Introduction to Genetic Analysis—Industrial Design: New Frontiers

1 1 The Genetics Revolution in the Technology as a Determinant Life Sciences of Object Shape Denis A. Coelho and Filipe A. A. Corda Universidade da Beira Interior KEY QUESTIONS Portugal

s 7HAT CONSTITUTES BIOLOGICAL INFORMATION AND HOW DOES IT 1. Introduction GENERATE FORM FROM RANDOM ENVIRONMENTAL COMPONENTS In a globalized world, we are confronted everywhere with the encouragement to s (OW IS LIFE ABLE TO PERSIST DOWN consumption, the purchase of goods and services. This is something characteristic of the THE GENERATIONS consumer society in which we live, whether it is caused by consumption needs and their satisfaction or because saturation has already set in, or it may even be caused by social s 7HAT IS THE BASIS OF HEREDITARY statement (Baudrillard 1995).

VARIATION The intention of this chapter is to focus on the study of technology as a determinant of the shape of products that incorporate technology. The acceptance ofs a(OW DID SPECIES ARISE ON THE product by consumers, and how important the shape and look of it is to the success ofPLANET the product, has been previously studied (Bloch 1995). Research has also been carried out to study the s (OW HAS GENETICS AFFECTED determinants of the shape of products (Crilly, Moultrie & Clarkson HUMAN SOCIETY 2009), which shows that several aspects determine the final shape of a product. The form development process is (OW DOES GENETIC RESEARCH driven by the designers' efforts to guide or constrain the way in s which the product will be WORK experienced, and the success of the final design may be determined by the degree of (Crilly, Moultrie & correspondence between designer intent and consumer response s (OW WILL GENETICS AFFECT OUR FUTURE of product shape Clarkson 2009). This chapter does not intend to focus on all determinants and does not aspire to focus on the acceptance of a product on the market or to reflect on the role of the personal taste of the industrial designer in determining the shape of the product.

The aim of this chapter is to study the influence of one aspect in particular, technology as a determinant of the form of products, for products that embed technology.

The study of materials and their development also fits this line of inquiry, since there is a 'ENETIC VARIATION IN THE COLOR OF CORN KERNELS %ACH KERNEL REPRESENTS A SEPARATE INDIVIDUAL This historical synergy between the development of technology and of materials. OUTLINE WITH A DISTINCT GENETIC MAKEUP 4HE PHOTOGRAPH SYMBOLIZES THE HISTORY OF HUMANITY S INTEREST IN HEREDITY (UMANS WERE BREEDING CORN THOUSANDS OF YEARS BEFORE THE ADVENT OF THE MODERN relationship, while not the main focus of this work, is also of 1.1 interest and merits some 4HE NATURE OF BIOLOGICAL DISCIPLINE OF GENETICS %XTENDING THIS HERITAGE CORN TODAY IS ONE OF THE MAIN RESEARCH ORGANISMS comments. The advent of new materials and the development and improvement INFORMATION of others IN CLASSICAL AND MOLECULAR GENETICS ;William Sheridan, University of North Dakota; photograph makes it possible to improve the application of new technologies and the consequent

by Travis Amos.]

1.2 (OW INFORMATION BECOMES development of new products. Man, machine, materials and production are closely linked in BIOLOGICAL FORM modern industry and this link is becoming increasingly strong. Advanced materials are ur planet Earth teeming with life (Figure 1-1), and this living 'ENETICS AND EVOLUTION critical toismany new technological applications, sinceworld the latter1.3 depend strongly on the has been a subject of great curiosity and investigation since the dawn of advances of the former (i.e. the high-speed train, Maglev, is based on technology already 1.4 'ENETICS HAS PROVIDED A civilization. However, in the last 60 years a revolution has taken place in materials developed and tested but its large-scale implementation awaits improvements POWERFUL NEW APPROACH TO in our understanding of the living world, and the foundation for this revolution technology so that cryogenic preservation can be maintained economically, so that it may be BIOLOGICAL RESEARCH has been the discoveries of genetic research. Today, most of the main questions possible to create the magnetic levitation consequent propulsion the vehicle). of biology have been answered through genetics, largelyand through an under1.5 of -ODEL ORGANISMS HAVE BEEN standing of molecular and cellular mechanisms centered on DNA. The molecule CRUCIAL IN THE GENETICS REVOLUTION deoxyribonucleic acid (DNA) is the central topic of interest to geneticists, but 1.6 'ENETICS CHANGES SOCIETY it has also become a kind of logo for all of the life sciences. The unfolding of our 1.7 'ENETICS AND THE FUTURE understanding of the nature of DNA and how it operates has not only provided

O

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Figure 1-1 4HE RICHNESS COMPLEXITY

Mastering the state of the AND BEAUTY OF LIFE HAVE INSPIRED THE opportunities, due largely to QUESTIONS THAT DRIVE RESEARCH IN BIOLOGY

Industrial Design – New Frontiers

Earth and on technological solutions offers vast art in materials Life a greater understanding and greater control of their basic characteristics. As such, new materials play an important role in the development of innovative technologies. For example, without knowledge of materials such as quartz crystal or piezoelectric ceramics, the production of energy that occurs with the deformation of these materials could not be put to use. Knowledge about materials catalyzes more technological knowledge. A recently created metallic material, with platinum-based nanopores, expands and contracts under the action of an electric current thereby converting electrical energy into mechanical energy and vice versa, depending on the state of the material. In conclusion, materials in general and bio-mimetic nano-materials in particular, form together with intelligent materials and organic polymers, among other materials, a wide range of examples of materials whose importance is recognized in the field of technology and product design.

The approach that is central to this chapter is bounded by the larger process of industrial design, where it gives a contribution that may take place at the stage of concept generation as well as the stage of detailed design. The bounding process of design that is considered is in line with the report of Lewis and Bonollo (2002). These authors performed an experimental investigation to unveil the design skills most influential to professional success, in order to have design education adequately train students in those skills. In order basic answers the core harnessed questions ofaallfive areas of biology, but hasprocess also led of to to structure their research, theseto authors stage operational spectacular applications in many areas of human endeavor such as medicine design, based on selected literature of their choice (Hales 1991). This process is comprised of and agriculture. five sub-ordinate processes (Table 1).

In this chapter, we will provide an overview of the genetics revolution and how Product development is part of any company's industrial innovation process (Roozenburg & it has come to pass. In doing so, we will see how the old mists have parted, leaving Eekels 1995). Industrial innovation all activities preceding the organism, launch of a popunew us with a clear viewincludes of the central processes of life at the cell, and product into the marketplace, lation levels.such as basic and applied research, design and development, market research, production, and sales. The development of new First, wedistribution need to deďŹ ne genetics.

Broadly, genetics is the study technological of all aspects of genes. Inthe turn, genesfor areapplications, deďŹ ned as the which fundamental unitscases of biological in many has ledinformato the possibilities has triggered search tion. They becases thought as uncommon the words in that the language of the living instead process. unveiling of new products.

In can such it isofnot the design process Muchand was the known about genes before discovery of DNA, butfor now we know that is the driven by the search technological of centring on the user potential market in virtually all cases, genes are composed of DNA. Thus, the discovery of DNA led applications. biological science into a realm called molecular genetics. By and large, molecuIn practice, technology influenced design may lead the way, in some cases, to a lar genetics deals with genes one or a few at a time. However, more recent technoin Table 1, little room is gene givensets to(called new simplification of thelogical design process have depicted innovations led to genomics, theas study of complete concept generation,genomes). since the Hence, conceptinformation is determined by the application of technology to can be analyzed not only at the level of the enable a particular “words,� functionality andmore as such, circumvents search and for “grammar.� new ideas,Today, and but at the complex level of life’s the “sentences� the termof genetics embracesproduct both molecular genetics and genomics.may well be promotes the continuation a particular archetype.

Such archetype tied to market requirements and perceived consumer acceptance, as well as to technological constraints and salient features that hamper shape alterations. What is proposed in this 1.1 The Nature of Biological Information chapter is to study the influence of technology as a determinant of the final shape of a product that incorporates technology.

This isbyintended to demonstrate is planet. a key Life on Earth is represented all the organisms currently how livingthis on the One of the most fascinating properties of life is that it regenerates itself every aspect for the possible deconstruction of product archetypes which have endured for many generation from single cells such as zygotes (fertilized eggs).

This regeneration years. To this end, some new product concepts are presented that incorporate emerging has abeen goingofon sincedistinct the origin of the life,existing and every organism on Earth today, technologies, reflecting change form, from hitherto. from the smallest such as bacteria to the largest such as whales, is a result of This chapter seeks to demonstrate the influence of technology in the form of the product. It millions of cycles of regeneration. This simple observation has led biologists also seeks to unveildown casesthe of ages product shapewhat changes brought aboutis from influence of to wonder kind of information insidethe these single cells technology in three categories given that gives them thebelow: ability to rebuild a complex adult organism. The word information literally means “that which is necessary to give form.� Hence, the question was, “What constitutes biological information?� Since the early twentieth century, scientists reasoned that in animals and plants, the information must lie within chromosomes, the worm-shaped, densely staining bodies found within

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1.1 The Nature of Biological Information

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Technology as a Determinant of Object Shape

Figure 1-2 3UCCESSIVE

cell of an a complement 1.Each Changing theorganism form in a has visible way (but not of theDNA product as an objectENLARGEMENTS BRING THE $.! OF AN ceases to exist); 2. Changes in the product in situations in which technology changesORGANISM INTO FOCUS in not reflected in gene changing the form of the product much but is responsible for modification of existing product as an object; performance (performance), keeping thegene 3. Cessation of existence of the productgene as such, in situations where the change in technology leads to a deconstruction of the product as an object, leaving behind the archetypes and stereotypes in a way hitherto associated with the product.

Organism (human)

A human body is made up of trillions of cells.

Each cell nucleus contains an identical complement of chromosomes in two copies.

Each copy is a genome.

One specific chromosome pair

Each DNA is a chromosome is one long DNA double helix. molecule, and genes are functional regions of this DNA.

the nuclei of cells (Figure 1-2). Chromosomes were considered likely information carriers because they are passed intact from generation to generation through precisely orchestrated nuclear divisions called meiosis and mitosis.

In the 1940s, several lines of research showed that the element that carries biological information within the chromoDNA is biological information somes is the molecule DNA. Eventually, the detailed molecular structure of DNA was elucidated by James Watson and Francis Crick in the 1950s. They inferred from this structure that DNA contains information written in a genetic code. DNA is a linear series of four molecular building blocks called nucleotides. The speciďŹ c sequence of nucleotides constitutes the language of the code. DNA, as part of the chromosome, is passed intact from one generation to the next, so all cells in each generation contain the same set of DNA with the same information-containing nucleotide sequence. Hence, one of the big secrets of life had been answered: the architectural blueprint for life is DNA. This discovery was to be a key step in the genetics revolution. In order to see how DNA plays its role, we need to understand its structure and its arrangement in cells.1. Operational Model of the Design Process (Lewis & Bonollo 2002, Hales 1991) Table Before embarking on our broad view of the current state of genetics, it is worth mentioning that most of the items cov2. Aims ered in this chapter will be revisited for detailed treatment in subsequent chapters; thean treatment herequestion is descriptive There is important thatrather impinges on the future of the practice of industrial than analytical, and the goal is to provide a general overview design – will there be objects that are at risk of deconstruction, to merge with the of the subject. environment, in view of the technologies that are developed for the near future and that will replace the existing ones? The overall objective of the work (Corda 2010) reported in this The molecular structure of DNA chapter was to carry out a survey of the evolution of form, taking into account the A molecule of DNA is made up of two long molecular technology of a selected range of consumer technology products in order to deconstruct strands of nucleotides wound around each other in a double archetypes that aredifferent fixed and new concepts, with particular regard to emerging helix (Figure 1-3).

There are four kindspropose of nucleotides in DNA:technologies. each nucleotide has a deoxyribose sugar, a Withand thea nitrogenous aim of enabling the sugars widespread use of the methods utilized to answer the phosphate group, base. The and aforementioned question and meet the specific objectives underlying the goal of this study, phosphates are identical in each nucleotide, but there are four different bases: adenine (A), thymine (T), guanine (G), and cytosine (C). In each strand, the sugars and phosphate groups form a chain rather like the sides of a ladder. Figure 1-3 4HE DOUBLE HELICAL STRUCTURE OF $.!

SHOWING THE The bases face the center, and each base is hydrogen bonded SUGAR PHOSPHATE BACKBONES IN BLUE AND PAIRED BASES IN BROWN

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Industrial Design – New Frontiers

to the base facing it in the opposite strand to constitute the “rungs� of the

Complementary base pairing this chapter presents the systematic methodology used so that it can be replicated in other ladder: adenine in one strand is always paired with thymine in the other,

is paired intended present thebonding methodologies product or technology contexts.

This chapter whereas guanine is always with to cytosine.

This speciďŹ city O 5´ developed duringOthe study and to explain the course of each of the methodologies andofthe is based on complementarity of shape and charge.

It is the sequence A, P 3´ O of Oa categorization is on divided into three types. the coded information carried T, G, that and C one strand that represents O emergence H N H 5´ CH2 that by The methodology is the meant analyse the 1-4). feasibility of applying an emerging DNAto molecule (Figure T N H N A O O 4´ technology in a given product was applied to three cases (Corda 2010), and is made up of 2´ 3´ 3´ O five steps1´in order to analyze and compare the technologies. The intent of this methodology 1´ 2´ 4´ -ESSAGE $.! IS BIOLOGICAL INFORMATION ENCODED AS A SEQUENCE OF O is to attempt Oto predict ifNUCLEOTIDES $.! IS A DOUBLE HELIX OF TWO NUCLEOTIDE CHAINS HELD TOGETHER BY the emergent technology is viable for application in a given 5´ CH2 P O any technology product; as such, that is incorporated, or has been incorporated, in a COMPLEMENTARY PAIRING OF ! WITH 4 AND OF ' WITH # O O N H O O P O particular product is considered in the analysis and compared with the emerging O CH2 C O that is intended to come to be incorporated in the product. As a result of O H N G Ntechnology DNA is organized into genes andsame chromosomes 3´ of each selected technology in a this methodology, one becomes aware of the performance O N H An organism’s complete set of genetic information, encoded in its DNA, is O given product, and gets to compare the performance of the product depending on the O CH2 its genome. In eukaryotes (organisms whose cells have nuclei), the bulk of O technology thatP enables the productis features (specific were considered O the genome found in the nuclei,and eachgeneral) of whichthat has the same DNA conO O P H O forOthe analysis.

This methodology is complemented with the use of another N important tent.

The nuclear DNA is divided into physically separate pieces, each a O 5´ CH 2 methodology, determining thedouble causality ofAn changes in technology on(Figure the external shapejust of O N T long helix. individual chromosome 1-5) contains H O N A the product. one of these double helices in a highly coiled condition. The set of chromoO O each technology, in order number to verify The awareness of the strengths and weaknesses somes in organisms from theof same species has a characteristic of O CH2 whether there Pis Oany viability in embedding an emerging technology a product, is chromosomes and appearance.

An example is seen ininFigure 1-6, which O O showsofthe of have a cell from one species of of a small Indian deer by the thechromosomes changes that occurred by way deployment of O N H followed O examination O P O called a muntjac.

CH different technologies in the product. The methodology for determining the causality of 2 C N H N G O O This illustration reveals someshape interesting features of chromochanges caused by technology (changes in the external of thegeneral products analysed) also O consists somes.

The lower part shows the chromosomes from one nucleus, spread H N of five steps and connects the shape changes occurred in the products with the O out as a result of breaking the nuclear membrane.

The chromosomes have O various technologies that incorporate each particular product.

CH2 H been stained by special uorescent molecular probes called chromosome It is important to3´ provide a comprehensive perspective to support peers who intend to O paints. In this preparation, the probes were designed so that each type of O P pursue the implementation of the two methods mentioned above, providing a (tripartite) C chromosome is painted the same color. This staining reveals that the total of categorization which is primarily a catalogue of the typological consequences of the 5´ O influence of technology on the form of a product, as a result of applying the two Figure 1-4 ! mATTENED REPRESENTATION methodologies presented in the process of technological product design.

The nuclear genome

OF $.! SHOWING HOW ! ALWAYS PAIRS WITH 4 AND ' WITH # %ACH ROW OF DOTS BETWEEN THE BASES REPRESENTS A HYDROGEN BOND 3. Methodologies

Eukaryotic cell

developed

This section is intended to communicate to peers Nuclear(industrial chromosomes designers and product engineers) the methodological results achieved. These concern stepwise methods to study technologies as determinants of a product’s shape and to propose new shapes for products embedding emerging technologies. A number of technologies are considered in relation to a set of products, as a means to show how technology has influenced object shape and how new technologies (e.g. OLED – organic light emitting diodes, MEMS – micro-electro-mechanical systems and energy harvesting) may promote archetype renewal.

Technology is a key player in today's society; it is the engine of our development and our innovation. Predicting its future uses necessitates systematic approaches, attempting to build future scenarios about the way science, technology, society and economy will evolve, DNA–protein supercoil in order to promote their benefits and make the most of the impacts that the future may bring (Glenn, Gordon & Florescu 2008 as cited by Damrongchai & Michelson 2009) .

According to this report, the look to the future is optimistic as it will bring progress in various fields, including technology, which promises to have the ability to make the world DNA

Gene

Gene

Gene

Figure 1-5 4 HE NUCLEAR GENOME IS COMPOSED OF A SPECIES SPECIlC NUMBER OF CHROMOSOMES /NE CHROMOSOMAL REGION HAS BEEN EXPANDED TO SHOW THE ARRANGEMENT OF GENES

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Structural comparison of the eukaryotes, prokaryotes, and viruses work in a better waygenome than itcomponents does today. of There are a number of technologies that,

according to Bengisu (2003) and Bengisu & Bekhili (2006), will be the most promising Protists for the near future. This selection was established based on an approach that relates the number of scientific publications with the number of patents over the years.

Those reports acknowledge the existence of many emerging technologies such as Eukaryotic cell nanotechnology, biotechnology, super-insulating materials and structures, hydrogen storage and combustion technology. OLED, MEMS and Energy harvesting were chosen Animals Plants because they are emerging technologies that already are used and are soon to emerge on a Nuclear chromosomes Chloroplast large scale in the market. Additionally, because the technology and product pairs focused Mitochondrial chromosome chromosome and the product had to be in this chapter were chosen simultaneously, the technology(plants) mutually compatible, so they could be articulated (technology and product) enabling the creation of new designs.

Organic Light Emitting Diodes (OLED), which are also called Light Emitting Polymers (LEP), are a technology which is at the forefront of bright screens and monitors, and has been steadily developing in recent years. OLEDs reached the media headlines in 2003 with one million units sold as part of a small application for an electric shaver from Philips, which gave an indication of the level of battery charge. Sometime later, a colour screen DNA (OLED) also appeared with great success as a monitor on the back of a camcorder; Kodak (a Gene Gene Gene Gene Gene major driving force in developing this technology) finally launched this image technology for the world market (Salmon 2004).

DNA–protein supercoil The development of MEMS, or micro-electromechanical systems, is responsible for an endless number of modern features and applications. This is a technology that has existed for some time but has expanded greatly in recent years, becoming an increasingly promising technology for the future. As we move into the third millennium, the number of applications for MEMS in our daily lives continues to increase, promoting continuously Gene Gene Gene et al. 2004). falling production costs for these devices (Beeby Energy harvesting (EH) approaches, form a group of means to harvest energy, which due to scarcity of natural resources such as crude oil, and increasing pollution of the planet by Prokaryotic cell to gain some forms of energy production (such as polluting power plants), have began Viruses Bacteria Bacterial importance and relevance in chromosome the production of clean energy. Increasingly there is awareness that every contribution that can save on energy from pollutant sources is welcome. As such, Plasmid the use of personal devices, with the ability to produce a few milliwatt of power (a thousandth of the electric power needed for a common light bulb), coming from sources DNA captured by forms of micro energy harvesting, are aligned with this purpose.

Gene The first approach that was developed in the study reported in this chapter was to verify the potential application of an emerging technology in a given product, evaluating the application of OLED technology in TV sets. Five specific aspects and five general aspects DNA were selected that were considered crucial to the performance and the quality of this Gene case, this methodology was used Gene to predict Gene Gene of applying Gene In the second product. the feasibility EH technology (which is an approach to self-powering of technological devices, a grouping Figure 1-11to %UKARYOTES PROKARYOTES AND VIRUSES ALL CONTAIN CHROMOSOMES ON WHICH of forms of energy harvesting) the clothes pressing warm iron, and likewise five general RESIDE THE GENES BUT THERE ARE SOME DIFFERENCES IN THE GENOMES &OR EXAMPLE PROKARYOTIC and five specific aspects were chosen that were considered relevant for this product and that CHROMOSOMES ARE CIRCULAR WHEREAS VIRAL AND THE NUCLEAR EUKARYOTIC CHROMOSOMES ARE enable the full unfolding of the methodology. The third case of deployment of this LINEAR 4WO EUKARYOTIC ORGANELLESˆTHE MITOCHONDRIA AND CHLOROPLASTSˆCONTAIN SEPARATE

methodology consisted in attempting CIRCULAR CHROMOSOMES to assess the feasibility of application of MEMS to the vacuum cleaner. Each of the five steps that make up this methodology will be explained in this section, as well as their limitations. circular. Prokaryotes often have small circular chromosomes called plasmids in addition to the main chromosome. The genomes of viruses are much smaller and usually linear.

A general representation of genomes is shown in Figure 1-11.

Fungi technologies

DNA

DNA

DNA

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1.2 How Information Becomes Biological Form

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Industrial Design – New Frontiers

We all know, from trying to build anything, that a plan or blueprint is needed.

Another methodology is demonstrated in this section. It is intended to assist in determining Thus, knowing that the blueprint of life is based on DNA and having an underthe structure causality and of changes in istechnology towards the external shape of products. It standing of DNA how DNA organized in cells waschanges a giant in step hence aims at assessing technology’s causality in relation to the changes that have occurred forward not only for genetics, but for all biology. in the shape of the products under study (TV, iron and vacuum cleaner) as technology changed in them, attempting to predict which aspects of shape may arise and disappear the implementation in these products ofForm the selected emerging technologies. This 1.2 Howwith Information Becomes Biological methodology was applied first to the TV set, and was used to compare the shape in this Once scientistsproduct, knew thedepending nature of the information the obvionbiological the technology thatmolecule, comprised it. Then the same methodology was ous question was, How is information contained in the DNA molecule converted employed to try to determine the aspects of form of warm clothes pressing irons according into “form,â€? the stuff that we see when looking at an organism? An organism’s to the technology that they embody, and finally, to determine those aspects of the shape of form is its physical essence, including its size, shape, color, smell, behavior, and so vacuum cleaners, also depending on technology. on. The main elements of form in organisms are proteins: when you look at a livObservation of results and data taken from the application of these two methodologies gave ing organism, you are looking either at proteins or material that has been made by rise can to the to create a comprehensive categorization of all cases of changes occurring in proteins. Proteins be need classiďŹ ed into three basic types: structural, enzymatic, technology they incorporate, resulting the products, derive directly from the and regulatory.

Asform their of name suggests,which structural proteins contribute to outward in a categorization, consisting of three variations that embrace distinct types of shape physical structure such as hair, nails, and muscle and also to structural elements changes in products. within the cell such as the cytoskeleton. Enzymatic proteins catalyze the reactions going on within cells, reactions that make all the main types of molecules, including proteins themselves, nucleic acids, carbohydrates, and fats. Regulatory pro3.1 Feasibility analysis of the implementation of an emerging technology in a given teins act to turn on or turn off gene activity at the appropriate time and place. product Hence, the main of the livingfor system is to convert theofinformation of the of an emerging technology Thetask methodology feasibility analysis the implementation DNA of genes in into proteins. a product consists of five steps (Table 2).

Molecular geneticists worked out the basic mechanism of conversion soon after the discovery of DNA. The remarkable discovery was that not only is DNA the information storage system for virtually all organisms, but in addition the genetic coding language is virtually the same in all organisms and so is the mechanism whereby DNA is converted into proTranscription and translation in a eukaryote teins. This remarkable uniformity in the informational system is a result of all organisms sharing a common evolutionary ancestor.

Transcription

Nucleus

DNA

In the ďŹ rst stage of the protein-synthesis process, the DNA of a Initial gene is copied to make another linear molecule called ribonuRNA Transcription transcript cleic acid (RNA). The copying process is called transcription.

RNA is also composed of nucleotides, but the sugar is ribose, and the base uracil replaces the base thymine. Whereas DNA is RNA processing and a double-stranded helix, RNA is single stranded. Nevertheless, intron removal the nucleotide sequence of one strand of the DNA double helix Table 2. Stages of the methodology for feasibility analysis, considering the implementation is copied precisely onto the nucleotide sequence in RNA, except of an emerging technology in a product. that uracil appears wherever thymine would appear in the origiMature mRNA Amino acid nal DNA. In most eukaryotes the initial transcript is modiďŹ ed by chain Transporttechnology, to The first step of this methodology is implemented by choosing an emerging excising the introns. The ďŹ nal form of gene transcripts destined cytoplasm which is intended for study, followed by the choice of product for which the test of for protein synthesis is called messenger RNA (mRNA). The feasibility applying is intended. This is followed by the identification of word messenger is used toofconvey the this idea technology that this molecule mRNA so that one can establish the comparison the technologies used and in use in this is the vehicle that conveys the information from a geneproduct, to and proceed with the remaining actions prescribed in the methodology.

The collection of Translation the protein-generating machinery. Each transcribed region is step, in which one should gather as much information on technologies makes up the second anked by one or more regions that determine when the tranRibosome information as place possible, scription of that gene will take and inincluding which cells.the advantages and disadvantages of the technologies that the productunit uses, and even used as well as the available data on the emerging The overall transcriptional composed of has an mRNAproducing region plus its anking regulatory elements is the unit we have called Figure 1-12 )N A EUKARYOTIC CELL M2.! a gene. It is in this sense that the gene is the basic functional unit of the genome: IS TRANSCRIBED FROM $.! IN THE NUCLEUS a gene is in fact a unit of transcription. The production of eukaryotic mRNA is AND THEN TRANSPORTED TO THE CYTOPLASM FOR TRANSLATION INTO A POLYPEPTIDE CHAIN diagrammed at the top of Figure 1-12.

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flow of information a eukaryotic cell technology. TheseThe enable drawing up ainTable split between the advantages and External disadvantages depending on the technology (view example in Table Nuclear chromosomes 3, developed for a Gene 1 signal specific technology – plasma, used on TVs). The third step consists in compiling the data that were considered relevant, after the drafting of the previous step, to create a Table technology containing the technologies selected in the first step, including the emerging Internal signal Gene 2 and with the MEMS emerging (view example in Table 4 – developed for the vacuum cleaner technology in mind). Five general aspects considered important to the product (for which the study of the feasibility of Intron applying the emerging technology is intended) and five removal that influence the product’s performance are chosen. specific issues which relate to factors Nuclear Gene 3 This membrane Table is populated with a range of attributes ranging from acceptable, satisfactory, mRNA 1 good, very good or excellent, to qualitatively describe the suitability of the technologies in the ten areas selected for comparison. The comparison of the data collected and the ranking fourth step of this methodology, which of technologies in order of feasibility, comprise the mRNA mRNA 3 2 transforms the scale of words used in the previous step in a numerical scale ranging from one to five, where number one corresponds to acceptable and number five to excellent and the remaining values follow the order of the verbal scale.

Endoplasmic reticulum

mRNA 4 Golgi apparatus Gene 4 Circular organelle chromosome Mitochondrion or chloroplast Cell membrane

Key Protein-coding region of DNA Noncoding region Protein-coding region of RNA Noncoding region Promoter Regulatory proteins

RNA polymerase Secreted protein Proteins used in cell Protein encoded by mitochondrion or chloroplast Amino acid chain Ribosome

Figure 1-13 Simplified view of gene action in a eukaryotic cell. The basic flow of genetic information is from DNA to RNA Table 3. Advantages and disadvantages of the PDP (Plasma Display Panel) technology in TV

to protein. Four types of genes are shown. Gene 1 responds to external regulatory signals and makes a protein for export; gene 2 respondssets. to internal signals and makes a protein for use in the cytoplasm; gene 3 makes a protein to be transported into an organelle; gene 4 is part of the organelle DNA and makes a protein for use inside its own organelle. The promoter is the region.

The fifth step entails a transcriptional matrix (an enzyme. example such is given in introns, Table 5, where transcription is initiated, and RNAdrawing polymeraseup is the Mostof eukaryotic genes contain concerning technologies pertaining to theof clothes upgenes the regions (generally noncoding) that are cut out in the preparation functionalironing messengerproduct) RNA. Note which that manysums organelle have introns and that an RNA-synthesizing enzyme is needed mRNA These have been omitted turn had beensynthesis. assigned bydetails matching words and values assigned in the fourth step, whichfor inorganelle from the diagram or the organelle for clarity.

numbers in step three. General aspects are added, which enables concluding which technology has greater suitability, according to these aspects. Finally, the results of general and specific featuresTranslation are summed up, and it is then estimated which is the technology that is more feasible to apply thesecond product in general (of the two each kinds of aspects, both In the stageselected of the protein-synthesis process, mRNA is translated into one specific protein. Hence, the sequence general and specific).

DNA l RNA l protein has become one of the operational mantras of biology. Indeed, it is one of the greatest insights into biology ever deduced and has been the foundation for much of biological research in the past half century. Like all rules, there are exceptions,

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Industrial Design – New Frontiers

and in some situations RNA can be reverse transcribed into DNA. For example, reverse transcription is used to maintain the telomeres that form the chromosome tips.

The details of translation are complex and intricate, as we will see in Chapter 9, but at the basic level it is quite simple (bottom of Figure 1-12). Every protein has a three-dimensional structure, but essentially it is a long chain of amino acids called a polypeptide. There are 20 main amino acids in cells, and it is the various combinations of these 20 that give each protein its speciďŹ c shape and function.

The chain of amino acids is folded or coiled to give the right shape for function.

How does the nucleotide sequence in mRNA become translated into an amino acid sequence in protein? Groups of three nucleotides, called codons, constitute the three-letter “wordsâ€? of the genetic coding language. Every combination of three stands for one of the 20 speciďŹ c amino acids. The codons in mRNA are “readâ€? consecutively starting at one end by the translational machine, called the ribosome. Hence, a speciďŹ c linear sequence of nucleotides is converted into a linear sequence of amino acids constituting a speciďŹ c protein. The translational system involves a number of cellular components.

-ESSAGE -OLECULAR GENETICS HAS SHOWN THAT BIOLOGICAL FORM IS GENERATED BY TRANSLATING

THE CODON SEQUENCE OF M2.! INTO THE AMINO ACID SEQUENCE OF PROTEIN

Some RNA molecules are never translated into protein but nevertheless play an important role in themselves. The existence of this general class of functional RNAs has been known for some time. Early examples were ribosomal RNA (rRNA), part of ribosomes, and transfer RNAs (tRNAs), whose role is to carry amino acids to the translational system. Recent research has revealed that there are many more types of functional RNAs that are essential for proper cell function.

The transcription and translational mechanisms outlined are just the bare bones of the complex process of how an undifferentiated zygote becomes a complex organism with many different operating systems. Clearly, the cells that are producing hair in the skin must be acting very differently from those producing insulin in the pancreas. How is this differentiation achieved? It is known that each of the trillions of cells of a multicellular organism has the same full complement of DNA, so logically, different sets of genes must be active in cells of different types. Indeed, it can be shown that most mRNA molecules are synthesized at speciďŹ c developmental stages and not others. Gene transcription is controlled by regulatory proteins, and these regulatory proteins in turn are made by other genes in response to speciďŹ c signals that may come from either outside or inside the cell. Some of the main elements of transcription and translation are illustrated in Figure 1-13, which outlines transcription and translation in a eukaryotic organism.

How does life replicate itself?

One DNA double helix becomes two

Chromosome

DNA replication

Daughter

Another perennial conundrum of traditional biology was, How can life perpetuchromosomes ate itself through time? People have babies, dogs have puppies, and maple trees Legend: * - General characteristics, applicable to technological products; ** - Concerning the envisaged have maple seedlings. How can this constancy of form through the ages be concept presented in Figure 6, # - Specific features of the product family in question. achieved? Again the answer lies in DNA, which constitutes the basis of descent through time of both4.cells and organisms.

Table Qualification of characteristics of technologies concerning the vacuum cleaner.

The structure of DNA lends itself to replication. Although quite a complex process in its detail, the idea, originally proposed by Watson and Crick, is simFigure 1-14 7HEN NEW CELLS ARE MADE

ple: the two strands of DNA separate and newly synthesized nucleotides are $.! REPLICATION ENABLES A CHROMOSOME deposited on the old strands, each paired with its appropriate partner, A with T TO BECOME DAUGHTER CHROMOSOMES AND PASS INTO NEW CELLS and G with C (Figure 1-14). The nucleotides in the new array are then ligated

12

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The Genetics Revolution in the Life Sciences

Technology as a Determinant of Object Shape

DNA replication is the basis for the perpetuation of life through time Testes

Ovaries

DNA REPLICATION

DNA REPLICATION

Division of gonad cells

Division of gonad cells

Sperm

Egg

11

(joined) while held in place by the old strand. Thus, two DNA molecules arise, each carrying one of the old separated strands plus a newly synthesized strand. This DNA replication process takes place every time somatic cells divide and also when sex cells (gametes) are formed (Figure 1-15). Hence, it is the way that life perpetuates its blueprint through time, both in producing new generations and in regenerating a new living organism from a single progenitor cell such as a fertilized egg.

-ESSAGE 4HE PERPETUATION OF LIFE THROUGH TIME IS BASED ON HIGH lDELITY REPLICATION OF A GENOME S $.!

Change at the DNA level Legend: *- General characteristics, applicable to technology products # - Specific to this particular type of product.

Species have established characteristics that deďŹ ne them, so we Zygote

canin(for example) always tellproduct a porpoise from pressing a whale. However, Table 5. Classification of technologies comparison, for the clothes iron. there is a great deal of variation within a species. Much of this is DNA to be neutral variation in that it hasunfolds; no demonstrable Tables 2 to 5 illustrate how the firstthought methodology presented in this chapter its first REPLICATION effect survival, but it does allowofindividuals to be distinapplication demonstrated was to test theonfeasibility of application OLED technology in guished. example, individual killer whales are easily distintelevisions. It has proven very efficient and For straightforward to conduct the entire process, as guished by the dorsal relevant ďŹ n and thedata, size and shapeas of Division of the abundance of data is large, which made it shape easieroftothecollect as well the white body markings. asexual (body) performing the choice between specific and general issues for comparison between cells The basis for variation has long been a topic of great curiostechnologies. Another advantage, which allowed the development of this methodology, was ity to humans, particularly as it relates to human variation. that the emerging technology (OLED) has to be applied to the product concerned (TV) and Geneticists took a huge step toward understanding variation Repeat andthat were and for as such values and considerations already existed divisions when they discovered thealready DNA in atested genome canproven be changed. their practical implementation in the product.

With regard to further application of this Their discovery of the mechanisms of change in DNA has proTVs, allthe thebasis technologies selected methodology in the case of the OLED technology vided a key piecewithin of insight into of variation, knowlfor comparison are currently in useedge in this ofreaping product, so this not a product with a thattype is now rewards in is medicine and many other single dominant technology as is mostly case for irons and vacuum cleaners. In the other areas the of research.

Comparisons of DNA from different individuals show that two cases of deployment of this methodology, for EH and MEMS technology, the feasibility the differences are often caused by a minor difference in a of implementing these procedures for the products iron and vacuum cleaner, respectively, Figure 1-15 gene’s DNA sequence.

A change to the DNA sequence is called was verified. Of particular importance was the fact that these technologies do not have Mutations occurand naturally either as a result of products, as such it became more commercial in the chosen A mutantwidespread gene causes albinism applicationa mutation. chemical analyses mistakes in processing in the cell orbetween by expodifficult to collect data and make accurate of DNA the aspects in comparison sure to environmental agents such as high-energy radiation or technologies. This was offset by the emergence of estimates and by basing the assessments reactive chemicals. As random changes to the molecular on envisaged concepts developed for these two products with the incorporation of the machine, most mutations are detrimental, but some have no emerging technologies. Another hardship was that predecessors of the technologies effect orfound are even advantageous.

If mutations arise in the germ used in the products iron and vacuum cleaner, are completely obsolete and are notcan used cells, such as the egg or sperm, then the mutation be anymore, which also hampered the passed collection of some data. on to progeny and contribute to variation between indiIt should be noted that this methodology is deemed suitable application fora mutamost viduals. A striking example of the to potential effect of tion inofa single seen in theofhuman condition albinism technologies, and serves the purposes testinggene theisfeasibility applying a particular 1-16). that can be improved with the emergence technology within a product. It is a(Figure methodology Mutations can lead to serious conditions.

They arefocused. the cause of new data and of results of the application of emerging technology in the product of human diseases that are passed on from one generation to the next, known as hereditary diseases. For example, Tay-Sachs dischanges thedystrophy shape of(affecting the 3.2 Determining causality in cases where technology ease (affecting nerves) and muscular musproduct cles) are caused by mutations in single genes that radically alter The methodology for determining or theknock causality of gene’s changes in technology, changes in the out that function.

Such mutations originate in external shape of the products, is composed of and fiveso steps (Table on 6). in egg or sperm. Figure 1-17 the gonads are passed shows some examples. Mutations in cells that are not germ cells Figure 1-16 ! NONFUNCTIONAL VERSION OF A SKIN PIGMENT GENE RESULTS IN LACK OF PIGMENT )N THIS CASE BOTH MEMBERS OF THE GENE do not have the same consequences: often such mutations simply kill a cell, which has no impact at all on the organism’s funcPAIR ARE MUTATED ;Copyright Yves Gellie/Icone.]

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Industrial Design – New Frontiers

shows that environmental exposure can affect the function of genes, often in a negative way. Current research is aimed at delineating the “epigenome,â€? that part of the genome that is susceptible to epigenetic modiďŹ cation.

In addition, some natural variation in individuals is caused by environmental effects not acting on the DNA. For example, dietary differences between individuals can affect size, shape, and function. These changes are generally not heritable.

-ESSAGE ( EREDITARY CHANGE IS CAUSED MOSTLY BY MUTATIONS IN $.!

BUT ALSO BY EPIGENETIC EFFECTS

The understanding of the basis of genetic variation between individuals of species also provided insight intoofhow different arise, inchange other words, Table 6. Stages of theone methodology for identification causality of species technological in how evolution occurs, which we consider next. the shape alterations of a specific product over time.

The first step of this methodology is to choose the target product for the analysis in terms of form, which is followed a historical study the evolution of that product shape from its 1.3 byGenetics and on Evolution beginnings to the present. An analysis of the product is then made according to the In addition to the has provided(the in cell and organismal biology, genetics technology that it incorporates, andinsights may it incorporate emerging technology that has is now a key component in the study of evolution.

The planet Earth is currently been selected for the product). Then the form search begins, composed of the observation of home to a multitude of different life-forms, and the fossil record shows that it was a wide range of issues, consulting catalogues and product photos, which are used to infer all home to many more species in the past, now extinct. Perhaps one of the biggest the salient features and of shape and are organized to been the technology incorporated, most controversial questionsaccording that has ever asked about the living world completing the second step thisforms methodology.

Creatingarose.

Tables with the characteristics of is how allin these (including humans) the product form (which had been collected in the previous step) split according to the technology that theNatural product selection incorporates, embodies the third step, which gives rise to a series of Tables. TheInfourth step consists of highlighting the most significant differences that the nineteenth century, Englishmen Charles Darwin and Alfred Russel Wallace proposed an explanation for the natural origin of species.

Both men were occurred in the product shape according to technological change, in several Tables listing impressed not only by the vast diversity of life, but also by the clear patterns of these changes. This does not only concern similarities, as gains and losses of form features between Forisexample, although humans, birds, and porpoises to provide a systematic overview of the are also of interest.similarity The purpose of species. this step are very different species occupying different ecological niches, their forelimbs existing changes with the onset of another technology in a product. In the fifth step, the have the same number of bones in the same relative positions. The interpretation results from the previous step on the influence of technology in the form of a product are was that these similarities between species are due to common ancestry and that gathered in a systematic way. are This enables describing theselection similarities in appearance, differences due to the force of natural in different habitats. and the changes in form, for Natural the product under study, on which a new technology is tocharbe selection is the process whereby individuals with a particular implemented. This acteristic step concludes the deployment of the methodology usedinto assistenviin (such as better vision) may reproduce better than others a given ronment.

Since these individuals haveoccurring more offspring, the relative shape in TVs, clothesabundance pressing determining technology’s causality in changes inwill of individuals with the characteristic in question will increase. Similarity due to irons and vacuum cleaners. ancestry from a common ancestor is called homology. concerns theThis factall-embracing that in the The main limitationshared observed of the use of this methodology notion of natural selection acting on variation became widely accepted asthat the case of irons and vacuum cleaners there is no model that uses the emerging technology theory of evolution. This theory has been called the greatest intellectual revoluhas been associated with each of these products. For television sets, it was not necessary to tion in the history of humanity, a radical new way of seeing ourselves and our resort to the verification the living concept developed in the form of a TV with OLED relationsof to the world. technology, because actual examples exist of this product OLED Genetics has madealready a large contribution to the theory ofincorporating evolution. Wallace and is acause vastofvariety of forms, is yetselection another technology. The factDarwin that in most products there had no idea what could be the the variation for natural to act on, but genetic research has shown that it is change in the DNA that generates hardship in the deployment of this methodology, to the extent that it would be impossible to which acts as the material for evolution.

DNA change can be analyze them all. variation, Moreover, the then existence of raw many technologies (mainly non-electric simple mutation within a gene or larger-scale changes involving whole chromotechnologies, in the case of irons and vacuum cleaners) would yield very large lists, covering or genomes. only a small set ofsomes products that used these technologies. As a way to overcome this The ďŹ eld of population genetics has provided a complete mathematical underobstacle, all non-electric technologies were considered jointly and a note was made of the pinning for population change leading to evolution. Furthermore, the study of large-scale chromosomal changes at the genomic level has revealed speciďŹ c mechanisms for evolution. In the above ways, genetics has provided substantial support for this greatest insight.

15

1.3 Genetics and Evolution

13

Technology as a Determinant of Object Shape

Evolutionary tree aspects based on of cytochrome DNA common of comparisons the products embedding them.c In the case of the vacuum cleaner, non-

Human Monkeyelectric technologies were grouped together under the manpower label, comprising 0.2 Dog Horse Donkey Pig Rabbit Kangaroo technologies that enhance the functionality of the product, such as tightening mechanisms, 0.8 0.9 0.1 Pigeon Duck Chicken Penguin levers and mechanical cranks.

1.3 2.7 1.1 1.0 3.0 2.7 1.6 1.1 Turtle applicable Snake This methodology, which is deemed to most types of products and technologies, 4.6 Tuna 1.7 –0.6 1.0 6.9 is intended to convey 1.2 a 0.5 the aspects of form that make up a product process to collect 1.4 4.9 Screwdepending and to relate the change of its shape with 1.4 on the3.3technology it incorporates, Moth worm 16.5 technology implementing a specific new in this product. Figures 1, 2 and 3, depict sketches 6.5 9.9 1.1 Candida analyzed, according to the type of 17.2 of the salient shape contours of the three products Saccharo3.3 technology that they embedded. myces Neurospora

–0.2

5.4

17.4

5.7

23.4

28.1 15.2 9.6

2.1

Figure 1-18 !

TREE BASED ON THE $.! SEQUENCE OF THE CYTOCHROME C GENE 4HE NUMBERS ESTIMATE THE NUCLEOTIDE SUBSTITUTIONS THAT HAVE OCCURRED ALONG THE LINEAGES IN Non electric iron THE GENE CODING FOR THIS PROTEIN THE DISTANCES ARE PROPORTIONAL TO NUCLEOTIDE DIFFERENCES BETWEEN ORGANISMS !LL DIFFERENCES ARE SMALL COMPARED TO THE SIZE OF THE GENE ;Š 1994 Fig. 1. The evolution of form in the modern clothes pressing iron.

Encyclopedia Britannica.]

Electric iron

While the fundamental shape archetype is unchanged as the clothes iron passed from non-electric to electric energy (Figure 1), over time there has been a gradual evolution of Constructing the evolutionary form features lineages in this product, resulting in a lighter and more streamlined product.

Neanderthal man An evolutionary tree is a treelike branched diagram that shows theright descent of variFundamentally, the product depicted in the sketch still consists of a V-shaped metal ous modern and speciesto through intermediate forms over time. archetype has endured over basefossil attached a handle, and as ancestral such, this basic product DNA sequencetime. is a powerful tool for constructing evolutionary trees. Differences in DNA sequences are quantiďŹ ed, with similar sequences placed closer The evolution and of species the shape of the TV setare (Figure 2) has clearly been influenced by together in the tree of relatedness. Such DNA trees can be used to test patterns of technology, in particular by the leap from CRT (Cathode Ray Tube) to LCD (Liquid evolutionary relationships previously proposed exclusively on physical homology. substitutes Display).

The most recentgroupings. technological They can also Crystal reveal new and unexpected taxonomic DNA homology is for LCD technology (Plasma, LED and OLED) have so far not promoted a fundamental often striking; for example, the DNA and amino acid sequence of the gene for thechange to the new archetype of the flat andcytochrome thin TV set. notwithstanding, thereofisorgana clear direction in the evolution of electron-transport-protein c isThis homologous across the range the shape of TV sets towards ultra-thin panels isms on the planet, spanning bacteria, fungi, worms, insects, display mammals, and so(and on flexible display panels are in (Figure 1-18). the Thishorizon). type of revelation, together with the demonstration of great homology of the processes atanalysed work in cells, has led to a new awareness the vacuum cleaner (Figure 3) is the case Ofbiochemical the three products in this chapter, that humans are indeed “cousins� to all the life-forms on Earth. where more striking form changes took place as an effect of changing technologies and Genetics has provided crucial input human The chimpanzee physical principles that on make up evolution. its fundamental functionality. In this product, several genome sequence shows that chimpanzees are our closest living relatives, supportarchetypes of shape have coexisted over time, but clearly, each form archetype is associated ing Darwin’s hypothesis that humans evolved from apes. Recently, DNA obtained to a particular technology, even if the same basic technology underlies several product form from bones of the extinct Neanderthal people (Figure 1-19) has been used to generof electric archetypes (this isgenome especially true As in expected, the case this ate a nearly complete Neanderthal sequence. genome isvacuum cleaners, from the preintelligence era). Furthermore, interesting clues about even closer toartificial ours than chimpanzees’.

Figure 1-19 4HE GENOME OF Neanderthals emerge, such as that one important gene for speech is in the same .EANDERTHALS IS THE CLOSEST TO MODERN form as it is in humans, whereas the chimpanzee form is different. This observation HUMANS OF ALL THOSE SEQUENCED ;imagebroker/Alamy.] leads to the fascinating speculation that Neanderthals had the ability of speech.

16

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Industrial Design – New Frontiers

DNA sequences from people around the world have been compared: these comparisons show that most likely, Homo sapiens evolved in Africa and then migrated to the far reaches of the planet. Indeed, speciďŹ c migration routes can be mapped by analyzing these comparisons (Figure 1-20). Studies on genes from people of different races have made the important ďŹ nding that there are no major discontinuities between the races, telling us that the race concept is not meaningful at the genetic level.

One spin-off of the discovery of DNA homology is to simplify the daunting task of determining the functions of genes in a huge genome such as the human genome. Because genes of similar structure in different species often have similar functions, insight can be obtained from previous research on homologous genes whose functions have been well established in experimental organisms.

In providing a deep understanding of the way DNA works and changes over CRT TVview of humanity’s position in time, genetics has given us a novel philosophical the universe, including our own evolution. DNA trees show that we are merely the end of one line of a complex web of evolutionary branching. We are not in any special position, but survivors like all other existing species.

Figure 1-20 #OMPARISON OF SITES

IN MITOCHONDRIAL $.! MT$.! AND 9 CHROMOSOME $.! REVEALS THE ROUTES TAKEN BY Homo sapiens IN COLONIZING THE PLANET $IFFERENT LINES OF THE SAME COLOR ARE THE RESULTS OF STUDIES WITH DIFFERENT REGIONS OF $.! ;The

-ESSAGE ' ENETICS HAS MADE KEY CONTRIBUTIONS TO UNDERSTANDING EVOLUTION AND

CONVERSELY KNOWLEDGE OF EVOLUTIONARY HOMOLOGY AT THE $.! LEVEL ALLOWS EXTRAPOLATION FROM ONE SPECIES GENETIC SYSTEM TO ANOTHER

Genographic Project.]

DNA-based migration routes of Homo sapiens

LCD TV

Arctic Ocean

LCD+LED TV

Europe North America North Pacific Ocean

North Atlantic Ocean

Africa

Indian Ocean

Australia

PDP TV

Fig. 2. The evolution of form in modern Television sets.

Y chromosome DNA Mitochondrial DNA

South Pacific Ocean

OLED TV South America

South Atlantic Ocean

17

1.4 Genetics Has Provided a Powerful New Approach to Biological Research Technology as a Determinant of Object Shape

15

1.4 Genetics Has Provided a Powerful New Approach to Biological Research The genetics revolution has radically influenced the way that biological research is done today. Genetics takes a unique approach to answering biological questions that relies on discovering genes relevant to that question. The investigator starts with a biological function that he or she wants to understand, then looks for mutant genes in which that function has been disrupted. This approach first defines the set of genes underlying the function of interest; then the normal and abnormal functions of those genes can be explored. Seeing how a mutant gene goes wrong can provide great insight about its normal function. Finally, all the genes discovered via such “mutational dissection” can be pieced together to construct the overall system at work in the cell. Every gene identified in this way reveals an important “word” in the genetic program underlying the function, while finding a set of genes all affecting the same function reveals the “sentences” that define the program. This type of genetics works in two ways, called forward Mechanical predecessor to the vacuum cleaner and reverse genetics.

Forward genetics The starting point of forward genetics is to treat cells of the normal wild-type form of the organism with some agent such as X rays or certain chemicals that causes mutations. Then descendants of these cells (usually organisms growing from them) are screened for abnormal manifestation of the function in question.

For example, if we are interested in the biological function “color” and the wild type is purple, then we might look for mutations producing any other color (blue, red, pink, and so on) or even the absence of color (white). The first question asked is, Are these properties inherited as a single mutated gene? That question can be answered by crossing each presumptive mutant organism to a wild-type organism, then inspecting the ratios of wild-type to mutant progeny in the subsequent generations of descendants. The ratios indicating single-gene inheritance were originally established by the “father of genetics,” Gregor Mendel, in the 1860s. A Electrical Vacuum gene discovered in this way can be mapped or isolated, often leading to its DNA cleaner (without artificial intelligence) sequence.

The next step is to determine the function of each gene that has been identified. Returning to our example, we would ask, How does that gene act to influence flower color? The biochemical properties of each mutant obtained are studied at the molecular level and the defective protein encoded by that gene deduced, an important step in piecing together the overall system of reactions responsible for color. Hence, overall forward genetics can be represented by the sequence Robotic (automatic) vacuum cleaner Mutation gene discoveryofl sequence and function Fig. 3.l The evolution theDNA form of the vacuum cleaner.

The relatively new field of genomics has facilitated this approach: once a gene technology driven shape changes in Categorization encompassing threesequence, kinds of then for a specific 3.3 property has been mapped in the genomic that products gene’s sequence is known, and if that gene has been studied in experimental The methodology for determining causality changes in technology, changes in the organisms, then because of evolutionary homology, it isthe very likely thatofa function is already known for it. For example, human genes forand proteins promote tranfor the analysis of feasibility of external shape of the products, the that methodology scription haveapplication been identified by emerging their homology with thein genes of fruit flies and of an technology a product, encompass the collection of data on the yeast. Many heritable disorders have complex inheritance (heart disease, diabecharacteristics and performance of products according to the technology that they embody, tes, and cleft palate are as some several genes; genomic analysis as well of examples) the data involving on the morphological differences occurred due to that technology has begun identifying these genes too. change. Encompassing the various kinds of form changes occurring in technology products,

Reverse genetics The reverse genetics approach starts with a gene sequence (probably learned from a genome sequence) that has no known function and then attempts to find

18

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The Genetics Revolution in the Life Sciences

16

Industrial Design – New Frontiers

that function. As in forward genetics, an important step is to obtain mutations in necessitates creating a categorization that considers the many changes in technology that gene. Several experimental approaches exist that can target mutations to an products. This is a tripartite which isare divided into threedirected variations. individualcategorization, gene. These approaches generally termed mutagenesis. One This categorization served throughout the study reported in this chapter frame the kind such approach is to completely knock out the gene’s functiontoby eliminating the of change that occurred in then the to product after another incorporated it. Thus, gene and look for the effects on thetechnology organism’s function.

Alterations in the changes were classified according to variations that occurred during the passage of function of the mutant gene reveal aspects of the gene’s biochemistry when fulLCD, LCD + LED, PDP andthat OLED), as well as television sets by various technologies ďŹ lling its normal role.(CRT, (The technique works well for genes are found as only one copy.from It hasthe been discovered fromby genomics some genes(non-electric, are present in the shape changes resulting passage of irons variousthat technologies more than oneof copy, and inharvesting such cases it-isEH), possible knock them all out.) Reverse electric power and the principle energy and,tofinally the changes in the genetics can be summarized by technologies the sequence (mechanical - human strength, vacuum cleaner with the emergence of various electrical - without Artificial Intelligence, robotics and MEMS).

Gene (DNA sequence) l mutation l function Thus it is possible to characterize the changes that occur in the products that were studied, within the following three categories: -ESSAGE " OTH FORWARD AND REVERSE GENETICS WORK BY ANALYZING MUTATIONS AND THEIR 1st type - change in the shape of the product caused by changing technology (appearance of EFFECTS BY SHOWING HOW A GENE GOES WRONG WE DEDUCE ITS NORMAL FUNCTION a new technology or application of an existing technology but that was never used in this type of product) which leads to a visible shift in the product shape, yet the product as an Manipulating DNA object remains; Like all scientists, geneticists a largechange proportion of reflected their inferences by technology is not so much 2nd type - product change, in situations where make manipulating the system observing for the modification effects. Hence,of there is always a need in changing the shape of the product, but isand responsible performance and manipulate genomeasin an speciďŹ c ways.object Genomes billionstoofsurface nucleoimproved efficiency,tokeeping thethe product existing andcontain proceeding tide pairs and are too big to handle as one unit, and so most DNA manipulation shape change in order to signal the increased performance to consumers, and, finally, 3rdis on parts of the genome, often single genes. Forty years type - cessation of performed existence by of focusing the product as such, in situations where the change in ago, this was impossible, but it is now routine in research and in applications such technology leads to a deconstruction of the product as an object, leaving behind the as medicine and agriculture. How is it possible to get one’s hands on a small segarchetypes and stereotypes hitherto with isthe product. ment of DNA? Theassociated basic approach called DNA cloning, which means taking a DNA fragment and replicating it many times over until there are many copies so that essentially it can be treated like a reagent in a test tube. The process of replicating a DNA sequence is called “amplifying,â€? in the same way as a guitar The aim of this chapter was multiplies to undertake a study about the influence of technology in the ampliďŹ er the volume of sound. form of products that incorporate a standard methodology developed Fragments oftechnology, the genome using are obtained by cutting the DNA in some way;for for this purpose. Examples of products and their or shape changes over timeenzymes. were presented. example, by vigorous agitation scissoring it with certain Fragments are inserted into a small called vecAttempts to understand the individually extent to which theseself-replicating changes arechromosome consequences ofa the tor (carrier).were The vectors with their loads then introduced individuallyasinto developments in technology put forward, and theare importance of technology a separate live bacterial cells.

The vector replicates as the cell divides, and its determinant of the shape of products that incorporate technology was demonstrated based inserted fragment is thus automatically replicated too. As each cell divides on three cases. repeatedly, it becomes a colony, which contains a clone (multiple replica) of one A review of the evolution of form, taking into account the technology of a selected range of DNA insert. consumer products thatA incorporate technology, the aim of deconstructing DNA clone can be used in awith number of ways; for example, the archetypes DNA can be that are fixed andmodiďŹ ed propose new ideas was accomplished.

In particular, a range of and reintroduced back into the original organism, introduced into a diftechnologies that are foreseen fortothe future were considered, and theseand were the ferent organism create a transgenic organism, or sequenced the also sequence with otherand cloned genomic sequence.

Cloned subject of study in assembled this contribution, are sequences expected totoproduce enable anew designs and future is used many syntheses of industrial such as enzymestothat forms for a great DNA variety of inproducts, which in some proteins, cases may bethesubject a make sugar from cornstarch, and of medically important proteins, such as human deconstruction of the archetype of the object's shape. growth hormone. from a historical perspective, one could see what have Selecting specific cases of products, been the determinants of their speciďŹ c shape, which led to the establishment of their archetypal Detecting sequences of DNA, RNA, and protein form. A comparative methodology was developed, in order to hint at the role of technology Whether studying gene structure or function, geneticists often need to detect as a determinant of the shape of products. a DNA, RNA, or protein speciďŹ c to one gene of interest. For example, they Understanding the importance oftotechnology asimplicated a modelling for products’ might attempt isolate a gene in a influence human hereditary diseaseform, along what is its responsibility as a major element what role this has inwith the its consumer society and RNA transcript and the associated protein. How can speciďŹ c molecules be detected among the thousands of types in the cell? One extensively used method for detecting speciďŹ c macromolecules in a mixture is probing. This method makes use of the speciďŹ city of intermolecular binding—for example, the binding afďŹ nity of an mRNA to the DNA sequence from which it was tran-

4. Conclusion

20

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The Genetics Revolution in the Life Sciences

17

Technology as a Determinant of Object Shape

speciďŹ c type of cancer. An example of such a result is A probed microarray in the DNA deconstruction of the archetypes shown of form was also in this also contribution.

The in Figure 1-22.focused This technique has a wide range

influence of technology in the transformation products was demonstrated, considering of otherof uses. three distinct types of alterations caused by changes in technology, in a tripartite view.

Detecting and amplifying sequences using the polyFollowing the study of the technologies, which was methodologically structured, and merase chain reaction (PCR) If a region has been seconcerned the technologies embedded in the three analysis, in the pastregion and quenced, it is products possible toin detect homologs of that with a forward view (technology that isinforeseen for the future), a scenario is proposed, an unknown sample using the polymerase chain rewith new designs for the products that have(PCR). been The studied (Figures 4, inspection 5 and 6). ofIt the is action method requires may disappear may be single-stranded dissolved in emphasized that the product as a physical object genome sequence and pickingortwo short the environment or building architecture, with the advent of emerging and DNA segments that ank the regiontechnologies in question. These their new capabilities. segments can be used as primers to initiate DNA replication across that region. Technical details will be given in Chapter 10, but in brief, the replication process shuttles back and forth across the region, with each synthesized copy acting as the template for a new round of synthesis.

The process expands exponentially, giving multiple copies of a DNA segment that is the equivalent of that region (Figure 1-23). The primers will work only if the unknown Figure 1-22 %ACH SPOT IN THIS sample contains a homolog of the target region in question (including of course MICROARRAY IS A DIFFERENT $.! SAMPLE the primer sequences), and so if any PCR product is obtained, the test acts as a ATTACHED TO AN INORGANIC SURFACE 4HE diagnostic for the presence of that DNA in the sample.

DIFFERENT COLORS REPRESENT DIFFERENT The PCR technique has found widespread use throughout the life sciences, AMOUNTS OF LABELED C$.! PROBES including forensics, medicine, and agriculture: it can rapidly detect the presence DERIVED FROM M2.! TRANSCRIPTS THAT HAVE BOUND TO THE SAMPLES IN THE ARRAY 4HE of speciďŹ c segments of interest in any type of diagnostics. Target DNA present in PATTERN SHOWS WHICH GENES ARE ACTIVELY very small amounts cannot be detected, but DNA samples can be ampliďŹ ed with TRANSCRIBED IN THAT CELL TYPE ;Alfred PCR, allowing the sequence in question to be identiďŹ ed if it is present. Detecting Pasieka/Photo Researchers.] a particular sequence is often the goal (as in forensics), but the ampliďŹ ed product can also be sequenced and studied further if required. For example, dry tissue from fossil or museum specimens can be subjected to PCR ampliďŹ cation, revealing DNA sequences of animals and plants long extinct.

PCR primers detect and amplify a speciďŹ c genomic region Region to be

Fig. 4. Multiple applicationsDNA of OLED technology in amplified a living room (lighting, shading, dynamic wall art gallery, TV monitor).

Primer 1

Primer 2

In the case presented in Figure 4, dematerialization of a product (TV set) and its blending with architecture is enabled by the ultra-thin OLED technology. This technology also enables new applications, including, as depicted, lighting, shading and a dynamic wall art gallery. This case leads to question the role of industrial design in this foreseen evolution.

Understanding people and their relation to artefacts, interaction design and concept creation (even if devoid of a three dimensional form) are bound to be design domains that industrial designers should focus on in supporting this kind of design endeavour.

The conceptual design presented for an energy self-sufficient travel iron (Figure 5), represents an archetypal leap from the traditional shape of this product, which caters to sustainability concerns. Independence of energy supply is bound to be another guiding theme to foster the creation by industrial designers of new product archetypes to perform functionality that had been tied to a fixed product concept.

Figure 1-23 3HORT SYNTHETIC $.!S HOMOLOGOUS TO mANKING REGIONS CAN PRIME THE SYNTHESIS OF MULTIPLE COPIES OF THE mANKED SEQUENCE PROVIDING A LARGE SAMPLE OF THAT $.!

FOR ANALYSIS

Multiple copies of region

1.5 Model Organisms Have Been Crucial in the Genetics Revolution

18

Industrial Design – New Frontiers

Probing for a speciďŹ c RNA It is often necessary to detect an RNA transcript in some particular tissue. For this purpose, a modiďŹ cation of the Southern analysis is useful. Total mRNA is extracted from the tissue, separated into fragments of different sizes using electrophoresis, and blotted onto a membrane (this is called a Northern blot). The cloned gene is used as a probe, and its label will highlight the mRNA in question if it is present (see Figure 1-21b).

Probing for a speciďŹ c protein Probing for proteins is generally performed by using antibodies as probes. An antibody is a protein made by an animal’s immune system; it binds with high afďŹ nity to a molecule such as a speciďŹ c protein (which acts as an antigen) because the antibody has a speciďŹ c lock-and-key ďŹ t with it. For protein detection, a protein mixture extracted from cells is separated into bands of distinct proteins by electrophoresis and then blotted onto a membrane (this is a Western blot). The position of a speciďŹ c protein of interest on the membrane is revealed byFig. bathing the membrane in a solution antibody obtained from a 5. Energy self-sufficient travel of iron. rabbit or other host into which the antigen has been previously injected. The position of the protein is revealed by the position of the label that the antibody carries (see Figure 1-21c).

-ESSAGE .UCLEIC ACIDS CAN BE USED AS LABELED PROBES OR PRIMERS FOR DETECTING

HOMOLOGOUS NUCLEIC ACIDS ON GELS ON INORGANIC SURFACES OR IN SOLUTION )NDIVIDUAL PROTEINS CAN BE DETECTED USING LABELED ANTIBODIES

1.5 Model Organisms Have Been Crucial in the Genetics Revolution As you read this textbook, you will encounter certain organisms over and over.

Fig. System for andSaccharomyces battery charge of robotic vacuum cleaner.

Organisms such as 6.

Escherichia coli unloading (a bacterium), cerevisiae (baker’s yeast), Drosophila melanogaster (fruit y), and mice have been used repeatedly as The conceptual design presented in Figure 6 represents an incremental shape evolution the subjects of experiments that have revealed much of what we know about how from the current shape archetypes for vacuum As growing automation and genetics works.

Whyone doesofscientiďŹ c research make use of a relatively smallcleaners. group of organisms? convenience for consumers proceeds, industrial designers are also bound to play an important role in organisms, establishing links with because past erathey designs, and as such provide consumers in These species, called model were chosen are well suited to studythis of the biological investigation.

Part of the suitabildigital age, question objects under that enable reminiscing of past eras, with a shape that cues their ity of model organisms is biological: thata organism should that functionality, providing deliberate a linkhave withproperties traditional shapes. lend themselves particularly well to that investigation.

A suitable model organism There are limitations in the methodologies presented in this chapter, which will be also has the beneďŹ t of expediency: small organisms that arenecessary easy and cheap to alleviated if the prerequisites that are for their effective use are met. The maintain and grow quickly are very convenient for research. Because of evolumethodologies and categorization are only deemed suitable for application in products tionary homology, what is learned from a model organism such as the fruit y can that incorporate technology for their operation. It is important for the deployment of often be applied to other species, even humans. theseofmethodologies to haveare knowledge on emerging technologies and on the history of Some examples genetic model organisms as follows (some are illustrated the product or devices that have been used for in Figure 1-24). The genomes of all these model organisms have been sequenced.implementation of a particular Because offunctionality. their small size, billions of bacteria can be used in an experiment. have failed, and that were put aside, There some permits historical of technologies The use of such largeare numbers thecases detection of extremely that rare genetic events. Also, bacteria be spread special of solid medium that becausecan there was on ana arrest the market byautomatically a technology already implemented. This selects for a speciďŹ c rare genetic event (such mutations or video new DNA combinahappened for example withasSony’s Beta system, which was of higher quality than tions). Thus, the system is said to have a high resolving power between the rare(despite the better quality of the Philip’s VHS (Video Home System), but the latter prevailed and the wild-type genetic state. Bacteria are also particularly handy because bacBeta video system), because films existed in greater quantities in the VHS format, which led teriophages (bacterial viruses) can be used as vectors to carry pieces of DNA from to the decrease of availability of films in Beta format. There is no guarantee that the three one bacterial cell to another. For these reasons, most of the early discoveries in molecular genetics were made in bacteria. For example, bacteria were the model organisms used in the experiments that revealed the sequence DNA l RNA l protein. Later on, the art of DNA cloning and manipulation was pioneered in bacterial systems.

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Technology as a Determinant of Object Shape

19

Some organisms models in genetic emerging technologies selectedused will as have a future in the research market, or even a future in the product (or application) that has been studied. The fact that emerging technologies are still developing, makes their performance characteristics modifiable and changeable in a short time span. It is also noteworthy that the current concerns about environmental sustainability have led governments to constrain the free operation of markets which can alter the dynamics of competition for emerging technologies, seeking to accelerate the implementation of more sustainable alternatives, and restricting the widespread adoption of other technologies, which may discourage the implementation of some emerging technologies.

5. References Baudrillard, J. (1995). Sociedade de consumo [in Portuguese – The consumer society], Lisboa: ediçþes 70. (a) Beeby, S., Ensell, G., Kraft, M. & White, N. (2004). MEMS Mechanical Sensors, Southampton, United Kingdom: Artech House.

Bengisu, M. (2003). Critical and emerging (b) technologies in materials, manufacturing, and industrial engineering: a study for priority setting, Scientometrics, Vol. 58, No. 3, 473-487.

Bengisu, M. & Bekhili, R. (2006). Forecasting emerging technologies with the aid of science and technology databases, Technological Forecasting & Social Change, Vol.73, 835844.

Bloch, Peter H. (1995). Seeking the ideal form: product design and consumer response, Journal of Marketing, 59(3), 16-29.

Corda, F. A. A. (2010). A tecnologia como determinante da forma dos objectos [in Portuguese – Technology as a determinant of object shape], Master of Science Dissertation in Technological industrial Design, Dept. Electromechanical Engineering, Universidade da Beira Interior, Portugal. Available on-line at http://webx.ubi.pt/~denis/MDIT/dissertacao_FilipeCorda.pdf Crilly, N., Moultrie, J. & Clarkson, P.J. (2009). Shaping things: intended consumer response and the other determinants of product form, Design Studies, 30(3), 224254.

Damrongchai, N. & Michelson, S.E. (2009). The Future of Science and Technology and pro(c) (d) poor applications, Foresight, 11(4), 51-65.

Glenn, J.C., Gordon, T.J. & Florescu, E. (2008). 2008 State of the Future. The Millennium Project, Washington, DC. Designyeast Process in an Industrial C., (1991). Analysis of thefungi Engineering Figure 1-24Hales, 3OME MODEL Ascomycete such as baker’s (Saccharomyces cerevisiae)Context, and the ORGANISMS A "ACTERIOPHAGE moldGants Neurospora crassa have their products of meiosis enclosed in a small sac, Eastleigh, UK: Hill Publications.

L ATTACHED TO AN INFECTED which made them ideal subjects for studies skills on meiosis and mating.

Yeast later Lewis, W. P., Bonollo, E., (2002), An analysis of professional in design: implications for Escherichia coli CELL PROGENY became the center of studies of the genes that regulate cell division; many such education and Research. Design Studies No.23, pp. 385-406.

PHAGE PARTICLES ARE MATURING genes were demonstrated to be important in human cancer.

INSIDE THE CELL B Neurospora Roozenburg, N. F. M. & Eekels, J., (1995). Product Design: Fundamentals and Methods, Arabidopsis thaliana is a miniature owering plant that can be cultured in GROWING ON A BURNT TREE AFTER A Chichester:large Johnnumbers Wiley &inSons. the greenhouse or laboratory. It has a small genome contained FOREST lRE C Arabidopsis. D display – CRT bymany flat-panel Salmon, R. (2004).

The changing world ofIt has TV been Caenorhabditis elegans. ;(a) Lee in only ďŹ ve chromosomes. an ideal modelchallenged for exploring aspects display, EBU technical review, pp.1-9. of plant parts ranging from roots to D. Simon/Science Source/Photo of plant biology, such April as the2004, development Researchers; (b) courtesy of David owers in higher plants.

Jacobson; (c) Wally Eberhart/ The common fruit y, Drosophila melanogaster, has only four chromosomes in Visuals Unlimited; (d) Sinclair its genome.

In the larval stage, these chromosomes have a well-marked pattern of Stammers/Photo Researchers.] banding that makes it possible to observe large-scale chromosomal alterations,

1.6 Genetics Changes Society

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Industrial Design – New Frontiers

which can then be correlated with genetic changes in morphology and biochemTseng, F., Cheng, A., & Peng, Y. (2009). Assessing market penetration combining istry. The development of Drosophila produces body segments in an anterior– scenario and the technological posterior order that exempliďŹ es theanalysis, basic bodyDelphi, plan common to invertebrates andsubstitution model: The case of thebeen OLED TV market, Technological Forecasting & Social Change, Vol.76, 897– vertebrates, and much has learned from the fruit y on this topic.

909. mouse, has been the model organism for vertebrates, Mus musculus, the house especially for humans. its(2004). small size, the mousedisplay has beentechnologies used in manyfor the best image performance, de Vaan,Because A. J. S.ofM. Competing genetic analyses, including studies of mutation, development, and transgenesis.

Journal of the SID, 15, 657-666.

-ESSAGE -OST GENETIC STUDIES ARE PERFORMED ON ONE OF A LIMITED NUMBER OF MODEL ORGANISMS WHICH HAVE FEATURES THAT MAKE THEM ESPECIALLY SUITED FOR SCIENTIlC STUDY

1.6 Genetics Changes Society Many beneďŹ ts to humanity have resulted from the applications of genetics in medicine, agriculture, and industry. Consider modern agriculture. Most crops and farm animals of today are only distantly related to wild species found in nature since their genomes have been extensively modiďŹ ed by systematic breeding programs.

This is also true of garden plants and domestic pets. Although this selection process began centuries ago, traditional and molecular genetics have streamlined it to produce valuable varieties in a much shorter time. Now there is almost no limit to the possible gene combinations that can be produced. Even combinations of genes from different species can be produced by introducing a “foreignâ€? gene into an organism. The foreign gene is called a transgene, and the organism into which geneticists have inserted a “foreignâ€? gene is called a transgenic organism (Figure 1-25). Crops modiďŹ ed with transgenes for insecticide and herbicide resistance are being widely farmed. Animals have been modiďŹ ed too: for example, certain transgenic goats produce the medically useful anti-blood-clotting protein antithrombin and secrete it in their milk for convenient extraction. Transgenic bacteria are in use industrially for synthesizing important drugs such as human insulin and human growth hormone. Transgenic strains of yeast are used in making the bread we eat and the beer and wine we drink.

In medicine, the results have been just as striking. As we have seen above, many diseases have been identiďŹ ed that are caused by mutations in single genes. Such knowledge allows more rational genetic counseling of families at risk. Perhaps more important, every time a gene causing a disease is identiďŹ ed, it is the beginning of a line of research that will reveal the gene’s function and then lead to possible therapy. A good example is in the discovery of the gene for phenylketonuria (PKU), a discovery that led to the alleviation of the disease through special diet.

The ability to modify genomes has inspired the tantalizing hope of correcting genetic disease at the DNA level, a process generally known as gene therapy. The development of the technology for transgenesis has made replacing defective genes with normally functioning ones a distinct possibility. Indeed, such gene therapy has been successful in animal models. In humans, more effective methods are needed for delivering the transgenic DNA and ensuring that it will function properly once in the genome. However, there have been some successes. In a recent case, gene therapy partially cured blindness resulting from the disease Lieber’s congenital amaurosis, caused by a mutation of a gene active in the retina.

A signiďŹ cant impact of genetics has been in forensics. Each genome, whether human or animal or plant, can be treated to prepare an individualistic “DNA

A transgenic organism

Figure 1-25 4HESE TRANSGENIC

MOSQUITO LARVAE ARE EXPRESSING A JELLYlSH GENE FOR GREEN mUORESCENT PROTEIN 4HE GENE IS EXPRESSED AT SPECIlC SITES IN EACH SEGMENT ;Sinclair Stammers/Photo

Researchers.]

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A DNA ďŹ ngerprint

ďŹ ngerprintâ€? (Figure 1-26). Most DNA ďŹ ngerprint approaches are based on the observation that certain regions of the genome are found in multiple adjacent copies (repetitive DNA), and the number of copies at any chromosomal position is highly individualistic. Comparison of several such sites reveals a personal ďŹ ngerprint.

DNA ďŹ ngerprints can be prepared even from minute amounts of bodily uids (blood, sweat, saliva, semen) by chemically amplifying the DNA Carlosusing A. M. Versos and A. Coelho a method called PCRDenis (see above).

PCR and Universidade da Beira Interior DNA ďŹ ngerprinting have revolutionized the identiďŹ cation of suspects in crimes. Portugal

6

Biologically Inspired Design: Methods and Validation

1. Introduction

1.7 Genetics and the Future

The genetics revolution has occupiedinspired much of Design inspired by nature, bionic design, biomimetism, biomimicry, or biologically the last 100 years, and this chapter so has design, despite having been a source of inspiration for design activities for a long time,far have shown the great impact of genetics on the life sciences over this time, both on Figure 1-26 $.! lNGERPRINTS FROM recently, under pressure from sustainability concerns, gained a role as part of a standard set basic research and in applied research areas. In research generally, the continual PATERNITY DETERMINATION INVESTIGATIONS of approaches to deal with design problems. Nature provides an important model to find "ANDS BLACK STRIPES IN COMMON SHOW and rapid advance of genetic technology means that the ability of biologists to solutions to the ecological crisis. The aim of this chapter is to establish a comparison among FROM WHICH PARENT A CHILD INHERITED $.! genetically dissect all biological functions will undoubtedly improve in ways that meant guide industrial designers in been carrying out activities ;Martin Shields/Alamy.] a set of design methods, we at present cantoonly guess.

The pattern has already established: powerful literature review are presented, with emphasis leading to bio-inspired design.that Theonce results ofsupreme techniques were challenges later become routine and applidrawn on existingcable documented approaches design that inspired nature, the more widely, especially totoorganisms are notbymodels and and that were presentation of the methods, a comparative thought toon bewhich genetically intractable. analysis is established. The parameters Perhapsare the set biggest willfive be ingeneral the areagoals of development.

Although a for the comparative analysis out,challenge based on that are considered great deal has been learned from model organisms about how speciďŹ cally the applicable to design problems, within the realm of industrial design. The presentation and body plan is laid down andby the that control thisimplications plan, there isfor stilltheory a long explanation of the comparisons is followed a genes discussion on their journey before a complete and detailed understanding of the building of a living and practice. organism is obtained. This information will be directly relevant to human develThe present day’s urgency in achieving environmental sustainability has promoted renewed opment and medical diagnosis and treatment. No doubt, over the coming decades, interest on gathering inspiration from nature in order create novel designbetter concepts. genetic disease (and indeed healthy humantofunction) will be much underDesign endeavoursstood in several technical disciplines may lead to ground-breaking new as a result of genetic research. a source of inspiration.

The focus of this concepts when natural As systems are considered as population increases put more and more pressure on land and other global chapter is on joiningresources, a bio-inspired to rely the creation of industrial design engineering societyapproach will have to more heavily on the most powerful technologies to provide the food,to clothing, housing, and health of of its members. concepts with a systematic approach design.

The conduction industrialInevitably, design the power of genetic technologies will be called on.

Any powerful new scientiďŹ c engineering projects is inherently structured and supported by methods set forth in the technology(e.g. leadsHales to ethical application.

Good examples are the systematic design literature 1991,dilemmas Hubka in & its Eder 1992, Roozenburg & Eekels nuclear and chemical industries, which although beneďŹ cial in many ways 1995, Pahl & Beitz 1996, Ulrich & Eppinger 2004). Hence, in order to be useful andhave of contributed to global pollution and deaths from accidents and exposure to toxins. practical value to the generation of industrial design engineering concepts, bio-inspired The question any individual scientist must ask is whether or not his or her discovdesign methods should bebeable to fit to into that follow systematic ery will applicable thedesign generalendeavours good. Even discoveries thata do not seem approach to design. directly applicable to societal problems nevertheless contribute to the general of nature, of what it created, tested The main purpose ofpool bionics is to carry benchmark of knowledge thatout canabe used or abused. and has evolved over millions of years, in order to improve creates artificially One of the greatest temptations may be in thewhat area ofman eugenics.

Broadly, eugenics has been “improving the quality of human births.�

When the journey (Benyus 1997). A number ofdeďŹ ned designas methods, intended especially to guide industrial of gene began in theofearly twentieth century, human behavioral designers in carrying out discovery the development biologically inspiredmany design, have been traitsestablishes were prematurely attributed to genes.

As a result, eugenics movements proposed. The chapter a comparative analysis between five methods, retrieved up in North Americainand Europe, and laws for theof sterilization from literature. The sprang methods are presented similar depth, andwere the passed parameters analysis (and even euthanasia) of people with traits that were considered undesirable in the population. Regrettably, these decisions were based on erroneous genetic understanding, in many cases backed up by societal and political prejudice.

However, what might our position be when genetics has advanced to the stage at which we do have a good understanding of complex human genetic conditions?

Key Terms

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Industrial Design – New Frontiers

Gene therapy is just one relevant area: if it is possible for a couple to have a baby are also described. The five bio-inspired design methods discussed, following an analytical free of genetic disease or suffering via gene therapy, why shouldn’t the technology direction thatTaking involves seeking inspiration in nature to solve a given problem, were be made available and used? the logic further, should parents be allowed from literature andsafe areways—for summarily presented.

These methods are analysed in this to have a babyretrieved genetically tailored in specific example, given high with regard to their perceived capacity to basis support the satisfaction of the five chosen intelligence orchapter athletic or musical ability.

As more is learned about the of our highwill level aims.

These aimsfreedoms? were selected considering individuality, how thisdesign knowledge affect human If a sound genetic their high degree of perceived basis is foundrelevance for certainto types of antisocial behavior, how willproblems. the legal system A critique of the bio-inspired design industrial design engineering deal with the methods responsibilities and is rights If we can accurately predict retrieved laid involved? out, informed by comparison between the methods regarding their susceptibility to various types of disease, how will this affect our relationships and is based on the scrutiny of the ability to support the satisfaction of the goals. The analysis attitudes toward each other (such as in mate selection), and of course how will five methods, in relation to the support given towards the satisfaction of five goals, health insurance deal with it? One thing is clear: these kinds of societal decisions considered of paramount importance, and which are present in typical design projects, will need to be made, and ultimately they will depend on a public and a governalbeit and translated into ainnumber ofofrequirements, specific to the problem at hand. The ment well educated knowledgeable the subject genetics. comparative analysis is intended to support designers in the process of selecting a design method that is adequate to the problem at hand. The analysis also identifies goals where the Summarymethods considered offer no or reduced support for their satisfaction, hence identifying the need for novel methodological proposals. The need to integrate validation activities in the The impact ofbio-inspired genetics on biological research and applichangeasrelevant Evenand afterfollowed species diverge design processes is its also emphasized a resulttoofevolution. the analysis cations has been so far reaching that it has been called “the during evolution, the DNA sequences of these species conthrough by the proposal of explicit procedures for validation of the satisfaction of goals genetics revolution.” Genetics is now part of the analytical tinue to show considerable similarity (homology). This sought by those pursuing biologically inspired design. This approach is intended to enable framework of virtually all areas of biology. It has provided DNA homology is convenient for research in that what is the evaluation of main outcomes attained with thelearned use of bio-inspired fundamental insights into all the questions of biology in one speciesdesign can bemethods, applied tooffering another. DNA to pursue the validation of bio-inspired methodological support to designers in order that were previously unanswerable. homology is used extensively for making evolutionary trees. concepts generated byhow them.

These validation procedures are of demonstrated in a specific One perennial question has been living systems The incisiveness the genetic approach is based on the design withcomponents the purpose of in exemplifying theofapplication of thea biological validationfunction steps can be generate “form” fromcase random taken as concept genetic dissection: nutrients. Biological information (that which is initially needed toconsidered picked apart through the use of mutations—each mutation proposed.

The requirements for the development of the product generate form) was shown to be encoded in our DNA, the represents another gene in the overall program behind the functionality considered in the case are also presented and a solution that is proposed to function in question.

Technological advances have allowed central molecule of life.

The information encoded in DNA is fulfil these requirements, generated using a bio-inspired approach, is evaluated, according individual genes to be isolated, studied, and moved into the perennial to blueprint that is handed down through genthe validation approach presented. other species for research and for making “designer organerations. Form is largely a product of an organism’s proThe deployment of the validation process proposed is done within an iterative design case, isms.” The advent of genomics has expanded genetics to teins. The DNA molecule is divided into functional units consisting of a novel CD rack, which draws inspiration form as its main solution further allow complete genenature, sets (genomes) to be analyzed, called genes. Most genes encode a specific protein. The proprinciple is steps: inspired on 1the spider-web. The extending process of makes use ofgenetic surveys, thevalidation ability to see complete systems at tein is synthesized in two in step (transcription), conceptual-analytical arguments and standard engineering design procedures. work in normal and disease situations.

RNA is transcribed from DNA, and in step 2 (translation), Human society has benefited from the genetics revolution. the RNA is “read” to synthesize a protein. The subunits of The deep level of understanding that genetics brings about the DNA (nucleotides) are read in groups of three, each corre2. Bio-inspired design nature and evolution of life has allowed humans to philosophisponding to an amino acid in that gene’s protein. DNA The term system, ortobio-inspired generally hasand two usual interpretations, cally see their own other species in a new way and to structure is ideally suitedbionic to enable copies be made of systems, concerning different every application domains. popular interpretation, based frequently on design applications in medicine, agriculture, and industry. itself. DNA molecules are replicated time a cell or an The The future, with its increasing pressuresand on resources, organism reproduces, enablingisthe information persist science fiction, associated to to more or less fantastic super-powers, to cybernetics to will inevitably draw heavily on genetic technology. endlessly through time. a robotic creations or additions to organisms. In this line of thought, bionics is presented as However, with thedevices likely progress comes a set human of ethicalbeings dilemmas surAlthough DNA structure persists through it does producing science uniting biology and time, mechanics, that capacitate rounding the application of the new discoveries, dilemmas undergo random in powers, the process of mutation. with change enhanced whether to compensate for innate or acquired physical limitations, regarding human individuality and our treatment of other Mutation is the source of much variation between individuor for mere enhancement. Besides this interpretation, the term bionics is associated with the organisms and the environment. For all these issues, a firm als of a species. If acted on by natural selection over time, meaning (bios – life,understanding mimesis – imitation). to Benyus of genetics According will be required to make wise mutation can original produce new speciesofinbiomimetism the process of evolunature, representing a novel mindset based (1997), biomimetism is a way to see and value decisions. tion. Genetics has been crucial in showing mechanisms of not on what can be extracted from the natural world, but what can be learnt from it. This interpretation is the one of concern in this contribution. In this view, the main purpose of KEY TERMSbionics is to carry out a benchmark of nature, of what it created, tested and has evolved over millions of years, in order to improve what man creates artificially. forward genetics (p. 17) adenine (A) (p. 3) deoxyribonucleic acid (DNA) (p. 1) diploid (p. 5) functional RNA (p. 11) centromere (p. 7) DNA cloning (p. 18) gene (p. 2) chromatin (p. 7) epigenetic (p. 13) gene pair (p. 6) codon (p. 11) extranuclear (p. 7) genetic code (p. 3) cytosine (C) (p. 3)

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103

genetics (p. 2) model organism (p. 21) reverse genetics (p. 17) In the following sub-sections, the origins bionics areacid summarily genome (p. 4) molecular genetics (p. 2)and evolution of ribonucleic (RNA) (p.reviewed, 9) while recalling a few well known examples of bio-inspired design solutions.

Arguing mutation (p. 12) genomics (p. 2) ribosomal RNA (rRNA) (p. 11)for the of design inspired designers, the section ends guanine (G) (p. 3) growing importancenatural Southern blot (p. 19) selection (p. 14)by nature for industrial that will(p. come with the presentation of fiveblot bio-inspired design methods telomere haploid (p. 5) 7) under scrutiny in Northern (p. 21) haploid number (p. 5)the remaining sections theory of evolution (p. 14) nucleosome (p. 7) of the chapter. histone (p. 7) thymine (T) (p. 3) nucleotide (p. 3) homolog (p. 5) transcription (p. 9) polymerase chain reaction (PCR) 2.1 Origins and evolution of bio-inspired design homologous chromosomes (p. 5) transfer RNA (tRNA) (p. 11) (p. 20) Although the terminology of this area of design is relatively recent – appearing for the first homology (p. 14) translation (p. 11) polypeptide (p. 11) time in the U.S.A. in 1958, by the hand of Jack E. Steele (Lloyd, 2008) – the practice, creation messenger RNA (RNA) (p. 9) Western blot (p. 21) probing (p. 18) and inspiration through learning about nature comes from the most remote and pre-historic times. Primitive human beings used bone harpoons, which were serrated on their edges, to PROBLEMS improve their piercing ability. This feature was likely inspired by animal teeth.

Leonardo da Vinci was compreprobably the first systematic of the possibilities bionics 9. In Figure 1-14,student what do the colors blue and goldofrepresent?

In each chapter, a set of problems tests the reader’s (Lage and Dias, 2003).

From the classical times of the Icarus legend, to the drawings of hension of the concepts in the chapter and their relation to 10. From Figure 1-17, locate the chromosomal positions of Leonardo da Vinci, man’s dream to fly originated in the observation of bird and insect flight. concepts in previous chapters. Each problem set begins with three genes involved in tumor production in the huLeonardo realized arms some problems based on the figuresda in Vinci the chapter, whichthat the human man body.were too weak to flap wings for a long embody important concepts. are followed by problems time, These and hence developed several sketches of machines he called ornitopters (Kindersley, 11. In Figure 1-18, calculate the approximate number of of a more general nature.

1995). Human flight would only be possiblenucleotide in the XXth century,between with thehumans aid of the differences andinternal dogs in engine the propeller, but the inspiration from nature is anyway at its onset.

Most of the problemscombustion are also available forand review/grading the cytochrome c gene. Repeat for humans and moths. design is Velcro, invented 1948, Onewww.yourgeneticsportal.com. of the most disseminated examples ofConsidering bio-inspired through the that the gene is several hundredinnucleoby Swiss engineer George de Mestral, from inspiration he got while observing thistles and tides long, do these numbers seem large or small to way they got caught in his dog’s tail and adhered you?

Explain.to clothes. In current times, designers WORKING WITH THEthe FIGURES Luigi Colani and Ross Lovegrove have 12. been in are portraying the useofofbands bionics in Ininstrumental Figure 1-21, why colored ladders shown 1. In considering Figure 1-2, if you were to extend the diause of biodynamic forms in products such as their creations. Colani became notorious byinthe all three electrophoretic gels? If the molecular labels gram, what would the next two stages of “magnificaused inhalf all cases were radioactive, you thinkand the automobiles and airplanes, during the second of the XXth century do (Pernodet tion” beyond DNA be? bands in the bottom part oforganic the figure would all Mehly, 2000). Lovegrove’s designs typicallyblack demonstrate a link between shapes and 2. In considering Figure 1-3, be a radioactive? material science (Lovegrove, 2004). While bio-inspired approach to design may not a. what do the small blue spheres represent? represent a universal tool that is applicable to any problem, it may provide support to b. what do the brown slabs represent?(Colombo, 2007). A set of five bio-inspired approaches to design, design activities BASIC QUESTIONS in literature, presented in the following sub-section. c. do you agree documented with the analogy that DNAare is struc13. In this chapter, the statement is made that most of tured like a ladder? the major questions of biology have been answered 3. In Figure 1-4, can2.2 you tell if thefor number of hydrogen Methods bio-inspired design through genetics. What are the main questions of biolbonds between adenine thymine is the same methods as designers organized process The goaland of bio-inspired design consists ogy, andindooffering you agree with the an above statement?

(State that between cytosine and to guanine? you think in order attain aDomodel thatthat may be applied in design, inspired by the relations between your reasons.) a DNA molecule with high function content ofin A T would be forma and nature (Colombo, 2007).

Despite the success several cases 14.

It has been said that the attained DNA l in RNA l protein more stable thanfrom one with high content of G

C? the use of this approach in design, the bio-inspired stillDohave discovery was the design “Rosettaapproach stone” of may biology. you 4. From Figure 1-6,room can you how manyinchromoforpredict improvement, order to become more systematic. Five existing methods have agree? somes there would be in a muntjac sperm?

How many been collected from literature and are presented in you Tables 1 to 5. the greatest impact on biology, 15. Who do think had purple chromosomes would there be in a sperm cell? the or importance environmental and The design method presented in Table 1 emphasizes Charles Darwin the researchofpartners James Watson 5. In examining Figure 1-7, state one major difference be-in the development economical sustainability factors and evaluation of the project by the and Francis Crick? tween the chromosomal “landscapes” of yeastshows and Drodesigner.

This method little support forgenetics organization method 16. How has affected problems. (a) agriculture,The (b) medicine, sophila. presented in Table 2 provides a detailed description the(d) procedures involved in natural (c) evolution,ofand modern biological research?

6. In Figure 1-8, is itsample true that the direction of transcripcollection and analysis.

It also prescribes completely listing the working principles of 17. Assume for the sake of this question that the human tion is from rightthe to natural left as written all the genes system.for However, this method body doescontains not include any procedures concerning the a trillion cells (a low estimate). We know shown in these chromosomal segments? design transfer of the features found in thethat natural samples. design method presented a human genomeThe contains about 1 meter of DNA. 7. In Figure 1-9, estimate what of DNA is shown in Table 3 length gives emphasis to the in product life cycle, giving consideration to issues If all the by DNA in your body were laid end tosuch end, as do the right-hand part of the figure. you think it could stretch to the Moon and back? Justify your answer with a calculation. (Note: The average 8. From Figure 1-12, what is the main difference in the distance to the Moon is 385,000 kilometers.) locales of transcription and translation?

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manufacturing processes, packaging and recycling of the product in development. In this method, iterations are implicit, and evaluation of the result of every step is also recommended.

Evolution of Genes and Traits Phase

Description

1. Analysis

Choice and analysis of a natural system.

The purpose of this phase is to understand the form, structure and functional principles of the natural system.

Extrapolation of mathematical, geometrical and statistical principles through a process of abstraction and simplification.

2. Transformation KEY QUESTIONS Transformation, by the analysis of the analogy, of the characteristics of s mechanical 7HAT ARE THE BASIC PRINCIPLES OF the biological system into technical and terms.

EVOLUTION BY NATURAL SELECTION Implement the principles of the relationship between form and s 7HAT OTHER PROCESSES IN 3. Implementation structure found in the natural system analysis, for the development of ADDITION TO NATURAL SELECTION new products.

PLAY A MAJOR ROLE IN MOLECULAR Development and evaluation of a new product taking the 4. Product environmental and economic factors for all lifeEVOLUTION stages of the product development into account. s (OW DO TRAITS AND GENES EVOLVE Table 1. The Aalborg bio-inspired design method (Colombo, 2007).s 7HAT ARE THE SIGNATURES OF NATURAL SELECTION OR ITS ABSENCE IN $.! SEQUENCES Description Phase s 7HY ARE REGULATORY SEQUENCES Identification of an unmet need in a satisfactory manner and that IMPORTANT IN THE EVOLUTION OF 1. Identification of allows the satisfaction of a particular problem and accurately, for subsequent analysis of the environment inMORPHOLOGICAL TRAITS search of potential need solutions. s (OW DO NEW GENES AND PROTEIN Practical process step involving the selection ofFUNCTIONS EVOLVE samples in nature that 2. Selection and fit the problem and the need at hand. Involves the search for samples 4HE THEORY OF EVOLUTION BY NATURAL SELECTION WAS DEVELOPED INDEPENDENTLY BY TWO INTREPID in nature and some knowledge about the habitat of the samples to be sampling "RITISH NATURALISTS #HARLES $ARWIN n AND !LFRED 2USSEL 7ALLACE n

collected and of the equipment to be used for the collection.

IN THE COURSE OF THEIR RESPECTIVE LONG VOYAGES [Darwin, at left: The Gallery Collection/Corbis; Wallace, at right: Hutton Archive/Getty Images.] Observation and analysis of the components of the morphological 3. Observation of structure, functions and processes, of the distributions in time and space of the Islands relationship the environment. Classification of the sample harles Darwin (1809–1882) arrived in theand GalapĂĄgos in 1835,with well into the sample. the fourth year of what was supposed to be a two-year voyage. One might think that these islands, now inextricably linked Darwin’s of name, were analysis, morphology and Through the with information functional 4. Analogy of Far thefrom it. Darwin found the islands hellishly hot, the young naturalist’s paradise. structure, the designer has the capacity to start considering the their broken blacknatural volcanicsystem rock scorching under theand hot feasibility sun. In his of diary he ob- of an analogyOUTLINE possibility application between the thetrees product served that “the with stunted show little signs of life .sample . . the plants also smell un-product to design. studied and the 20.1 %VOLUTION BY NATURAL pleasantly. . . . The black lava rocks on the beach are frequented by large (2–3 ft.)

Considering the feasibility of application SELECTION of the sample most disgusting clumsy lizards. . . . They assuredly well become the land they inhabcharacteristics to the design and from the functional, formal and 20.2 -OLECULAR EVOLUTION THE it.� Other than the lizards and the tortoises, the animal life on the islands was scant 5. Design structural as well as thedid needs and requirements and unimpressive.

He could not wait to leave the place.analysis, The 26-year-old explorer NEUTRAL THEORYof the implementation product, analysis of the system is held at this not know that his ďŹ ve weeks in the GalĂĄpagosproposed would inspire a seriesan of radical ideas 20.3 .ATURAL SELECTION IN ACTION that, some 24 years later with the publication of his On the Origin of Speciesstage.

(1859), AN EXEMPLARY CASE would change our perception of the world and our place in it.

Table 2. The biomimicry design method (Junior et al., 2002).

20.4 #UMULATIVE SELECTION AND THE Several months after leaving the islands, on the last leg of the voyage home to England, Darwin had his ďŹ rst ash of insight. He had begun to organize his copiPATHS TO FUNCTIONAL CHANGE ous ďŹ eld notes from his nearly ďŹ ve years of exploration and collecting. His plan 20.5 -ORPHOLOGICAL EVOLUTION was for experts back in England to lead the study of his collections of fossils, 20.6 4HE ORIGIN OF NEW GENES AND plants, animals, and rocks. Turning to his observations on the birds of the GalĂĄpaPROTEIN FUNCTIONS gos, he recalled that he had found slightly different forms of mockingbirds on

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three different islands. Now, there was a puzzle. The prevailing view of the origin Description of species in 1835, held by most of Darwin’s teachers and much of the scientific establishment, was that species were specially created Godthe in details their present Development of the Design Brief for a human needby with and 1. Identify form, unchangeable, and placed in the habitat to which they were best suited. specifications of the problem to be solved.

Why, then, would there be slightly different birds on such similar islands? Darwin Biological view of thenotebook: problem. Questioning the Design Brief from the jotted in his ornithology 2. Interpret perspective of nature. Translation of the functions of the project into When I see these Islands in sight of eachin other and possessed of but a scanty tasks performed nature. stock of animals, tenanted by these birds but slightly differing in structure Find the the same best natural modelsIto answer / address filling place in Nature, must suspect they are the onlychallenges varieties. . . . If 3. Discover posed. there is the slightest foundation for these remarks, the zoology of Archipelagoes will be well examining;most for such facts would undermine Select the "champions" withworth the strategies relevant to a particular 4. Abstract the stability of species [emphasis added]. challenge of the project.

Darwin’s insight was that species might Thismodels was nottowhat he had Developing ideas and solutions based change. on natural mimic 5. Emulate learned at Cambridge University.

This was heresy.

Although Darwin decided aspects of form, function and of the ecosystem as much as possible. to keep such dangerous thoughts to himself, he was gripped by the idea. After Evaluate the design solution considering the principles of life.

Identify arriving home in England, he filled a series of notebooks with thoughts about ways to improve the design and bring forward questions to explore species changing.

Within a year he had convinced himself that species arise 6. Evaluate issues such those related to packaging, naturally fromas preexisting species, as naturallymarketing, as children transportation, are born from parents and parentsnew fromproducts, grandparents.

He then pondered how species change and additions and refinements. adapt to their particular circumstances. In 1838, just two years after the concluand and refine design briefs lessons learnedhis from sion Develop of his voyage before he had yetbased turnedon30, he conceived answer— 7. Identify evaluation of life's principles. natural selection. In this competitive process, individuals bearing some relative advantage over others live longer and produce more offspring, which in Table 3. The spiral design method turn inherit the(Biomimicry advantage. Institute, 2007).

Darwin knew that to convince others of these two ideas—the descent of species from ancestors and natural selection—he would need more evidence. He Description Phase spent the next two decades marshaling all of the facts he could from botany, zool1. Problem Selection of a problem to solve and performing further definition of it ogy, embryology, and the fossil record. through functional decomposition and optimization. definition He received crucial information from experts who helped to sort out and characterize histhe collections.

Gould pointed outterms. to Darwin Redefining problem Ornithologist using broadlyJohn applicable biological 2. Reframe the that what the young naturalist thought were blackbirds, grossbeaks, and Asking the question: "How do biological solutions perform this problem finches from the Galápagos werefunction?" actually 12 (now recognized as 13) new and distinct species of ground finches (Figure 20-1). The Galápagos species, though Find solutions are relevant to theinbiological problem with clearly finches, exhibitthat an immense variation feeding behavior and in the bill 3.Biological techniques such as changing constraints, analysis of natural champions shape that corresponds to their food sources. For example, the vegetarian tree adaptation, a family solutions and multisolution search finchofuses its heavy variation bill to eat within fruits and leaves,ofthe insectivorous finch has a bill with a biting tip for eating functionality. large insects, and, most remarkable of all, the woodpecker finch grasps a twig in its bill and uses it to obtain insect prey by 4. Define the Identifyholes the structures probing in trees. and surface mechanisms of the biological system biological related to the recast function.

This diversity of species, Darwin deduced, must have arisen from an original solution population of finch that arrived in the Galápagos from the mainland of South Extraction the important principles of the solution the form of a America and of populated the islands.

The descendants of theinoriginal colonizers 5. Principle neutral solution, requiring a description that removes, as much asfrom spread to the different islands and formed local populations that diverged extraction possible, the various structural and environmental constraints. one another and eventually formed different species.

The finches illustrate the process of adaptation, in which the characteristics of themodified bio-inspired principleinextracted into a Darwin new ofTranslation a species become to suitsolution the environments which they live.

6. Principle area, involving an interpretation of a domain space (e.g., biology) provided one level of explanation for the process, natural selection, but he to could application another (e.g., varied mechanics) introducing new constraints. not explain how traits or howby they changed with time because he did not understand the mechanisms of inheritance. Understanding the genetic basis of Table 4. Bio-inspiredadaptation design method (Helms 2009). has been one of et theal., long-standing goals of evolutionary biology.

A first step toward this goal was taken when Mendel’s work pointing to the existence of genes was rediscovered two decades after Darwin died. Another key emerged a half century later, when the molecular basis of inheritance and the genetic code were deciphered. For many decades since, biologists have known

Phase

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A diversity of species may result from adaptation Phase Description 1. Biological From the observation of natural phenomena on a macro scale and / or Seed eaters solution micro level, a potential solution to apply is sought to transfer to a Bills ofaseed eaters are adapted human problem. identification for harvesting and crushing seeds.

2. Define the The components or systems involved in the phenomenon in question Large are identified in ground order finch to outline the biological solution in functional biological (Geospiza magnitrostis) Large-billed finches can notation. solution crush large, hard seeds.

Medium ground finch 3. Principle From the analysis of the biological solution in schematic notation, the (G. fortis) extraction fundamental principle of the solution is extracted.

In Small this case, reframing forces designers to think in terms of how ground finch 4. Reframe the Small-billed finches cannot crush (G. fuliginosa) humans might view the usefulness of the biological function being large seeds as well, but are more solution achieved. adept at handling small seeds.

Sharp-billed ground finch Whereas search in the biological domain includes search through some (G. difficilis) 5. Problem finite space of documented biological solutions, the search may include search defining new problems (this is much different than the solution search Large cactus finch (G. conirostris)step in the problem-driven processes).

Cactus finches are adapted to opening cactus fruits and By analogy with the definition of the solution in schematic notation, extracting the seeds.

6. Problem the problem is outlined similarly. The aim is thus to establish a parallel Cactus finch between the systems(G.and components of the biological solution and the definition scandens) problem.

Once the solution principle is established, it is transformed into a Bud eater 7. Principle The bud working principle of the eater’s heavy bill is adapted fortechnological concept that is needed. This and wrenching buds from in branches. activity will culminate the embodiment of a bio-inspired solution of application grasping a technological product or system.

Vegetarian Table 5. Bio-solution in search of afinch problem method (adapted from Helms et al., 2009).

ANCESTOR FINCH from South American For the mainland.

(Platyspiza crassirostris)

method presented in Table 4, the process of problem definition and searching for biological solutions is supported by elucidative techniques, suggestions and practical examples. The method presented in Table 5 supports an iterative formulation of the bioInsect eaters The bills of insect eaters vary because they eat inspired design principle. types and sizes of insects and they The application ofdifferent bionic principles in a design project can be accomplished by following capture them in different ways. any of two opposing directions: finding a solution to a problem in nature, or looking for a problem for which a solution has been found in nature. The former approach starts with the Small tree finch identification of a problem (human applications, such as developing orThe improving products large tree finch uses its heavy (Camarhynchus parvulus) bill tofrom twist apart woodor to reach or services) or the need of a project, followed by looking for inspiration nature an larvae inside. tree finch analogy to foster a solution to theLarge problem (a bionic solution proposal). This approach is (C. psittacula) well suited to designers seeking inspiration for the development of a particular product. The The small and medium tree finches other approach is based on the observation of nature and its structures in order to collect and mangrove finches pick insects Medium tree finch useful information (bionic inspiration based solution) for human from applications (design leaves and branches and (C. pauper) explore crevices for hidden prey. problems to be sought).

Mangrove finch (C. heliobates)

3. Generally applicable goals for bio-inspired design Woodpecker finch

The woodpecker finch uses its long beak to probe into dead wood, crevices, and bark for insects.

This section presents an analysis the likelihood of satisfaction of selected goals with the (C.of pallidus) use of the five methods for bio-inspired design, retrieved from literature and presented in The warbler finch uses quick motions to capture insects on Warbler finch the previous section. Five general goals are proposed that are deemed to encompass many plant surfaces.

(Certhidea olivacea) of the requirements pertaining to design projects for which inspiration from nature is

Figure 20-1 4HE SPECIES OF lNCHES FOUND IN THE 'ALĂ–PAGOS )SLANDS [After W. K. Purves, G. H. Orians, and H. C. Heller, Life: The Science of Biology, 4th ed. Sinauer Associates/W. H. Freeman and Company, 1995, Fig. 20.3, p. 450.]

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that species and traits evolve through changes in DNA sequence. However, the sought. The goals were selected basedchanges on their perceived level of importance andortheir elucidation of specific in DNA sequence underlying physiological moralbeit translated into a number perceived ubiquitous relevance across design projects, phological evolution has posed considerable technical challenges. Advances of in requirements, specific to the problems at hand.genetics, Communication effectiveness, molecular genetics, developmental and comparative genomics areform now optimization, multiple requirements satisfaction, and paradigm revealing the diverse mechanismsorganization underlying theeffectiveness evolution of genes, traits, and innovation for improved functional performance are the goals considered. organismal diversity. of a language that may be based on Effectiveness of communication depends on examine the sharing In this chapter, we will the molecular genetic mechanisms underlyvariation in appropriate and evolutiontoofthe traits and theand adaptation organisms to a code, gestures, oring on the signal that is activity context.ofFor effective their environments.

Wethat willthe firstmessage examine is theclearly evolutionary process general and communication to accrue it is necessary delivered andinreceived in then focus on specific examples which the and molecular bases of the a timely fashion, without noise, and that it is for relevant to genetic the situation or event that is phenotypic differences between populations or species have been pinpointed. All ongoing. of theofexamples will focus on the evolution of relatively simple traits controlled by can result directly from the balanced Optimizing the shape an object or structure a single gene.

These relatively simple examples are sufficient to illustrate the funsatisfaction (with concessions on both sides - trade-offs) of several key requirements, such as damental process of evolution at the DNA level and the variety of ways in which the reduction of material and, or, size, or the satisfaction of greater stability, or reduced the evolution of genes affects the gain, loss, and modification of traits. drag, depending on the targeted objectives. It is not always possible to achieve an optimal configuration, with maximization of all properties due to inherent conflicts that they sometimes impart (e.g. contradiction between low weight Selection and high strength or high volume 20.1 Evolution

by Natural or stability). Thus, optimization requires that the configuration reached is the one that best The modern of evolution so desired completely identified with Darwin’s name, addresses the contradictions andtheory conflicts betweenisthe properties. people think Darwin himself proposed concept that organisms Nature is rife with many effective solutions in order to first enable, in athe limited space, a systemhave to evolved, but that is not the case. TheCompliance idea that life changed over timerequirements was circulating with multiple perform various tasks or fulfil several functions. in scientific circles for many decades The great quesreflects the achievement of several key points thatbefore are Darwin’s inherenthistoric to thevoyage. problem at hand, tion was, How did life change?

For some, the explanation was a series of special creaiming for viability and profitability of a small number of structures and elements that are ations by God. To others, such as Jean-Baptiste Lamarck (1744–1829), change was to be used in performing more than one function. This simultaneous satisfaction opens the caused by the environment acting directly on the organism, and those changes way for consideration of new objectives to add value and profitability to the designed acquired in an organism’s lifetime were passed on to its offspring. product or system. Compliance with various targets, carried out by a limited set of features, What Darwin provided was a detailed explanation of the mechanism of the structures or entities implies streamlining for functional efficiency, which will result in evolutionary process that correctly incorporated the role of inheritance. Darwin’s resource savings. theory of evolution by natural selection begins with the variation that exists multiple structures (which The effectiveness of among organization depends the coordination organisms within aon species.

Individuals ofofone generation are qualitatively also includes communication) for the performance of activities with the need of differentiation. different from one another. Evolution of the species as a whole results from the The coordination of fact multiple entities in joint to of more effective results than that the various typesactivity differ inmay theirlead rates survival and reproduction. entity, such asthe that “the whole is greater the performance of the activity separately bymore eachoffspring, Better-adapted types leave and so relative frequencies of the than the sum of itstypes parts”.

An over example of excellent and to effectiveness the change time. Thus, the threecoordination critical ingredients evolutionary of change resulting organization can be from observation of the Darwin putinferred forth were variation, selection, andnatural time: system comprised of a pack of wolves. The group can hunt animals larger than the wolf, while a lone wolf may only Can it, then, be thought improbable. . . that variations useful in some way to hunt smaller animals or of a scale similar to his. The organization of the roles of each element each being in the great and complex battle of life, should sometimes occur within the pack is a pre-condition for achieving this result. in the course of thousands of generations? . . . Can we doubt (remembering Finally, the fifth goal considered in achieving in the paradigm that many consists more individuals are change born than canconventional possibly survive) that used to implement a feature, replacing with an innovative latter may be individuals having it any advantage, however paradigm. slight, over The others, would have proposed based on thethe observation of structures, behaviours and, or, processes of nature best chance of surviving and of procreating their kind? On the other that enable improvedhand, performance of sure the that function or feature. can be we may feel any variation in theThe least features degree injurious characterized by transformation of physical state, association or state variations hierarchy, to would be rigidly destroyed.

Thisstate preservation of favorable and rejectionto of represent injurious variations I call Natural Selection.

(On the Origin name a few. This goal the is deemed one of the most commonly sought goals by of aSpecies, IV) designers inclined to use bionicChapter approach.

Darwin’s writings and ideas are well known, and justifiably so, but it is very 3.1 Likelihood of achieving goals selected by alone usinginbio-inspired methods important the to note that he was not arriving at this concept of natural undera focus analysed terms Considering the fiveselection. goals presented, the Wallace five methods Alfred Russel (1823–1913), fellow were Englishman whoin explored the jungles of the and the Malay Archipelago for a total of 12 years, of their perceived support offered to Amazon designers making use of them towards the satisfaction reached a very similar conclusion in a paper that was co-published with an excerpt from Darwin in 1858: The life of wild animals is a struggle for existence. . . . Perhaps all the variations from the typical form of a species must have some definite effect, however

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slight, on the habits or capacities of the individuals. . . . It is also evident that of each goal. In what concerns the effectiveness of organization, a method oriented from the most changes would affect, either favourably or adversely, the powers of (Aalborg) is species considered applicable prolongingsolution existence.to. .the . If,problem on the other hand, any should produce a to support the satisfaction of this goal, demonstrating that there are a few gaps remaining in order to lead to the full variety having slightly increased powers of preserving existence, that variety satisfaction of this agoal.

None of the problem-oriented methods analyzed is considered fully must inevitably in time acquire superiority in numbers.�

(On the Tendency of to achieve Varieties toadequate Depart IndeďŹ nitely fromthis the goal.

Original Type, 1858) With regard to satisfying multiple requirements, methods oriented from the solution to the While today Darwin’s name tends to be exclusively linked to evolution by natproblem show, from the analysis, gaps in support to achieve this goal. The methods ural selection, in their day, the theory was recognized as the Darwin-Wallace thein the contrary direction of analysis, are providing guidance isinatimplementing projects ory. Perhaps the current perception least in part duebionic to Wallace himself, who very heterogeneous.

While the method of bio-mimicry offers was always deferential to Darwin and referred to the emergent theory of evolu- no support for the pursuit of this goal, in the opposite extreme, with considerable support, is the method of bio-inspired tion as “Darwinism.� design. considering the goal of form optimization, one is faced with a relatively -ESSAGE $ When ARWIN AND 7ALLACE PROPOSED A NEW EXPLANATION TO ACCOUNT FOR THE PHENOMENON OF EVOLUTION 4HEY UNDERSTOOD THAT THE POPULATION OF A GIVEN SPECIES homogeneous landscape, with the methods only offering partial support to attain this goal.

AT A GIVEN TIME INCLUDES INDIVIDUALS OF VARYING CHARACTERISTICS 4HEY REALIZED THAT THE The exception of the method of spiral design is highlighted, as it is considered significantly POPULATION OF SUCCEEDING GENERATIONS WILL CONTAIN A HIGHER FREQUENCY OF THOSE TYPES THAT applicable in order to achieve this purpose (this method provides guidance in following the MOST SUCCESSFULLY SURVIVE AND REPRODUCE UNDER THE EXISTING ENVIRONMENTAL CONDITIONS direction from problem to solution).

4HUS THE FREQUENCIES OF VARIOUS TYPES WITHIN THE SPECIES WILL CHANGE OVER TIME In what concerns the innovation of paradigm for improved functional performance, all methodsbetween provide guidelines which There is ananalyzed obvious similarity thesatisfactory process of evolution as Darwin andcan support the achievement of Wallace described it and the process by which that the plant or animal breederthat has been recommended for this purpose.

This demonstrates the primary approach improves a domestic Thecentres plant breeder selects the highest-yielding plants bionic stock. design on the functionality.

Moreover, except for individual cases, the from the current population and uses them as the parents of the next generation. remaining goals have been given a minor importance. Although the Aalborg and If the characteristics causingmethod the higher yield were are heritable, the next generabiomimicry ratings similarthen (except for organizational effectiveness), the steps tion should produce a higher yield.

It was no accident that Darwin chose the former, and there is a descriptive of the latter are more detailed than the ones of the term natural selection to describe his model of evolution through in the complementarity between both. The needdifferences to integrate validation activities in the biorates of reproduction shown by different variants in the population.

As a model inspired design processes is emphasized, as only a few of the methods (the spiral design and for this evolutionary process in the wild, he had in mind the selection that breedAalborg design methods) entail some evaluation and iteration. The development and testing ers exercise on successive generations of domestic plants and animals. of improved methods, providing broad support to pursuing a large scope of design goals, We can summarize the theory of evolution by natural selection in three principles: with support for validation of the quality of results attained, is hence necessary. The results of the overall analysis are presented in Table 6.

1. Principle of variation.

Among design individuals within population, there is vari- with shortcomings" with regard The bio-mimicry method isany only deemed "applicable ation in morphology, physiology, and behavior. to attaining the goals of optimizing form and improving effectiveness of organization. For 2. Principle of heredity.

Offspring their derives parents more resem-of iteration in order to pursue the first goal, the resemble assessment fromthan thethey absence ble unrelated optimization individuals. (observing the morphological structure is what is suggested in the method that may provide support to pursuing this goal).

For the second goal, the assessment 3. Principle of selection.

Somelimited forms are more successful at surviving and reprodirect account of organizational aspects, but takes into account that the method supports no ducing than other forms in a given environment. only does that indirectly through structural analysis. The evaluation also results in A selective process can produce change in the population composition only suggesting the applicability of the method to support the pursuance of the goal of paradigm if there are some variations among which to select. If all individuals are identiinnovation increased functional performance, and onhow the other hand, enables suggesting cal, no differences in thefor reproductive rates of individuals, no matter its non-applicability if the goal is to achieve satisfaction extreme, will alter the composition of the population. Furthermore, the varia- of multiple requirements and communication effectiveness. tion must be in some part heritable if these differences in reproductive rates are The spiral genetic designcomposition. method wasIf granted the rating "Applicable with shortcomings� with to alter the population’s large animals within of a popularespect to than the do goal of ones satisfying tion have more offspring small but theirmultiple offspringrequirements. are no larger onIn this method, satisfaction of multiple requirements according to their explanation in the initial average than those of small animals, thenmay there take will beplace no change in population composition from one generation to another. if all variant leave, specification, if natural modelsFinally, demonstrating thetypes reunion of the functions and, or, qualities on average, the same number of offspring, then we expect the population to not explicitly consider a way to guide the sought are analysed.

However, thecan method does remain unchanged. quest to satisfy multiple requirements. The goal of organizational effectiveness receives the same evaluation, as the aspect of organization is not considered directly in this method, but

-ESSAGE 4HE PRINCIPLES OF VARIATION HEREDITY AND SELECTION MUST ALL APPLY FOR EVOLUTION TO TAKE PLACE THROUGH A VARIATIONAL MECHANISM

Heritable variation provides the raw material for successive changes within a species and for the multiplication of new species. The basic mechanisms of those

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changes (as discussed in Chapter 18) are the origin of new genetic

The interplay of evolutionary it is only implicit in the consideration analysis ecosystems and of natural variationofbythe mutation, theof change in frequency alleles social within forces inuences conditions.variation For the other goals at hand, this method proves to be applicable to support their populations by selective and random processes, the divergence of

satisfaction if the target is form optimization (especially given the nature of are thisdifferent iterative different populations because the selective forces or method, which favours systematic optimization) innovation paradigm with regard to because of randomor drift, and the reduction of variation between is perceived to attain the goal of those communication populations by migration (Figure 20-2).

From basic mechaMutation a A performance features.

Mutation A No a support effectiveness. nisms, a set of principles governing changes in the genetic composition of populations can be derived. The application of these Genetic drift Genetic drift principles of population genetics provides a genetic theory of evoGoals sought lution. Generally, as Table 20-1 shows, forces thatParadigm increase or Migration Migration maintain variation within populations prevent populations from Bio-inspired innovation diverging from oneMultiple another, whereas forces that make each popudesign Communication Form Organization for Balanced polymorphism lation less variable (e.g., homozygous) cause populations to requirements methods effectiveness optimization effectiveness improved diverge. satisfaction functional Directional selection performance -ESSAGE %VOLUTION THE CHANGE IN POPULATIONS OR SPECIES OVER TIME

Applicable Bio-mimicry Applicable IS THE CONVERSION OF HERITABLE VARIATION BETWEEN INDIVIDUALS WITHIN Selection against heterozygotes POPULATIONS INTO HERITABLE DIFFERENCES BETWEEN POPULATIONS IN TIME Not applicable with Applicable (Junior et Not Applicable with AND IN SPACE BY POPULATION GENETIC MECHANISMS shortcomings al., 2002) shortcomings Spiral Applicable Applicable We will now turn from this general genetic description of evo0.0 0.1 0.2 0.3 0.4 design 0.5 0.6 0.7 0.8 0.9 1.0 Not Applicable Applicable with with lutionary change to the examination of evolution atApplicable the molecular Allelic frequency of A (Biomimicry shortcomings shortcomings level.

Inst., 2007) Figure 20-2 4HE EFFECTS ON ALLELE Bio-inspired ApplicableEvolution: The Neutral Theory 20.2 Molecular FREQUENCY OF VARIOUS FORCES OF EVOLUTION design 4HE BLUE ARROWS SHOW A TENDENCY TOWARD Not Applicable Applicable Not applicable Applicable with (Helms et Darwin and shortcomings Wallace conceived of evolution largely as “changes in organisms INCREASED VARIATION WITHIN THE POPULATION THE RED ARROWS DECREASED VARIATION al., 2009) brought about by natural selection.â€? Indeed, this is what most people think of as the meaning ofApplicable “evolution.â€? However, a century after Darwin’s theory, as molecuApplicable Aalborg lar biologists began to confront evolution of proteins and DNA molewith at the level Applicable Applicable (Colombo, Not Applicable with cules, they encountered and identiďŹ ed another dimension of the evolutionary 2007) shortcomings shortcomings process, neutral molecular evolution, which did not involve natural selection. An Bio-solution understanding of neutral molecular evolution is crucial to grasping how genes Applicable Applicable seeks change over time.

Not with Applicable problem Not Applicable with applicable (Helms et shortcomings The development of theshortcomings neutral theory al., 2009) By the 1940s, three branches of evolutionary biology—population genetics, (the definition andbyclassification of species), and paleontology— Table 6. Analysis of systematics perceived support provided the five bio-inspired design methods had become incorporated in what was dubbed the “Modern Synthesis� of evoselected in attaining five fundamental design goals. lutionary theory. This synthesis reflected general agreement that the princisupport offered to designersby if the goal is The bio-inspired design shows gaps in the ples method operating at the level of populations, as illuminated population genetics, were account foristhe evolution of design species to achieve optimal form, since thesufficient focus in to this method setlarger-scale on function.

In some processes supported by the procedures inherent to this method, the search for a biologically inspired solution to perform given function could lead to ( ) considerations of form.

Table 20-1 aHow the Forces of Evolution Increase or Decrease ( ) for optimization and does not explicitly However, the method does not provide Variationprocedures Within and Between Populations consider form, or shape.

The method is also deemed applicable manner to Force Variation withinin a satisfactory Variation between problems where the targeted goal is either paradigm innovation for improved functional populations populations performance, or to satisfy multiple requirements, or a combination of both. However, it is Inbreeding or genetic drift

not applicable to support the pursuance of the goals of effectiveness of either Mutation

communication or organization.

Migration

Directional selection

/ Balancing

Incompatible

20.2 Molecular Evolution: The Neutral Theory

110

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rd M s/re am p m ti l e al s R ep s/re pt til es ile /fi s C sh ar p/ la m V pr in ert ey se eb ct ra s te s/

s

Bi

M am m al

Number of amino acid substitutions per 100 residues

and higher taxa as documented, for example, in the fossil Proteins differ in mutation rate In the Aalborg method, which provides guidance in the direction from the solution to the record. However, at this time there was no understanding problem, the degree of applicability to the goals of form optimization and satisfaction of 220 of the molecular basis of either heredity (DNA) or evoluwith shortcomings".

For the first goal, multiple conditions, was assigned as "Applicable tionary change.

200 despite the focus form, were theredeveloped is no effort to optimize. Secondly, because shape, structure In the 1950s and early 1960s,on methods 180 functional principlesthe are amino considered that enabled and biologists to determine acid in this method the, implementation of multiple principles form and structure may result160from the analysis but is not explicitly sequences of proteins.

Thisofnew capability raised the pros140 pect that the fundamental of evolutionary change was considered. basis For the goals of innovation of paradigm for improved performance of functions Fibrinopeptides ďŹ nally at hand.

However, as the sequences of proteins from and for effectiveness of organization, this method 120is deemed applicable. a variety of species deciphered, paradox For thewere bio-solution in asearch of emerged. a problem method, which is directed from the solution to 100 The sequences of globins and cytochrome c, for example, the problem, as this method focuses on extracting and implementingHemoglobin the solution principle 80 typically differ between anyboth two the species at aofnumber of the shape form nature, aspects optimizing and satisfying multiple requirements, amino acids, and that number increases with the time are bound to be sidelined at the expense of the 60 functional principle. The evaluation of this Cytochrome c elapsed since their divergence from a common ancestor Separation 40 method and the previous one only differ significantly on the applicability to provide (Figure 20-3). Yet, the function of these proteins is the same of ancestors effectiveness, because in this method support carry to theand pursuance of thetogoal ofin organizational 20 of plants in different species—to deliver oxygen tissues and animals there is no focus on the organizational structure of the biological system centred upon.

The the case of hemoglobin and to shuttle electrons during cel0 100 200 300 400 500 600 700 800 900 1000 1100 1200 1300 method is deemed applicable to support attaining the goal of paradigm innovation for lular respiration in the case of cytochrome c.

Millions of years since divergence performance.

The puzzleincreased then wasfunctional whether the amino acid replacements between species reected changes in protein function and adaptations to selective conditions. Biochemists Linus Pauling and Emile Figure 20-3 .UMBER OF AMINO 4. Validation of goal satisfaction in the bio-inspired design process ACID SUBSTITUTIONS IN THE EVOLUTION OF Zuckerkandl did not think so. They observed that many substitutions were of one THE VERTEBRATES AS A FUNCTION OF TIME amino acid forThe another with similar properties.

Theyprevious concludedsection that mostidentified amino analysis presented in the goals where the methods SINCE DIVERGENCE 4HE THREE PROTEINSˆ acid substitutions were “neutralâ€? or “nearly neutralâ€? and did not change the funcconsidered were deemed to either offer no support, or only offer lBRINOPEPTIDES HEMOGLOBIN AND reduced support, towards tion of a protein whatsoever. (the spiral design their pursuance and satisfaction. Moreover, only two of the methods CYTOCHROME CˆDIFFER IN SUBSTITUTION RATE This line of reasoning was rejected at ďŹ rst by many evolutionary biologists, BECAUSE DIFFERENT PROPORTIONS OF THEIR method and the Aalborg method) entail some evaluation procedures, albeit limited in scope. who at the time viewed all evolutionary changes as the result of natural selection AMINO ACID SUBSTITUTIONS ARE SELECTIVELY This leads to suggest the integration of validation activities in bionic design processes, in and adaptation. Paleontologist George Gaylord Simpson, an architect of the ModNEUTRAL ascertain the desired mightneutral be met by the use of the concepts ern Synthesis,order arguedtothat “there iswhether a strong consensus thatgoals completely methods. generated with the support of bionic design genes or alleles must be rare if they exist at all. To an evolutionary biologist itThe current section presents a proposed validationthat approach, depicted on Table 7, based on considering therefore seems highly improbable proteins . .summarily . should change in a regular specific but non-adaptive way.â€? validation procedures matching each of the five goals focused in the previous Zuckerkandl and Pauling asserted that the similarity or differences among section. organisms need not be reected at the level of protein—that molecular change and visible change were not necessarily linked or proportional.

4.1 Bio-inspired design case requirements The debate was resolved by an onslaught of empirical data and the decipherFive methods that are intended to support the generation of bio-inspired design concepts, ing of the genetic code. Because multiple codons encode the same amino acid, a literature, in this Three of these methods shared a mutation thatretrieved changes, from say, CAG to CACwere doesanalysed not change the chapter. amino acid common direction analysis, which departs from given encoded. Therefore, variation can of exist at the DNA level that has no aeffect onproblem and seeks the proposal of solutions byneutral gathering insight andBut inspiration form natural systems. This approach begins protein sequences, and thus alleles do exist. even more important the identification of a problem or the needs project, which is followed by looking for populationwith genetics was the development of the “neutral theory of of amolecular evolution�for

by Motoo Kimura, Jack nature L. King, or andseeking Thomas Jukes.

These authors inspiration from an analogy with a natural solution to foster the proposed thatemergence most, but not mutations thatproblem are ďŹ xed(aare neutral or nearly of aall, solution to the bionic solution proposal). neutral and any between species such sitesout, in DNA evolve by anranapproach combining three of the A differences bionic design project wasat carried following dom genetic drift. methods reviewed (Junior et al. 2002, Biomimicry Inst. 2007, Helms et al. 2009). The problem The “neutral theoryâ€? marked a profound conceptual shift away from a view of considered was the storage and the physical display to enable browsing of personal music evolution as always guided by natural selection. Moreover, it provided a baseline collections, focusing on CDs and DVDs. The conduction of the design process led to seek assumption of how DNA should change over time if no other agent such as natuinspiration form nature, having selected the spider web as a natural example that was the ral selection intervened. basis for the analogy of working principle established. The requirements established for the project and their corresponding goals are listed in Table 8. Moreover, environmental -ESSAGE 4 HE NEUTRAL THEORY OF MOLECULAR EVOLUTION PROPOSED THAT MOST MUTATIONS IN $.! OR AMINO ACID REPLACEMENTS BETWEEN SPECIES ARE FUNCTIONALLY NEUTRAL OR NEARLY NEUTRAL AND lXED BY RANDOM GENETIC DRIFT 4HE ASSUMPTION OF NEUTRALITY OFFERS A BASELINE EXPECTATION OF HOW $.! SHOULD CHANGE OVER TIME WHEN NATURAL SELECTION IS ABSENT

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Biologically Inspired Design: Methods and Validation

The rate of neutral substitutions

Validation procedures to evaluate goal accomplishment As we saw in Chapter 18 (see Box 18-5), we can calculate the expected rate of neutral Validation is made according to the level of communication involved. changes in DNA sequences over time. If M is the rate of new mutations at a locus per Passive communication (triggered by observation) - the gene copy per generation, then the absolute number of new mutations that will effectiveness mayofbe evaluated by assessing the degree of the are subappear in a population N diploid individuals is 2NM. The new mutations overlap the meaning intended bepopulation, incorporated into thewill ject to randombetween genetic drift: most will be lost fromtothe while a few and the readings of signification product or system by the designer Communication become ďŹ xed and replace the previous allele. If a newly arisen mutation is neutral, bya users or observers verification). thenmade there is probability of 1/(2N)(empirical that it will replace the previous allele because effectiveness Active communication (synchronous process between sender and of random genetic drift. Each one of the 2NM new mutations thatawill appear in a a receiver) effectiveness evaluated from thetaking assessment of population. the population has a- probability of 1/(2N) of eventually over that Thus, the absolute substitution rate k isfrom the mutation rate and multiplied overlap between the messages the sender what by is the probabilityperceived that any one will eventually take over by drift: bymutation the receiver, which should conform to what is desired by the sender (empirical verification).

K rate of neutral substitution 2NM r 1/(2N) M Validation based on a comparative approach with regard to a That is, we expect that, in every generation, there will be Mto substitutions conventional product with functionality that is similar the one in the population, purely from the genetic drift of neutral mutations. intended for the bionic concept. Examples: Form Reducing material and weight - analysis from solid modeling.

-ESSAGE 4HE RATE OF SUBSTITUTIONS IN $.! IN EVOLUTION RESULTING FROM THE RANDOM optimization Stability static analysis of mass centre (force vector modeling).

GENETIC DRIFT OF NEUTRAL MUTATIONS IS EQUAL TO THE MUTATION RATE TO SUCH ALLELES M Resistance for maximum capacity - finite element method and prototype testing.

TheObject signature of- purifying selection on DNA storage capacity, maximum capacity; quantification.

Validation based onofobjectively verifying, as much as possible, thefor neuWhen measurements molecular change deviate from what is expected Multiple level that has been reached for each property in every tral changes, that is an important signal—a signal implicit that selection has intervened.

That signal mayThis reveal that selection has favored some speciďŹ c change or that it requirement. is followed by checking if the resolution of conflicts requirements has rejected others. We willproperties examine the latter casewith ďŹ rst,compromises as the most pervasive between non-compatible was made satisfaction inuence of natural selection onthe DNA is to conserveconcerned. gene function and sequence. established on every side of requirements The case of positive natural selection will be covered in Section Validation based on the comparison between two or more20.4. systems All classes of DNA sequences, including exons, introns, regulatory sequences, performing the same function (including the proposed system), but and sequences in between genes, show nucleotide diversity among individuals Organization with different methods of organization. Collect measures of the levels within populations and between species. Of course, not all mutations in DNA are Figure 20-4 4HE AMOUNT OF NUCLEOTIDE effectiveness of operation effectiveness the or (real or simulated) neutral with respect to gene from function organismal ďŹ tness.systems Mutations of DNA DIVERGENCE AT SYNONYMOUS SITES IS (including the proposed system), such as execution time, energy may also be deleterious, reducing the probability of the survival and reproducGREATER THAN THE AMOUNT OF DIVERGENCE AT expended, resources expended, resources generated.geneticists NONSYNONYMOUS SITES OF THE B GLOBIN GENE tion of theirmaterial carriers. The laboratory mutantsorused by experimental The evidence of paradigm change depends onsome the type of paradigm usually have mutations with deleterious effect on ďŹ tinvolved.

Consider these examples of two kinds of paradigm change: ness. A third possibility is that mutations may increase Mutation rate is higher at synonymous ďŹ tness by increasing efďŹ ciency, by expanding the range of Paradigm change at the organizational level could involve sites than at nonsynonymous sites conditions in whichmaking the species make a changing from environmental a centralized model of decision to acan process living, or making by enabling the organism to adjust to by changes in Paradigm of cooperative decision distributed and performed Synonymous the environment. innovation for multiple system elements. sites The ratelevel of neutral substitutions improved Paradigm change at theconstant technical – could involve predicts that, if the number of nucleotide differences between two species 3.0 functional drive fundamental changes in working principle, shape archetype, were plotted against the time since their divergence from a performance technology or kind of energy supplied. common ancestor, the result should be a straight line with The verification of the satisfaction of this goal may centre on a slope equal to M. That is, evolution should proceed according 2.0 conceptual-analytical between to aargument moleculardistinguishing clock that is ticking at the the rateexisting M. Figure 20-4 and the new paradigm, possibly illustrated by descriptive imagery shows such a plot for the B-globin gene. The results are quite and, or, technical schemes. consistent with the claim that nucleotide substitutions have neutral in the of past 500 million years.

Two sorts of of neu1.0 Table 7. Specific procedures suggested been for consideration the processes of validation tral nucleotide substitutions are plotted: synonymous subNonsynonymous goals sought in bio-inspired design endeavours. stitutions, which are from one alternative codon to another, sites making no change in the amino acid, and nonsynonymous substitutions, which result in an amino acid change. Figure 0 1 2 3 4 5 20-4 shows a much lower slope for nonsynonymous substitu8 Divergence time (Ă— 10 ) tions than for synonymous changes, which means that the Number of substitutions per nucleotide

Goal

111

20.3 Natural Selection in Action: An Exemplary Case

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Industrial Design – New Frontiers

mutation rate to neutral nonsynonymous substitutions is much lower than that to concerns were expressed in terms of reduced environmental impact of materials, ease of synonymous neutral substitutions. maintenance asunder wellnatural as low weightMutations of the product (and its package) for This outcome is precisely and what repair, we expect selection. transportation.

These requirements were dealt with in the that cause an amino acid substitution should have a deleterious effect moredesign project, impinging on the selection of materials (selection of achange bio-polymer andSuch an organic elastomer) and on the often than synonymous substitutions, which do not the protein. designwill ofbethe project (impinging the goalselection of paradigm innovation for improved deleterious variants removed from populations on by purifying (see performance).

Chapter 18). functional A lower-than-expected ratio of nonsynonymous to synonymous changes is a signature of purifying selection. It is important to note that these observations do not show that synonymousRequirements substitutions have no selective conGoals sought* straints on them; rather, that these constraints are,the on user the average, not an 1. Nicethey andshow appealing shape, enabling to develop as strong as those for mutations that changeinterest amino in acids.

So, a synonymous aesthetic product Communication change, although it has no effect on the amino acid sequence, does change the effectiveness 2. Sending a message of an avant-garde character, creative and mRNA for that sequence and thus may affect mRNA stability or efďŹ ciency at youthful which the message is translated.

3. Enhanced stability against a dynamic disturbance compared Purifying selection is the most widespread, but often overlooked, facet of natwith a conventional solution†ural selection. The “rejection of injurious variations,â€? as Darwin termed it, is perForm optimization 4. Increased lightness compared to conventional solution†vasive. Purifying selection explains why we ďŹ nd many protein sequences that are unchanged or nearly unchanged over vast spans of of evolutionary time. For exam5. Proper positioning of the title the CDs, DVDs and books for ple, there are several dozen genes that exist in all domains of life—Archaea, bacteenhanced readability ria, fungi, plants, and animals—and encode proteins whose sequences have been Organization Storage with of preserve CDs, DVDs books largely conserved over 36.billion years of versatility evolution. To suchor sequences, effectiveness variants that have arisen at random in billions of individuals in tens of millions of Paradigm innovation species have been rejected by selection over and over again. for improved 7. Enhanced gripping of objects compared with a conventional functional solution -ESSAGE 0 URIFYING SELECTION IS A PERVASIVE ASPECT OF NATURAL SELECTION THAT REDUCES performance GENETIC VARIATION AND PRESERVES $.! AND PROTEIN SEQUENCES OVER AEONS OF TIME *- Satisfaction of multiple requirements is implicit in the consideration of the several requirements;

Another prediction of therequirements, theory of neutral evolution is that different proteins †- Conflicting requiring a trade-off. will have different clock rates, because the metabolic functions of some proteins Table 8. Listing of requirements set for the bio-inspired design case presented and their will be much more sensitive to changes in their amino acid sequences. Proteins in corresponding that were sought. which every amino acid makes goals a difference will have a lower rate of neutral mutation because aThe smaller proportion of theircarried mutations will be neutral compareddesign case used are summarily validation processes out within the exemplified with proteins described, that are more tolerant of substitution.

Figure 20-3 shows comand an overview of the evidence used and athe results obtained is provided in the parison of the clocks for ďŹ brinopeptides, hemoglobin, and cytochrome c. That following sub-sections, considering the goals depicted in Table 7. In what concerns the goal ďŹ brinopeptides have a much higher proportion of neutral mutations is reasonable of satisfaction of multiple requirements, a conflict was detected between the requirement of because these peptides are merely a nonmetabolic safety catch, cut out of ďŹ brinostabilityreaction. and lightness.

This conflict was solvedare by means of an approach akin to gen to activateenhanced the blood-clotting It is less obvious why hemoglobins by change of state, in the second TRIZ (Altshuller 1994), with the contradiction solved less sensitive to amino acid changes than is cytochrome c. iteration of the design. Bionic tower 2 hence encompasses a reservoir in the basis which may -ESSAGE 4HE RATE OF NEUTRAL EVOLUTION FOR THE AMINO ACID SEQUENCE OF A PROTEIN be filled with water or sand for added stability, while lightness is still guaranteed, for the DEPENDS ON THE SENSITIVITY OF THE PROTEIN S FUNCTION TO AMINO ACID CHANGES sake of environmental concerns, especially focusing on the production and distribution phases of the product’s life-cycle.

The conservation of gene sequences by purifying selection and the neutral evolution of gene sequences are two crucial dimensions of the evolutionary pro4.2ofValidation of communication effectiveness cess, but neither them account for the origin of adaptations.

In the next three enabling the development of an The perception by the user of pleasantness sections of the chapter, we will illustrate several examples of theand waysappeal, in which aesthetic interest in thediversity. product (first requirement in Table 8) was validated through a genetic changes are linked to organismal questionnaire where, among other things, each of the two bionic CD towers was visually compared, with a conventional tower (Figure 1). The validation of this requirement is necessarily subjective, the key issue that arises relates to the taste and sensitivity of 20.3 Natural Selection inbecause Action: each individual questioned. Respondents, answering by email, accounted to 85, aged

An Exemplary Case

For nearly a century after the publication of On the Origin of Species there was not one example of natural selection that had been fully elucidated, that is, where the agent of natural selection was known, the effect on different

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Figure 20-5 ! BLOOD SMEAR OF AN

between 18 and INDIVIDUAL WITH THE SICKLE CELL TRAIT 4HIS specialities.

INDIVIDUAL IS HETEROZYGOUS FOR THE SICKLE CELL MUTATION 5NDER NORMAL OXYGEN CONCENTRATIONS THE RED CELLS APPEAR DISK SHAPED left "UT WHEN DEOXYGENATED

THE CELLS ASSUME THE SICKLE SHAPE right

cells inwith someone with sickle-celland traitknowledge 60, both maleRed andblood female, and diverse professional

[Photo from A. C. Allison, 1956, ScientiďŹ c American 195, 87–94, used by permission.]

genotypes could be measured, the genetic and molecular basis of variation was identified, and the physiological role of the gene or protein involved was understood.

Fig. 1. Depiction of awell conventional CD tower, and the two bio-inspired CD tower racks ďŹ rst such “integratedâ€? natural selection designed: conventional The tower(A), bionic tower 1example (B) and of bionic tower 2 (C).on a molecular variant was elucidated in the 1950s, before the genetic code was even deciphered.

Each respondent indicated which the CD work racksrevealed was personally more aesthetically Remarkably, this of trailblazing natural selection operating on pleasing and appealing, from 3 paired comparisons presented.

The paired comparisons humans. It still stands today as one of the most detailed and important examples approach applied toof this case by of natural three objects 8 possibilities of response, two of evolution selectionenables in any species. story when Tony Allison, a Kenyan-born, Oxford medical which are incongruent,The since no began ranking of preference can be established out of them.student Three undertook a ďŹ eld of study of blood types comparisons. among Kenyan Thus, tribes. the One analysis of the blood out of the 85 respondents reported incongruent paired of tests he ran was for sickle cells, red blood cells that form a sickle shape on exporesults was carried out for 82 responses. The results were analysed on the basis of the sure tothe the Kendall reducing coefficient agent sodium or after standing for a few days of betasulďŹ te concordance (Siegel & Castellan 1988). procedure for calculating (Figure 20-5).

The deformed cells are a hallmark of sickle-cell anemia, a disease The average ranking obtained was bionic tower 1 (first place), bionic tower 2 (second place) ďŹ rst described in 1910. These cells cause pathological complications by occluding and conventional tower (third place). This result is considered significant to represent the blood vessels and lead to early mortality. overall opinion of respondents to a confidence level of 99%. These results support the In 1949, the very year Allison went into the ďŹ eld, Linus Pauling’s research validation of the first requirement depicted in Table 8. Both the firsthad anda hemoglobin second bionic group demonstrated that patients with sickle-cell anemia protowers received the tein preference respondents the conventional with an of abnormal charge over (Hemoglobin S, or HbS)tower, in theirwhich blood, supports compared aesthetic appeal, for versions of the validation of thewith gains terms of pleasantness theinhemoglobin of unaffected and individuals (Hemoglobin A,both or HbA).

This was the bio-inspired design. the ďŹ rst demonstration of a molecular abnormality linked to a complex disease. It at thethat time that carriers ofto sickle were of heterozygous In what concerns was thegenerally second understood requirement contributes thecellgoal effective and thus had mixture of and HbS AS),of whereas aficted individucommunication, validation wasa sought byHbA means of a(denoted technique anthropomorphizing alsattribution were homozygous for the HbS allele (denoted first phase, a translation of products through the of personality dimensions.

In aSS).

Allison collected blood specimens from members the Kikuyo, Masai, the requirement into a product personality profile (Jordan 2002) of was proposed.

In Luo, the and other tribes across the very diverse geography of Kenya.

While he did not second phase of the process, a sample of specialized public (eight undergraduate Industrial see any particularly striking association between ABO or MN blood types among Design students) assessed the personality profile of the three objects shown in Figure 1. In the tribes, he measured remarkably different frequencies of HbS. In tribes livthehighlands, designerthe was transmitted towas theless public such, whether or not message ingthe in arid centralintended Kenya or by in the frequency of HbS than could be verified. 1 percent; however, in tribes living on the coast or near Lake Victoria, the frein aand number of concepts to promote The second requirement setofinHbS Table 8, was decomposed quency often exceeded 10 percent approached 40 percent in some the matching process envisaged. led to considering the attributes of modern, elegant, locations (TableThis 20-2). youthful, joyful, flexible and dynamic. Moreover the attributes consisting of lightweight and fourth requirements.

The correspondence stable were also considered from the third Table 20-2 Frequency of and HbS in Particular Kenyan Tribes between product attributes intended by the designer to be perceived by the public and Tribe Ethnic afďŹ nity District/region % HbS Luo Suba Kikuyu

Nilotic Bantu Bantu

Kisumu (Lake Victoria) Rusingo Island Nairobi

25.7 27.7 0.4

20.3 Natural Selection in Action: An Exemplary Case

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Industrial Design – New Frontiers

The allele frequencies were surprising for two Malarial within red outcome blood cells product personality dimensions (Jordan 2002) are parasites shown inlive Table 9. The of reasons. First, since sickle-cell anemia was usually personality profiles is also shown, based on analysis on the respondents assessment of the lethal, why were the frequencies of the HbS allele so evaluation Kendall’s coefficient high? And second, givenofthe relatively short dis-of concordance (Siegel & Castellan 1988).

For everywhy personality pair, analysis was performed as exemplified for the pair energetic – tances between regions, was the HbS frequency non energetic energy, the average ranking of the panel of respondents (with a significance of high in some places and not others?

99%, given bythe theterrain, assessment Kendall ‘s coefficient) resulted in the following rank order: Allison’s familiarity with tribes,ofand 1st C, 2nd B, 3rd A. As a conclusion tropical diseases of Kenya led him to the crucial to this result, it is understandable that tower C (bionic tower realized 2) is considered more energetic than the tower B (bionic tower 1), and that tower C explanation. Allison that the HbS allele was (conventional tower) considered at high frequency in low-lying humidis regions with less energetic than tower B. This means that tower C is very high levels of malaria nearly absentof at the highthree towers and that C is the tower that emerges as the deemed theand least energetic altitudes suchmost as around Nairobi. bydynamic, mosqui- thus validating this communication requirement. dynamic andCarried the less toes, the intracellular parasite Plasmodium falcipaSignificance rum, which causes malaria, multiplies inside red level of blood cells (Figure Designer’s 20-6). Mosquitoes Personality and the disease Average Kendall’s Conclusion ranking are prevalent throughout sub-Saharan Africa in message profile coefficient of humid, low-lying regions near bodies of water where 1st- 2nd – 3rd Figure 20-6 ! BLOOD SMEAR OF AN INDIVIDUAL INFECTED WITH MALARIAL concordance the mosquitoes reproduce. Allison surmised that the PARASITES ! RED BLOOD CELL SAMPLE WAS TREATED WITH 'IEMSA STAIN TO REVEAL HbS allele might, by altering red blood cells, confer PARASITES WITHIN CELLS RED DOTS [PhotoSample courtesy ofdid Dr. not Mae Melvin, revealCDC Public Modern – Dim BHealth – A –Image C Library.]

Not significant some degree of resistance to malarialBright infection. agreement

Simple – The selective advantage Lightweight of HbS

Tower A is considered A–B–C 99% Complex most simple (lightweight) In order to test this idea, Allison carried out a much larger survey of HbS frequenGentleTanzania, – Sample did not reveal cies across eastern Africa, including Uganda, and C Kenya. examined B and – A He Not significant Violent agreement about 5000 individuals representing more than 30 different tribes. Again he Elegant found HbS frequencies of up to 40 percent in malarial areas and frequencies as Moderate Sample did not reveal A–B–C Not significant low as 0 percent where malaria was absent.

Excessive agreement The link suggested that the HbS allele might affect parasite levels, so Allison Towers B and C are the Liberal – also undertook a study of the level of parasites in the heterozygous B blood and Cof- A 99%AS most liberal (youthful) Authoritarian children versus wild-type AA children. In a study of nearly 300 children, he found Rebel –lower in AS children (27.9 percent) Tower C is the most the incidence of malarial parasites was indeed C–B–A 99% Youthful spirit Conformist rebellious (youthful) than in AA children (45.7 percent) and that parasite density was also lower in AS children. The results indicated that AS children had Optimistic – a lower incidence and severSample did not reveal Badvantage – C – A in Not significant ity of malarial infection and would thus have a selective areas where Pessimistic agreement malaria was prevalent.

Light-hearted The advantage to AS heterozygotes was especially striking in light of the disTower C is the most light– SeriousC–B–A 99% ease suffered by SS homozygotes. Allison noted: hearted (joyful) minded Joyful The proportion of individuals with sickle cells in any population, then, will Kind – Towers B and C are the be the result of a balance between two factors: theBseverity and C of - Amalaria, which 95% Unkind most kind (joyful) will tend to increase the frequency of the gene, and the rate of elimination of Sample did not reveal Flexible – the sickle-cell genes in individuals dying of sickle-cell Flexible Canaemia. – B – A . . . Genetically Not significant agreement Inflexible speaking, this is a balanced polymorphism [emphasis added], where the heterozygote has an advantage over either homozygote.

Energetic – Tower C is the most Dynamic C–B–A 99% Unenergetic energetic (dynamic) In other words, the sickle-cell mutation was under balancing selection (see Chapter 18) in areas where malaria wasStable present.

Positive selection operating on Sample did not reveal Stableby natural selection operating B – against A – C AANot significant AS individuals is balanced individuals agreement Unstable susceptible to malaria and SS individuals who would succumb to sickle-cell Table 9. Analysis of the results of the survey on the personality profile of the towers for CD anemia.

DVD storage verificationexperience? of messages perceived from observation of the objects by How muchand of an advantage doand AS individuals This can be calcuthe pannel of undergraduate industrial design students. lated by measuring the frequency of the HbS allele in populations and examining how these frequencies differ from the frequencies expected under the assumptions of the Hardy–Weinberg equation (see Chapter 18). A large-scale survey of 12,387 West Africans has revealed an HbS allele frequency (q) of 0.123.

The frequencies calculated from the Hardy–Weinberg equation are lower for the

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Table 20-3 The Fitness Advantage Sickle-Cell According to ofthe findingsHeterozygotes obtained, the communication of a message of young spirit, SS AS AA Total

Observed phenotypeand Expected phenotype Ratio of observed/ advantage (relativetower fitness)2) Selective dynamism joyfulness were validated.

Tower CW(bionic is the one which, frequency frequency expected according to the survey, more effectively conveys the desired messages, is considered the

29dynamic, the most 187.4 0.155/1.12 0.14 most rebellious, most0.155 joyful and, together with tower B (bionic tower 1), 1.0/0.88 1.136the 2993 2672.4 1.12 1.12/1.12

1.00 most kind and most liberal. Regarding the transmission of the message of lightness, 9365 9527.2 0.983 0.983/1.12

0.88 personality profile related (simple - complex) did not translate so well the associated 12,387 12,387have led respondents to identify tower A (conventional) as the requirement. This might simplest, and therefore, according to the tenuous association, the lightest of the three. homozygous phenotypes higher forabsence the heterozygous phenotype of (Table Interpretative meanings vary from person toand person.

The of actual experience use assumed thatwho the AS heterozygote a fitness of 1.0, then thehave relaof the towers on the20-3). partIfofit is respondents, just exercised has visual perception, may tive contributed fitness of the other genotypes can be estimated these differences also influenced and to vagueness and lack of from agreement among (see the Table 20-3). The relative fitness of the heterozygous AS genotype is 1.0/0.88 = respondents.

1.136, which corresponds to a selective advantage of approximately 14 percent.

This selective advantage has been well documented by long-term survival 4.3 Validation of form optimization studies of AA, AS, and SS children in Kenya. These studies have found that AS to the satisfaction ofand theSSgoal of form The results concerning requirements contributing individuals have a pronounced survival advantage over AA individuals in the firstin fewTable years of10life(enhanced (Figure 20-7). optimization are shown stability – according to force vector analysis), Table 11 (increased lightness – solid modelling analysis), Figure 2 (enhanced Message The sickle-cell hemoglobin allele, HbS, is under balancing selection in readability of CD titles – graphical depiction) and Figure 2 (scheme illustrating analytical malarial zones and conveys a large survival advantage in heterozygotes over the first stability modelling). few Foryears the of first life.of the three requirements concerned by this goal, bionic tower 2 ranks in first place, while for the second requirement, bionic tower 1 is clearly the lightest, while for the last of the three requirements both bionic towers achieve a tie ahead molecular origins of validation HbS of the conventionalThe tower.

The results support of the achievement of the goal After Allison’salbeit discovery, wastowers keen interest in determining the molecular sought of form optimization, boththere bionic are deemed equivalent in this basis of the difference(s) between HbS and HbA. Protein sequencing determined respect.

Survival analysis of sickle-cell genotypes

Maximum lateral disturbance to 1.02 maintain stability

Conventional tower

Bionic tower 1

Bionic tower 2

At maximum 0.97 capacity

49,96 N

49,59 N

74 N

HbAS 35,11

29,57 N

56,34 N

At medium capacity Estimate of relative survival

Genotype

0.92

N

Table 10. Comparison of results for the maximum lateral disturbance tolerated without loss 0.87 of stability in the three concepts.

HbAA

Total mass0.82

Conventional tower

Bionic tower 1

Bionic tower 2

Transport mode

11,049 Kg

4,763 Kg

8,087 Kg

11,049 Kg

4,763 Kg

Use mode

0.77

0.72

HbSS

0 30of mass 180 data 360 among 540 the 720three 900 1080 Table 11. Comparison objects.

17,087 Kg 1260

1440

1620

1800

2140

Time until death (days)

Figure 20-7

The relative survival of approximately 1000 children from Kisumu is plotted from birth through the first few years of life. Sickle-cell heterozygotes experienced a significant advantage in overall survival from ages 2 to 16 months. [From M. Aidoo et al., The Lancet 359, 2002, 1311–1312.]

20.3 Natural Selection in Action: An Exemplary Case

116

739

Industrial Design – New Frontiers

that HbS differs from HbA by just one amino acid, a The geography of sickle-cell hemoglobin and malaria valine in the place of a glutamic acid residue. This single amino acid change alters the charge of hemoglobins and causes it to aggregate into long rodlike structures within red blood cells. Once the genetic code was deciphered and methods for sequencing DNA were developed, HbS was determined to be caused by a single point mutation (GAG l GTG) in the glutamic acid codon encoding the sixth amino Distribution acid of the B-globin subunit within the hemoglobin of malaria protein.

Interestingly, Allison also noted a high incidence of HbS outside of Africa, including in Italy, Greece, and India. Other blood-type markers did not indicate 2. Graphical depiction readability of content titles for the three objects (from left to strong geneticFig. relationships among theseofpopulaFrequency of sickle-cell trait right: conventional tower, bionic tower 1 and bionic tower 2). tions. Rather, Allison observed that these were also 1 â&#x20AC;&#x201C; 10% > 20% areas with a high incidence of malaria. The correla15 â&#x20AC;&#x201C; 20% < 1% tion between HbS frequency and the incidence of malaria held across not only East Africa, but the African continent, southern Europe, and the Indian subcontinent. Allison composed Figure 20-8 4HESE MAPS SHOW THE CLOSE CORRESPONDENCE BETWEEN THE maps showing these striking correlations (Figure 20-8) and inferred that the HbS DISTRIBUTION OF MALARIA left AND THE alleles in different regions arose independently, rather than through spreading by FREQUENCY OF THE SICKLE CELL TRAIT right migration. Indeed, with the advent of tools for DNA genotyping, it is clear that the ACROSS !FRICA [Based on A. C. Allison, HbS mutation has arisen independently in ďŹ ve different haplotypes and then Genetics 66, 2004, 1591; redrawn by increased to high frequency in particular regions. Based on the limited genetic Leanne Olds.] diversity of malarial populations, it is believed that HbS mutations arose in just the past several thousand years, once populations began living around bodies of water with the advent of agriculture.

Fig. 3. Schematical depiction of analytical stability modelling for a lateral disturbance in the conventional CD rack, as well as in both the bionic towers designed.

MALARIA WAS THE lRST EXAMPLE OF NATURAL SELECTION TO BE ELUCIDATED WHERE THE AGENT

-ESSAGE 4HE ROLE OF SICKLE CELL HEMOGLOBIN S MUTATION IN CONFERRING RESISTANCE TO

OF SELECTION WAS DEMONSTRATED THE RELATIVE lTNESS OF DIFFERENT GENOTYPES COULD BE MEASURED AND THE GENETIC AND MOLECULAR BASIS OF FUNCTIONAL VARIATION WAS PINPOINTED 4.4 Validation of organization effectiveness

To validate the goal of organization effectiveness, the proof of achievement of the The role ofrequirement HbS in conferring resistance to malaria illustrated three important DVDs or books was sought by means of a of storage with versatility of CDs, facets of the evolutionary process: graphical depiction (Figure 4) which is deemed self-explanatory with regard to this satisfaction.

1. Evolutionrequirementâ&#x20AC;&#x2122;s can and does repeat itself. The multiple independent origins and expansions of the HbS mutation demonstrate that given sufficient population size and time, the same mutations can arise and spread repeatedly. Many other examples are now known of the precise, independent repetition of the evolution of adaptive mutations, and we will encounter several more in this chapter.

2. Fitness is a very relative, conditional status. Whether a mutation is advantageous or disadvantageous, or neither, depends very much on environmental conditions. In the absence of malaria, HbS is very rare and disfavored. Where malaria is present, it can reach high frequencies despite the disadvantages imparted to SS homozygotes. In African Americans, the frequency of HbS is on the decline because of selection against the allele in the absence of malaria in North America.

3. Natural selection acts on whatever is available, and not necessarFig. 4. Depiction of threevariation possibilities of dynamic storage of objects in the bionic towers. ily by the best means imaginable. The HbS mutation, while protective against malaria, also causes a life-threatening condition. In areas where malaria is prevalent, which includes over 40 percent of the worldâ&#x20AC;&#x2122;s population, the imperative of combating malaria counterbalances the deleterious effect of the sickle-cell mutation.

740

CHAPTER 20

Evolution of Genes and Traits

Biologically Inspired Design: Methods and Validation

117

20.4 Cumulative Selection and performance 4.5 Validation of paradigm innovation for improved functional To validate the achievement of the goal Paths of paradigm innovation for improved functional Multistep to Functional performance, verification of the achievement of the requirement of enhanced gripping of Change objects in the bionic towers was sought.

Because so much sequence evolution is neutral, there is no simple relation between the amount of change in a geneâ&#x20AC;&#x2122;s DNA and the amount of change, if any, in the encoded proteinâ&#x20AC;&#x2122;s function. At one extreme, almost the entire amino acid sequence of a protein can be replaced while maintaining the original function if those amino acids that are substituted maintain the enzymeâ&#x20AC;&#x2122;s three-dimensional structure.

In contrast, the function of an enzyme can be changed by a single amino acid substitution. The sheep blowďŹ&#x201A;y, Lucilia cuprina, has evolved resistance to organophosphate insecticides used widely to control it. Richard Newcombe, Peter Campbell, and their colleagues showed that this resistance is the consequence of a single substitution of an aspartic acid for a glycine residue in the Fig. 5. Illustration ofactive the changes in enzyme geometry ofisthe web that generate object securing force. site of an that ordinarily a carboxylesterase (splits a carboxyl ester, Râ&#x20AC;&#x201C;COOâ&#x20AC;&#x201C;R, into an alcohol and a carboxylate). The mutation causes comForce and strength plete of material calculations were performed numerically and analytically, loss of the carboxylesterase activity and its replacement by esterase activresulting in an estimation of approximately vertical force per CD ity (splits any ester, Râ&#x20AC;&#x201C;Oâ&#x20AC;&#x201C;R, 0,5 intoNanofacid and ancompression alcohol). Three-dimensional from that thethe physical comprehension of abilthe (based on analytical calculations developed modeling of the molecule indicates substituted protein gains the phenomenon - Figure Finite element modelling wassite pursued resulting in organophossuccessful ity to5).bind a water molecule close to the of attachment of the phate. for Thefull water molecule then reacts with the organophosphate, validation of the design capacity (Figure 6 â&#x20AC;&#x201C; stress analysis under full splitting capacity;it in two.

Figure 7 â&#x20AC;&#x201C; displacement under full load), yielding a safety factor of 166% and a maximum elastic (recoverable) displacement of 7.7 cm.

-ESSAGE 4HERE IS NO PROPORTIONATE RELATION BETWEEN HOW MUCH $.! CHANGE TAKES PLACE IN EVOLUTION AND HOW MUCH CHANGE IN FUNCTION RESULTS

Selection clearly plays a role in the evolution of insect carboxylesterase and insecticide resistance. In many cases, however, the amino acid replacements that alter the function of the protein are more numerous and accumulate through repeated rounds of mutation and selection, what is referred to as cumulative selection. The power of cumulative selection to drive greater changes in a moleculeâ&#x20AC;&#x2122;s function is one of the least appreciated facets of evolution by natural selection. One reason is that the role of selection in each of the multiple replacements is more difďŹ cult to ascertain.

-ESSAGE # UMULATIVE SELECTION CAN DRIVE THE lXATION OF MANY CHANGES IN EVOLVING MOLECULES

In order to understand the role of selection in cases of multiple substitutions, two major approaches are taken: empirical experimental analysis and statistical methods. We will illustrate the former ďŹ rst.

Multistep pathways in evolution When mutations arise at multiple sites in the evolution from one phenotypic state to another, there are multiple possible orders in which these mutations can appear, each representing a different pathway through the genetic space that Fig. 6. Rendering of evolution Von Misesmight stresstake. analysis bionic tower 2 frame under full load, Suchfor multistep pathways of evolutionary change are obtained from educational 3D CAD software. referred to as adaptive walks.

Suppose that the difference between the original phenotype and the evolved form is a consequence of mutations at ďŹ ve sites, A, B, C, D, and E. There are many different orders in which these mutations could have occurred over evolutionary

20.4 Cumulative Selection and Multistep Paths to Functional Change

118

Industrial Design – New Frontiers

time. First, site A may have been fixed in the population, then D, then C, then E, and, finally, B. On the other hand, the order of fixation might have been E, D, A, B, C. For five sites there are 5 r 4 r 3 r 2 r 1 120 possible orders. Two important questions in understanding evolution are, How many of these alternative evolutionary pathways are possible? and, What are the probabilities of the different possible pathways relative to one another?

Daniel Weinreich and his colleagues have characterized in detail such a set of adaptive walks through genetic space in their study of the evolution of antibiotic resistance in the bacterium E. coli. Resistance to the antibiotic cefotaxime is acquired through the accumulation of five mutations at different sites in the bacterial B-lactamase gene. Four of the mutations lead to amino acid changes, and the fifth is a noncoding mutation. When all five mutations are present, the minimum concentration of antibiotic required to inhibit bacterial growth increases by a factor of 100,000. The experimenters first measured the resistance conferred by a mutation at a given site in the presence of all 24 16 possible combinations of mutants and nonmutants at the other four sites. In most combinations, but not all, a mutant at one site was more resistant, irrespective of the state of the other four sites. For example, a mutant at site G238S showed significant resistance, irrespective of the mutant or nonmutant state of the other four sites (Table 20-4). On the other hand, the mutation at the noncoding site g4205a conferred significant resistance in eight combinations, negligible change in resistance in six cases, and a decrease in resistance in two combinations (see Table 20-4). This dependency of the fitness advantage or disadvanFig. 7. Rendering of maximum elastic displacement forisbionic tage of a new mutation on the mutations that have previously been fixed what tower 2 frame under full load, obtained fromepistasis. educational 3D CAD software. the experimenters call sign Weinrich and colleagues measured the resistance at every stage in the temporal sequence adding mutations one site after another. If a mutation in one 5.ofConclusion of the 120 possible orderings did not confer a higher resistance, then presumFrom anpath industrial design perspective, the comparative analysis presented suggests that ably that evolutionary would terminate, because there would be no selection either in current favor of methods the mutation or even bionic againstdesign, it. Theyreported found that, the to support in of literature, despite supporting specific 120 possible goal pathways througharethe history,theonly 18 spectrum provided of typical design goals. All the satisfaction, notmutational effective across whole increased resistance at each mutational step. adequate Thus, 102/120 85 percent of the for paradigm innovation, but methods surveyed provide support to the search possible mutational pathways to maximum resistance were not accessible form optimization, organization effectiveness and multipletorequirement satisfaction are only evolution by natural selection. Finally, we assume that, in a population evolving adequately supported by some of the methods, albeit without any case of adequate support resistance, the likelihood that a particular accessible pathway will actually be to all five goals found. Communication effectiveness is typically not supported in existing followed is proportional to the magnitude of the increased resistance at each methods.

The Aalborg (Colombo, 2007) is step. Under that assumption, only 10 ofmethod the 18 accessible pathways willdeemed accountto adequately support attaining organization effectiveness, while the spiral design method (Biomimicry Institute, 2007) is deemed to adequately support attaining form optimization. Finally, the bio-inspired design (Helmsof the et Fitness al., 2009) for problems seeking multiple Table 20-4 method The Dependence Effectsisof deemed Mutations applicable on Prior requirements especially where trade-offs have to be established. Moreover, little Mutations in E. satisfaction, coli support is given in the methods validation activities, concerning the satisfaction of proportional Mutation* Number of alleles on which meantowardsMean the goals set for the design.

The approaches to validation proposed in this chapter, combines increase mutational effect is engineering social science approaches to validation, in accordance with the Positive approaches Negative with Negligible nature of each of the goals focused. This validation process was demonstrated in a design g4205a 8 2 6 1.4 case. Two variations of a novel bionic design for CD and DVD storage were designed using A42G 12 0 4 5.9 a combination of bio-inspired methods, and were then analysed in terms of satisfaction of E104K 15 1 0 9.7 requirements and 3validation 5of satisfaction of M182T 8 2.8the goals sought, in comparison with a conventional solution for the0 same problem.

G238S 16 0 1.0 rThis 103 design case hence demonstrated the deployment of the validation process proposed in this chapter. *The mutations leading to antibiotic resistance are designated by their nucleotide or amino acid position. Of the 16 possible allelic combinations of the four other sites, the positive, negative, or neutral effects of the mutation are indicated along with the mean proportional increase in fitness for mutations at the indicated site.

741

CHAPTER 20

Evolution of Genes and Traits

Adaptive walks to antibiotic resistance â&#x20AC;&#x201C;â&#x20AC;&#x201C;+â&#x20AC;&#x201C;â&#x20AC;&#x201C;

A42G

â&#x20AC;&#x201C;++â&#x20AC;&#x201C;â&#x20AC;&#x201C;

G238S

04

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+ + â&#x20AC;&#x201C;Cassidy â&#x20AC;&#x201C;+ + + +David â&#x20AC;&#x201C;+ Li, Tom and Bromilow E104K

362

38

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4K

â&#x20AC;&#x201C; + â&#x20AC;&#x201C; â&#x20AC;&#x201C; + M182T

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1. Introduction

1.41

A4

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1650University

362

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4100 23 8S Instructions T Product in the Digital Age 2 G 18 42 4K 0.13

â&#x20AC;&#x201C;â&#x20AC;&#x201C;â&#x20AC;&#x201C;â&#x20AC;&#x201C;â&#x20AC;&#x201C; Wild type

3

â&#x20AC;&#x201C; + + â&#x20AC;&#x201C; + M182T â&#x20AC;&#x201C; + + + + g4205a

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of Leeds United Kingdom

â&#x20AC;&#x201C;++++ 2050

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2 consumers to use products Product instructions are guides with the purpose of helping A4 g4 properly when they cannot be communicated through the design of the product itself. They â&#x20AC;&#x201C; â&#x20AC;&#x201C; â&#x20AC;&#x201C; + + E104T â&#x20AC;&#x201C; â&#x20AC;&#x201C; + + + are usually â&#x20AC;&#x153;on the product itself or its packaging or in accompanying materialsâ&#x20AC;? (ISO/IEC g4 32.0 362 20 tasks and the good ones benefit both the GUIDE 37, 1995, iv). They perform many different 5a users and the manufacturers. They should ensure users can operate products properly and safely. For manufacturers, instructions can add value + â&#x20AC;&#x201C;to â&#x20AC;&#x201C; +the + products, encourage sales and reduce time for customer service which makes good business sense.

362 In recent times, products tend to be designed for intuitive use. However, this is not the case for every user and for every product. ThusThird product instructions are still necessary and have First mutation Second mutation mutation Fourth mutation Fifth mutation their unique values. For example, many newly developed products are very complex and involve multiple functions, these functions are experimented with only when necessary and Figure 20-9 4HE MUTATIONAL STEPS FOR THE MOST PROBABLE TRAJECTORIES FROM WILD TYPE when the user guides are available. Thus, instructions for these products have to be SUSCEPTIBILITY TO THE ANTIBIOTIC CEFOTAXIME TO MAXIMAL RESISTANCE %ACH CIRCLE REPRESENTS AN carefully prepared ifALLELE WHOSE IDENTITY IS DENOTED BY A STRING OF lVE OR SYMBOLS CORRESPONDING left the current trends are to continue. to In this research, the right TO THE PRESENCE OR ABSENCE OF MUTATIONS G A ! ' % + - 4 AND ' 3

authors investigate problems of product instructions as well as suggest RESPECTIVELY .UMBERS INDICATE DEGREE OF CEFOTAXIME RESISTANCE IN MICROGRAMS PER MILLILITER possible explanations for those problems. The study aims to find solutions to enhance the 4HE RELATIVE PROBABILITY OF EACH BENElCIAL MUTATION IS REPRESENTED BY THE COLOR AND WIDTH effective and inclusive performance of product instructions in a commercial environment in OF ARROWS GREENÂ&#x2C6;WIDE HIGHEST PURPLEÂ&#x2C6;MEDIUM MODERATE BLUEÂ&#x2C6;NARROW LOW AND produce product instructions that this digital age. The REDÂ&#x2C6;VERY NARROW LOWEST ideal was to find a method [From D. to Weinrich et al.,durable Science 312, 2006, 111â&#x20AC;&#x201C;114.] can be easily accessed, understood, stored and updated for all; meanwhile fulfilling the requirements of being to produce and environmentally friendly. forcheap 90 percent of the cases of evolution of bacterial resistance to the antibiotic E1

742

(Figure 20-9).

2. Product instructions

-ESSAGE 4HE ORDER IN WHICH MUTATIONS OCCUR IS OF CRITICAL IMPORTANCE IN DETERMINING

In the Oxford EnglishTHE PATH OF EVOLUTION AND WHETHER EVOLUTION BY NATURAL SELECTION WILL OR WILL NOT ACTUALLY online dictionary (2006), the word â&#x20AC;&#x153;productâ&#x20AC;? is defined as â&#x20AC;&#x153;that which REACH THE MOST ADVANTAGEOUS STATE "ECAUSE THE ORDER OF OCCURRENCE OF MUTATIONS IS is produced by any action, operation, or work; a production; the result. Now that which is RANDOM MANY ADVANTAGEOUS PHENOTYPES MAY NEVER BE ACHIEVED EVEN THOUGH THE produced commercially for saleâ&#x20AC;?. Another word â&#x20AC;&#x153;Instructionâ&#x20AC;? is described as â&#x20AC;&#x153;making INDIVIDUAL MUTATIONS OCCUR known to a person what he is required to do; a direction, an order, a mandate (oral or written) (www.oed.com, 2006)â&#x20AC;?.

Thus the â&#x20AC;&#x153;Product refers to the guides A key factor, then, in term determining theinstructionsâ&#x20AC;? evolutionary path a population may associated with products to provide detailed operating instructions.

In one of these follow is the randomness of the mutational process. After the initial genetic variainternational standards, for selective the use and of products of consumer are tion isâ&#x20AC;&#x153;Instructions exhausted by the random ďŹ xation of alleles,interestâ&#x20AC;? new variation defined as: â&#x20AC;&#x153;the means of conveying information the user how to use the product a arising from mutation can be theto source of yeton further evolutionary change.in The correct and safe mannerâ&#x20AC;?

(ISO/IEC GUIDE 1995, iv). particular direction of this 37, further evolution depends on the particular mutations occur and theistemporal order in which arise. vitalthey information to users, and help The initial purpose that of instructions to communicate A very clear illustration of this historical contingency adaptive walks is a them to use products correctly when this cannot be achieved through the of design of products selection experiment carried out by Holly Wichman and her colleagues. They forced the bacteriophage FX174 to reproduce at high temperatures and on the host Salmonella typhimurium instead of its normal host, Escherichia coli. Two independent lines of viruses were established, labeled TX and ID, and kept separate, although both were exposed to the same conditions. Both evolved the ability to

20.4 Cumulative Selection and Multistep Paths to Functional Change

40

Industrial Design â&#x20AC;&#x201C; New Frontiers

reproduce at high temperatures in the new host. In one of the two lines, the abilthemselves. They are crucial parts of products and they should allow and promote proper ity to reproduce on E. coli still existed, but, in the other line, the ability was lost. use ofhas manufactured also direct help to avoid The bacteriophage only 11 genes,goods and so theoffer experimenters were able tomishandling which may lead to danger.changes Although not compensate forproteins flaws of product design, instructions record the successive in thethey DNAshould for all these genes and in the products, failures or inefficient should be the ableselection to reduce risksThere of damaging encoded by them during process. were 15 DNA changes consequent in operations. strain TX, located in six different genes; in strain ID, there were 14 changes located in four different genes.

In seven the changes the two It is believed bycases, Petterson (2002)tothat thestrains designwere of identiproduct instructions is the design of cal, including instructional a large deletion,messages but even these appeared in each Design. It is closely related to and itidentical is one changes sub area of Instruction line in a different order (Table 20-5).

So,itfor the change at subject.

DNA site It takes influences from many information design and is example, an interdisciplinary 1533, causing established a substitutionareas of isoleucine for threonine, was areas the third change in language, art and aesthetics, of research.

The main may involve the ID strain but the 14th change in the TX strain (see Table 20-5). information discipline, communication, behavioural and cognitive study and so on.

Thus, the Incourse evolution followed by the initially identical manyof perspectives, product instruction design viruses and information design share their depended on the mutations available at any given time in the cumulative selecsimilarities. Both these areas are not clearly defined yet and their histories are not easy to tion process. Contrast this situation with the repeated origin of the sickle-cell trace. The preparation, presentation, analysis and understanding of a message need to be allele HbS: in this case, the same mutation arose and spread ďŹ ve times. Clearly, in embraced through a selected medium.

Also, productand instruction design and information some cases there are many molecular â&#x20AC;&#x153;solutionsâ&#x20AC;? to selective conditions in design both involve multi-disciplinary and global concerns.

They have influences from others just one or very few. similar areas and they both need to inform the intended users. When studying the design of instructions, the authors have taken inspiration from the information design field.

-ESSAGE 5 product NDER IDENTICAL CONDITIONS OF NATURAL SELECTION TWO POPULATIONS MAY ARRIVE AT IDENTICAL OR TWO DIFFERENT GENETIC COMPOSITIONS AS A DIRECT RESULT OF NATURAL SELECTION

3. The trends and problems

The experimental dissection of evolutionary pathways is very time consuming and expensive.Peopleâ&#x20AC;&#x2122;s In addition, it is often practical for experimenters to engineer demands onnot product instructions more or less depend on how much information every possiblethey genotype in an adaptive walk in populations or to attempt to the mea-design of product instructions is need for the operation of the products. Therefore sure relative ďŹ tness of many organisms in the wild.

The antibiotic-resistance and In the product design field, closely related to the design and development of products. viral-host examples are cases where both genetic engineering and ďŹ tness meaproducts are restructured and redesigned from time to time to follow different trends. surements areDesigners readily executed in bacteriaabout and their viruses in the laboratory.creating In are passionate using newer technology, appealing appearances for other situations, statistical methods have been devised to uncover a signature products, minimise then simplify them (Redhead, 2000). indicating that selection has acted on DNA and protein sequences.

The past ten years has been the fastest changing period for technologies; extraordinary changes have been brought to society. The emergence of mass information, new products Table 20-5 and Molecular Substitutions in Two F-X174prevalent Bacteriophages, redesigned products is more than ever. New technology allows products to TX more and ID,complicated During Adaptation be to use but their appearance is getting simpler. Users are very often Order* TX site Amino ID site Amino change Products both more confusing overwhelmed by acid newchange technology, products and acid information. and more exciting 1 782 E72, T lthan 1 ever. 2167 F388, H l Q The choices for customers are wide,from products 2 1727 1613 F242, Ll F F204, T l S like computers and mobile phones to 6 consumer products, for example, shampoo 1533 3 2085 F177, Tand l I chairs, almost everything has been F361, Al V rethought from scratch.

Consumers, after experiencing high technologies and pleasant 4 319 1460 F153, Q l E C63, Vl F appearances of Ginventions, start1300 to requireF99, more control and urge for personalisation. They 5 2973 silent H15, lS 3 personal, want products to be â&#x20AC;&#x153;more seductive, more 1305 6 323 F101, G l D more availableâ&#x20AC;? (Redhead, 2000, P54).

C64, D l G 3 The trend of customisation allows more customers 4110 1308 7 A44, H l Y F102, Y l C to personalise their products. For 1 example, Appleâ&#x20AC;&#x2122;s such4110 as the iPod and iShuffle allow customers to have their own 8 1025 A44, Hl Y F8, E l products K 7 name on the back of the product.

Similarly, Nike let the buyers decide the colour, detail and 3166 4637 A219, silent 9 H79, A l V 4 the ID of their own trainers.

And now, personalised products are developed in most 965-91 10 5185 deletion A402, T l M 2 5 industries; ranging from fashion products to computers or furniture, even picture frames.

5365 1305 11 F101, G l D A462, M l T These4 trends and existing changes the Qdesign 965-91 41687 on A63, 12 deletion l R of new products require product 5 2 instructions to follow up and to be as exciting.

3166 5365 13 A462, M l T H79, A l V The change of products needs their 1 instructions to be clearer, quicker to access and K easier 1533 1809 14 F177, T l I F269, l R to understand. However, while we are 6 surfing in the 4168 15 A63,ocean Q l Rof newer and more charming products, product instructions are not as interesting as they should be. They are not redesigned and updated quickly enough to catch *Changes are listed in the order in which they appeared in each of the two bacteriophage selection lines. The nucleotide position is listed, followed by the protein affected, Aâ&#x20AC;&#x201C;H, with the number of the amino acid residue and the nature of the amino acid substitution.

Parallel changes are shown in boldface, and a superscript indicates the order of those changes in the other virus selection line.

Source: H. A. Wichman et al., Science 285, 1999, 422â&#x20AC;&#x201C;424.

743

744

CHAPTER 20

Evolution of Genes and Traits

41

Product Instructions in the Digital Age

The signature of positive selection on Table 20-6 Synonymous andthe Nonsynonymous Polymorphisms up with changes in emerging products. With the majority of product instructions, users Organism

and Species Differences for Alcohol Dehydrogenase are mainly suffering from problems in DNA three sequences design aspects: the effectiveness, the in Three Species of Drosophila The demonstration of the molecular clock argues that accessibility and the inclusiveness.

Species differences Polymorphisms most nucleotide substitutions that have occurred in

evolution were neutral, but it does not tell us how Nonsynonymous 3.1 Effectiveness 7 2 much of molecular evolution has been adaptive change Synonymous 42are important Although 17 product instructions andbynot replaceable, suggests positive selection.evidence One way of detectingthat the Ratio 0.29 0.71 0.05 0.95 as theydriven existing instructions are not as good should be.

The fact is that the user satisfaction adaptive evolution of a protein is by comparing the rate on product instructions is only 31% according to the authorsâ&#x20AC;&#x2122; survey in 2006.

Users Source: J. McDonald and M. Kreitman, â&#x20AC;&#x153;Adaptive Protein Evolution at the synonymous and nonsynonymous nucleotide polyAdh locus in Drosophila,â&#x20AC;?

Nature 351,about 1991, 652â&#x20AC;&#x201C;654. complain many problems with product instructions such as they explain what morphisms within species withdo thenot synonymous and the users really need; they are either too wordy or difficult to understand, hold unusual nonsynonymous nucleotide changes between species. Under the operation of technical terms, contain badevolution translations and bad visuals 1). neutral by random genetic drift,(Figure polymorphism within a species is simply a stage in the eventual ďŹ xation of a new allele. So, if all mutations are neutral, the 4ratio of nonsynonymous to synonymous nucleotide polymorphisms within a other species should be the same as the ratio of nonsynonymous to synonymous nuclevisually poor 37 otide substitutions between species. doesn't match product 26 On the other hand, if the amino acid changes between species have been driven by positive selection, there ought53 to be an don't explain w hat I need excess of nonsynonymous changes between species. Table difficult to understand 42 20-6 shows an application of this principle by John MacDonald and Martin Kreitman to the alcohol too detailed and w ordy 43 too much jargon 48 Clearly, there is dehydrogenase gene in three closely related species of Drosophila. of amino species over what is expected.

0 an excess 5 10 15 acid 20 replacements 25 30 between 35 40 45 50 55 60 Therefore, we conclude that some of the amino acid replacements that helped Frequencies form the enzyme were adaptive changes driven by natural selection.

Fig. 1. Problems with instructions (authorsâ&#x20AC;&#x2122; survey 2006).

These criticisms suggest that many accompanying instructions are not effective and they are 20.5 Morphological Evolution not designed for all.

One of the most obvious and interesting categories of evolving traits is that of 3.2 Accessibility organism morphology. Among animals, for example, there is great diversity in the number, kind, size, shape, andmaterials color of body adult form theleaflets, product The majority of instructions in accompanying are parts. in theSince physical formsis of of 2). embryonic changes in the formauthors must be(2008) the result of changes in manuals, CD (Figure Anotherdevelopment, survey carried out by showed that the what during development.

Recent genetic vast majority (92%) of happens product instructions often are advances printed.in understanding Other forms the such as CD/DVDs are also adopted but only used by a very small number of users.

Contrasting colors of the Pinacate desert

Videotapes 0%

Other 2%

CDs/DVDs 6%

Printed leaflets and Manuals 92%

Fig. 2. Types of accompanying instructions.

Figure 20-10 ,AVA mOWS IN THE

0INACATE DESERT HAVE PRODUCED OUTCROPS OF BLACK COLORED ROCK ADJACENT TO SANDY COLORED SUBSTRATES [Photograph courtesy of

Michael Nachman, University of Arizona.]

20.5 Morphological Evolution

42

745

Industrial Design â&#x20AC;&#x201C; New Frontiers

control of development (see Chapter 13) have enabled researchers to investigate Many printed instructions take a huge amount of storage space and are not easy to be kept the genetic and molecular bases of the evolution of animal form. We will see that shared.

For example, products, such as office machines and equipment, are shared some dramaticand changes in animal form havesome a relatively simple genetic and molecor the passed around andgoverned instruction manuals become in the process. For example, in the ular basis, while evolution of traits by many â&#x20AC;&#x153;toolkitâ&#x20AC;? genes lost involves survey carried out by from the those authors (2008), 72% of participants (155) intended to keep all molecular mechanisms that are distinct we have examined thus far. We will examine cases in which coding substitutions, gene inactivation, and regulatory instructions which accompany products (Figure 3). sequence evolution, respectively, underlie morphological divergence.

Adaptive changes in a pigment-regulating protein No, 61, 28%

Some of the most striking and best-understood examples of morphological divergence are found in animal body-color patterns. Mammalian-coat, birdâ&#x20AC;&#x201C;plumage, ďŹ sh-scale, and insect-wing color schemes are wonderfully diverse. Investigators have made much progress in understanding the genetic control of color formation and its role in the evolution of color differences within and between species.

In the Pinacate region of southwestern Arizona, dark rocky outcrops are surrounded by lighter-colored sandy granite (Figure 20-10). The rock pocket mouse, Chaetodipus intermedius, inhabits the Pinacate as well as other rocky areas of the Yes, 155, 72% Southwest. The mice found on the lava outcrops are typically dark in color, whereas those found in surrounding areas of sandy-colored granite or on the desert ďŹ&#x201A;oor are usually light colored (Figure 20-11). Field studies suggest that Fig. 3. Do users intend to keep instructions? color matching of coat color and environment protects mice against being seen by predators. Among them, only 5% participants (3%) never lose the instructions and another 37 The rock pocket mice give(24%) an example melanismâ&#x20AC;&#x201D;the occurrence of a darkadmit that they lose product participants rarelyof lose them. 12% participants form within a population or species. Melanism is one of the most common types instructions very often. The majority users (61%) replied â&#x20AC;&#x153;sometimesâ&#x20AC;? (Figure 4). of phenotypic variation in animals. The dark color of the fur is due to heavy deposition of the pigment melanin, the most widespread pigment in the animal Very often, 18, kingdom. In mammals, two types of melanin are produced in 5, melanocytes (the Never, 3% pigment cells of the epidermis and hair follicles): eumelanin, which forms black12% or brown pigments, and phaeomelanin, which forms yellow or red pigments. The relative amounts of eumelanin and phaeomelanin Rarely, 37, 24%are controlled by the products of several genes. Two key proteins are the melanocortin 1 receptor (MC1R) and the agouti protein. During the hair-growth cycle, the A-melanocyte-stimulating

Melanism in the rock pocket mouse

Sometimes, 95, 61%

Fig. 4. Do users lose instructions?

On the other hand, for manufacturers, it is expensive to have these accompanying materials produced. Paper based product instructions such as leaflets and manuals are typical examples. Some of them contain many pages as all useful information has to be included (Figure 5).

Figure 20-11 ,IGHT AND DARK COLORED Chaetodipus intermedius FROM THE the price of energy and Costs for producing them have been continuously increasing since 0INACATE REGION OF !RIZONA ARE SHOWN paper has climbed. In recent years, there are more and more product instructions available ON SANDY COLORED AND DARK LAVA ROCK online for free download. However, they are mostly digital orBACKGROUNDS scanned versions the of [Photographsof courtesy Michael Nachman, from M. W. Nachman, H. E. Hoekstra, and S. L. Dâ&#x20AC;&#x2122;Agostino, â&#x20AC;&#x153;The Genetic Basis of Adaptive Melanism in Pocket Mice,â&#x20AC;? Proc. Natl. Acad. Sci. USA 100, 2003, 5268â&#x20AC;&#x201C;5273.]

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43

(A-MSH) binds to the MC1R protein, which triggers the inducAmino acid replacements cluster in andhormone traditional instructions, areofstill limited compared to other by tion pigment-producing enzymes.

The instructions agouti proteindelivered blocks MC1R one part of the MC1R protein physical media.

activation and inhibits the production of eumelanin.

Michael Nachman and his colleagues examined the DNA sequences MC1R NH of the mc1r genes of light- and dark-colored pocket mice. They found the presence of four mutations in the mc1r gene in dark mice that cause the Extracellular MC1R protein to differ at four amino acid residues from the corresponding protein in light mice. Findings from biochemical studies suggest that Intracellular such mutations cause the MC1R protein to be constitutively active (active at all times), bypassing the regulation of receptor activity by the agouti protein. Indeed, mutations in mc1r are associated with melanism in all Fig. 5. Examples of paper based instructions. sorts product of wild and domesticated vertebrates. Many of these mutations alter residues in the same part of the MC1R protein, and the same mutaL100P (mouse) tions have occurred independently in some species (Figure 20-12).

3.3 Inclusiveness L99P (cow, pig) D121N In many ways, we can think of these dark mice analogs of DarProduct instructions should help all users to use different products andasfulfill different (pig, sheep) winâ&#x20AC;&#x2122;s ďŹ nches and the lava outcrops as new â&#x20AC;&#x153;islandâ&#x20AC;? habitats produced tasks. When designing product instructions, designers are planning instructional materials E94K by the same volcanic activity that produced the GalĂĄpagos Islands. The and in some way designing a learning process for product users. Designed instructions (mouse, C125R sandy-colored form of the mouse appears to be the ancestral type, akin chicken, (fox) be easy to follow by users with all kind of intelligence references and learning styles. should to the continental ancestral ďŹ nch that colonized the GalĂĄpagos. The bananaquit) Therefore the instructions should useofvaried styles of to delivery, customized for selection specific advantage being less visible predatorsberesulted in natural However, this is not achieved most people and help everyone to and forunderstand coat color, and thelearn. invasion of the lava-rock islands by the in mice led to the spread of an allele that was favored on the black-rock background cases. selected against on are the sandy-colored mutations either text,New images or a Currently, the majority of and product instructions presented bybackground. in the mc1r dominated gene were essential to this adaptation to the changing mixture of both. Product instructions by text certainly enable aural learners to S71L (mouse) M73K (sheep) landscape. follow easily, however, they are not as straightforward to use for other readers with The evolution of melanism in the pocket mice illustrates how ďŹ tness different strengths. Instructions full of pictures and charts can help visual learners to process depends on the conditions in which an organism lives. The new black mutation Figure 20-12 !MINO ACID information effectively and useonproducts quicklybut butdisfavored yet again might not be the living best REPLACEMENTS ORANGE CIRCLES ASSOCIATED was favored the lava outcrops in they the ancestral population WITH MELANISM VARY SLIGHTLY IN LOCATION choice for other users, for example, kinesthetic learners. on sandy-colored terrain.

IN DIFFERENT SPECIES BUT ARE LOCATED IN Additionally, it is difficult to locate a piece of information among instructions, as they are THE SAME PART OF THE -# 2 PROTEIN 4HE -ESSAGE HE RELATIVE lTNESS OF A NEW VARIANT DEPENDS ON THE IMMEDIATE SELECTIVE often very lengthy. Users have 4to scan all information and evaluate them to select the part UPPER PART OF THE lGURE SHOWS THE GENERAL CONDITIONS ! MUTATION THAT MAY BE BENElCIAL IN ONE POPULATION MAY BE DELETERIOUS IN they need. This works well when the assimilating learning style is favoured. However, TOPOLOGY OF THE -# 2 PROTEIN 4HE REGION ANOTHER IN WHICH REPLACEMENTS ARE LOCATED IS when an accommodating learning style is preferred, users will be annoyed, often because ENLARGED IN THE LOWER PART OF THE lGURE they are forced to go through lots of instructions, instead of getting hands on experience [After E. Eizirik et al., â&#x20AC;&#x153;Molecular Genetics quickly. and Evolution in the Cat Family,â&#x20AC;?

Curr.

Gene inactivation Biol. 13, 2003, 448â&#x20AC;&#x201C;453; reprinted with permission from Elsevier.]

It has long been noted that cave-dwelling animals are often blind and uncolored.

Darwin noted in The Origin of Species that â&#x20AC;&#x153;several animals belonging to the most 4. Current solutions different classes, which inhabit the caves of Carniola [in Slovenia] and Kentucky, Facing all these problems some have been to are blind.with As it product is difďŹ cultinstructions, to imagine that eyes, actions though useless, couldtaken be in any alleviate the frustrations.

To make productliving instructions more and effective, way injurious to animals in darkness, theircomprehensible loss may be attributed to disuse.â&#x20AC;?

Many species of ďŹ sh live in and cavestextual have lost their eyes color. standards for formulating instructions are that available materials on and howbody to write Because these species belong to many different families that include surfaceinstructions are provided. Meanwhile, info-graphics have been studied by some designers dwelling, so eye-bearing species, can the loss of eyestoand has clearly and academic researchers that graphics be used aidpigmentation the presentation of occurred repeatedly. For example, the Mexican blind cave ďŹ sh (Astyonax mexicainformation. However, related standards are limited and dated; research focused on the nus) belongs to the same order as the piranha and the colorful neon tetra. About accessibility and inclusive design of product instruction is very rare; problems of product 30 cave populations of ďŹ sh in Mexico have lost the body color of their surfaceinstructions are not dwelling completely and(Figure successfully relatives 20-13). solved and users are continuing to suffer from annoyance caused by poor product instructions.

It is innecessary carry out a Genetic studies have indicated that albinism the PachĂłntocave ďŹ sh populathe performance of aproduct instructions, systematic and up tion to date to recessive improvemutation. is duestudy to a single Furthermore, cross between a Molino cave age. individual and a PachĂłn cave individual produced only albino offspring, sugespecially in this digital gesting that the albinism in the two populations is due to the same genetic locus.

To identify the gene responsible for albinism in the ďŹ sh, researchers investigated the genotypes of ďŹ sh at several pigmentation loci known to cause albinism in mice or humans. They found that one of these genes, Oca2, mapped to the albino locus.

20.5 Morphological Evolution

44

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Industrial Design â&#x20AC;&#x201C; New Frontiers

They also found that there was a perfect association between the genotype of the Evolution of albinism in 5.the Possible solutions Oca2 locus and phenotype of albinism in F2 offspring that were a backcross blind cave ďŹ sh between Molino Molino/surface F1 progeny product or PachĂłn and PachĂłn/surface Theand people who are producing instructions should be trained to write and produce F1 progeny. effective product instructions. They should understand standards for formulating Further inspection of theand Oca2 thewhile PachĂłndoing population was instructions begene ablerevealed to applythat them their jobs. homozygous for a deletion that extended from an intron through most of an exon To make product instructions easily accessible, easily stored and updated, they could be and that the Molino population was homozygous for the deletion of a different created and distributed digitally, through networks, for example Internet or 3G networks. exon. Functional analyses proved that each deletion in the Oca2 gene caused loss cave around the This will provide product instructions available at anytime, from Molino anywhere of Oca2 function. world and could lesions be translated into multiple languages gene of the two cave pop- with a very low budget for The identiďŹ cation of different in the Oca2 maintenance.

There were 1,966,514,816 Internet users around the world in June 2010. The ulations indicates that albinism evolved separately in the two cave populations. number has grown by 444.8 % between 2000 to 2010, and it is still growing There is also evidence that a third cave population carries yet a third, distinct (internetworldstats.com, On the other hand,can based on Nielsen's estimate (2010), 50% Oca2 mutation.

It is known from other 2010). vertebrates that albinism evolve through mutations other genes.

What might account for the inacti- users by 2011, which means of USinmobile subscribers (142.8 million) willrepeated be Smartphone PachĂłn cave are actually vation of the they Oca2 could gene? get There are two explanations.

First, on Oca2 mutaaccess to a likely 3G network very easily their phones. Similar trends tions appear to cause no serious collateral defects other than loss of pigmentahappening everywhere across the world. tion and vision. pigmentation genes, when mutated in ďŹ sh, cause intelligence levels and learning styles, To Some fulfilother requirements from users with different dramatic reductions in viability.

The effects of Oca2 mutations appear, then, to music, animation etc., as well instructions could involve multiple media for example, sound, be less pleiotropic and have effects on overall ďŹ tness that are less harmful than as the traditional media of text and images. Product instructions might also be interactive so those of mutations in other ďŹ sh pigmentation genes. Second, the Oca2 locus is that they could be read in almost any order. Once instructions are designed to be interactive very large, spanning some 345 kb in humans and containing 24 exons. It presSurface rather than can bethat read by disrupt choice. gene This funcshould enable the users to reread ents a very large target forlinear, randomthey mutations would instructions and to repeat the tasks when an are error is discovered.

This will also minimise the tion; Oca2 mutations are therefore more likely to arise than mutations at Figure 20-13 3URFACE FORMS OF THE lSH inexperienced users who smaller loci. amount of time spent on reading instructions, especially for thoseAstyanu mexicanus APPEAR NORMAL BUT have little prior knowledge.

Also, a combination of when minimalist and systematically complete The loss of gene function is not what we usually think about we CAVE POPULATIONS SUCH AS THOSE FROM THE think about evolution.

Butmight gene inactivation is certainly what we shouldlearning preinstructions be able to offer the most productive experience.

-OLINO AND 0ACHÂ&#x2DC;N CAVES IN -EXICO HAVE dict to happen when selective conditions change or when populations or speREPEATEDLY EVOLVED BLINDNESS AND ALBINISM [Photographs courtesy of Meredith Protas and cies shift their habitats or lifestyles and certain gene functions are no longer 6.

Design challenges Cliff Tabin, Harvard Medical School.] necessary.

Ideally, multimedia instructions should help people with different leaning styles and

-ESSAGE ' strengths ENE INACTIVATING MUTATIONS MAY OCCUR AND RISE TO HIGH FREQUENCY WHEN to operate products easier, quicker and safer. However, it has been suggested Wing spots on fruitby ďŹ&#x201A;ies HABITAT OR LIFESTYLE CHANGES RELAX NATURAL SELECTION ON TRAITS AND UNDERLYING GENE Tapscott ( 2009) that Digital Natives (those who have FUNCTIONS

grown up with digital devices) and Digital Immigrants (those who learnt to use digital devices as an adult) learn things differently and have different opinions on digital products and interactive works. Therefore Regulatory-sequence evolution the key challenges for this study were to find differences between improved traditional and multimedia instructions use;potential to discover As discussed instructions above, a major constraint on gene evolution in is the for if multimedia instructions are harmful side going effects to caused by mutations codingofregions that alter protein perform better ininterms their effectiveness and inclusiveness; to determine if function. These effects can be circumvented by mutations regulatory sequences, multimedia instructions can be better in solutions for all users, including the Digital Natives which play a major role in the evolution of gene regulation and body form. and the Digital Immigrants.

The examples of body-coloration evolution we have looked at thus far have the coat or scale pattern changing over the entire body. The evolution of solid 7. Prototyping andcoloration user testing black or entirely unpigmented body can arise through mutations in pigmentation To genes.

However, many color schemes are often made up of twofor or a particular product, a lighting find the answers to the above questions, instructions more colors in some spatial pattern. In such cases, the expression of pigmentatable (Figure 6) were chosen and rewritten according to the standards and regulations for tion genes must differ in areas of the body that will be of different colors. In planningorproduct Two versions of product instructions were then produced: a different populations species,instructions. the regulation of pigmentation genes must 7); a multimedia version product printed version text and evolve by some mechanism thatcombining does not disrupt the images function(Figure of pigmentation rosophila Figure 20-14of Dthe instructions, which used the same text and imagery information but involved extra sound, melanogaster MALES LACK WING SPOTS proteins. top WHEREAS Drosophila animation and were interactive 8).ofParticipants for the tests biarmipes were display extensive(Figure diversity The species of the fruit-ďŹ&#x201A;y genus designed Drosophila as MALES bottom HAVE DARK WING SPOTS body and wingseparated markings.into A common patternDigital is the presence a black spotImmigrants. near two groups: Natives of and Digital THAT ARE DISPLAYED IN A COURTSHIP RITUAL the tip of the wing in males (Figure 20-14). The production of the black spots 4HIS SIMPLE MORPHOLOGICAL DIFFERENCE requires enzymes that synthesize melanin, the same pigment made in pocket IS DUE TO DIFFERENCES IN THE REGULATION mice. Many genes controlling the melanin synthesis pathway have been well OF PIGMENTATION GENES [Photographs by studied in the model organism Drosophila melanogaster. One gene is named Nicolas Gompel.]

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Product Instructions in the Digital Age

Changes in regulatory sequences can underlie evolutionary differences

Wing

Body

Bristle

Wing

Reporter

Wing

Body

Bristle

Wing

Reporter

Yellow D. biarmipes

Yellow D. melanogaster (a) Pupal expression

(b) yellow gene

Figure 20-15 The evolution of gene regulation and morphology in the case shown is due to evolution in cis-acting regulatory sequences. (a) In spotted fruit flies, the Yellow pigmentation protein is expressed at high levels in cells that will produce large amounts of melanin. (b) The yellow locus ofFig. Drosophila 6. A photo species contains several discrete cisacting regulatory elements (red) that govern yellow transcription in different body parts. Exons are shown in gold.

Arrows indicate the point of the start and direction of transcription of the gene. (c) The “wing” regulatory element from D. biarmipes drives reportergene expression in a spot pattern in the developing wing, whereas the homologous element from the unspotted D. melanogaster does not drive a spot pattern of reporter expression. This difference in wing cis-acting-regulatoryelement activities demonstrates that changes in the cis-acting-regulatoryelement function underlie differences in Yellow expression and pigmentation between the two species.

(c) Reporter expression

yellow because mutations in the gene cause darkly pigmented areas of the body to appear yellowish or tan. The yellow gene plays a central role in the development of divergent melanin patterns. In species with spots, the Yellow protein is expressed at high levels in wing cells that will produce the black spot, whereas in species without spots, Yellow is expressed at a low level throughout the wing blade (Figure 20-15a).

The difference Yellow expression between spotted and unspotted species of the selected productinand its original instructions. could be due to differences in how the yellow gene is regulated in the two species.

Either or both of two possible mechanisms could be at play: the species could differ in the spatial deployment of transcription factors that regulate yellow (that is, changes in trans-acting sequences to the yellow gene) or they could differ in cisacting regulatory sequences that govern how the yellow gene is regulated. To examine which mechanisms are involved, investigators examined the activity of yellow cis-acting regulatory sequences from different species by placing them upstream of a reporter gene and introducing them into D. melanogaster.

The yellow gene is regulated by an array of separate cis-acting regulatory sequences that govern gene transcription in different tissues and cell types and at different times in development (Figure 20-15b). These regulatory sequences include those controlling transcription in the larval mouthparts, the pupal thorax and abdomen, and the developing wing blade. It was discovered that, whereas the wing-blade cis-acting regulatory element from unspotted species drives low-level expression of a reporter gene across the wing blade, the corresponding element from a spotted species, such as D. biarmipes or D. elegans, drives a high level of reporter expression in a spot near the tip of the wing (Figure 20-15c). These observations show that changes in sequence and function of a cis-acting regulatory element are responsible for the change in yellow regulation and contribute to the origin of the wing spot. The cis-acting regulatory element of the spotted species has apparently acquired binding sites for transcription factors that now drive high levels of gene transcription in a spot pattern in the developing wing.

Thus, evolutionary changes in cis-acting regulatory sequences play a critical role in the evolution of body form. The location of change in the regulatory sequence rather than the gene itself can be best explained in light of the many different effects that can appear as the result of a coding mutation in a “toolkit” gene. In this instance, the yellow gene is highly pleiotropic: it is required for the pigmentation of many structures and for functions in the nervous system as well. A coding mutation that alters Fig. 7. Layout for the redesigned printed version of product instructions.

Yellow protein activity would alter Yellow activity in all tissues, which might have a negative consequence for fitness. However, because individual cis-acting regulatory sequences usually affect only one aspect of gene expression, mutations in these sequences provide a mechanism for changing one aspect of gene expression while preserving the role of protein products in other developmental processes.

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Evolution of Genes and Traits Industrial Design â&#x20AC;&#x201C; New Frontiers

The differences in pelvic morphology have evolved repeatedly in just the past 10,000 years, since the recession of the glaciers of the last ice age. Many separate lakes were colonized by long-spined oceanic sticklebacks, and forms with reduced pelvic spines evolved independently several times. Because the ďŹ sh are so closely related and interbreed in the laboratory, geneticists can map the genes involved in the reduction of the pelvis. David Kingsleyâ&#x20AC;&#x2122;s group at Stanford University along with Dolph Schluterâ&#x20AC;&#x2122;s group at the University of British Columbia mapped one major factor involved in pelvic differences to the Pitx1 gene, which encodes a transcription factor. Like most other developmental toolkit genes, the Pitx1 gene has several distinct functions in ďŹ sh development. However, in the form of the stickleback with a reduced pelvis, its expression is lost from the area of the developing ďŹ sh embryo that will give rise to the pelvic-ďŹ n bud and spines (see Figure 20-16).

The fact that the difference in pelvic morphology between the two forms mapped to the Pitx1 locusversion and was of associated the loss of gene expression sugFig. 8. Screen examples for the multimedia productwith instructions. gested that changes in Pitx1 regulatory sequences were responsible for the difference in phenotypes. most pleiotropic toolkit genes,totheensure expression the planned in order that of their The choices of the participants had toLike be carefully Pitx1 gene in different parts of the developing ďŹ sh is controlled by separate cishuman performance characteristics were checked prior to the beginning of the tests. This acting regulatory elements.

Chan and colleagues that the was done using a method traditionally usedFrank by work-study officers demonstrated to establish what a regulatory element that controls Pitx1 expression in the developing pelvis hundred percent effort or rating looks like. A full pack of cards is dealt into four hands inhas a been inactivated by large deletion mutations in multiple, independent populaperiod of 52 seconds. It was ensured that the participants could all carry out this task in tions of pelvic-reduced ďŹ sh (Figure 20-16, bottom). Furthermore, it was observed periods between 50 that and heterozygosity 56 seconds. Thus their human could pelall was reduced aroundperformance the cis-acting characteristics sequences controlling be considered similar. vic expression relative to other nearby sequences. This observation is consistent for the product the They were asked with to follow either thebeing printed the deletion allele favoredinstructions by natural selection acting on the or bottompelvic-reduced form. multimedia ones todwelling, complete the same set of given tasks. The tasks included 1) using these ďŹ ndings further illustrate how mutations in regulatory instructions to find Thus, information, 2) checking components of the product sequences and 3) circumvent the pleiotropic effects of coding mutations in toolkit genes and that assembling. Their actions were monitored; timing was recorded; errors were observed adaptive changes in morphology can be due to the loss as well as the gain of gene and feedback was collected at the end. expression during development.

-ESSAGE !

DAPTIVE CHANGES IN MORPHOLOGY CAN RESULT FROM INACTIVATION OF REGULATORY 8. Analysis and interpretation SEQUENCES AND LOSS OF GENE EXPRESSION AS WELL AS THE MODIlCATION OF REGULATORY

Data from the experiment was gathered and interpreted to clarify the communicating effects SEQUENCES AND THE GAIN OF GENE EXPRESSION of instructions, mainly from two aspects of task performance: efficiency and accuracy.

Circumventing the potentially side effects of coding mutations Results from different user groups were compared harmful and examined to find out which typeisofa veryeffective important factor in explaining why acts by generating new roles instructions were more and inclusive in terms of evolution communication. for transcription factors that may regulate dozens to hundreds of target genes.

Changes in the coding sequences of a transcription factorâ&#x20AC;&#x201D;for example, the DNA8.1 Task analysis binding domainâ&#x20AC;&#x201D;may affect all target genes, with catastrophic consequences for given to the ofparticipant and product In the test, all components product the animal.of Thethe constraint on were the coding sequences highly pleiotropic proteins, instructions were provided on either a printed sheet or a laptop computer.

By using with many functions, explains the extraordinary conservation of the DNA-binding Hierarchical task analysis (HTA), main (see goalFigure and sub-goals the other tasks transcription were expressed as domains of Hoxthe proteins 13-8) andof many factors below (Figure 9). over vast expanses of evolutionary time. But, although the proteinsâ&#x20AC;&#x2122; biochemical functions their regulation does diverge.

The to evolution the As shown in figure9, tasks 1 are andconstrained, 2 were skill-based tasks. Users were asked follow of clear expression patterns of Hox and other toolkit genes plays a major role in the and simple instructions to carry out actions and they did not have to make judgements on evolution of body form. the aim and plan of their actions. Task 3 was more complicated, it contained 12 steps and sections: 3-A, 3-B, 3-C and 3-D, depending these 12 little tasks were groupedevolution into different Regulatory in humans on their goals. Many parts of task 3 required users to recall or understand some rules then Regulatory evolution is not limited to genes affecting development. The level, should carry out, in may order towithin achieve the make their own decisions onspatial whatpattern action ofthey timing, or the expression of any gene vary popularequired results. tions or diverge between species. For example, as noted earlier (see Chapter 18), the frequencies of alleles at the Duffy blood-group locus vary widely in human populations. The Duffy locus (denoted Fy) encodes a glycoprotein that serves as a receptor for multiple intercellular signaling proteins. In sub-Saharan Africa, most members of indigenous populations carry the Fynull allele. Individuals with this

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Product Instructions in the Digital Age

20.6 The Origin of New Genes and Protein Functions Evolution consists of more than the substitution of one allele for another at loci of deďŹ ned function. A large fraction of protein-coding and RNA-encoding genes belong to gene families, groups of genes that are related in sequence and typically in biochemical function as well. For example, there are over 1000 genes encoding structurally related olfactory receptors in a mouse and three structurally related opsin genes that encode proteins necessary for color vision in humans.

Within families such as these, new functions have evolved that have made possible new capabilities. These new functions may be expansions of existing capabilities. In the examples above, new receptors appeared in mice with the ability to detect new chemicals in the environment, or in the case of humans and their Old World primate relatives, new opsin proteins appeared that can detect wavelengths of light that other mammals cannot. In other cases, the evolution of new gene families may lead to entirely novel functions that open up new ways of living, such as the acquisition of antifreeze proteins in polar ďŹ sh. Here, we will ask, Where does the DNA for new genes come from? What are the fates of new genes?

And how do new protein functions evolve?

Expanding gene number There are several genetic mechanisms that can expand the number of genes or parts of genes. One large-scale process for the expansion of gene number is the formation of polyploids, individuals with more than two chromosome sets. Polyploids

Fig. 9. The main goal and sub-goals of the refined tasks.

Even chromosome numbers are more common than odd numbers

Number of species

8 8.2 Performance on efficiency 11 1100 To examine efficiency of different types of instructions, the following indices were used: 1. Time for finishing all tasks, (from the beginning to the end).

1000task section.

2. Time for each Overall, Data suggested that all participants, who used multimedia instructions, used on 900 average 1379 seconds (22minutes 59 seconds), with a standard deviation of 220 seconds, which seemed to be slightly shorter to those of printed instruction users, who spent 1390 800 14 seconds (23 minutes 10 seconds), with a standard deviation of 213 seconds (Table 1). The difference was small therefore the authors were keen to find out if there was statistically 700 significant difference between the total time consumption of different instruction.

Null hypothesis: T1 = T2 600 There is no significant difference between the average total time of users using either printed or multimedia instructions. 16 18 500 Alternative hypothesis: T1 â&#x2030; T2 There is a significant difference between the average total time of users using either printed 400 or multimedia instructions.

20 24 significant difference between the The authors assumed that there was no statistically 300 22 groups. A t-test was then carried out. to find out the confidence level of this hypothesis. The 2-tailed t- test returned a P-value of 0.89. Since the P-value (0.89) was greater than the 200 28 significance level (0.05), the null hypothesis was 26 accepted.

This indicated that there was no 36product instructions.

34of significant difference between the efficiency of two versions 30 32 100

Figure 20-18 &REQUENCY DISTRIBUTION OF HAPLOID CHROMOSOME NUMBERS IN DICOTYLEDONOUS PLANTS [After Verne Grant, The Origin of Adaptations.

Columbia University Press, 1963.

38 40

0

1

5

10

20

30 Haploid number

40

50

60

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Industrial Design â&#x20AC;&#x201C; New Frontiers

Printed product instructions

Average duration (s): Average duration (s): ď &#x20AC;1375 ď &#x20AC;1390

any signiďŹ cant frequency, as is the fate of many new mutations (see Chapter Digital Digital Immigrants (DI) 18). But letâ&#x20AC;&#x2122;s consider next Natives the more(DN) interesting scenarios: suppose the duplication survives and new mutations begin to occur within the duplicate gene Average Duration (s) Average Duration (s) pair.

Keeping in mind that the original and duplicated genes are initially exact copies and therefore redundant, once new mutations arise, there are several possible fates: 1. An inactivating mutation may occur in the coding region of either duplicate.

Printed (DN)a pseudogene Printed(DI) ď &#x20AC;1284 and ď &#x20AC;1497 to The inactivated paralog is called will generally be invisible natural selection. Thus, it will accumulate more mutations and evolve by random genetic drift, while natural selection will maintain the functional paralog (Figure 20-19b).

2. Mutations may occur that alter the regulation of one duplicate or the activity of one encoded protein. These alleles may then become subject to positive selection and acquire a new function (neofunctionalization) (Figure 20-19c).

Multimedia product instructions

3. In cases where the ancestral gene has more than one function and more than Multimedia Multimedia ď &#x20AC;1425 one regulatory element, as for most toolkit genes, a third possible outcome is that ď &#x20AC;1332 (DN) (DI) initial mutations inactivate or alter one regulatory element in each duplicate.

The original gene function is now divided between the duplicates, which complement each other. In order to preserve the ancestral function, natural selection will maintain the integrity of both gene-coding regions. Loci that follow this path of duplication and mutation that produce complementary paralogs are said to be DN 20-19d).

All DI subfunctionalizedAll (Figure ď &#x20AC;1308 ď &#x20AC;1461 Average(s) Average(s) Some of these alternative fates of gene duplicates are illustrated in the history

of the evolution of human globin genes. The evolution of our lineage, from ďŹ sh ancestors to terrestrial amniotes that laid eggs to placental mammals, has required Table 1. Average time for all tasks a series of innovations in tissue oxygenation. These include the evolution of additional globin genes with novel patterns of regulation and the evolution of hemoglobin proteins with distinct oxygen-binding properties.

Adult hemoglobin is a tetramer consisting of two A polypeptide chains and two B chains, each with its bound heme molecule. The gene encoding the adult A chain is on chromosome 16, and the gene encoding the B chain is on chromosome 11. The two chains are about 49 percent identical in their amino acid sequences; this similarity reďŹ&#x201A;ects their common origin from an ancestral globin gene deep in evolutionary time. The A-chain gene resides in a cluster of ďŹ ve related genes (A and Z ) on chromosome 16, while the B chain resides in a cluster of six related genes on chromosome 11 (E, B, D, and G) (Figure 20-20). Each cluster contains a pseudogene, 9A and 9B respectively, that has accumulated random, inactivating mutations.

Each cluster contains genes that have evolved distinct expression proďŹ les, a distinct function, or both. Of greatest interest are the two G genes. These genes are expressed during the last seven months of fetal development to produce fetal

Some duplicates of the hemoglobin genes evolved into nonfunctional pseudogenes (9A and 9B) Figure 20-20

60

#HROMOSOMAL DISTRIBUTION OF THE GENES FOR THE A FAMILY OF Fig. 10. Time to achieve GLOBINS ON CHROMOSOME AND THE B FAMILY OF GLOBINS ON CHROMOSOME IN Chromosome 11 HUMANS 'ENE STRUCTURE IS

SHOWN BY BLACK BARS EXONS 5 AND COLORED BARS INTRONS

50

40

30

20

10 kb

Chromosome 16

all tasks in each user 2group.

1

2

1 3

5 G

A

3

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Summary Product Instructions in the Digital Age

49

hemoglobin (also known as hemoglobin F), which is composed of two A chains Similarly, Figure 10 potentially the than Digital and two G chains.

Fetal hemoglobin has a greatersuggested affinity forthat oxygen doesNatives performed better, when than using either the printed or multimedia instructions, adult hemoglobin, which allows the fetus to extract oxygen from the mother’s the digital immigrants. On the hand, the Digital seemed to perform circulation viaother the placenta.

At birth, up toNatives 95 percent of hemoglobin is thebetter fetal using print instructions than multimedia opposite happened withamount the Digital Immigrants. Again, t- tests were type, then expression of theand adultthe B form replaces G and a small of D glocarried The out order to findofout the confidence level of the significant bin is also produced. appearance of globin chains during develop-differences. showed After another 3 sets set of 2-tailed t-tests, the results ment is orchestrated by a complex of cis-acting regulatory sequences and,that the amount of time Digital Natives and Digital Immigrants used to complete all tasks was not much different. Also, remarkably, follows the order of genes on each chromosome. different types of instructions did not have a huge impact in The G genes are restricted to placental mammals. Their distinct developmen- terms of the overall efficiency. were as efficient as printed ones for that multimedia product instructions tal regulationThis and suggested protein products mean that these duplicates have evolved Digital and Digital differences inboth function thatNatives have contributed to Immigrants. the evolution of the placental lifestyle. Interestingly, regulatory variants of these genes are known that cause expression of the fetal hemoglobin to persist into childhood and adulthood. These naturally occurring variants appear to moderate the severity of sickle-cell anemia by suppressing the levels of HbS produced. One widespread strategy for the treatment of sickle-cell anemia is to administer drugs that stimulate the reactivation of fetal-hemoglobin expression.

Summary The theory of evolution by natural selection explains the through cumulative selection. Such multistep, adaptive changes that take place in populations of organisms as walks may follow different paths even when the conditions being the result of changes in the relative frequencies of of natural selection are the same. This is because the paths different variants in the population. If there is no variation available to any population at any given moment depend on within a species for some trait, there can be no evolution. the chance occurrence of mutations that may not arise in Moreover, that variation must be influenced by genetic difthe same order in different populations. Furthermore, the ferences. If differences are not heritable, they cannot previous steps taken may affect whether a new mutation is evolve, because the reproductive advantage of a variant favored, disfavored, or neutral. will not carry across generational lines. It is crucial to Before the advent of molecular genetics, it was not posunderstand that the mutational processes that generate sible to know whether independent evolutionary events Fig.the 11.genome Average to achieve task in each group. variation within acttime at random, butall that thesections might haveuser given rise to the same adaptation multiple selective process that sorts out the advantageous and distimes.

By pinpointing the genes and11), exact mutations By looking at the time, which has been spent on each task section in detail (Figure it was involved in changes in function, we now appreciate advantageousdiscovered variants is not random. that multimedia product instructions generally have a positive impact on Digital that evolution canapply and does repeat itself by acting on is the same The abilityImmigrants to study evolution at the level efficiency. of DNA andYet, this does not when a spatial judgement in terms of their genes to produce similar results in independent cases. For proteins has transformed our understanding of the evoluinvolved in knowledge- based tasks. For Digital Natives, different types of instructions have example, changes to the same genes are responsible for tionary process. Before we had the ability to study evoludifferent effects on time consumption; depending on the nature of each task. Printed independently arising cases of melanism and albinism in tion at the molecular level, there was no inkling that much instructions were more efficient to be scanned when skill-based tasks were simple enough to some vertebrates or for the loss of pelvic spines in different of evolution was in fact a result of genetic drift and not natcompleted When instructions are necessary topopulations. follow for skillbasedmay tasks, theitself by stickleback-fish Evolution repeat ural selection.be A great deal of intuitively. molecular evolution seems to time difference between the use of multimedia instructions and printed instructions was altering the very same nucleotide in the case of indepenbe the replacement of one protein sequence by another one little.

Although it also took longer for thearising Digital Natives to use that multimedia dently sickle-cell mutations lead to adaptive of equivalent very function.

Among the evidence for the prevaa spatial to judgement instructions fulfil a complicated malaria. was needed; multimedia lence of neutral evolution isto that the number of aminojob acidwhen resistance instructions were significantly more efficient to An useimportant for a transferable (rule-based constraint process on the evolution of coding differences between two different species in some moletasks).

Therefore the authors believe that multimedia instructions are not always efficient as sequences is the potentially harmful side effects of mutacule—for example, hemoglobin—is directly proportional to expected, for since example particular types they are still multiple more effective tions. Ifbut a protein serves functionsininterms different tisthe number of generations theirfor divergence from a of tasks; of their efficiency in general, especially for Digital Immigrants. sues, as is the case for many genes involved in the regulation common ancestor in the evolutionary past. We would not of developmental processes, mutations in coding sequences expect such a “molecular clock” with a constant rate of may affect all functions and decrease fitness. The potential change to exist if the selection of differences were depen8.3 Performance on accuracy pleiotropic effects of analysis coding mutations can be circumvented dent on particular changes in the environment.

The accuracy of users’ performance was evaluated through error in this investigation by mutations in noncoding regulatory sequences.

So much sequence evolution is neutral that there is no a and it was achieved by observations. Every time a user failed to achieve the planned goal,Mutations in these sequences may selectively change gene expression in simple relation between the amount of change in a gene’s only one tissue or body part and not others. The evolution of DNA sequence and the amount of change, if any, in the cis-acting regulatory sequences is central to the evolution of encoded protein’s function. Some protein functions can morphological traits and the expression of toolkit genes that change through a single amino acid substitution, whereas control development. others require a suite of substitutions brought about

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CHAPTER 20

Evolution of Genes and Traits

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Industrial Design – New Frontiers

New protein functions often arise through the duplicavation of one duplicate, the splitting of function between two human mutation. error was found The failures mainly in two different ways tion of genes and subsequent New DNAand may recorded. arise duplicates, or the gain ofappeared new functions. but the actions were deficient; actionscontinwere (Hollnagel, 1993): the user’s plan was adequate by duplication of the entire genome (polyploidy), a frequent Overall, genetic evolution is subject to or historical carried out as planned but the intention was wrong according to the given tasks. occurrence in plants, or by various mechanisms that produce gency and chance, but it is constrained by the necessity of To genes defineorand the tasks,tothree questions were referenced (Reason, duplicates of individual sets classify of genes.human The fateerror of in organisms survive and reproduce in a constantly chang1990), anddeal theyonall duplicate genes depends a great theclosely naturerelated of muta-to intentions: ing world. “The fittest” is a conditional status, subject to 1. Were Possible actionsfates guided by prior tions acquired after duplication. are the inacti-goals?change as the planet and habitats change.

2. Have actions been proceed as planned?

3. Was the desired end achieved?

KEY TERMS The questions then were used to categorize discovered errors into three main kinds: slips, (Figure 12). pseudogene (p. 754) adaptation (p. 728) lapses and mistakes molecular clock (p. 734) retrotransposition (p. 753) adaptive walk (p. 740) natural selection (p. 728) sign epistasis (p. 741) cumulative selection (p. 740) neofunctionalization (p. 753) subfunctionalization (p. 754) gene duplication (p. 753) nonsynonymous substitution synonymous substitution (p. 734) gene family (p. 752) (p. 734) SOLVED PROBLEMS SOLVED PROBLEM 1. Two closely related species of bacteria are found to be fixed for two different electrophoretically detected alleles at a locus encoding an enzyme involved in breaking down a nutrient. How could you test statistically whether that divergence is more likely to be a result of natural selection or of neutral evolution?

Polymorphisms Species differences

Replacement Synonymous

Replacement

Synonymous

a c

b d

Solution

(a b c d )(ad bc )2 C2 a. Obtain DNA sequences of the gene from a number of (a c )(b d )(a b)(c d ) separate individuals or strains from each of the two species. Ten or more sequences from each species would be SOLVED PROBLEM 2. In the above example, how could desirable. The polymorphic sites within populations are you test experimentally whether the divergence in enzyme then classified into nonsynonymous (a) and synonymous sequences may have caused differences in function and (b) sites. The fixed nucleotide differences between species fitness? are classified into nonsynonymous (c) and synonymous (d) differences.

Fig. 12. Generic Error Modelling SystemSolution (GEMS) (Reason, 1990) In order to test whether the enzymes have different b. Tabulate the nucleotide differences among individuals functional properties, one could devise both in vitro and within each species 8.3.1 (polymorphisms), and classify these Slips and lapses in vivo experiments.

If the process substrates of differences as either those aminowere acid changes in the execution so and that properties users failed Both that slipsresult and in lapses errors that happened the enzyme are known, one could purify the enzyme (replacement polymorphisms; a inthe thedesired table below) or those to achieve goals.

The intentions were proper, but results were not right. A slip from each species and measure directly whether there that do not change the amino acid (synonymous polymormainly involved actions that were not happening as planned, while lapses were the errors are functional differences. Alternatively, an indirect test phisms; b in the accompanying that weretable). caused by failures of memory. would be whether each species grew as well on the parc. Make the same tabulation of replacement (c) and synticular nutrient that the enzyme broke down. onymous (d) changes for the fixed differences between the 8.3.2 Mistakes Ideally, in order to measure fitness differences, one species, counting only those differences that completely processes; are species errors Mistakes referred to failures in the planning would and/or replace judgemental the enzyme-coding regionthey of one differentiate the species. That is, do not count a polymorusers’ intentions They involve the selection of objectives, or the withmight the enzyme-coding region from the second species phism in one species in that includes a variant(Norman, that is seen1983). in and vice versa.

Then the growth of each wild-type and decisions of means, even actions for achieving the objectives.

They are normally caused by the other species. strain could be compared on the nutrieither a failure of expertise or lack oftransgenic expertise(Reason, 1990).

They could be same effectively d. If the divergence between the species is purely the media, withingrowth beingusing an indicator of avoided or reduced by communicatingent-containing sufficient information, this case, product result of random genetic drift, then we expect a/b to be fitness.

If there areusers differences in the relative fitness of instructions.

Therefore, the number of mistakes left by after each test was the main equal to c/d. If, on the other hand, there has been selective the transgenic and wild-type strains, then it is possible criteria to excess evaluate the accuracy performance of the product instructions. divergence, there should be an of fixed nonsynonythat the enzymes have diverged under natural selection. mous differences, and so a/b should be less than c/d.

If not, then it is likely that the enzymes have evolved neue. Test the statistical significance of the observed ratio by a 2 r 2 C2 test of the following table:

trally or that the effect of selection is too small to measure experimentally.

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CHAPTER 20

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Product Instructions in the Digital Age

20. It has been claimed here that “evolution repeats itself.”

Does this result support neutral evolution of the gene?

Print DI Multimedia What is the evidence for this claim Print from DN Does it supportDN an adaptiveMultimedia replacementDI of amino Slips 2 1 1 2 acids?

What explanation would you offer for the a. the analysis of HbS alleles? observations?

Lapses 0 1 0 0 b. the analysis of antibiotic resistance in bacteria?

25. In humans, two genes encoding Mistakes 4 2 1 0 the opsin visual pigc. the analysis of experimentally selected bacterioments that are sensitive to green and red wavelengths phage FX174? Table 2. Error analysis of light are found adjacent to one another on the X d. the analysis ofDuring Oca2 mutations in cave fish? chromosome.

They encode proteins that aretheir 96 percent the tests, by referring to given instructions, users observed and corrected own e. the analysis oferrors stickleback Pitx1 loci? identical.

Nonprimate mammals possess just by gene the in the performing progress. When errors were not detected or corrected one encoding (Table an opsin the red/green waveparticipants, were recorded 2).sensitive In thistoexperiment, Digital 21. What is the molecular evidencethey that natural selection and evaluated Natives and Digital Immigrants have bothlength. made errors. The numbers of slips and lapses includes the “rejection of injurious change”? were similar in two user groups.

They were caused by each individual’s of of action or a. Offer one explanation for thefailures presence the two 22. What are three alternative fates of a new gene duplicate? solved by improving product failures of memory. Unfortunately, they cannot be perfectly opsin genes on the human X chromosome.

23. What is the evidence that gene duplication has been instructions.

When looking at the number of mistakes made by participants, b. How would you test your the explanation furtherdata and the source of the A and B gene families for human revealed that multimedia instructions are better for avoiding mistakes, for both Digital pinpoint when in evolutionary history the second gene hemoglobin?

Natives and Digital Immigrants compare toarose? the traditional instructions.

24. DNA-sequencing studies for a gene in two closely relat26. About 9 percent of Caucasian males are color-blind ed species produce the following numbers of sites that and cannot distinguish red-colored from green-colored vary: Print Multimedia Print Multimedia objects.

Synonymous polymorphismsTasks 50 (DN) (DI) (DI) (DN) a.

Offer one genetic model for color blindness.

Nonsynonymous 2 1 species differences Finding information 0 0 0 0 Synonymous species differences 18 b. Explain why and how color blindness has reached a 2 UnpackingNonsynonymous polymorphisms 20 check parts 0 frequency of 90 percent in0this population. 0 Section 3-A: Make the frame base 1 0 0 0

Section 3-B:

Finish the frame

0

3

0

2

Section 3-C:

Fix the top sheet

0

1

0

0

Section 3-D:

Attach the accessory

0

0

0

0

Table 3. Mistakes in each task section.

When each task section was examined (Table 3), it was more evident that multimedia instructions can help users to avoid mistakes, especially in some complicated tasks for example task section 3-B. This section contained the most time consuming jobs in the whole experiment. It was a combination of many small knowledge-based tasks and some tasks required users to make critical decisions. Both Digital Natives and Digital Immigrants have made a few mistakes in this job section when traditional instructions were provided.

However, when multimedia instructions with equivalent contents were presented, all users either avoided mistakes or realised errors on their own. Thus it is not difficult to conclude that multimedia instructions are better than traditional instructions (with only images and text) in terms of ensuring accuracy of actions.

9. Conclusion Although multimedia instructions are not always more efficient than traditional ones, the authors believe that they are quicker to use for many types of tasks. They allow more flexibility in action and more importantly can help to reduce human errors significantly in the working process. They are effortless to access, can be transferred between different digital platforms and easy to update or replace. It is also proved that they can be used easily by people who have grown up with or without ubiquitous of digital media.

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Industrial Design – New Frontiers

During the time for the development of this project, technology has changed and improved A Brief Guide to Model Organisms as fast as usual. Smart phones have become more popular and more portable digital devices

like the iPad have come into the market and our daily lives. We are more comfortable with Escherichia coliand Saccharomyces crassa devices.

Arabidopsis thaliana dependent cerevisiae on with Neurospora portable digital The authors believe that multimedia Caenorhabditisinstructions elegans Drosophila melanogaster

Mus musculus could be and soon will be better solutions for many of our daily products, to help us use products easily and safely.

However, this will not cause the complete death of the traditional instructions. Although they are not as good to ensure accuracy of performance, they can still be used in many cases. his brief guide collects inthey one place mainchoice features genetics simple owe a great deal to more century of For example, are athe better forofperforming skill-based tasksthan on aproducts inwork on model organisms as they relate to genetics.

Each of seven model organisms. terms of efficiency, especially for Digital Natives, less patient or busy people. Therefore, in model organisms given itsinstruction own two-page spread; the format All model far more product, than one useful theisfuture, designers may want to analyse tasksorganisms for usinghave a particular is consistent, allowing readers to compare andtocontrast feature for genetic or or multimedia other biological study.

Hence, after a then decide either they need designthe traditional instructions ones to satisfy features of model organisms.

Each treatment focuses on the model organism has been developed by a few people with users’ requirements for efficiency and accuracy of operation. special features of the organism that have made it useful as specific interests, it then acts as a nucleus for the The authors accept that, as with any research project, there are certain limitations associateddevelopa model; the with specialthe techniques that have been developed ment of a research community—a grouphad of researchers study. Every effort was made to ensure that the participants chosen similar with for studying the organism; and the main contributions that an interest in various features of one particular model organlevels of human performance characteristics. In other words, they all had the same degree of studies of the organism have made to our understanding of ism. There are organized research communities for all the normal flexibility, intelligence, adaptability and dexterity. However, even with the test genetics. Although many differences will be apparent, the model organisms mentioned in this summary. The people in applied (dealing cards) and observations made on the participants, it was still impossible to general approaches of genetic analysis are similar but have to these communities are in touch with one another regularly, completely eliminate the human factor. be tailored to take account of the individual life cycle, ploidy share their mutant strains, and often meet at least annually level, size and shape, and genomic properties, such as the at conferences that may attract thousands of people. Such a 10. Contribution presence of natural plasmids and transposons. community makes possible the provision of important serModel organisms have always been at the forefront of vices, such as databases of research information, techniques, Overall, this study, a problem-driven wasDNA adopted.

Inspiration genetics. Initially, in thefor historical development of a model design genetic strategy stocks, clones, libraries, and genomicwas sequences. taken from fields like information design, product design, graphic design, and instructional organism, a researcher selects the organism because of some Another advantage to an individual researcher in design in education andofergonomic science. feature that lends itself particularlyplus well cognitive to the study a belonging to such a community is that he or she may develop to organism” solve problems product Asin related studies and isstandards genetic process which the researcher interested. are The not “asufficient feeling for the (a phrasewith of maize geneticist and this“Choose digital age, research should makeMcClintock). an originalThis contribution advice of the instructions past hundredespecially years has in been, your this Nobel laureate Barbara idea is difficult to in this field. It will bothfungi, users such and manufacturers it aims at finding solutions to ways organism well.”

For example, the benefit ascomycete convey, but itsince implies an understanding of the general improve the quality of product instructions.

Furthermore, this study should have economic as Saccharomyces cerevisiae and Neurospora crassa, are well of an organism. No living process takes place in isolation, and costsprocesses, of product instructions reduced.the general ways of an organism is often benefisuited to the value study as of the meiotic such as crossingcan be so knowing over, because their unique feature, the ascus, holds together cial in trying to understand one process and to interpret it in the products of11. a single meiosis. its proper context.

References Different species tend to show remarkably similar proAs the database for each model organism expands Entner, (2010). Smartphones to Overtake in U.S. by 2011.

October 2010, cesses, even across theR.members of large groups, such as Feature (whichPhones it currently is doing at a great pace 27, thanks to genomAvailable from: expect <http://blog.nielsen.com/nielsenwire/consumer/smartphonesthe eukaryotes. Hence, we can reasonably that what ics), geneticists are more and more able to take a holistic is learned in one species can be at least partly applied to view, encompassing the integrated workings of all parts of the to-overtake-feature-phones-in-u-s-by-2011> others. In particular, geneticists have kept anofeye open for organism’s makeup.

In this way, model organisms Mahwah, N.J. ; London : Lawrence Erlbaum. become Hollnagel, E. (1993) Handbook cognitive task design, new research ISO findings thatISO/IEC may apply to our37: own species. not only for isolated processesinterest. but also models of (1995).

GUIDE 1995(E) Instruction for models use of products of consumer Compared with other species, humans are relatively diffiintegrated life processes.

The term systems biology is used to Miniwatts Marketing Group.

(2010). Internet usage statistics - The Internet Big Picture.

October cult to study at the genetic level, and so advances in human describe this holistic approach.

25 2010, Available from: <http://www.internetworldstats.com/stats.htm> Norman, A.D. (1983). Design Rules Based on Analyses of Human Error. Communication of the ACM, Vol 26 254-258 OED. (2006). Oxford English online dictionary , January 14 2006, Available from: <www.oed.com> Pettersson, R. (2002.) Information design: an introduction, Amsterdam, Philadelphia : John Benjamins Pub. Co., c.

Reason, J. T. (1990). Human error , New York: Cambridge University Press Redhead, D. (2000) Products of our time, London, Birlhauser.

Tapscott, D. (2009) Grown up digital: how the net generation is changing your world, New York ; London : McGraw-Hill.

T

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Escherichia coli Key organism for studying: Transcription, translation, replication, recombination Mutation Gene regulation Recombinant DNA technology

Genetic “Vital Statistics” Genome size: Chromosomes: Number of genes: Percentage with human homologs: Average gene size: Transposons:

4.6 Mb 1, circular 4000

Part 2

Culturally Inspired Design 8%

Genome sequenced in:

1 kb, no introns Strain specific, 60 copies per genome 1997

The unicellular bacterium Escherichia coli is widely known as a disease-causing pathogen, a source of food poisoning and intestinal disease. However, this negative reputation is undeserved. Although some strains of E. coli are harmful, others are natural and essential residents of the human gut. As model organisms, strains of E. coli play an indispensable role in genetic analyses. In the 1940s, several groups began investigating the genetics of E. coli. The need was for a simple organism that could be cultured inexpensively to produce large numbers of individual bacteria to be able to find and analyze rare genetic events. Because E. coli can be obtained from the human gut and is small and easy to culture, it was a natural choice. Work on E. coli defined the beginning of “black box” reasoning in genetics: through the selection and analysis of mutants, the workings of cellular processes could be deduced even though an individual cell was too small to be seen.

E. coli genome. Electron micrograph of the genome of the bacterium E. coli, released from the cell by osmotic shock.

[Dr. Gopal Murti/Science Photo Library/Photo Researchers.]

Special features Much of E. coli’s success as a model organism can be attributed to two statistics: its 1-Mm cell size and a 20-minute generation time.

(Replication of the chromosome takes 40 minutes, but multiple replication forks allow the cell to divide in 20 minutes.) Consequently, this prokaryote can be grown in staggering numbers—a feature that allows geneticists to identify mutations and other rare genetic events such as intragenic recombinants. E. coli is also remarkably easy to culture. When cells are spread on plates of nutrient medium, each cell divides in situ and forms a visible colony. Alternatively, batches of cells can be grown in liquid shake culture. Phenotypes such as colony size, drug resistance, ability to obtain energy from particular carbon sources, and colored dye production take the place of the morphological phenotypes of eukaryotic genetics.

Bacterial colonies. [Biophoto Associates/ Science Source/Photo Researchers.]

760

Life Cycle Conjugation and Escherichia coli reproduces transfer of F factor asexually by simple cell + + F a F a+ fission; its haploid genome replicates and partitions F– a – a with the dividing cell. In the 1940s, Joshua Lederberg and Edward Tatum discovered that E. coli also F a+ + + has a type of sexual cycle F a in which cells of genetically differentiated “sexes” F a– fuse and exchange some + – F a or all of their genomes, sometimes leading to recombination (see Chapter 5). “Males” can convert “females” into males by the transmission of a particular plasmid. This circular extragenomic 100-kb DNA plasmid, called F, determines a type of “maleness.” F cells acting as male “donors” transmit a copy of the F plasmid to a recipient cell. The F plasmid can integrate into the chromosome to form an Hfr cell type, which transmits the chromosome linearly into F= recipients. Other plasmids are found in E. coli in nature. Some carry genes whose functions equip the cell for life in specific environments; R plasmids that carry drug-resistance genes are examples.

–

Length of life cycle: 20 minutes

A Brief Guide to Model Organisms

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Industrial Design – New Frontiers

Geneticists5.have also taken advantage of some unique geGenetic engineering Embodiment design netic elements associated with E. coli. Bacterial plasmids and Transgenesis. E. coli plays a key role in introducing transgenes phages are usedEmbodiment as vectors to clone the genes of other organisms design is well known in producttodevelopment. first organother organismsKesselring (see Chapter(1954) 10). It was is thethe standard harnessed within E. coli. Transposable elements from E. coli areand isma used cloning genes of any organism.

E. coli plasmids or to refer to Embodiment Design introduced set offorprinciples: minimum manufacturing to disrupt genes in cloned eukaryotic DNA. Such bacterial elebacteriophages are used as vectors, carryinghandling. the DNA sequence costs, minimum requirements, minimum of weight, minimum losses and optimal ments are key players in recombinant DNA technology. to be cloned. These vectors are introduced into a bacterial cell

These principles are often calculated at the end of the design process and are typically used

by transformation, if a plasmid, or by transduction, if a phage, where they replicate in the cytoplasm. Vectors are specially modSpontaneous E. The coli mutants show aofvariety of DNA changes, rangPahl and Beitz (1996) as be follows: definition embodiment design according ified to to include unique cloning sites runs that can cut by a variety ing from simple base substitutions to the insertion of transposable “Embodiment Design is the part of the design of process starting from the “shuttle” principle solution or restriction enzymes.

Other vectors are designed to elements. The study of rare spontaneous mutations in E. coli is feamove DNA fragments from yeast (“the eukaryoticwith E. coli ”) into concept of a consumer product.

The design should be developed in accordance sible because large populations can be screened. However, mutaE. coli, for its greater ease of genetic manipulation, and then back engineering and economical gens also are used to increase mutation frequencies. criteria”. This is a pure technical and economical consideration into yeast for phenotypic assessment.

To obtain of specific mutant phenotypes repre- has more aspects than only the technical and Embodiment Design. that But might a product sent defects in economical a process underones. study,A screens or selections mustbring aspects about emotion, beauty, appeal and product can also pBR322 be designed. For example, nutritional mutations and mutations vectorif the happiness the other values in live. People like to pay for these values earnings are EcoRV 185 conferring resistance to drugs or phages can be obtained on plates NheI 229 higher than the cost of the basic needs.

Scal 3846 supplemented with specific chemicals, drugs, or phages. Null mutaBamHI 375 Pvul 3735 Sphlabout 562 The gene Embodiment phase the part of the design process which is concerned tions of any essential will result inDesign no growth; these is mutations Sal l 651 Pst l 3609 can be selected the by adding penicillinof (anthe antibacterial isolatedthe engineering and the economical feasibility. The production productdrug concept, Eagl 939 from a fungus),production which kills dividing cellsthe but parts not themaking nongrowing Ppal 3435 contains and the product assembling.amp R Nrul 972 tet R mutants. For conditional replicathe plating be Howeverlethal thismutations, doesn’t open newcanperspective of embodiment design. We propose aBspM newl 1063 used: mutated colonies on a master plate are transferred by a felt 4.4 kb definition of embodiment design and it runs as follows “Embodiment Design is designing pad to other plates that are then subjected to some toxic environwith material, manufacturing and to fulfill a new function or updating of the ment. Mutations affecting the expression of a specific gene geometry of inori terest can be screened by fusing to a reporteraspects gene such as the function”.

Theitemotional such as: use, interaction ergonomics, etc. have to meet the lacZ gene, whoserequirement protein product can make a blue dye,aspects. or the GFP with the physical gene, whose product fluoresces when exposed to light of a particuA plasmid designed as a vector for DNA cloning. Successful lar wavelength. insertion of a foreign gene into the plasmid is detected by inactivation of After a set of mutants affecting the process of interest have either drug-resistance gene (tet R or ampR). Restriction sites are identified. been obtained, the mutations are sorted into their genes by recombination and complementation. These genes are cloned and Targeted gene knockouts. A complete set of gene knockouts is sequenced to obtain clues to function. Targeted mutagenesis can being accumulated. In one procedure, a kanamycin-resistance be used to tailor mutational changes at specific protein positions transposon is introduced into a cloned gene in vitro (by using a (see page 517). transposase). The construct is transformed in, and resistant coloIn E. coli, crosses are used to map mutations and to produce nies are knockouts produced by homologous recombination. specific cell genotypes (see Chapter 5). Recombinants are made by mixing Hfr cells (having an integrated F plasmid) and F cells. GenMain contributions erally an Hfr donor transmits part of the bacterial genome, forming Pioneering studies for genetics as a whole were carried out in a temporary merozygote in which recombination takes place. Hfr E. coli. Perhaps the greatest triumph was the elucidation of the unicrosses can be used to perform mapping by time-of-marker entry versal 64-codon genetic code, but this achievement is far from alone or by recombinant frequency. By transfer of F derivatives carrying on the list of accomplishments attributable to this organism. Other donor genes to F , it is possible to make stable partial diploids to fundamentals of genetics that were first demonstrated in E. coli study gene interaction or dominance. include the spontaneous nature of mutation (the fluctuation test, page 558), the various types of base changes that cause mutations, Techniques of Genetic Modification and the semiconservative replication of DNA (the Meselson and Standard mutagenesis: Stahl experiment, page 262). This bacterium helped open up whole Chemicals and radiation Random somatic mutations new areas of genetics, such as gene regulation (the lac operon, Transposons Random somatic insertions pages 385ff.) and DNA transposition (IS elements, page 529). Last but not least, recombinant DNA technology was invented in E. coli, Transgenesis: and the organism still plays a central role in this technology today.

On plasmid vector Free or integrated On phage vector Free or integrated Other areas of contribution Transformation Integrated Cell metabolism Fig. 6. Embodiment Design Model Targeted gene knockouts: Nonsense suppressors Null allele on vector Gene replacement by Colinearity of gene and polypeptide recombination The operon Engineered allele on vector Site-directed mutagenesis by Plasmid-based drug resistance gene replacement Active transport

Genetic analysis as verification.

Saccharomyces cerevisiae Key organism for studying: Genomics Systems biology Genetic control of cell cycle Signal transduction Recombination

Genetic “Vital Statistics” Genome size: Chromosomes: Number of genes: Percentage with human homologs: Average gene size: Transposons: Genome sequenced in:

12 Mb n 16 6000

4

Culturally Inspired Design: Product 25% 1.5 kb, 0.03 intron/gene Personalities to Capture Cultural Small proportionAspects of DNA

Mating type Mitochondrial inheritance Gene interaction; two-hybrid

1996

Denis A. Coelho, Ana S. C. Silva and Carla S. M. Simão

Universidade da Beira Interior Portugal The ascomycete S. cerevisiae, alias “baker’s yeast,” “budding yeast,” or simply “yeast,” has

been the basis of the baking and brewing industries since antiquity. In nature, it probably grows on the surfaces of plants, using exudates as nutrients, although its precise niche 1. Introduction is still a mystery. Although laboratory strains are mostly haploid, cells in nature can be diploid or polyploid. In approximately 70 years of genetic research, yeast has become “the E. coli of eukaryotes.”inspired Because itdesign, is haploid,with unicellular, and forms compact colonies on This chapter, focusing ontheculturally emphasis on Portuguese and plates, it can be treated much the process same way(Fig. as a bacterium. it has Lusophone cultures, is developed in a in two stage 1). In theHowever, first part, an eukaryotic effort to meiosis,identity cell cycle,reflected and mitochondria, and these been at is thepursued. center of the identify the Portuguese in the design of features existinghave products In yeast success story.

the second part of this work, product design specifications are created based on the Yeast personalities cells, Saccharomyces cerevisiae. assignment of product to capture Portuguese and Lusophone cultural aspects.

Both stages of this contribution give rise to new product concepts, which are aimed at ing dominant mutations, sheltering mutations, performing Special features exemplifying the profile in existing Lusophone design production (in lethal comparison with other complementation tests, and exploring gene interaction.

As a model organism, yeast combines the and best of worlds: it design origins) attwo demonstrating the transfer of selected cultural values to designed has much of the convenience of a bacterium, but with the key feaobjects. tures of a eukaryote. Yeast cells are small (10 Mm) and complete their cell cycle in just 90 minutes, allowing them to be produced in huge numbers in a short time. Like bacteria, yeast can be grown in large batches in a liquid medium that is continuously shaken.

And, like bacteria, yeast produces visible colonies when plated on agar medium, can be screened for mutations, and can be replica plated. In typical eukaryotic manner, yeast has a mitotic celldivision cycle, undergoes meiosis, and contains mitochondria housing a small unique genome. Yeast cells can respire anaerobically by using the fermentation cycle and hence can do without mitochondria, allowing mitochondrial mutants to be viable.

Genetic analysis

Life Cycle Yeast is a unicellular species with a very simple life cycle consisting of sexual and asexual phases. The asexual phase can be haploid or diploid. A cell divides asexually by budding: a mother cell throws off a bud into which is passed one of the nuclei that result from mitosis. For sexual reproduction, there are two mating types, determined by the alleles MATA and MATa. When haploid cells of different mating type unite, they form a diploid cell, which can divide mitotically or undergo meiotic division. The products of meiosis are a nonlinear tetrad of four ascospores.

Total length of life cycle: 90 minutes to complete cell cycle Performing crosses in yeast is quite straightforward. Strains of Fig.simply 1. Depiction two streams opposite mating type are mixed onofanthe appropriate me- of analysis departing form an empirical and an abstract Fusion a reaching at new product concepts. dium. The resulting a/Alevel, diploids are induced to undergo meiosis (n) (n) by using a special sporulation medium. Investigators can isolate (2n) Intetrad both by stages the research, ascospores from a single using of a machine called a an mi- array of product features was drawn up, in the first case from observation, the second case from matching of cultural traitsMitosis with product features, cromanipulator. They also have the option of in synthesizing a/a or A/A diploids for specialthrough purposesthe or creating partial diploidspersonality by use of the product assignment approach. + using specially engineered plasmids.

Culture may inform design by a process of context-informed practice.

Hence, collectively(2n) Meiosis Ascus (2n) Because a huge array of norms yeast mutants and DNA constructs culture into the design held of practice shared within contexts may well introduce (n) a (n) are available within the research community, special-purpose a practice (n) (n) process, even if indirectly.

Geographical context may influence the and results of strains for screens and selections can be built by crossing various design in twoalleles ways. the onebyhand, everyday specific features of a location (availability yeast types. Additionally, new mutant canOne be mapped Mitosis Mitosis of technology materials, climate, local modes of exchange and even cultural factors crossing with strains containing an array and of phenotypic or DNA markers of known map position. affecting business activities) produce particularized actions, which may however be (n) (n) a The availability of both haploid and diploid cells provides flexibility for mutational studies. Haploid cells are convenient Culture Culture for large-scale selections or screens because mutant phenotypes colony colony are expressed directly. Diploid cells are convenient for obtain-

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contrasted with perceived globalized, mainstream and dominant modes of practice. On the Techniques of Genetic Manipulation other hand, when viewing design as a mode of communication, peripherization and Standard mutagenesis: engagement of a consciousness of difference may emerge, depending on location (Julier Chemicals and radiation Random somatic mutations Transposons 2007). No factual Random somatic data withinsertions a substantial depth about the cultural traits of the nations

Transgenesis:portrayed in this chapter was found in literature, with the exception of the work by the Integrative plasmid Inserts by Geert homologous Dutch social scientist Hofstede. Hofstede developed and published, in 1980, four recombination national measures of culture applied to a set of selected countries. Portugal and Brazil were Replicative plasmid Can replicate autonomously the only Lusophone countries included in Hofstede’s study. The national measures of (2M or ARS origin of (a) culture presented by this author were: Power Distance, Masculinity, (b) Individuality and replication) Uncertainly Avoidance.

The nature of the national measures of culture presented

by Geert Cell-cycle mutants. (a) Mutants that elongate without dividing.

Yeast artificial chromosome Replicates and segregates as (b) Mutants that arrest without budding. a chromosome Hendrik Hofstede, was not deemed adequate to advance the development of the goals set Shuttle vectorfor the secondCan replicate in yeast orin this chapter. A literature survey was hence pursued, project reported Main contributions E. coli informing, through the perspectives of several authors, on the Portuguese and Lusophone Thanks to a combination of good genetics and good biochemistry, Targeted gene knockouts: cultural traits. yeast studies have made substantial contributions to our underGene replacement Homologous recombination The current geo-strategic setting gives some added importance to the Portuguese-speaking standing of the genetic control of cell processes. replaces wild-type allele claiming themselves as regionalgenes powers world. Both Brazil and Angola, in part, have been Cell cycle. The identification of cell-division through their with null copy (in South America and sub-Saharan Africa, temperature-sensitive respectively). In mutants this context, the design ofa power(cdc mutants) has led to model for the genetic control division. The and different Cdc products as part of the cultural expression offul people is associated withofitscellproduction Genetic engineering phenotypes reveal the components of the machinery required to industrial capacity, and can be seen as a front for disseminating advancement of culture, execute specific steps in the progression of the cell cycle. This work Transgenesis. Budding yeast provides more opportunities for while its existence is related to the relative importance of this culture in the globalized has been useful for understanding the abnormal cell-division congenetic manipulation than any other eukaryote (see Chapter 10). world. is easily not mandatory tocell joinwalls Brazilian and Angolan, trols that caneventually lead to human cancer. or the design of Exogenous DNA is takenItup by cells whose have design, other Portuguese-speaking countries, with Portuguese design.

In the cultural andmolecular Recombination. Many of the key ideas forsphere, the current been partly removed by enzyme digestion or abrasion. Various that underlies this work component, will be difficult to model) modelscultural of crossing over (such asitthe double-strand-break types of vectorsthe areapproach available. For a plasmid to replicate free has of a strong on tetrad analysis of gene conversion yeast the chromosomes, it must contain normal yeast replication disentangle the ahistorical and culturalorilegacyare of based the area of language, as this is oneinof the(see page 150).

Gene conversion (aberrant allele ratios such as 3 : 1) is quite gin (ARS) or a main replication origin from a 2-Mm plasmid found in ways to define and mark broad cultural groups. Thus, in this work, it is considered common in yeast genes, providing an appropriately large data set certain yeast isolates. The most elaborate vector, the yeast artifithat the combination of design production in the countries of official Portuguese language is for quantifying the key features of this process. cial chromosome (YAC), consists of an ARS, a yeast centromere, relevant.

Gene interactions. Yeast has led the way in the study of gene inand two telomeres.

A YAC can carry large transgenic inserts, teractions. The techniques of traditional genetics have been used to which are then inherited in the same way as Mendelian chroreveal patterns of epistasis and suppression, which suggest gene inmosomes. YACs1.1 have been important vectors in cloning and seAims teractions (see Chapter The two-hybridof plasmid system for findquencing large genomes such as the human genome. is to seek the 6). identification a possibly The main purpose of the first part of this chapter ing protein interactions was developed in yeast and has generated existent identity of Portuguese and Lusophone Design, according to different perspectives complex interaction maps that represent the beginnings of systems Selectable yeast marker (e.g. form, brand, material, archetype), from the (see study selected Whiledouble it is mutants biology page of 514).

Syntheticcases. lethals—lethal based the material properties of products acknowledged that an analysis which is mostly created byon intercrossing two viable single mutants—also are used to is necessarily limited in scope, the consideration of experience or use related qualities, given plot networks of interaction (see page 233).

Selectable Bacterial replication origin bacterial Mitochondrial Mutants withby defective visually asgenetics. their assessment actual mitochondria use the breadth of this survey, was inferred, albeit marker are recognizable as very small colonies called “petites.” would not be feasible. Initially, a historical perspective of Portuguese and Brazilian designThe availability of these petites and other mitochondrial mutants enabled was drawn up. Since the existing information concerning existing design of other Cloned region the first detailed analysis of mitochondrial genome structure and of interest is very limited, it was chosen to analyse Portuguese and Brazilian Lusophone countries function in any organism. design only, and identities,Genetics extrapolate a proposed Lusophone of mating type. Yeast MAT allelesdesign were the first A simple yeast vector. This type of vectorfrom is calledthese a yeasttwo integrative From this analysis, similarities were level. plasmid (YIp). identity, focusing on material properties mostly. mating-type genes to be characterized at the molecular Interestingly, yeast undergoes switching perceived between Portuguese and Brazilian (Lusophone) designs, spontaneous according to the from one mating type to the other.

A silent “spare” copy Targeted knockouts.

Transposon mutagenesis (transposon taganalyzed products. Another analysis of designed products was then carried out, focusing of onthe opposite MAT allele, residing elsewhere in the genome, enters ging) can be accomplished by introducing yeast DNA into E. coli on countries with design production of great international appreciation so that it would be into the mating-type locus, replacing the resident allele by homologous a shuttle vector; the bacterial transposons integrate into the yeast possible to differentiate this against Lusophone design. The analyzed regions and countries, recombination. Yeast has provided one of the central models DNA, knocking out gene function. The shuttle vector is then transtheand purpose of differentiation, were Scandinavia, includes thedetection Nordic and countries, for signalwhich transduction during responseasto mating ferred back intofor yeast, the tagged mutants replace wild-type well as Italy and Germany.

To conclude the first stage of this research, and project it in a hormones from the opposite mating type. copies by homologous recombination. Gene knockouts can also be practical twowith conceptual designs were developed. accomplished by replacingcomponent, wild-type alleles an engineered Other areas of contribution null copy through homologous recombination. By using these Genetics of switching between yeastlike and filamentous techniques, researchers have systematically constructed a comgrowth plete set of yeast knockout strains (each carrying a different knockout) to assess null function of each gene at the phenotypic level.

Genetics of senescence

Culturally Inspired Design: Product Personalities to Capture Cultural Aspects

57

The secondcrassa part of this chapter reports on a project aimed to identify the cultural traits Genetic “Vitalthat Statistics” Neurospora of the Portuguese speaking countries, with regard to both an internal Genome size: 43 Mb perspective as well as

an outsider’s perspective. Subsequently, Chromosomes: the translation of these traits into design 7 autosomes (n product 7) Number of genes: 10,000 was intended, attempting to give a Portuguese and Lusophone projected cultural identity to Key organism for studying: withinhuman products. To this end, a methodology wasPercentage developed several stages. For the application of Genetics of metabolism and uptake homologs: 6% the methodology, several studies were carried out.

The personality attributes of products Genetics of crossing over and meiosis Average gene size: 1.7 kb, 1.7 introns/gene were analyzed using a technique known as Product Personality Assignment (Jordan 2000) in Fungal cytogenetics Transposons: rare Polar growth order to mediate the transfer from the identified traits to product design Genome sequencedcultural in: 2003 Circadian rhythms requirements. Patrick W. Jordan used positive and negative characteristics of people, Interactions between nucleus and amitochondria developing list with 209 descriptors of personality and, after a collation and synthesis of work arrived at a list of 17 pairs of dimensions of personality. These dimensions are composed of pairsNeurospora of opposing descriptors, / Simple.

Thus, crassa,personality the orange bread mold, was such one ofas theComplex first eukaryotic microbes to be adopted by geneticists as a model organism.

Like yeast, it was originally chosen because its the Personality Assignment to a product is a tool that explores the emotional ties existing in of haploidy, its simple and rapid life cycle, and the ease with which it can be cultured.

Of particurelationship between user and product.

lar significance was the fact that it will grow on a medium with a defined set of nutrients, making it possible to study the genetic control of cellular chemistry. In nature, it is found in many parts of world growing on vegetation.

Because fire activates dormant ascospores, 2. Characterization ofthe the identity ofdead existing Portuguese and its Brazilian designit is most easily collected after burns—for example, under the bark of burnt trees and in fields of In this section, an attempt and Brazilian identities reflected in the crops suchto as identify sugar canethe thatPortuguese are routinely burned before harvesting.

design of existing products is carried out. This contribution gives rise to new concepts, at representing cultural traits embedded in objects. An array of product features is drawn up from observation of a sample of designed objects (208), whose pictures design web-blogs and design museums which were found Special features were readily available from Life Cycle through web searches, to empirically assess the existence of a Lusophone design style, in Neurospora holds the speed record for fungi because section is to seek the comparison with origins. main N. crassa has a The haploid eu- purpose of this Sexual each hypha grows more than 10 cm per day.other This design spores grow to adults karyotic life cycle.

A haploid identification of a possibly existent identity of Portuguese and Lusophone Design, according rapid growth, combined with its haploid life cycle and asexual spore (calledmaterial, a conid- archetype), from the study of selected tomedium, different form, brand, ability to grow on defined has perspectives made it an or- (e.g. ium) germinates produce awhich is mostly based on the material ganism of choice for studying of cases.biochemical While itgenetics is acknowledged that antoanalysis germ tube that extends at its nutrition and nutrient uptake. properties of products is necessarily limited in scope, the consideration Asci of experience or use tip.

Progressive tip growth and Another unique feature of Neurospora (and rerelated qualities, given thebranching breadthproduce of thisa mass survey, was inferred, albeit visually as their of lated fungi) allows geneticists to trace the steps of assessment by actual use would not be feasible.

Initially, a historical perspective of branched threads (called hysingle meioses. The four haploid products of one phae), which forms a compact Since the existing information concerning Portuguese and Brazilian design was drawn up. meiosis stay together in a sac called an ascus. Each Meiosis colony on growth medium. designsa of other Lusophone countries is very limited, it was chosen to analyse of the four products of existing meiosis undergoes further Becauseonly, hyphae have no cross mitotic division, resulting in a linear and octadBrazilian of eight design Portuguese and from these two identities, extrapolate a proposed walls, a colony is essentially ascospores (see pages Lusophone 96–97). This feature designmakes identity, focusing on material properties mostly. From this analysis, one cell containing many hapNeurospora an ideal system in which were to study crosssimilarities perceived between loid nuclei.Portuguese The colony and budsBrazilian (Lusophone) designs, according ing over, gene conversion, chromosomal rearrangeto the analyzed products. off Another analysis of designed products was then carried out, Synchronous division and fusion millions of asexual spores, ments, meiotic nondisjunction, and the genetic conto form diploid meiocytes focusing onalthough countries design great international appreciation so that it canproduction disperse in airofand trol of meiosis itself. Chromosomes, small,with which repeat the asexual cycle. would be possible to differentiate this against Lusophone design. The analyzed regions and are easily visible, and so meiotic processes can be CrossIn N. crassa’s were sexualScandinavia, whichfertilization countries, forchromosomal the purpose of differentiation, includes the Nordic studied at both the genetic and the cycle, there are two identicallevels. Hence, in Neurospora, fundamental studies countries, as well as Italy and Germany. To conclude the first stage of this research, and apply looking mating types MAT-A have been carried out on thea mechanisms underlyit in practical component, two conceptual designs were developed (Fig. 2 and 3). and MAT-a, which can be ing these processes (seeOne page 127). of the designs concerns a refrigerator (Figure viewed as simple “sexes.”

As2) that intends to reflect the Portuguese identity, without disregard in toyeast, new the options, both in two mating typesterms of currently available material and Genetic analysis technology. The other conceptual design are determined by twoconsists alleles of a sofa with a special focus on Genetic analysis is straightforward (see page 96). of one gene.

When colonies of may assume an array of different Lusophone related features (Figure 3). The latter Maternal nucleus Maternal nucleus Stock centers provide a wide range of mutants afMating type A Mating type a different mating type come configurations, and it differs from similar products in its versatility, having as main function fecting all aspects of the biology of the fungus. contact,for their walls of the users’ feet, and converting into a that of a sofa, includinginto a footrest thecell support Neurospora genes can be mapped easily but by crossing and nuclei fuse. Many transient diploid nuclei arise, each of which undergoes set of table with threeloci stoolsmeiosis, if necessary. them with a bank of strains with known mutant producing an octad of ascopores. The ascospores germinate and proNeurospora crassa growing on sugarcane. which are aimed

or known RFLP alleles. Strains of opposite mating type are crossed simply by growing them together.

A geneticist with a handheld needle can pick out a single ascospore for study. Hence, analyses in which

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duce colonies exactly like those produced by asexual spores.

Length of life cycle: 4 weeks for sexual cycle

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Industrial Design – New Frontiers transgene, inserted at a random ectopic location. Because of this duplication of material, if the strain is crossed, it is subject to RIP, a genetic process that is unique to Neurospora. RIP is a premeiotic mechanism that introduces many GC-to-AT transitions into both duplicate copies, effectively disrupting the gene. RIP can therefore be harnessed as a convenient way of deliberately knocking out a specific gene.

Main contributions

Fig. 2. Refrigerator designed with inspiration on the Portuguese “postigo” door or as the model George Beadle and Edward Tatum (small used Neurospora window within a regular door) (designed by the third in author). organism their pioneering studies on gene–enzyme relations, Wild-type (left) and mutant (right) Neurospora grown in a petri dish.

in which they were able to determine the enzymatic steps in the synthesis of arginine (see page 219). Their work with Neurospora established the beginning of molecular genetics. Many comparable studies on the genetics of cell metabolism with the use of Neurospora followed.

either complete asci or random ascospores are used are rapid and straightforward.

Because Neurospora is haploid, newly obtained mutant phenotypes are easily detected with the use of various types of Mutant for Mutant for Wild type screens and selections. A favorite system for study of the mechagene 1 gene 2 nism of mutation is the ad-3 gene, becauseobject ad-3 mutants are pur-shelf, stools and footrest) designed with inspiration Fig. 3. Multi-purpose (sofa, table, ple and easily detected. taken from the traditional “canapé” (multiple seat wooden chair) (designed by the third Although vegetative diploids of Neurospora are not readily obauthor). tainable, geneticists are able to create a “mimic diploid,” useful for complemenation tests and other analyses requiring the presence of two copies of2.1 a gene (see pagedeployed 225). Namely, fusion of two design profiles Methods to the unveil existing different strains produces a heterokaryon, an individual containing The overall goal of the study was to identify from various perspectives (brand, material, two different nuclear types in a common cytoplasm. Heterokaryons among the test, contours of a possibly existing identity of Lusophone design, also enable the archetype, use of a version of the others) specific-locus a way to from study of selected cases.

Thea /m guiding specific objectives were the following: recover mutations in athe specific recessive allele. (Cells from gene 1 gene 2 and seeking - plated Identifying the various types of associations that support cultural identity heterokaryon are and m/m colonies are sought.)

enzyme 2 Nonpigment enzyme 1 Yellow Normal to illustrate them by adopting a historical perspective. precursor precursor orange carotenoid Analyzing products of international recognition to identify a possible identity of pigment Techniques of Genetic Manipulation Portuguese and Lusophone design.

Pathway synthesizing orange caroteinoid pigment in Neurospora.

Standard mutagenesis: PlacingRandom the proposed identification of traces of Lusophone cultural identity in the Chemicals and radiation somatic mutations context Not of other traditions, as a means of differentiation.

Pioneering work has been done on the genetics of meiotic Transposon mutagenesis available processes,tosuch as crossing over and disjunction, and on cowhat was found, while adopting Proposing solutions or concepts in continuity Transgenesis: nidiation rhythms.

Continuously growing cultures show a daily emerging technology.

Plasmid-mediated contemporary Random or insertion rhythm of conidiospore formation. The results of pioneering To assist in achieving these objectives the following research questions were developed: transformation studies using mutations that alter this rhythm have contributed the for appearance traces, signs or Over time is there a continuity and perseverance to a generalin model the genetics of of circadian rhythms.

Targeted gene knockouts: marks on production Lusophone space, in Portugal? serves as aand model for the multitude of pathoRIP GCthe l AT mutations inof objects within theNeurospora genic filamentous affecting crops and humans because Are theretransgenic materials, shapes, graphic markings, colours, fungi and other product properties duplicate segments these fungi are often difficult to culture and manipulate genetibefore a cross (Lusophone), and, or, typically Portuguese with international acceptance? cally. It is even used as a simple eukaryotic test system for muQuelling Somatic Are there any posttranscriptional identifiable differences between the products of Lusophone production tagenic and carcinogenic chemicals in the human environment. inactivation of transgenes and the most visible design currents with a geographical identity, suchbyasusing Scandinavian, Because crosses can be made one parent as female, Italian or German design? the cycle is convenient for the study of mitochondrial genetics and nucleus–mitochondria interaction.

A wide An extensive review of Portuguese and Lusophone design was carried out in order to range betterof linear Genetic engineering and circular mitochondrial plasmids have been discovered of this study are based on results from in natunderstand it.

The new designs created in the course Transgenesis. The first eukaryotic transformation was accomural isolates. Some of them are retroelements that are thought to is easily transformed plished in Neurospora.

Today, Neurospora the analysis pertaining to the products shown in the following sections. The selection of be intermediates in the evolution of viruses. with the use of products bacterial plasmids carrying transgene, comprised inthe thedesired analysis presented (including iconic designs identified in design plus a selectable marker such as hygromycin resistance to show web-blogs, items for sale at the Museum of Modern Art, New York, red dot design awards Other areas of contribution that the plasmid has entered. No plasmids replicate in Neurofair) has necessarily influenced the results design fair catalogues, e.g. Milan Fungal diversity and adaptation spora, and so a and transgene is inherited only if it integrates into adesign

chromosome.

Targeted knockouts. In special strains of Neurospora, transgenes frequently integrate by homologous recombination. Hence, a transgenic strain normally has the resident gene plus the homologous

Cytogenetics (chromosomal basis of genetics) Mating-type genes Heterokaryon-compatibility genes (a model for the genetics of self and nonself recognition)

59

Culturally Inspired Design: Product Personalities to Capture Cultural Aspects

attained. Had other objects produced Genetic in the “Vital sameStatistics” geographic spaces been considered, Arabidopsis thaliana different results probably would haveGenome been size: found. An underlying hypothesis for the 125 Mb

Chromosomes: 5 autosomes 10) not are capital even(2nwhen approach deployed in this chapter is that cultural influencesdiploid, of genes: consciously considered by designers, andNumber are hence reflected in25,000 the design production itself. with human A possibly existing design identity andPercentage its continuity over time was sought, in order to Key organism for studying: homologs: 18% products.

Design recognize characteristics and similarities among Average gene size: 2 kb,production 4 introns/genewas not only Development examined within the Lusophone space, but its international acceptance and appreciation Transposons: 10% of the genome Gene expression and regulation Genome sequenced in: 2000 Plant genomics was also considered, so that, through this analysis, it would be possible to recognize the character and contours of the design culture in order to give continuity to a tradition of centuries. It then became imperative to perform a new product search to investigate the differentiation against highly visible design traditions, as is the case of Scandinavian, Italian and German designs. Finally, and from the analytical treatment performed to the data collected in the survey mentioned above, two design concepts are presented which combine Portuguese and Lusophone design tradition, respectively, with contemporary materials and technologies. Ultimately, the aim of these concepts was to establish an alliance between the cultural backgrounds of Portuguese design with the numerous technological possibilities that are presented everyday and athat enable theBrassicaceae achievement of product at Arabidopsis thaliana, member of the (cabbage) family ofimprovements plants, is a relatively late arrival as a genetic model organism.

Most work done inperformance the past 20 years. various levels. These improvements focus on aspects suchhasasbeen product andIt has no of economic it grows prolifically as a weed in many temperate parts of the increasing the quality humansignificance: life.

world. However, because of its small size, short life cycle, and small genome, it has overtaken the more traditional genetic plant models such as corn and wheat and has become the domi2.2 Product characteristics associated identity nant model for plant molecularwith genetics.

This section seeks identification of various types of associations that support cultural identity and seeks to illustrate them by adopting a historical perspective. The aim is also Arabidopsis thaliana growing in the wild. The versions grown in the to seek answers to the question: over www.missouriplants.com.] time is there a noticeable continuity and laboratory are smaller.

[Dan Tenaglia, perseverance in the appearance of traces, signs (materials, shapes, graphic markings, colours, and so on) in the production of objects within the Lusophone space, and Portugal? To answer this question a web based search for products with origins in Life Cycle Special features Portugal and Brazil was carried out. As was observed throughout the many examples In comparison with other plants, Arabidopsis in regard familiar plant cycle, with a dominant encountered in ouris small review, over timeArabidopsis there is has a the continuity andlifeperseverance in the to both its physical size and its genome size—features that are diploid stage.

A plant bears several flowers, each of which the appearance of traces, signs (materials, shapes, graphic markings, colours, and other) in advantageous for a model organism. Arabidopsis grows to a produces many seeds. Like many annual weeds, its life cycle production of objects within the Lusophone space (represented only by Brazil), and height of less than 10 cm under appropriate conditions; hence, is rapid: it takes only about 6 weeks for a planted seed to proWith regard to the continuityduce of Portuguese design, analyzing the set of iconic it can be grown in largePortugal. numbers, permitting large-scale mutant a new crop of seeds. screens and progeny analyses.

Its encountered total genome size of 125 Mb the similarities at technical and conceptual levels) the products (regarding Total length of life cycle: 6 weeks made the genome relatively easy to sequence with colours that are mostcompared used are white, beige, black, green, metallic grey, red, brown and other plant model organism genomes, such as the maize ge2n 2n yellow. The materials most used are ceramic, wood, Adult porcelain, cork, metal and Adult leatherette. nome (2500 Mb) and the wheat genome (16,000 Mb). sporophyte sporophyte In what concerns form, the products are characterized by simplicity, rationality, curved Meiosis appeal. Portuguese designers innovate Genetic analysis shapes, elegance and convening an organic Meiosis especially in incorporating several features to objects, they take care in choosing n n n n the most n n n n The analysis of Arabidopsis mutations through crossing relies on Haploid Haploid tried and true methods—essentially those

by Mendel.

Plant are usually easyMany to use and provide appropriate andused up-to-date material, and the products spores spores Many mitoses mitoses stocks carrying useful great mutations relevantwith to the in comfort, noexperiment graphic markings. n Adult n Adult hand are obtained from public stock centers. Lines can be manugametophyte gametophyte analyzing the set of iconic products In terms of the continuity of Brazilian design, ally crossed with each other or self-fertilized. Although the flowMitosis Mitosis encountered (regarding the similarities between technical and conceptual qualities), ers are small, cross-pollination is easily accomplished by removing undehisced anthers (which are sometimes eaten bydesigners the experi- seem to show a preference suggests that Brazilian white, black and n Gametesfor brown, n Gametes menter as a convenient green means of disposal).Materials-wise, Each pollinated flower colours. a higher adherence to wood, plastic, leather and metal is 2n Zygote 2n Zygote then produces a long pod containing a large number of seeds. This visible. Brazilian products are characterized primarily by simplicity, rational and straight abundant production of offspring (thousands of seeds per plant) is a boon to geneticists searching for rare mutants or other rare events. If a plant carries a new recessive mutation in the germ line, selfing allows progeny homozygous for the recessive mutation to be recovered in the plant’s immediate descendants.

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Many mitoses

Many mitoses

2n Adult sporophyte

2n Adult sporophyte

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Industrial Design – New Frontiers

lines, wavy and winding forms. These designs are innovative, incorporate functional improvements and demonstrate savings in the materials used in the objects, while designers select the most recent materials and apply high mutability to their projects. The designers of this nationality do not use graphic markings and inferred ease of use of their products varies between easy to medium. In the following section, it is possible to define an identity for Lusophone design, based on the intersection of Brazilian and Portuguese design characteristics.

2.2.1 Portuguese and Brazilian design Regarding the possibility of a cultural identity of Portuguese design, one can thus conclude (ag), which results in flowers with only petals and sepals (no reproductive structures). (Right ) A that the most common colours area (described by decreasing double-mutant ap1, cal, which makes a flower that looks like cauliflower. (Similar mutations in frequency): white, black, brown, cabbage are probably the cause of real grey, cauliflowers.)

[Photos fromand Georgecork Haughn.] beige, metallic green, red, yellow. The materials preferably used by Portuguese designers in most objects are clay (pottery), wood, cork, porcelain, plastic, metal products, theseeven aredecades. characterized their and leatherette. Regarding the shape of themany years, perhaps This featureby is not possible for Techniques of Genetic Modification simplicity, rationality, curved lines, elegance, most organic character, softness and someCaenorhabditis cases populations of animal models.

Theinworm elStandard mutagenesis: egans can be preserved a frozen animal, flies of (Drosophila straightness of lines. This design culture stands out for its as innovation in but thefruit field Chemicals and radiation Random germ-line or melanogaster) cannot be frozen and revived. Thus, lines of fruit-fly materials, and it alsosomatic reflects concerns about the ease of use, comfort, very often the addition mutations mutants must be maintained as living organisms. oftransposons new materials and products T-DNA itself or Random taggedare aesthetically modern. Surveyed objects are mostly devoid contributions insertions of graphic markings, except for the productMain brand.

Finally, all objects are considered to As the first Transgenesis:require between easy and medium ability for their use. plant genome to be sequenced, Arabidopsis has provided an important model for plant genome architecture and T-DNA carriesBrazil the transgene insertion also shows Random important similarities between its designers’ production, in their choice evolution. In addition, studies of Arabidopsis have made key conTargeted gene knockouts: is of clear.

Theycontrol use the of colours such as brown, white, black and tributions green, this to oursimilarity understanding the genetic of plant deT-DNA or transposon-mediated Random insertion; velopment.

Geneticists have The isolated homeotic mutations affectmost common materials including wood, metal, plastic and leather. sampled products mutagenesis knockouts selected ing flower development, for example.

In such mutants, designed in this nation exhibit similarities among each other such as simplicity, straightone type with PCR of floral part is replaced by another. Integration of the action of RNAi Mimics targeted lines, rationality, and undulating and sinuous lines. Originality and innovation stand out these mutants has led to an elegant model of flower-whorl deterknockout improvements, material savings, and in the evident concern for comfort, functional mination based on overlapping patterns of regulatory-gene exconscious selection of materials by Brazilianpression designers through the mutability given in theand flower meristem.

Arabidopsis has also contributed broadly the genetic basis of plant gene of regulation, to their products. The objects are mostly devoid of to graphic markings and physiology, inferred ease Genetic engineering and the interaction of plants and the environment (including Transgenesis. use Agrobacterium T-DNA is alarge convenient vector for although most of these products were deemed varies between and medium, the genetics of disease resistance).

Because Arabidopsis is a natuintroducing transgenes easy to (see use.Chapter 10). The vector–transgene ral plant of worldwide distribution, it has great potential for the construct inserts randomly throughout the genome. Transgenesis amongdiversification the Portuguese language In identifying a possibly existing identity for studydesign of evolutionary and adaptation. offers an effective way to study gene regulation. The transgene countries, albeit it was based only in Portugal and Brazil, the following characteristics were is spliced to a reporter gene such as GUS, which produces a blue se colours mostly green; materials are typically ca dye at whateveridentified: positions in the plant the gene isused active.are white, brown, black and pe st Targeted knockouts. wood, Because plastic homologous and metal.recombination Moreover, isthe products are characterized mainly by their rare in Arabidopsis, specific genes cannot be easily knocked out C C C themselves by speaking simplicity, rationality and straight lines. The designers differentiate B B B B by homologous replacement with a transgene. Hence, in ArabiA A A of knocked the choice ofthe material, the comfort they bring to the objects, Aassigning more than one (a) dopsis, genes are out by random insertion of a Tto transposons their products arethe same time incorporating mutability into their DNA vector or functionality transposon (maize such as and Ac-Dsat used), and thendesigns. specific gene selected by applying Theknockouts objects are created within the Lusophone space are generally easy to use, Flower and gene- are expression pattern PCR analysis tomostly DNA from large pools of plants.

The PCR uses a devoid of graphic markings.

Arabidopisis mutants. (Left ) Wild-type flower of Arabidopsis. (Middle ) The agamous mutation

sequence in the T-DNA or in the transposon as one primer and a (b) B C Gene class A sequence in the2.2.1.1 gene ofSampled interest asPortuguese the other primer.

Thus, PCR designs The establishment of whorl fate. (a) Patterns of gene expression amplifies only copies of the gene of interest that carry an inserset offates.

26 other products Besides the 46repeating productthe designs section, antoadditional the different whorl From outermost to tion. Subdividing the pool and process showed lead to thein thiscorresponding innermost, the fates are sepal (se), petal (pe), stamen (st), and was analyzed in this study, but are not shown due to space and size restrictions (Fig. 4;carpel specific plant carrying the knockout. Alternatively, RNAi may be (ca). (b) The set shaded of the cross-sectional of the used to inactivate a specific gene. are in the public domain; for a complete images shown of regions references see Simão &diagrams Coelho, developing flower indicate the gene-expression patterns for the genes Large collections 2011).of T-DNA insertion mutants are available; of the A, B, and C classes. they have the flanking plant sequences listed in public databases; so, if you are interested in a specific gene, you can see if the colOther areas of contribution lection contains a plant that has an insertion in that gene. A convenient feature of knockout populations in plants is that they can Environmental-stress response be easily and inexpensively maintained as collections of seeds for Hormone control systems

Culturally Inspired Design: Product Personalities to Capture Cultural Aspects

Caenorhabditis elegans Key organism for studying: Development Behavior Nerves and muscles Aging

61

Genetic “Vital Statistics” Genome size: 97 Mb Chromosomes: 5 autosomes (2n 10), X chromosome Number of genes: 19,000 Percentage with human homologs: 25% Average gene size: 5 kb, 5 exons/gene Transposons: Several types, active in some strains Genome sequenced in: 1998

Caenorhabditis elegans may not look like much under a microscope, and, indeed, this 1-mm-long soil-dwelling roundworm (a nematode) is relatively simple as animals go. But that simplicity is part of what makes C. elegans a good model organism. Its small size, rapid growth, ability to self, transparency, and low number of body cells have made it an ideal choice for the study of the genetics of eukaryotic development.

Pharynx

Ovary

Eggs

Intestine

Rectum Anus

Oviduct

Oocytes

Uterus

Vulva

Fig. 4. Images of Portuguese designed products sampled as a basis for analysis.

Photomicrograph and drawing of an adult Caenorhabditis elegans.

2.2.1.2 Sampled Brazilian designs

from Brazil shown in this section, an additional Special features Besides the 32 examples of product design simply by watching the worms under a light microscope. The reset of another 32 products was considered in the analysis presented in this study, but are not

Geneticists can see right through C. elegans. Unlike other multicelsults of such studies have shown that C. elegans’s development is dueflies to space and size restrictions (Fig.programmed 5; images shown the has public domain;small for lular model organisms, shown such as fruit or Arabidopsis, this tiny tightly and that are eachin worm a surprisingly a complete set references see Simão &and Coelho, 2011). worm is transparent, making it efficient to of screen large populations consistent number of cells (959 in hermaphrodites and 1031 in for interesting mutations affecting virtually any aspect of anatomy males). In fact, biologists have tracked the fates of specific cells as or behavior. Transparency also lends itself well to studies of develthe worm develops and have determined the exact pattern of cell opment: researchers can directly observe all stages of development division leading to each adult organ. This effort has yielded a lineage pedigree for every adult cell (see page 476).

W

P1

P2

P3,P4,P5, P6,P7,P8,P9

P10

Because the worms are small and reproduce quickly and prolifically (selfing produces about 300 progeny and crossing yields

L1

L3

P10.ppppp P10.ppppa P10.pppa P10.ppap P10.ppaa P10.papp P10.papa P10.paap P10.paaa P10.aapp P10.aapa

Adult

Life Cycle

C. elegans is unique among the major model animals in that one of the two sexes is hermaphrodite (XX). The other is male (XO). The two sexes can be distinguished by the greater size of the hermaphrodites and by differences in their sex organs.

Hermaphrodites produce both eggs and sperm, and so they can be selfed. The progeny of a selfed hermaphrodite also are hermaphrodites, except when a rare nondisjunction leads to an XO male. If hermaphrodites and males are mixed, the sexes copulate, and many ofas thea resulting zygotes will have been fertilized Fig. 5. Images of Brazilian designed products sampled basis for analysis. by the males’ amoeboid sperm. Fertilization and embryo production take place within the hermaphrodite, which then lays the eggs. The eggs finish their development externally.

Pn.aapp Pn.aapa

L4

s

P10.app P10.apa P10.aaap P10.aaaa Pn.p;vh Pn.app Pn.apa Pn.aaap Pn.aaaa P2.p;vh P2.app P2.apa P2.aap P2.aaap P2.aaaa P1.p;vh P1.app P1.apa P1.aaap P1.aaaa

W.aap W.aaa L2

W.pp W.pa

s

A symbolic representation of the lineages of 11 cells. A cell that undergoes programmed cell death is indicated by a blue X at the end of a branch of a lineage.

768

Genetic analysis

Total length of life cycle: 3 21 days

62

Industrial Design – New Frontiers

2.2.2 Comparison with Scandinavian, Italian Geneticand “VitalGerman Statistics”design Drosophila melanogaster of identifying the This section is intended to achieve the objective Genome size: 180 Mb

characteristics of Lusophone design identity in the contextChromosomes: of other geographically based design traditions, Diploid, 3 autosomes, X and Y as between the products a form of visible differentiation. Hence, it seeks to identify differences (2n = 8) Key organism for studying: Number of genes: 13,000 of Lusophone origin and products with a Scandinavian, Italian and German origin.

Percentage with human Transmission genetics As shown in this section, there are some differences between Lusophone design and homologs:

50% Cytogenetics Scandinavian, Italian and German design. This section enables establishing material and use Average gene size: 3 kb, 4 exons/gene Development based differences drawn from the four design origins included in the study.

Transposons: P elements, among others Population genetics differences With regard to colour preference very significant Genome sequenced in: 2000 do not exist, however, Evolution Lusophone design resembles Scandinavian design in this respect, differing from Italian and German design by the use of more subtle and neutral colours. The colours that are primarily The fruit fly Drosophila melanogaster (loosely translated as “dusky syrup-lover”) was one of used by the Italian current tend to be more flashy (Table 1). the first model organisms to be used in genetics. It was chosen in part because it is readily

Polytene chromosomes.

available from ripe fruit, has a short life cycle of the diploid type, and is simple to culture and cross in jars or vials containing a layer of food. Early genetic analysis showed that its inheriLusophone Space Scandinavia (23) to those of other Italyeukaryotes, (26) Germany tance mechanisms have strong similarities underlining its role as(23) (136) a model organism. Its popularity as a model organism went into decline during the years when WhiteE. coli, yeast, 25%and other White 35%were being White Black microorganisms developed as36% molecular tools.

However, 36% Drosophila has experienced a renaissance because it lends itself so well to the study Metallicof the Metallic 32%Drosophila’s importance 28% Browngenetic basis 17%of development, Red one of 30% the central questions of biology.

Grey Grey as a model for human genetics is demonstrated by the discovery that approximately 60 perin humans, Yellow as well as 70 percent genes, have 28% Blackcent of known 15% disease-causing Black genes30% 24% of cancer White counterparts in Drosophila.

Green

7%

Brown

26%

Special features

Black

20%

Blue

16%

Red

20%

Grey

12%

Drosophila came into vogue as an experimental organism in the Blue 16% Orange 12% early twentieth century because of features common to most Life CyclePink 12% model organisms. It is small (3 mm long), simple to raise (origiDrosophilaBrown has a short diploid nally, in milk bottles), quick to reproduce (only 12 days from egg 12%life cycle that lends itself well to genetic analysis. After hatching from an egg, the fly deto adult), and easy to obtain (just leave out some rotting fruit). It Green 12%stages and a pupal stage before velops through several larval proved easy to amass a large range of interesting mutant alleles emerging as an adult, which soon becomes sexually mature. that were used to lay the ground rules of transmission genetics.

Orange 12% Sex is determined by X and Y sex chromosomes (XX is feEarly researchers also took advantage of a feature unique to the male, XY male), although, in contrast with humans, the fruit fly: polytene chromosomes page 609).

In salivary glands Table 1.(see Colour characteristics prevalent across theis sampled products. number of X’s in relation to the number of autosomes deterand certain other tissues, these “giant chromosomes” are prominesinsex (see page 50).of choice for products, these are the material In relation to the material visible duced by multiple rounds of DNA replication withoutdifferences chromosomal segregation. Eachshown polytenein chromosome a unique Table 2. displays Portuguese speaking designers a special preference for wood Total length of have life cycle: 12 days from egg to adult banding pattern, providing geneticists with landmarks that could primarily, followed by plastic, while the materials of preference of Scandinavian, Italian and be used to correlate recombination-based maps with actual chroAdult German designers (metal) are the least utilized by Lusophone designers. mosomes. The momentum provided by these early advances, along with the large amount of accumulated knowledge about the organism, made Drosophila an attractive genetic model. Scandinavia Italy Germany Lusophone Space

(136)

Genetic analysis

(23)

17% Metals Crosses in Drosophila can beWood performed quite easily. The parents may be wild or mutant stocks obtained from stock centers or as Plastics 6% Plastics new mutant lines.

Metals

4%

Wood

1

1

3 2 –4 2 days

(26)

1 day

48%

Metals

52%

30%

Plastics

26%

Pupa Wood

Fabric

17%

Glass

17%

Metals

32%

40%

Wood 1 day

24%

24%

Leather

20%

Egg

First instar

Plastics 1 day 1

2 2 –3 days

Table 2. Materials that are prevalent across the sampled products.

Second instar

Third instar Wild type

Bar eyes

Vestigial wings

Two morphological mutants of Drosophila, with the wild type for comparison.

770

(23)

1 day

16%