Issue 23

ELEMENTS A MAGAZINE FOR SCIENCE AT THE UNIVERSITY OF PUGET SOUND

ISSUE 23 - FALL 2018

Critical History

Natural World

“We ignore public understanding of science at our peril.”

-EUGENIE CLARK (1922-2015)

LETTER FROM THE EDITOR These are trying times for scientists. It seems that we are being assaulted from all sides. The President has taken what is widely perceived to be a hostile stance toward the scientific community, mixing fact and fiction to suit his dubious political aims. Until his resignation in July of this year, the head of the U.S. Environmental Protection Agency, Scott Pruitt, actively opposed environmental regulations and undermined the science of climate change. Our community is plagued with the ethical issue of p-value hacking, leading us to question results that have long been held true. In the midst of these challenges, it is tempting to question if our efforts to share the joys of scientific inquiry with the Puget Sound community are even worth it. After all, what difference will it make?

To answer this, I would like to draw upon the opening quotation of this issue: “We ignore public understanding of science at our peril.” These words belong to Eugenie Clark, a biracial woman who broke into the male-dominated field of marine biology after World War II and revolutionized the way we think about one of the ocean’s most misjudged predators: the shark.

To me, Clark’s words are a rallying cry—we must not give in to hopelessness, especially in the face of the trials our times have brought. It is imperative that we foster the public’s understanding of our fields, because if they do not understand our work, they will not perceive its immense value.

With this in mind, readers may notice that this issue of Elements is not afraid to address some of the tense topics in today’s political and social conversations. We are excited to publish Elements’ first article on race, entitled “Genocide can look like many things, Racism and Genetics: commentary on ‘Trauma Marks’.” This article was inspired by the Race and Pedagogy National Conference, which was held on our campus in September. We are also proud to take a stand against eugenics in our community with the article “A Moral and Scientific Rebuttal to ‘Reconciling Eugenics for the Sake of Human Survival’.” We champion green energy solutions in Washington in our article “The Use of Ethical, Renewable Energy Sources in the State of Washington.”

I hope that you will find this issue of Elements both informative and inspiring during these times of doubt and insecurity. I have no doubt that together, we can make a meaningful difference.

Anna Marchand

STAFF Anna Marchand

Emily Nygard

EDITOR IN CHIEF

ASSOCIATE EDITOR

COPY EDITOR

Andrew Izzo

Annelise Phelps

Noah Bader-Fourney

ASSOCIATE EDITOR

ASSOCIATE EDITOR

Finn Dobkin

Allison Shapiro

ASSOCIATE EDITOR

DESIGN EDITOR

Cover illustration by Charlotte Nabors and Abby Rawson

Erin Stewart

OUTREACH MANAGER

The production of Elements Magazine is possible due to the funding and support of the Associated Students of the University of Puget Sound (ASUPS). We thank Media Board, ASUPS and, by extension, the student body for making this publication a reality. This magazine was printed by Print NW (Lakewood, WA).

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In this Issue 6

When Goats Fly: Relocation and Restoration on the Olympic Peninsula - Erin Stewart

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Genealogy of the Scientific Method - Finn Dobkin

11

Scientific Genesis - Emily Nygard

12

Ancient Polychromy - Sandra Brandon

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How far we’ve come: an overview of gene editing prior to CRISPR - Lily Rivin

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Rebuttal to “Reconciling Eugenics for the Sake of Human Survival” - Kaelie Coleman

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Race and Genetics, a discussion on “Trauma Marks” - Mason Culbertson

21

Cover Contest Runner-Up

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An Evolution of Ethics within the Doctor-Patient Relationship - Noah Bader-Fourney

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Treatment Non-Adherence and Depression - Morgan White

26

Cordyceps: The Truth Behind the Horror - Finn Kearney

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Languages From the Deep: Marine Animal Communication - Kaela Hamilton

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The use of Ethical, Renewable Energy Sources in the State of Washington - Anna Fryxll

33

100 Kmh - Josh Pi

36

Green Chemistry: Developing Novel Catalysts for Amide Synthesis - Alex Guzman

39

Professor Research Interviews - Andrew Izzo

40

Cosmo Nerd

41 Which Life Science Professor Are You? - Anna Marchand 42 43

Mad labs - Annelise Phelps Citations

When Goats Fly: Relocation and Restoration on the Olympic Peninsula Images: Wikimediia Commons

BY ERIN STEWART Late this summer, local news was saturated with pictures of blindfolded mountain goats suspended from helicopters.

As ridiculous as it looked, it was part of a serious restoration effort. Understanding the rationale for this effort requires knowledge of the history and ecological impacts of mountain goats on the Olympic Peninsula.

A Brief History of Mountain Goats in the Olympics The Olympic Peninsula is often compared to an island ecosystem due to the fact that is was largely cut off from the Cascade Range during the Pleistocene glaciation (1).

This isolation permitted the evolution of multiple endemic species and subspecies, including the Olympic marmot as well as twelve species and varieties of alpine plants (2, 3).

The region is also a refuge for rare species: a 1994 report from the National Park Service indicates that although the peninsula only comprises 8% of Washington’s surface area, it contains 27% of its rare vascular plants (4).

Between 1925 and 1929, eleven or twelve mountain goats (Oreamnos americanus) were released into this relatively isolated ecosystem (4). These goats came from British Columbia and Alaska, and were released near Lake Crescent and Baldy Ridge by Washington State wildlife agents, the U.S. Forest Service, and a sportsman’s club (3). While the historical record doesn’t explicitly identify the reason for

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these introductions, they were intended to establish a population of goats for sport hunting (3). This desire was never realized, however, as hunting became illegal in much of the Olympics following the establishment of the Olympic National Park in 1938 (3).

The goat population grew slowly but steadily, reaching an estimated 1,175 individuals by 1983 (4). Around this time, an Experimental Management Program was implemented by the National Park Service to test the effectiveness of different goat removal strategies – including foot snares, drop nets, sterilization, and chemical immobilization via tranquilizer darts (4). This program was followed by an Operational Management Program, which aimed to eliminate the goat population in the core of the Olympic National Park (4). As a result of these two efforts, 407 goats were either relocated or shot between 1981 and 1989 (4).

However, the goat population was not completely extirpated, and this allowed it to rebound. As of September 2018, there were an estimated 725 goats on the peninsula (5). This number was projected to increase by 45% in five years if no control measures were taken (5).

Mountain Goats and Alpine Ecology So why have goat removal programs been deemed necessary, both historically and currently? One motivation behind these programs is the desire to preserve the unique alpine ecosystems present in the Olympic National Park.

This is concerning primarily because the plants grazed or otherwise damaged by goats include a number of the peninsula’s endemic plant species (4). Of particular note, goats often trample Olympic Mountain milkvetch (Astragalus australis var. cottonii), an endemic alpine flower that is listed as threatened by the Washington Department of Fish and Wildlife (6). While it is unclear whether the injuries to individual plants by grazing and trampling could actually drive any of these species to extinction, they certainly increase the likelihood of extinction by fragmenting populations (4). Therefore, goat removal programs are in part meant to protect rare and endemic plant species.

Such alpine ecosystems are inherently vulnerable to disturbance as a result of short growing seasons, shallow soils, and extreme environmental conditions, all of which result in slow rates of plant growth and regeneration (3).

In fact, research suggests that alpine meadows may take an entire century to recover after a mere 500 passes by human hikers (3). Mountain goats cause significant disturbances in these ecosystems through grazing, trampling, and wallowing (3). The latter behavior creates “wallows” – 1-3 m2 areas in which rocks and vegetation have been eliminated (4). Through these actions, mountain goats leave quite visible marks on their habitats.

Mountain Goat Management: Planning and Implementation Over the years, there has been considerable controversy surrounding the prospect of goat removal. Issues have ranged from claims that goats may actually be native to the peninsula, to concerns about the humanity of removal techniques, to questions as to why wolf reintroduction, open public hunting, or sterilization measures aren’t being considered as viable means to reduce the goat population (3, 5, 7, 8). This combination of political, ethical, and

Images: Wikimediia Commons

Numerous studies have documented the effects of mountain goat presence on alpine vegetative communities in the Olympics. One study examined the relationship between goat density and grazing levels, and found that the percent of plant species grazed upon, as well as the average grazing intensity across all species, was higher in areas with elevated goat densities (4). Photographic comparisons the same alpine meadows at different times also bear out this negative correlation between goat density and vegetative coverage (4). Drawing a more causal link, another study found that human-controlled reductions in goat density led to an increase in the coverage of plant species preferred by foraging goats (4). Furthermore, this research indicated that goat presence actually mediates competition between plants: under grazing and wallowing pressures, non-preferred or disturbance-oriented plants dominated, while the removal of this pressure led to the dominance of preferred forage species (4). Overall, these studies show that goats significantly alter the coverage and species composition of alpine vegetative communities.

However, as is often the case with restoration projects, humans aren’t completely selfless in their motivations.

Goats in the Olympic Peninsula have become conditioned to seek salt from human urine, and are now considered a nuisance to hikers (6). In addition, worries about the hazardous nature of human-goat interactions have moved to the forefront of conversations following the fatal goring of a hiker by a mountain goat in 2010 (6). Thus, the relocation is as much a response to safety concerns as it is to ecological concerns.

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Image: PIXABAY.COM

logistical considerations has made population control a highly complex issue.

Due to the level of debate surrounding the issue, the National Park Service’s development of the contemporary removal plan involved an “extensive public engagement and environmental impact analysis effort that began in 2014” (9). The public engagement portion of this effort included consultations with other federal and state agencies, tribes possessing federally recognized ties to the Olympic Peninsula, and members of the general public (6).

Following this planning period, the National Park Service issued a finalized Environmental Impact Statement in April 2018, in which it outlined four different alternatives for goat management: A – no action B – capture and relocation C – lethal removal D – capture and relocation followed by lethal removal For each alternative, the agency analyzed the potential impacts on the park’s wilderness character, wildlife and vegetation (with particular attention paid to threatened and endangered species), acoustic environment, soils, archeological resources, visitor use and experience, and visitor and employee safety (6). Two months later, on June 18th, the National Park Service issued a press release announcing the approval of alternative D (9).

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The first relocation took place in mid-September, and by the end of the two-week period a total of 114 goats were relocated (5). For all relocations, goats were first tranquilized using darts or caught using net guns (5).

Next, they were carried via helicopters in “specially-made slings customized for mountain goats” to a staging area at Hurricane Ridge, where they were processed by a team of veterinarians (5). Finally, they were transported to a staging area in the North Cascades and released soon thereafter (5).

The North Cascades were chosen as the destination because their native goat population has shrunk significantly over the past few decades, and the infusion of new goats is expected to boost the population size and genetic fitness of this resident population (5, 6).

This management project represents a massive culmination of scientific research, assessment and planning, and political decision-making. Using the method above, the National Park Service estimates that it can relocate about half of mountain goat population (325-375 individuals) to the North Cascades, with the remainder to be removed through lethal measures (9). Over the next few years, Washingtonians can expect to hear more about relocation efforts as well as their initial ecological effects.

So, next time you see an area closure in the Olympics, make sure to go – you might just see a mountain goat in a customized sling flying through the air.

GENEOLOGY OF THE SCIENTIFIC METHOD

BY FINN DOBKIN In his seminal classic titled Les formes élémentaires de la vie religieuse, social theorist Emile Durkheim wrote “although the offspring of religion, science tends to replace religion in everything that involves the cognitive and intellectual functions” (2). To Durkheim, science and religion were both representations of human belief, which he argued were based off of the same premises. “There ought necessarily to be a certain number of fundamental representations or conceptions and of ritual attitudes which, in spite of the diversity of forms which they have taken, have the same objective significant and fulfill the same functions everywhere,” he stated. Durkheim’s writings on science and religion are foundational to his life’s work but more importantly, they reveal a copious amount about how we have studied science.

Considering Durkheim’s statements, it becomes clear that there is no identifiable time when scientific knowledge began. Despite this ambiguity, many observers would point to the Renaissance and Enlightenment eras as the beginning of science as a formalized procedure (3). During these eras, two figures were key in describing how science ought to be pursued. The first and perhaps most famous of these was astronomer Galileo Galilei.

Born in 1564 in Florence, Italy, Galileo’s academic career began at the University of Pisa where he taught and studied mathematics. In 1592, he was offered a position to teach at the prestigious University of Padua where he would further much of his scientific work. It was here that he continued the work of Nicolas Copernicus to put forward a Heliocentric theory (4). Though this work is certainly what brought him fame, his truly pioneering work was his advancement of a more methodical approach to science, which he details in his text Discourse e Dimostrazioni Matematiche Intorno a

ABOVE: Robert Hooke, father of modern cell theory, an art piece create by Rosie Rogers .

Due Nuove Scienze. In this writing, Galileo uses Aristotelian logic to argue that science must produce knowledge based on reasoned truths. That is, science must use proven axioms to explain the results of experiments (5).

Galileo’s work, though important, did not frame the modern scientific method quite as neatly as the work of Sir Francis Bacon. Bacon was critical of Galileo’s method.

He believed that there must be a master theory to explain science and philosophy, which Galileo’s work was incapable of producing (6). In order to fill this niche, Bacon proposed an inductive approach which “by slow and faithful toil gathers information from things and brings it to the understanding.” Bacon proposed this theory in his text Novum Organum where he also identified four Idola mentis (Idols of the Mind), which were false images that skewed the collection of knowledge. These false images included Idola tribus (Idols of the Tribe), which is the belief that there is more order in the world than actually exists, or apophenia.

The next is Idola specus (Idols of the Cave), which is a reflection of personal biases. After that is Idola fori (Idols of the Forum), which is the subjectivity of language. Finally, there is Idola theatri (Idols of the Theatre), which is one’s inability to question the current status of knowledge (7).

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ABOVE: Galileo Galilei, an Italian astronomer, physicist, and engineer. He has been called the “father of the scientific method” and “father of observational astronomy’ Taken as a whole, Bacon and Galileo’s work were highly influential to later scientists and philosophers, both of the Enlightenment era and of today. Though the importance of their work cannot be understated, one would not be doing justice to history to ascribe all credit for the scientific process to Bacon and Galileo alone. A more authoritative account of the scientific method instead begins with a corpus of writings from Islamic scholars beginning in the early 1000’s (3).

Ibn al-Haytham was born in 965 AD and is considered by many to be the founder of modern optics, though he also commented on mathematics, astronomy, and scientific theory. Although he didn’t explicate his theory on the scientific method in any one text, his writings show an emphasis on careful and detailed empirical work (8). In his most famous set of writings, titled Kitab al-Manazir, al-Haytham argues “The duty of the man who investigates the writings of scientists, if learning the truth is his goal, is to make himself an enemy of all that he reads, and ... attack it from every side.” The text itself is a compilation of the experiments he performed while imprisoned in Cairo, Egypt. What is clear from the writings is that he took careful observations which he then used to justify his theoretical propositions. He concludes by urging others to repeat his

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experiments to prove the validity of his conclusions (8).

The scientists of the Enlightenment and Renaissance eras owe much to the work of al-Haytham. However, the work of Abū Rayhān al-Bīrūnī is also noteworthy. Born twelve years after al-Haytham, al-Bīrūnī was a mathematician, philosopher, and theologian, amongst other pursuits. In his work on geology and psychology, al-Bīrūnī emphasized the importance of beginning with a question and narrowing down one’s work to an experiment, after which one could develop a theory about how the world works. Similarly, he emphasized the importance of multiple experiments to discern trends in one’s work (3).

As we trace back the history of the scientific method, from al-Haytham to Bacon, it becomes obvious that the scientific method of today is based off of centuries of the practice of science itself. There is something to be appreciated about the lack of formal origin of the scientific method. It shows that scientific procedures are almost inherent to human nature, as there is such great consistency across time and space.

Images: google image for reuse

SCIENTIFIC GENESIS

BY EMILY NYGARD

Currently, the relationship between science and religion routinely experiences significant conflict. Historically, this was not the case. Much of the genesis of science was supported, funded, and undertaken by the church (1). For decades, professors at Oxford University had to be ordained in order to teach (1). The relationship has since changed, but it is worth asking – where would science be without religion?

Science relies on pattern analysis to make meaning.

Claims are valid if they are replicable and methodical. It just so happens that a methodical, systematic approach to science works because in the natural world, there are a lot of patterns. The natural world is orderly and methodical, and that is how we approach science.

But why do we approach science in the mindset that it can be understood? Why do we look at leaves or rocks or bodies and expect to see systematic meaning? Historically, this was because science, formerly known as natural philosophy, was seen as a way to understand God’s divine order and plan (1). Because science began with a bias - that God is orderly and in control - early scientists believed they would see such order and planning in the world. And it just so happens, that the world has many patterns and systems.

Early scientists found what they were looking for because – though they did not know it – they were looking in the right direction.

But wait – aren’t human beings neurologically programmed to find patterns? Yep. Humans have what is called superior pattern processing (SPP) capabilities (2).

SPP is a product of evolution; individuals that could make mental maps to remember the locations of food, water, and threats were more likely to survive than their more spontaneous counterparts (2). Thus individuals who could remember events, assign significance to those events, and structure their lives around expected outcomes were more adaptive to their environment (2). This superior pattern processing applies to patterns that are explicitly useful – like those regarding food, trauma, and shelter. It also

Image: PIXABAY.COM

applies to vestigial patterns that have survived because they are not explicitly detrimental, such as forms of ‘magical thinking’, which includes religion, superstition, and imagination. Even if SPP functions like magical thinking are not specifically useful, they are a part of a larger SPP network that is explicitly helpful. SPP allowed for larger brains in humans as neural pathways were strengthened and expanded, and SPP continues to change the brain on an individual level. For example, individuals that believe in an Old Testament Christian God have different neurological pathways than those that believe in an New Testament Christian God; they process experiences with different parts of their brain (amygdala vs. prefrontal cortex and anterior cingulate cortex), and interact with the world using different neurological pathways (3).

Superior pattern processing in humans is a neurological explanation for religion - people look for meaning in experiences, and God as an overarching explanation for existence is developed and reinforced in human SPP abilities. However, it is important to note that religion preceded science as a product of human SPP. Many of the first ‘scientists’ were motivated by religious desire to know God through His second ‘book:’ the natural world, believed to be an important source of divine knowledge right alongside the Bible (1). For example, the study of zoogeography was invented to attempt to support a literal interpretation of the creation story in Genesis (1). This attempt was ultimately unsuccessful, but it is worth asking – how much longer would it have taken to develop the study of zoogeography without the religious foundation? In science, bias is seen as a significant handicap, but where would science be today without a foundational religious bias as a justification for funding, scientific hierarchy, and scientific presence in religious institutions?

Science may be the ultimate expression of human SPP, but it is important to note that it was the religious expectation of order that helped to urge science on its way.

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Ancient Polychromy: Because Blick Art Materials were not Available 2,000 Years Ago

BY SANDRA BRANDON Wikipedia: Polychrome is the “practice of decorating architectural elements, sculpture, etc., in a variety of colors.” The term is used to refer to certain styles of architecture, pottery or sculpture in multiple colors.

In the Ancient world, being an artist required an intensive training process. There was no walking to an art supply shop and picking up your favorite colors. All colors had to be formulated from pigments, crushed, and mixed to create the right consistency and opacity. In addition, these colors were applied on surfaces that might surprise you. The best surviving pieces of ancient art are the marble statues and temples that dot the landscapes of Greece and Rome. These pieces would’ve also been painted with a variety of bright colors.

Our best sources of information about the colors used to come from ancient literature. Many of these texts refer to painted statues and temples, but unfortunately the translations are often unclear.

Some terms have been crudely translated, like the term graphta andreia. Most commonly, this is translated as “paintings,” even though the phrase is closer to “painted statues.” Some point to this as an example of prejudice in individual authors. However, Quatremere and Walz conducted research in the beginning and middle of the 19th century that elaborated on incorrect references about painted sculptures.

So what do we know about ancient pigments from literary text? We must applaud Pliny the Elder, who wrote the anthology Natural History, in which books 33 through 37 are dedicated to the research of metallurgy and mineralogy.

From this we have been able to extract much information,

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and then connect the dots with what we can see with the naked eye. There have been several painted sculptures whose pigments are still preserved after thousands of years underground.

Unfortunately, pigments are usually faded or have worn off completely, and thus cannot be accurately identified. This is when we have to rely on modern technology to do the work for us. Scientific methods have evolved drastically since scholars began to study polychromy. We have gone from extremely damaging practices to methods that only require light to identify original colors. The range of less or nondestructive analytic methods that allow us to identify the pigments include light and fluorescence microscopy; UV-VIS absorption spectrometry; scanning electron microscopy; micro X-ray fluorescence analysis; and energy dispersive X-ray microanalysis. All of these tests can reveal a range of results by simply identifying the presence of pigments and/ or identifying the compounds of minerals to help identify the exact chemical composition.

However, some methods do require scientists to conduct damaging practices. Take, for example, the analytical research on the marble bust of Caligula from 40 AD that was conducted in 1998. In this sculpture there was a sufficient sample size of the white substratum on the bust to remove and conduct tests upon. The pigment was treated twice with a mixture of chloroform and methanol, followed by a methanol and oxalic acid. The extracts were analyzed by gas

Image: PIXABAY.COM

chromatography-mass spectrometry. The residue was then hydrolyzed with hydrochloric acid to analyze the amino acids that might have been released by the ion-exchange chromatography. The resulting amino acid profile tells us what protein media was used. The high ammonia content shows us a high denaturation rate of the proteins (essentially telling us that we are in possession of an ancient sample).

The high traces of the amino acid serine and other typical decay byproducts tell us that the binding medium used on this bust was egg.(1) This is a very complicated process which, in this case, tells us the binding agent and color minerals, and confirms the age of the product. Keep in mind that this test was only possible due to the substantial amount of the white pigment that was left on the statue, and that the sample had to be destroyed in order to conduct the test. Although these tests were groundbreaking in 1998, today they are outdated. Much of the information can now be discovered using noninvasive absorption spectrometry. Technology is constantly improving to make experiments faster and uncover even more information we thought was possible.

Yet, along the way we have unfortunately destroyed some of the evidence we have left.

Let’s talk colors: Black: This is a carbon-containing substance prepared by charring bones and then grinding them to produce a fine powder.

The Red Family: Madder is a herbaceous plant belonging to the family Rubiaceae. The color is extracted from

the dried and pulverized roots of the Rubia tinctorial L. plant. It’s actually colorless until you boil the roots in a solution of alum and then precipite the solution with soda, grape vine ash, etc. The pigment is a mixture of various anthraqinone compounds including alizarin, purpurin, and pseudopurpurine. Adjusting the proportions of these compounds creates the various shades that range from red to rose to brown. This pigment was incredibly popular during antiquity due to its chemical stability and natural resistance to fading.

Cinnabar produces the classic red you see in ancient art.

In his works, Pliny the Elder refers to this as cinnabris, which comes from the Greek word Kinnibari, meaning “dragon’s blood.” This is a mercuric sulphide found in Istria and Andalusia. Unfortunately, it is not light resistant, and over time, UV light changes the color to a brownish black.

Other red pigments include red ocher and hematite, but these are not as bright as cinnabar.

Yellow/Orange: Yellow ocher was a common mineral also used in Neolithic cave paintings. Another option was realgar, which is a soft crystalline mineral. Today we know it as sulphuric arsenic - a highly poisonous arsenic compound. According to the ancient geographer Strabo, mortality rates were so high for the extraction of sulphuric arsenic that only convicts were employed in the Anatolian mines.

Green: Malachite is a copper carbonate and a semiprecious stone that is pale green. It is the decomposed product of azurite, a blue mineral, which is why azurite will eventually fade to a green color.

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Image: PIXABAY.COM

Blue: The mineral azurite is used to create various shades of blue and was found in the Sinai Peninsula, Italy, and Spain. Because it fades to green over time, a synthetic blue was established in the 4th Egyptian Dynasty (around 26002500 BCE). Egyptian blue is a pulverized glass frit comprised of a compound of lime, quartz-sand, and copper ore.

So, if scholars have this much information about ancient polychromy, then why doesn’t the public know more about it? Why do scholars debate about the extent of polychromy?

There is a wide spectrum of beliefs, ranging from the total acceptance of polychromy to the total rejection the notion.

In the middle are a group of supporters that believe only in blue-red bichromy. It is true that blue and red tend to have the highest resistance to fading over time, but it is still a surprising argument considering the amount of evidence for polychromy. As for those pure white statues that you normally see, we can blame those on mid-14th century Europe and the Renaissance. When Roman and Greek sculptures started resurfacing, artists initially unaware of the full extent of polychromy created the notion of ‘high art’ that continued to persist through the 19th century.

While the works of Michelangelo and his contemporaries are beautiful, there is no excuse for those in the modern era to ignore the evidence for polychromy that has turned

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up on a large scale. It is one thing for Vincenzo Borghini to say, in 1584, that “the power and virtue of the sculptor lie in the effects of the chisel, and if some clumsy oaf in this field uses colors, it denies the very nature of that art,” than an individual in the modern world of today who has access to the wealth of polychromy information that has been discovered.

Special thanks to the Legion of Honor in San Francisco’s exhibit Gods in Color: Polychromy in the Ancient World and the published companions for enlightening me on the more technical aspects of pigment analysis.

A Moral and Scientific Rebuttal to “Reconciling Eugenics for the Sake of Human Survival”

BY KAELIE COLEMAN

Negative eugenics refers to the practice of preventing “undesirable” traits from becoming prevalent within the population. Its use has a sordid, bloody history that runs deep within our own nation. The methods directly mentioned by the article are somatic and germline tools, but traditionally the methods of negative eugenics have been far cruder, focused on limiting the right of reproduction to those deemed worthy, or flatly removing those deemed unworthy from society. In any case, the implementation of negative eugenics in this capacity largely rests on two possibilities, the first being the elimination of the disabled

Image: Google image for reuse

In December of 2016, an article entitled “Reconciling Eugenics for the Sake of Human Survival” was published in Sound Decisions, the bioethics journal at University of Puget Sound. The article argued that in the face of global threats like climate change, resource scarcity, and nuclear warfare, humanity must embrace the use of positive and negative eugenics in order to assure survival through novel problem-solving. The argument was two-fold: cognitive bio-enhancement would provide us with the capability to adapt beyond current solutions, and negative eugenics would relieve the burden imposed by cognitive disabilities.

The writer asserted that these dual actions would allow the human species to evolve past the concerns that currently threaten us. The moral permissibility of these measures rested on the philosophical paradigm of principlism to justify eugenics based on the understanding that cognitive disability is a “harmed condition,” and that anyone “would be better off protected from that reduced quality of life” (1).

Extending this line of reasoning, the writer stated that “if we truly wish to ensure the continuation of our species, we must eliminate any possibilities of genetic predispositions to death, to which mental disabilities belong” (1). While the viability of cognitive enhancement is, in itself, a debated stance, the use of negative eugenics to enhance cognition through the elimination of disabilities is impractical with current technology and would do little to nothing to help humanity. Further, the moral justification is lacking at best.

already living, and the second being the use of prenatal screening to allow selective termination of embryos found to have cognitive disabilities. The first solution doesn’t warrant a response for obvious reasons. The second proves to a be a slightly trickier issue.

Prenatal screening is becoming increasingly common in developed nations, leading to safer pregnancies worldwide.

But even with its increasing popularity, there are limitations to its applicability in terms of cognitive disability. In order to determine if an embryo will develop a cognitive disability, we must first understand where these disabilities arise, and that is a mystery that has yet to be solved in many cases. Recent advances in the field of genomic sequencing suggests that many forms of severe cognitive impairment occur as a result of random single-nucleotide variations or copy-number variations in a genome (2). These events are neither hereditary nor preventable, but simply a byproduct of development of the same sort that has driven evolution since life first came into being (3). By random chance, a single base pair in a single gene is either incorrectly copied

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“Eugenics is the ultimate expression of the medical model as a practice that not only entirely ignores the autonomy of disabled individuals, but also fails to question the good that comes from someone with a different thought process.” or copied twice during DNA replication, leading to a slightly different person than would otherwise have existed. On a very broad scale, these random changes in DNA replication lead to variation within a population, providing alternative means of existing — sometimes beneficial, sometimes harmful, but usually rather neutral. Without random mutation, no novel traits would arise in a population, leaving species stagnant and unable to adjust to their changing environment. If novel problem solving is the goal, eliminating the genetic diversity that arises in the form of disability isn’t a solution. Aside from that, these singular events could feasibly occur anywhere on the genome and are very difficult to find even after birth. Prenatal screening would need to be incredibly thorough in order to catch a mutation this small, requiring an incredible investment for each pregnancy.

Perhaps this investment would be well placed were it not for the utter lack of evidence that disabilities are a negative trait. While some may classify a disability as a harmed state, many within the disabled community would strongly push back against that classification. Arguments that center on saving the disabled from their existence tend to fall under the medical model of disability, a model that portrays their functional reality as a problem that requires a solution. This model focuses predominantly on getting people to a baseline of “typical” functioning and laments anything else as a failure (4). The social model of disability has arisen to challenge the notion that disabilities are inherently harmful, seeking to examine why different means of functioning are stigmatized, and whether these disabilities are truly less desirable, or if they are just harder to fit into societal norms.

To be clear, the question here isn’t whether abortion based on prenatal screening results should be allowed. The choice to continue or end a pregnancy — for any reason, under any circumstance — should be a choice left to the individual carrying, but they also deserve factual, unbiased

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information that can be used to make an informed decision.

Because of our medical system’s ties to the eugenics movement, this lack of bias can be hard to find, and even then, there is the consideration of how difficult it can be to function as a disabled individual without facing prejudice.

Should our joint understanding of disability shift towards the social model, perhaps the choice of whether to raise a disabled child would become less daunting.

The critiques brought up by the social model of disability reveal the underlying issue of arguments that rest on the benefits of eugenics. As a practice, eugenics forces us to place people within a hierarchy of value. By its very nature, eugenics is built on assigning superiority and inferiority and the right of the superior to oppress, and even eliminate, the inferior. In this sense, eugenics is the ultimate expression of the medical model as a practice that not only entirely ignores the autonomy of disabled individuals, but also fails to question the good that comes from someone with a different thought process.

If the purpose of utilizing eugenics is to encourage a greater problem-solving capacity, and in turn a greater ability to resolve global tensions without resorting to violence, then reducing genetic variation is counterintuitive. Practically by definition, disabilities force us to reconsider what was assumed to be granted. The opportunity for diversity of thought should be embraced.

Beyond that, those with cognitive disabilities should not need to prove their worth in terms of avoiding a global catastrophe in order to be treated as humans who deserve respect and autonomy. These are rights inherent to human dignity, indicating that the real issue being faced may not be in the value of the cognitively disabled, but rather the basic sense of empathy that is lacking in any argument advocating for eugenics.

HOW FAR WE’VE COME: AN OVERVIEW OF GENE EDITING PRIOR TO CRISPR

BY LILY RIVIN

Image: PIXABAY.COM

Everyone is raving about CRISPR right now- and with good reason. CRISPR has opened up an entirely new world for gene-editing research, making the process significantly faster, cheaper, easier, and more accessible. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It’s a DNA sequence found in certain bacteria that acts as an “adaptive immune system” (1). When paired with the enzyme Cas9, it can be used to splice DNA and replace it with new sequences (1). First discovered in 1993, it wasn’t successfully used as a gene editing tool until 2013, meaning that many of you reading this were still in high school when it took off (1). But this article isn’t about CRISPR. Twenty years before CRISPR had even been discovered, scientists were researching and utilising other gene editing technologies (2). It was these older gene editing techniques that paved the way for CRISPR. One such technique is RNA interference (RNAi), which was first published by Andrew Fire and Craig Mello in 1998. In 2006, they won a Nobel Prize in Physiology or Medicine for their discovery (3). Simply put, RNAi acts to edit genes by preventing their expression in a cell, also called gene silencing or gene knockdown. In this method, short double-stranded RNA, such as small interfering RNA (siRNA) or microRNA (miRNA), is injected into a cell. An enzyme called Dicer cleaves it into single-stranded siRNA. Then the siRNA binds the protein Argonaute and forms an RNA-induced silencing complex (RISC). RISC then travels along messenger RNA (mRNA), and if the siRNA construct has perfect complementary base pairing with this mRNA, Argonaute will cleave this target sequence. The mRNA is subsequently degraded. Since mRNA is translated to produce proteins, this method allows silencing of gene expression by preventing mRNA from ever producing its protein products (4). The downside of this method is that while creating siRNA constructs is fairly easy, it is difficult

to choose siRNAs that will have a high efficacy of silencing. siRNA knockdowns usually do not reduce protein levels to less than 20% of the original level and these protein levels usually return to baseline within a few weeks, meaning that the gene edits are neither fully effective nor permanent (5). Furthermore, this means that these mutations are not heritable.

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RIGHT: Repair outcomes of a genomic

double strand break for ZFN cleavage

Image: Wikimedia Commons

Another class of gene editing techniques uses nucleases, which are enzymes that cleave DNA and cause double stranded breaks in which both strands of DNA are severed.

There are two methods that fall under this technique: Zinc Finger Nucleases (ZFNs) and TAL Effector Nucleases (TALENS). Both of these are artificially engineered restriction enzymes, or enzymes that cleave DNA, and consist of two main domains: 1) a DNA-binding domain engineered to bind specific sequences of DNA, and 2) a DNA-cleaving domain, made up of a nuclease, which cuts the DNA at the desired location to create double-stranded breaks (6). The host cell then initiates DNA repair, which can either introduce mutations into DNA or incorporate new DNA sequences (6).

Zinc Finger Nucleases became popular in the early 2000s (2). The ZFN DNA-binding domain is made up of a zinc finger protein, named as such because someone thought it looked like a finger (6). Their DNA-cleaving domain, made up of the endonuclease Fok1, cuts the DNA at the desired location, causing double-stranded breaks and initiating one of two DNA repair pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). NHEJ is prone to error, adding insertions or deletions that lead to a knockout gene (7). (Note that while knockdown genes have reduced expression, knockout genes have no expression whatsoever.) On the other hand, homologous recombination (HR) can incorporate slight changes into the newly repaired DNA if a mostly homologous DNA template is introduced into the cell with the ZFNs (7). In other words, if the template DNA is mostly the same as the target region of DNA and has only minor base pair alterations, homologous recombination will incorporate that entire segment, including alterations, into the host

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DNA. Mario Capecchi, Martin Evans, and Oliver Smithies won a Nobel prize in 2007 for their work on targeting genes via homologous recombination in mice embryonic stem cells (8). In fact, the knockout mice strains that we take for granted were first created by these three scientists (8). The benefit of this method is that the mutations occur quickly and are permanent as well as heritable (9). Unfortunately, this method is incredibly expensive and engineering the customized ZFNs that undergo HR can take over 2 years (10).

Transcription Activator-Like (TAL) Effector Nucleases are the other type of nuclease gene editing technique.

Like ZFNs, TALENS are artificially engineered restriction enzymes that include a DNA-binding domain and a DNAcleaving domain. TAL effectors are a protein found in a specific bacteria (11). In TALENS, each DNA binding unit binds one nucleotide, whereas in ZFNs, one unit binds three (12). Because TALENS bind DNA more simply, they are easier to construct (10).

These are only some of the steps of gene editing discoveries and technologies along the way to our present body of knowledge. CRISPR is an incredibly exciting new tool that will be used in countless research papers, genetic modifications, and gene therapies. However, the CRISPR/ Cas9 technology could not have been developed without the knowledge about gene editing that we gained from understanding the mechanisms behind these previous techniques.

GENOCIDE CAN LOOK LIKE MANY THINGS RACE AND GENETICS: A DISCUSSION ON “TRAUMA” MARKS

BY MASON CULBERTSON

Dr. Melvin Rouse Jr., Dr. Juli McGruder, and Dr. Kristen Wilbur, faculty of the University of Puget Sound, gave a talk on racism and the impact of discrimination on the genes of African Americans in the US at the Race & Pedagogy National Conference this fall. Their talk explicated the development of a generational accumulation of illness in African Americans in our society. They provided several examples of programs dedicated to combating this effect, and called on the general medical and scientific community to recognize the persistent need for more lifesaving programs of this nature.

Following this overview, the concept of epigenetics was introduced. In discussing the ways our genes are permanently altered by our experiences in our own lifetimes, the bigger picture came into light. Namely, that genetic mutations can occur within lifetimes and be passed down to offspring. At this point the presentation turned towards a more socio-historic perspective. Dr. Rouse began discussing studies which linked early developmental experiences of animal and human models to changes in their gene expression, or epigenetic changes, that they passed on to their offspring (1, 2).

Dr. McGruder shifted the topic to discussing the ways that trauma can change our epigenetics for generations after the initial trauma. She discussed several studies from the last three decades which document and explore the

Image: PIXABAY.COM

The talk began with Dr. Rouse giving an overview of the genetic and biological processes that occur in the early development of a fetus in the womb. Dr. Rouse detailed the role of our genes in forming phenotypic and behavioral traits of humans. Certain DNA sequences control the expression of specific proteins and enzymes that contribute to forming the unique phenotypic coding of each person.

relationships between trauma from racial discrimination and the health outcomes of these traumas for people (3).

Dr. McGruder explained the ways in which historic sources of trauma (such as the North Atlantic slave trade), in conjunction with modern perceived racism, continue to affect gene expression and the lives of African Americans to this day (4). On average, whites were found to have slightly lower death rates due to heart disease and had higher access to medical and insurance benefits to treat diseases and illnesses. According to the CDC, the decrease in heart disease-related deaths among whites and blacks diverged in the late ’70s, when blacks’ rates plateaued while whites’ rates continue to decrease (5).

The speakers highlighted how multiple systems in our country’s social infrastructure arrange power dynamics

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Image: Google image for reuse

ABOVE: Sanctuary rally #LetThemStay in Melbourne such that African Americans are consistently underserved in medical and pharmaceutical fields (7,8). From 1968 to 2015, the CDC reported an increase in the number of states where the ratio of black-white mortality due to heart disease was greater than one to one, of 16 to 27 (5). These ideas culminate to posit that trauma can indeed affect humans on a genetic level, and that these effects can be passed onto offspring.

Dr. Wilbur ended the talk by discussing some of the programs in action which seek to combat the negative health effects of racism and other socially-based trauma.

One program that stood out to me was the Black Barber Health Outreach program. This program certifies and trains African American Barbers to screen their clients for basic symptoms of cardiac disease, making them able to refer their clients who have been found to be least likely to seek medical help for symptoms (7). This is happening in more than just our own city, and only through discussing these issues and bringing them into the light can we continue to make visible the markings of a traumatic past and learn how to undo the generational damage which resulted.

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In an interview following the talk, Dr. Rouse responded to the question of what he’d like to impart upon people who do not accept the link between social experience and genetics:

“…between 2010 and 2015 about 35-percent of the African American population in the Hilltop neighborhood of Tacoma were forced to move due to increasing rents and decreased affordability …most of these folk continued to work the same jobs, meaning that to actually get to those jobs, in many cases, their commute increased to a significant degree because of said gentrification. There is a significant body of data that shows that increased traffic exposure contributes to poor health and is a significant trigger for a cardiac event” (8).

COVER CONTEST RUNNER-UP

BY MORGAN DIONNE, 9 YEARS-OLD

“Suppose you came across a woman lying on the street with an elephant sitting on her chest. You notice she is short of breath. Shortness of breath can be a symptom of heart problems. In her case, the much more likely cause is the elephant on her chest. For a long time, society put obstacles in the way of women who wanted to enter the sciences. That is the elephant. Until the playing field has been leveled and lingering stereotypes are gone, you can’t even ask the question.”

-Sally Ride, the first American woman in space, when asked if men are simply predisposed to be better at math and science than women.

Here at Elements, five out of eight of our staff members are female. Nine out of the sixteen articles in this issue were written by women. We firmly believe that girls should be encouraged to pursue their interests in STEM (Science, Math, Engineering, and Technology), and were delighted to receive this submission for our cover contest. We applaud Morgan for her contribution to our magazine, and hope that she will continue to develop her interest in the natural world!

-Elements Staff, Fall 2018

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An Evolution of Ethics within the Doctor-Patient Relationship

Image: PIXABAY.COM

BY NOAH BADER-FOURNEY

“Alright, take off your pants, and I’ll check around” These words, for anyone who has ever received a physical from their primary care doctor, usually precede a rather awkward fumbling and prodding before your physician can give your health the “all clear.” However, for those with cultural practices that limit the display of such nudity, to what extent should the doctor be expected to adapt their practices to a patient’s ethics? The answer can be seen in

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the enormous shift within healthcare towards a patient centered model; no longer are patients thought of as only physical bodies, but beings with cultural, religious, and ethical nuances that accompany their identity. This has resulted in the relationship between doctor and patient becoming deeply personal, and based in discussion and collaboration. What does this mean exactly?

Until around the 1960’s, the ethics of Western Medicine were guided according to the Hippocratic Principle (1).

The physician’s moral purview was only to support a patient’s general well being, and certainly did not demand nuance or discussion during treatment. Defining success in terms of the quantity of patients treated, this hardline, pragmatic perspective seemed perfectly reasonable.

However, when physicians hold these views, it results in a loss of patient rights. Of course, your doctor grants you the basic human rights—they aren’t animals—but beyond such considerations, patients’ bodies were viewed as a collection of cells and interconnected organs whose only function was to be diagnosed and treated. Any input offered, if at all, by the patient regarding their treatment plan was to be accepted with a benevolent paternalism and thrown to the wayside (2).

Within the last decade, however, a movement has erupted within healthcare, demanding instead that our system emphasize a patient-centered approach, defined by “greater patient control, reduced physician dominance, and more mutual participation” (2). Today, we are requiring physicians to, on top of their already vast and comprehensive skill set, possess a strong and well-defined ability to create a comfortable and collaborative environment. What has been the catalyst for this movement? And has it led to greater patient control and voice?

I suspect that many readers will have heard of WebMD (an online publisher of diagnostic medical information) and have asked the invisible doctor to diagnose their curious pains and lumps. In fact, it is the very advent of widespread access to physician-quality health care information that has become one the largest catalysts for patient-centered healthcare. Previously, patients would find themselves forced to engage in a relationship wherein the doctor had complete and unrivaled power over the diagnosis, treatment options, and the very information discussed during the appointment. Today, not only are patients able to arrive with an idea of their diagnosis and preferred treatment plan, but are also able to research alternative therapies if the ones provided by their physicians are deemed inappropriate.

This has largely erased the skewed power dynamic between patient and doctor, promoting instead an environment of mutual participation and discussion.

Image: PIXABAY.COM However, access to widespread healthcare information isn’t always beneficial. The possibility of patients misdiagnosing themselves, gleaning misinformation about their condition, or just misinterpreting the science remains likely. In such cases, the physician must spend valuable time correcting these errors, while at the same time respecting the autonomy and intelligence of their patient. And this situation becomes only more difficult when the correction of such errors leads to an inevitable conflict in patient values. For example, think of the doctor who must tell their patient—a Hindu—that they must use a non-vegetarian medication for treatment in the pursuit of greater effectiveness or because it is the only option (3).

While many argue that the doctor-patient relationship should be immune from external, political, and social issues, the reality is just the opposite. Recent cultural movements, especially in the United States, away from archetypal stereotypes towards a culture of individualism and nuance, has influenced this relationship permanently (1). No longer can physicians brush aside the desires and values of the patient without being labeled as unthoughtful or inconsiderate. Today, they are required to engage in a shared decision-making process with the patient, wherein the physician becomes primarily responsible for guiding the medical science while the patient becomes the guide for how to best align their treatment with their values.

It seems that the effort of the physician to accommodate the ethical demands of their patients have, at least quantitatively, succeeded in bettering patient care. In fact, up from 88.4% in 2010, 92.3% of patients report having been involved in care or treatment by their regular doctor

as of 2016 (4). Additionally, it appears that physicians are embracing this culture whole-heartedly as 87.1% of patients, in 2016, felt they were given enough time to discuss and engage with their primary care doctors during consultations, up from 84.8% in 2010. (4) These numbers are shockingly high considering that as of the 1970’s the concept of patient satisfaction was non-existent. In fact, around 73% of patients would be likely to recommend their doctor to others. (5) To ignore the cultural and religious values of their patients is to deny them a piece of their humanity. It is nothing short of a regression towards an archaic, well-intentioned system rooted in paradox, where the doctor may succeed in curing the physical ailment but fail in treating the human being. If the doctor has any intention of truly treating their patient, they must understand what the disease means to the patient: what is means to them in terms of their cultural identity, their socioeconomic status, their family, etc.

I will close with a quote by Paul Kalanithi, M.D. Paul was the chief neurosurgery resident at Stanford just months away from graduation when he was diagnosed with stage IV metastatic lung cancer. He spent his final months reflecting on the very relationship I have examined here today and, I might add, with a far greater eloquence.

“Science may provide the most useful way to organize empirical, reproducible data, but its power to do so is predicated on its inability to grasp the most central aspects of human life: hope, fear, love, hate, beauty, envy, honor, weakness, striving, suffering, virtue” -Paul Kalanithi, When Breath Becomes Air

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Treatment, Non-Adherence and Depression

BY MORGAN WHITE Nonadherence to medical treatment in the general population has been a prominent issue in our society. The term “adherence” is used to describe patients’ continual taking of their prescribed treatment. Adherence is said to be associated with “a greater respect for the patient as an interactive part of the treatment,” and both “adherence” and “compliance” are said to relate to the patient’s relationship with their treatment and the medication advice of their provider (1). Forms of nonadherence differ from person to person. It has been reported that 12% of patients do not fill the prescription they are given at all; another 12% fill the prescription, but do not take any of the actual medication; 29% stop taking medication before it runs out; and 22% take less of the medication than is prescribed on the label (2).

Regardless of the form it takes, nonadherence to medical treatments causes 125,000 deaths annually and 10-25% of hospital and nursing home admissions (2).

Patients’ beliefs about their disorder and their beliefs about medications have a great influence on adherence to treatment, particularly in the case of patients taking antidepressants (1). In one study, a shocking 40-60% of patients could not correctly report what their physicians expected of them 10-80 minutes after they were given the information (3). Over 60% of patients misunderstood the medication directions when interviewed immediately after they visited the physician (3). Patients also reported concerns about their physicians overprescribing medication (4). These statistics emphasize the role of patient understanding and beliefs about medication in adherence rates.

Those with mood disorders are particularly at risk for nonadherence to treatment regimens because their conditions generally yield impaired cognitive focus, energy, and motivation. This can impact the patient’s willingness and ability to follow through with treatment (5). Those with depression are three times more likely to exhibit nonadherence than those without depression (5).

In another study of those with depression, it was found that there was an adherence rate of 40-90% among patients

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“Happy” pills Image: Google images for reuse treated with antidepressants, whereas adherence rate in those with physical disorders ranged from 60-92% (6). This wide range in adherence rates indicates that it is necessary for more research to be conducted on why those taking antidepressants do not adhere to treatment regimens.

This issue applies especially to those experiencing chronic mood disorders, because treatment of this type of disorder is primarily aimed at prevention of relapse and recurrence of disease, rather than treatment of physical symptoms (1). Adherence when referring to those with depression is generally associated with the patient’s ability to apply the recommended health behaviors (including attendance at consolation, taking the appropriate amount of medication for the appropriate amount of time, and engaging in productive healthy activities), as well as the physician’s role in ensuring that adherence takes place (1). Because depression generates a sense of hopelessness, adherence for the sake of long-term prevention seems useless (5).

This feeling of the medication being useless is perpetuated during periods in which the patient feels better and therefore does not see the need to take the medication. The side effects of the antidepressants may also arise before the effect of the drug itself takes place, which may motivate people to avoid antidepressants because the medication is not treating the symptoms of the disorder; it is instead preventing relapse and recurrence (1, 7). The reduction in the cognitive function that is involved in remembering and following through with tasks associated with depression may also contribute to the nonadherence, creating a

Image: PIXABAY.COM

feedback loop where depression causes the nonadherence and nonadherence further exacerbates the depression (2).

The rates of nonadherence are compounded in women with mental illness. In a study looking at the adherence rates of women, it was found that the use of prescription drugs was reported in 59.5% of the participants; out of those who reported using prescription medication, 66.4% of these participants did not adhere to the prescribed regimen.

It is said that men and women differ in their reasons for nonadherence, so the difference may be due to the type of measurement chosen to assess the nonadherence. Men were more likely than women to report forgetting to take their medication (51.8% vs. 49.0%), changing the dosage (21.4% vs. 16.9%), or recovering (14.3% vs. 13.7%). Meanwhile, more women than men reported filling the prescription but not taking the medication (26.2% vs. 19.3%) or developing adverse drug reactions (10.8% vs. 5.4%) (8).

Because there is no set way of measuring adherence to medication regimes, it is also important to discuss the ways in which the studies discussed conduct their measurement in order to create a complete picture of the impact of nonadherence issue. Examples of the methods of measuring adherence include case registers for populations, having patients and their relatives give reports of adherence, counting the “missing� medication, electronic registration of medication given in small boxes, and monitoring serum levels (1). The varying forms of measurement have different sets of pros and cons, and it is therefore difficult to claim that one is superior to the others.

In order to begin the resolution of the issue of gender differences in treatment nonadherence as well as treatment adherence in general, it is necessary to create a standard measurement with which to judge nonadherence. Methods that may improve adherence include having physicians work on making sure that patients understand their diagnosis and that they need to finish the prescriptions completely in order to prevent the emergence of a more serious condition (2, 6). Patients may also be more inclined to adhere to their medication regimes if they feel that they have a say in their treatment as well as if the side effects they may experience are explained to them during the initial explanation of the treatment (3). Physicians may also utilize medication-adherence improving aids and collaboration with patients to figure out how best to incorporate the drugs into the daily routine of the patient.

Adherence may be improved further if physicians assess their patients’ adherence during appointments, explore barriers to adherence, address any concerns patients have about taking medications, and reduce the complexity of medicinal regimen so patients do not get overwhelmed by number of pills they have to take. These practices will help increase adherence rates because patients will feel that they have a positive relationship with their provider and feel that they have control of their conditions.

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Cordyceps, the Truth Behind the Horror

BY FINN KEARNEY

Image: PIXABAY.COM The Zombie Fungus has captured the imagination of many curious students, whether they’ve seen it in nature shows such as Planet Earth, classes here at the University of Puget Sound (like Biology 101), or even the mainstream video game The Last of Us. The parasitic Cordyceps fungus infects its targets through airborne spores and seizes control of its host’s movement before killing them and using their body to propagate itself. The strain featured on Planet Earth forces infected rainforest ants to drag themselves to a high place, usually a branch in the lower canopy, and attach themselves there by clamping down hard with their mandibles. This ensures that when the fruiting body bursts from the host’s head (killing the ant in the process) it will be able to cover as large an area as possible with its spores (1). Traditionally, the belief has been that the fungus infects the host ant’s brain to control motor function, but recent research at Penn State University and the University of Notre Dame suggests that Cordyceps infects muscles instead, creating a vast fungal network within the host independent of the brain (2).

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The researchers used electron microscopy and 3D imaging to observe the ant-infecting Cordyceps and made numerous observations that suggested that the fungus avoided the brain entirely but saturated the rest of the host’s body.

Through a careful examination of the fungal cells within the ants’ heads, the researchers found that the fungal cells congregate outside of the brain but do not actually invade the neural tissue. Additionally, the fungus creates structures around the host’s muscles and in between the muscle fibers which allow it to seize direct control of motor functions, circumventing messages sent from the ant’s brain. These fungal structures are thought to communicate with each other independent of the host’s nervous system to coordinate movement throughout the body (2). One of the seven authors of the research paper, David Hughes, Ph.D., described how “almost like a puppeteer pulling the strings to make a marionette move, the fungus controls the ant’s muscles to manipulate the host’s legs and mandibles” (1). This means that the insect is fully aware as the fungus forces it to climb to a high point before killing it and

“...almost like a puppeteer pulling the strings to make a marionette move, the fungus controls the ant’s muscles to manipulate the host’s legs and mandibles”- David Huges, Ph.D releasing fungal spores.

Thankfully, this parasitic fungus is only known to affect insects, and some strains have even been used in traditional Chinese and Tibetan medicine. Healers collect the fungus from the mountainous regions of Sikkim in northeast India, having observed that livestock consuming the mushrooms grow “very strong and stout.” These Tibetan healers claim that the fungus acts as a tonic for “all illnesses” and improves energy, appetite, stamina, libido, endurance, and sleeping patterns for humans (3). In China, this traditional medicine has a longstanding tradition, but a surge in demand coupled with declining harvests of the fungus have driven prices to exorbitant levels. Today, the value of top quality Cordyceps is higher than the price of gold (4).

Science has not confirmed whether or not the fungus’ healing potential has a sound basis, but several studies have proven that there are some benefits to ingesting the fungus. A Chinese study tested the effect that orally ingested Cordyceps had on endurance and resistance to fatigue in a swim test involving lab mice. The study found that the mice who ingested the medicinal fungus were able to swim significantly longer than those who did not receive the medicine, showing a 30%-73% increase in endurance.

Another study conducted by the Beijing Medical University Sports Research Institute backed up these findings and found that Cordyceps medicine raises cell metabolism of lactic acid and so increases the rate of lactate clearance in subjects’ muscles. They concluded that the medicine would “allow athletes greater anaerobic physical performance” (3).

While Cordyceps has captured our imaginations with a real life zombie horror story, the reality is that while it is deadly to insects, the fungus could actually act as a medicine to humans and other animals. It is hard to imagine that such a horrific and deadly killer could possibly be beneficial, but the fact remains that it is an expensive and sought after medicine with some real scientific benefits behind it. At the very least, it’s clear that humans need not fear being puppeted by the Cordyceps fungus.

ABOVE: An ant with the parasitic Cordyceps growing out of its

head.

Images: google image for resuse UNIVERSITY OF PUGET SOUND | 27

Languages of the Deep: Communication in Marine Organisms

BY KAELA HAMILTON

The study of inter and intra-species communication is constantly uncovering new evidence for the complex interactions that occur between marine organisms. Although there are likely infinite ways in which communication occurs in the vast ocean ecosystems, generally, three modes are utilized: chemical, visual, and auditory. For the purposes of this article, communication will be broadly defined as the act of one organism purposefully sending a signal which a target organism receives and reacts to accordingly.

Chemical communication is the act of one organism releasing a chemical signal to convey some message. Due to the constant movement of water from tides and currents, this technique is most effective at short ranges, and is thus commonly used by shallow-water reef organisms. For example, copepods, a group of small, widely distributed crustaceans, use chemical communication to attract mates. Females spread a hydrodynamic wake packed with pheromones that chemoreceptive males are able to quickly and precisely track. This is an extremely effective method of finding a mate, as the female can increase her communication range by up to 100 times her body size (1).

Chemical communication techniques can also be used for defense and food tracking. The coral Acropora nasuta is damaged by contact with a toxic algae called turtle weed. If the coral senses the chemical signals of the algae nearby, it releases an odor that attracts its symbiotic partner, the goby fish, which trim back the turtle weed and save the coral from damage (2). In this relationship, the coral provides shelter for the gobies, which often become unpalatable to predators after eating the turtle weed.

A slightly more familiar mode, visual communication, involves the functional eyesight of both the signal sender and receiver. This mode is effective in high-light areas of the ocean, such as coastal and surface zones. Visual exchanges can be impaired by low light conditions, such as those found in the deeper zones of the ocean or at nighttime, or in locations with high concentrations of suspended sediments. Because long-distance visualization is less effective in water than on land, most visual communication

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techniques are short-range. One of the most widely recognized examples of this mode is pigmentation change in cephalopods, which use chromatophores under the skin to change their color and texture (3). Cuttlefish and octopuses are able to create complex patterns used for mating rituals (“look how many pretty colors I can make!”) or aggressive standoffs (“don’t come any closer!”).

On the other hand, physical movement can also effectively deliver information. Many cetaceans, such as orcas or

dolphins, spend part of their life cycle grouped together in surface zones, and are capable of using movements of their fins and tails, head shaking, and surface slapping for complex greetings, mating rituals, and signaling aggression (4). An exception to the light restrictive assumptions of the visual mode of communication is bioluminescence, in which an organism produces its own light. Studies have shown that bioluminescence in deep-sea fish is used for sexual selection, species recognition, and shoaling behaviors (5).

Likely the most common mode of marine communication, acoustic signals are utilized by organisms of every marine ecosystem and trophic level. Sound travels five times faster underwater than in air, but is still affected by temperature and pressure gradients. The blue whale, both the largest and loudest animal on the planet, can send its calls up to one thousand miles across open ocean at a pitch so low that it is inaudible to humans (6). Many social cetaceans, such as humpback whales, show group-specific vocalizations, and some, particularly dolphins, develop individualized sounds so that others can recognize their unique call (7).

Contrary to popular belief, non-mammalian marine organisms also utilize auditory communication techniques.

During courtship, seahorses produce sounds by rubbing the bones in their heads together, producing a click that is amplified by their swim bladders (8). Even fish make sounds to communicate, like the midshipman fish, which uses grunts and growls to defend its territory, but hums to potential mates (9).

Although these example organisms are great at demonstrating a particular mode of communication, many marine species utilize more than one mode to communicate, just like us! The ocean is so vast and so little of it is understood, that there are likely many, many more ways in which marine organisms communicate with one another that are unknown or unknowable to humans. The biggest takeaway from this emerging knowledge of marine life is that just because we don’t understand the language of marine animals doesn’t mean that it isn’t infinitely complex and meaningful to those that use it.

Images: PIXABAY.COM

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The Use of Ethical, Renewable Energy Resources in the State of Washington

Washington Net Electricity Generation by Source, Jul. 2018

BY ANNA FRYXLL In the midst of global warming and climate change, it is imperative that we rethink the types of sources from which we get our energy. Transitioning from nonrenewable resources such as fossil fuels to renewable energy sources provides climate change mitigation and is heavily researched today. In Washington state, more electricity is produced than consumed, and the excess electricity is sold to other western states and Canada (1). Washington ranks second in the nation for renewable energy consumption, with 45.3% of its energy consumption coming from renewable sources (1). This article will outline the mechanisms, advantages, and disadvantages of common renewable energy sources, with a focus on the state of Washington’s energy consumption and production.

Hydroelectric power, also known as hydropower, accounts for most of the renewable energy consumption in Washington. Hydroelectricity utilizes kinetic energy from water in rivers as it moves downstream. Turbines and generators then convert the kinetic energy into electricity that empties into the electric grid so that homes and businesses can use it. Hydropower ultimately comes from the sun because the water cycle is powered by solar radiation. Washington accounts for a quarter of the United States’ hydroelectricity, with 74% of its electricity production coming from hydropower (1, Figure 1). In the Columbia River, Washington’s Grand Coulee Dam is the largest dam and hydroelectric contributor in the United States! A disadvantage of hydropower is that it oftentimes involves dams, which disrupt aquatic ecosystems by creating a physical barrier and generating noise pollution; however, hydropower does not always involve dams, and it is a relatively inexpensive technology (2).

Another widespread form of renewable energy is wind turbines, formerly referred to as windmills. Wind turbines function by converting kinetic energy from wind into electricity. Like hydropower, wind energy is a byproduct of solar energy because the revolution of Earth around the

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sun, uneven solar radiation on the globe, and other large scale processes work together to create wind patterns.

Wind energy is largely a preferable form of renewable energy because there is plentiful wind on this planet.

However, wind turbines contribute to noise pollution, and they function best in open areas, which are remote from large cities where electricity is needed the most (2).

Solar panels are perhaps the most practical form of renewable energy in Washington because the eastern side of the state is mostly sunny, and even the cloudiest areas can provide a usable amount of solar energy. According to the Office of Energy Efficiency & Renewable Energy, the “amount of sunlight that strikes the earth’s surface in an hour and a half is enough to handle the entire world’s energy consumption for a full year” (2). One type of solar technology is photovoltaic cells used in solar panels, which absorb energy from sunlight and convert it into electricity.

Electricity can also be generated by heat from the reflection and concentration of sunlight via mirrors (2). Due to markedly increased research in the field, solar panels have exponentially decreased in cost and gained in efficiency, becoming much more widely used.

In all, renewable resources such as wind and solar energy are found everywhere on Earth and thus do not contribute to international arguments surrounding oil. Because renewable energy is a growing industry and is, by definition, a renewable resource, transitioning to sustainable energy is sure to cause economic growth and provide long-term jobs to communities across the globe. With Washington expanding and encouraging the use of these sources of energy, other states will likely be inspired to follow suit.

100 KMH

BY JOSH PI The pen slips in my hand as we make yet another abrupt turn, leaving just enough space for a soccer ball between us and the car ahead. I try to catch the stoplight flash from yellow to red as we round the corner – a quick flash, like the ones we see before a near death experience. It falls out of sight before I can witness the switch. As I try to remove my face from looking like that one emoji: , Alvin appears to be completely unaffected by the fact that he just almost crashed into the compact ahead. I turn to the backseat to find another pair of terrified eyes for solidarity. Everybody is passed out.

As my breathing re-stabilizes, I resume taking notes on Alvin’s response to my question: How would you change the environmental education (EE) system in Malaysia? He responds quickly and without hesitation: “We need more traditional ecological knowledge in EE. We need more anthropologists and a balance in designing textbooks and curricula,” he states. “Rudimentary knowledge of ecology is not enough if we want young Malaysians to want to protect the environment” (1).

Sarawak is one of two Malaysian states on the tropical

EE was formally implemented in Malaysia in 2004 by the Ministry of Education (MoE), 14 years after the U.S. passed the National Environmental Education Act (1990), which outlines EE here (2). In Malaysia, the MoE meant to implement EE across all disciplines including science, geography, and Kajian Tempatan (local studies – a mix of history, Malaysian geography, and civics), meaning that students would learn aspects of EE not only in the natural

Photo credits: Noah Dillon

Whether you call him a conservationist, an ecotourism guide, or an opinionated, loud man who’s not afraid to express his aversion towards non-government organizations, everyone involved in Sarawak conservation seems to recognize Alvin Danker’s name. Growing up in rural communities of Peninsular Malaysia, Danker was exposed to wildlife at a young age. He remembers capturing Siamese Fighting Fish as a child, and watching them duel in his house, amazed by both their beauty and vicious aggression. This appreciation for wildlife is what motivated Danker to begin his career in environmental advocacy and education. As a freelance tour guide and conservation activist, Danker leads trips across Sarawak, educating visitors about the spectacular wildlife in one of the worlds greatest biodiversity hotspots – and the threats they are currently facing of extinction.

island of Borneo in Southeast Asia, bordered by Sabah, Indonesian Kalimantan, and the country of Brunei. Our trip to the island this past summer, led by Professor Peter Wimberger, involved each student selecting and researching a topic about conservation issues in Southeast Asia. I chose to investigate environmental education (EE) in Malaysia.

That is how I found myself in the front seat of a sixteenpassenger van flying down the narrow streets of Sarawak at 110 kilometers per hour, dissecting the heavy accent of a Portuguese-Malaysian environmentalist roaring about the corruption involved with environmental education in Malaysia. SCREECH. Another sudden turn. This time, I caught the light change.

ABOVE: A picture of Alvin Danker and his wife, Christina at a Gawai celebration.

UNIVERSITY OF PUGET SOUND | 31

but also in social science, math, and language (3). Yet, even with this cross-subject implementation, Malaysia is still seen to be at a “functional” level of environmental literacy (2). As a country, Malaysians give less attention to EE compared to other disciplines, especially the STEM fields and English. In fact, many Malaysians feel general apathy towards EE. So why is this the case? With its unique geological history and high level of species endemism (species that exist only in the region), why is it that most Malaysians don’t seek to protect their home? “Perception,” Alvin says. This time, the word leaves his mouth softer, compared to his usual booming voice. “Society is the biggest enemy [to the environment]. Money is a huge driver, and people ignore EE because it does not bring in as much money.” I nod in agreement as I write his words into my notebook. In the ’90s, Southeast Asia experienced a natural forest decline of 1.4% per year (4). Especially vulnerable were the large, dipterocarp trees. You may not have heard of these before; however, you’ve probably seen them… in the form of coffee tables and other home furnishings. Whether for lumber sales or plantation conversion, logging diminishes species richness and population density in these primary forests (4). With the booming market in logging and habitat conversion for oil palm plantations, few Malaysians are involved in conservation and EE. Most are willing to ignore the consequences if the pay is high.

“Logging also prevents solving the problem, because

ABOVE: Visit to Semengoh Wildlife Centre in Kuching, Malaysia.

Photo credits: Lisa Long

32 | ELEMENTS

the most influential people who can change educational policies are involved in logging!” His voice goes back to its usual high volume. In Malaysia, some EE programs actually promote logging and oil palm expansion. Alvin begins a rambling soliloquy on government corruption in the educational system. By the time he finishes, I’ve only scribbled three words: “corruption in education???”

I’m skeptical, but corruption in logging is not new. Lukas Straumann’s Money Logging explores the inside networks of the Asian timber mafia and their hold on national governments (5). Straumann articulates similar arguments to the ones Alvin offers. Alvin, however, connects the issue to its effects on what is taught in the classroom. I wonder if he’s read the book.

Nevertheless, the largest challenge facing EE in Malaysia is not solely a lack of interest. Those who are interested in environmental protection have little resources to effect change. Teachers lack the funding and training to deliver effective programs for students (6). Additionally, those resources that do exist are not effective. This is why Alvin believes in opening the door in curricula design to multiple fields. “We need anthropologists. Not just scientists.” The field of EE cannot be limited to one specific discipline; otherwise, critical components of conservation are left unmentioned. Teachers need to be trained on not only rudimentary knowledge, but they also need to understand the history, economics, and societal views on environmental concerns in the country. On a larger scale, what EE needs is a shift in focus. Citizen engagement is limited in Malaysia and studies have found that students have a lack of authority and ownership to perform responsible environmental behaviors (7). Without a clear understanding of how individual impacts can create change, people fail to develop a sense of responsibility to protect the environment. This is true in both Malaysia and the U.S. We pull over to the right shoulder of the road, but not before crossing into the right lane facing the oncoming traffic. It reminds me of my first day in Sarawak, opening the door to the taxi’s driver seat only to remember that not everyone drives on the right side of the road. “Bathroom break!” Alvin announces. Waking grunts echo throughout the van as I hop out and look ahead to where we’re going.

A line of cars stretch to the riverbank waiting for the same ferry we’re about to board on our way to Serabang. While my classmates begin exiting the van one after the other, I review my notes. I trace every speed bump, illegal turn, and sudden stop in my writing. As I begin to jot down more questions for Alvin, I can’t help but feel relieved that for the next hour, I just might have legible notes.

Green Chemistry: Developing Novel Catalysts for Amide Synthesis

BY ALEX GUZMÁN

Image: google image for reuse

The increasing awareness of environmental health and sustainability is a tremendous opportunity for innovative development in the field of chemistry. The research that I conducted during the summer of 2018 in the lab of Professor Luc Boisvert in the UPS Chemistry Department aimed to create a more sustainable method for the production of pharmaceuticals with the simultaneous investigation of novel chemical processes. A fundamental concept behind the research is “Green Chemistry,” which has proven to be a critical tool in providing innovative solutions by making large scale industrial production of chemicals more sustainable and safe. There are twelve essential principles of green chemistry, which incorporate (among other things): waste reduction, safety, and the use of catalysts (1). The principles of green chemistry have caught the attention of many industries because any inefficiencies and toxic compounds involved in chemical reactions are magnified on the industrial scale. Notably, the pharmaceutical industry is particularly wasteful, as a lot of chemical waste is generated during the synthesis of pharmaceutical drugs. This is not a consequence of the

industry’s lack of initiative. Inefficiencies are mainly due to the complexity of pharmaceutical syntheses, which take an average of twelve steps (compared to 1–3 steps for bulk chemicals), producing undesirable by-products and waste, and using additional solvents (2).

Catalysts, which are added chemicals that speed up a chemical reaction without being consumed, are heavily used throughout the chemical industry to increase efficiency and safety. For example, as shown in Scheme 1, a new catalytic pathway has drastically improved the production of caprolactam, an essential component of nylon that contains an amide functional group, by eliminating all hazardous waste by-products and increasing atom efficiency (the ratio of product mass to reactant mass) in products by 46% (3, 4).

UNIVERSITY OF PUGET SOUND | 33

SCHEME 1

As shown in Scheme 1, amides are composed of a nitrogen atom attached to a double-bonded carbon-oxygen segment.

Amides are commonly found in many pharmaceuticals and biologically-produced chemicals. In fact, every protein and about 30% of pharmaceuticals contain an amide (5, 6).

The current industrial methods of forming amides usually involve the reaction of a carboxylic acid with an amine (Scheme 2).

SCHEME 2

The most successful amide formation catalysts to date are boronic acids, and their reactivity can be linked to their bifunctional attributes (7, 8). However, boronic acid catalysts have not found widespread use in the pharmaceutical industry due to inefficiencies and poor reaction times.

The need to improve amide formation catalysts prompted the Boisvert lab to investigate strongly hydrogen-bonding thiourea catalysts that have demonstrated great potential, especially the bifunctional variant (Scheme 4) (9).

SCHEME 4

Although this reaction is widely used and is very effective at forming amides, the reactants and by-products are toxic and corrosive, which can become very troublesome when these reactions are conducted on an industrial scale.

Alternatively, the catalytic formation of amides directly from a carboxylic acid and an amine is a much more attractive process as it produces water as the only byproduct (Scheme 3).

Over the course of the summer, I made progress in the synthesis of six catalysts: two quinoline thiourea catalysts (compounds 4 and 5), three pyrazine/pyrimidine thiourea catalysts (compounds 1–3), and a novel thiosquaramide catalyst (compound 6) (Scheme 5).

SCHEME 3

34 | ELEMENTS

Captions by ---

SCHEME 5 When working on the synthesis of the target compounds, I typically conducted reactions under reflux (a heating technique), isolated compounds by chromatography purification techniques, and took characterizing data.

Catalysts 1–3 were particularly difficult because the synthesis reactions were highly variable, but I made useful progress on these reactions. Catalysts 4 and 5 were more straightforward: I was able to synthesize the desired products, but isolation proved to be difficult because the reactions formed unexpected by-products. However, near the end of the scheduled research, I isolated compound 5 using a chromatotron (an alternative purification technique – thank you Professor Hanson!). Because literature procedures were available, the synthesis of thiosquaramide (6) was carried out smoothly. After successfully synthesizing catalysts 5 and 6, I conducted amide formation reactions to test their effectiveness by comparing the reaction rates to that of a boron-based catalyst (Figure 1). My research marks

the first time that a thiosquaramide catalyst effectively catalyzed an amide formation reaction.

I found that amide formation using catalysts 5 and 6 proceeded at a rates close to those observed for the boric acid catalyst. These are exciting results because the effectiveness of a simple thiosquaramide suggests a promising future for bifunctional thiosquaramides to be studied in the Boisvert Lab. Working in the Boisvert lab was an engaging and fun experience that required problem-solving and a high level of self-motivation. Over the summer, I gained confidence in a lab environment, and I learned a lot beyond new lab techniques, such as data organization, experiencing the research process, and improving scientific communication. I plan to continue research in the Boisvert lab my senior year.

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Professor Research Interviews

BY ANDREW IZZO

Exercise Science – Passive Stiffness Over the summer of 2018, Dr. Gary McCall and UPS Senior Angus Lamont worked on a way to measure exactly how stiff your sore muscles are. Using a term they call “passive stiffness,” they ran a study to test how resistant their participants’ muscles were to stretching before and after exercise. A key component of their study was looking at delayed-onset muscle soreness, which is the reason that you’re most sore the day after, or even two days after, a hard workout. This was achieved by testing the amount of resistance to passive movements, measured in torque, in the muscles of the participants before and after exercising.

“Can we make a more quantitative measurement of the stiffness?” asks Dr. McCall.

Prior to this research, all measurements of soreness and stiffness had been qualitative, such as a doctor saying “you feel less stiff than last week” or a patient saying “Wow, my left arm is much more sore than my right.” However, quantifying muscle stiffness wasn’t the goal when Dr. McCall’s research started. They initially planned to test how a particular kind of fitness water helped mitigate the impact of delayed-onset muscle soreness– but before they could begin the testing, the drink was discontinued. “We were in the development phase of the passive stiffness testing part, so that became the focus,” Dr. McCall said, “The model was just a means to test the effects of a product.” They then shifted gears to focus on the quantification method, and that has led their research to where it is now. “It’s very fundamental, very basic methodology kind of research,” Dr. McCall said. “It’s validating a tool.” Early results from the study are a little unclear. The participants in the study were of varying ages, fitness levels, and stages of training, so that created variables that have blurred the results. “We want to get through our first layer of analysis,” Dr. McCall said, later mentioning the ways that the methods of this study could be improved by being more intentional with the participant selection. Angus Lamont is continuing this research and data collection, and is working towards his senior thesis with this study.

36 | ELEMENTS

ABOVE: Device used for measuring passive stiffness

Photo credits: Angus lamont

Physics/Biophysics – Splash Cups Dr. Rachel Pepper is studying the science of splashing.

While it may seem that every infant in a bathtub is well on their way to becoming an expert in the subject, the reality is much more complicated. Dr. Pepper is looking at the splashing that is related to seed dispersal for plants with “splash cups.” Splash cups are a seed-dispersal structure that rely on raindrops falling in to them, taking seeds out with the splash. Plants of many sizes have splash cups like this, and they sparked Dr. Pepper’s interest while she was in her PhD program. Working at UPS has allowed her to start active research on this phenomenon, and she has been working on the physics of this method of seed dispersal since 2015. Seeds in these cups can end up meters away from the plant, which is quite a long distance for some of the smaller plants. “My overarching goal is to understand

how they do that” Dr. Pepper said. “What are the physics that lead to such a far dispersal?”

Dr. Pepper is currently working with UPS Senior Tom Daligault on the splash cups of a species of liverwort.

They are dripping water droplets from a custom-built rig into a replica splash cup from a height of 10 centimeters, mimicking a drop of rain falling from an overhanging leaf.

The splashes are filmed with a high speed camera so that the splash can be analyzed down to a fraction of a second.

These splashes are tested in cups with and without “seeds” in them. While the “seeds” are actually very small glass beads, this is still a big step, as most of the previous studies that have looked at this subject have tested splash cups without seeds in them, making their results approximations. Dr. Pepper and her team have found that there is an optimal shape for the splash cup to maximize the distance for seed dispersal. They have also found that it often takes more than one raindrop to get all of the seeds out of a splash cup; this could result in greater variation in the direction of seed dispersal. “The end goal is to understand everything,” Dr. Pepper said. “There’s a ton of stuff we haven’t tried yet.”

The ultimate goal of this research is to write a theory that will predict the best kind of splash cup, accounting for all possible variables. Dr. Pepper is continuing this research, and is looking for more students to be involved in the project.

Physics/Biophysics 2 – Microscopic Sessile FilterFeeders When someone says the phrase “filter feeder,” many people conjure the image of a great blue whale filtering hundreds of gallons of water through their baleen, sieving

BELOW: Still frame of experimental spash

ABOVE: Device used for measuring passive stiffness out tiny crustaceans to eat for lunch. However, like many organisms in this fabulous world of ours, filter feeders come in all shapes and sizes. One extraordinarily small, non-mobile type is a protist called Vorticella, one of many kinds of microscopic sessile filter feeders. Dr. Rachel Pepper studies the factors that influence Vorticella’s feeding ability. “This is the one we work with, but it has implications for all of them” Dr. Pepper explained. “They have this huge ecological role.” Vorticella and others are key players in keeping water clean, act as a significant food source for small animals, and perform an important role in the carbon cycle of their environments.

Vorticella create small feeding currents using cilia, and Dr. Pepper traces these feeding currents using tiny, stained Styrofoam pellets. Dr. Pepper and her team test how they feed positioned at different angles and in different currents. She has been working with Vorticella since earning her PhD. “I got interested in them because of this super-fast contraction that they do,” Dr. Pepper said.

Her interests have since changed to the feeding habits of Vorticella, and have led to results that are moving towards a greater understanding of how these little filter feeders eat. Data from Dr. Pepper’s lab suggest that the angle at which the Vorticella are positioned while feeding is a very important factor, and the influence of angle is different in flowing water versus still water. Dr. Pepper and several of her associates have received a National Science Foundation grant to continue this research, and she is planning to run more experiments to confirm the math behind her predictions. Future work with the project will involve 3D imaging of the feeding patterns, as well as using a specialized underwater microscope to do observations in the field. Olivia Perotti worked with Dr. Pepper over the summer of 2018 on this project, but Dr. Pepper does not have any students working on this project currently, and is looking for students to continue this research with her.

UNIVERSITY OF PUGET SOUND | 37

ABOVE: Vorticella feeding current still shot Photo credits: Dr. Rachel Pepper Organic Chemistry - Liquid Crystals When you’re doing pretty much anything on your phone, the images you’re seeing on the screen are actually the countless liquid crystals that make up the display, changing alignment as electricity dances through them. Liquid crystals are molecules that exist a curious phase of matter that isn’t quite solid and isn’t quite liquid. “It has more order than a liquid, but less order than a solid. And what’s special is that you can change the orientation of the molecules with an electric or magnetic field, and that changes the optical properties,” Dr. Eric Scharrer explained.

Dr. Scharrer and his team have been studying these liquid crystals for years. Dr. Scharrer initially picked up this field of study because he was trying to create research projects for undergraduates in the field of polymer chemistry and kept stumbling across ideas with liquid crystals. This blossomed into a multi-year effort, looking at all sides of liquid crystal chemistry, from the synthesis of new compounds to potential applications for screens. Most liquid crystal displays (LCDs) have a mix of molecules in them with different properties, and these combinations give useful properties to the display. They are also slower than other kinds of displays, such as a plasma screen. Dr. Scharrer and his team are working with a particular phase of liquid crystals, called the biaxial nematic phase, because liquid crystals in this phase can be changed faster than in other phases. That ability makes this phase of liquid crystals more useful for practical applications.

Dr. Scharrer works with a banana-shaped molecule that exists in this liquid crystal phase, and most of his research is focused on making modifications to the chemical structure of this liquid crystal so that it can have practical applications.

“You start with a basic, core structure, then make changes to it, and see how that changes the phase properties,” Dr.

38 | ELEMENTS

Scharrer said. A team of physicists in Italy is working with Dr. Scharrer’s team on the properties of these crystals, combining information from both physics and chemistry to move the project forward. His team is specifically focused on modifying the molecules so that they remain in the liquid crystal phase near room temperature, because like all states of matter, liquid crystals can only exist in certain temperature ranges. Blake Bordokas, Angela Lisovsky and Isabelle Warner worked on research with Dr. Scharrer over the summer of 2018. Blake and Angela are still working with Dr. Scharrer, and Blake is working towards his thesis with this research.

ABOVE: Biaxial nematic phase liquid crystal

Photo credits: Dr. Eric Scharrer’s lab

THE ALLIUM Teary-Eyed

“I don’t know what it is, but I just get SO emotional when I’m around you.”

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COSMOPOLITAN NERD Check ou t t h i s a vo g a d ro to a s t r e c ipe!

: E G R A H C RE- re tips a c f l s e n s o t o r p from ctrons e l e d an

Dirty talk HOT enough to cause combustion!

How t DRO o with P ACI D out

burn

ed

What ’s YO UR micro for th horoscope em 40 | ELEMENTS on th?

getti ng

LY L A U T AC u o y r o Do y r t s i m e h c b a l have r u o ty s u j e ? r e n is sh t r pa

It’s just another Wednesday afternoon in

(name of UPS building)

walk in, sit down, and place my

on the lab bench in front of me. Let’s get started. “Today, we’re

(noun)

going to use the microscopes to examine

(plural noun)

seems to be more

(Adjective)

. The clock chimes once. Time for lab! I

!” says the instructor. Professor

(name of UPS professor)

than usual today, and I can see why. Normally, I feel

(Adjective of emotion)

when we have to use the microscopes, but this lab has me excited. “Microscopy is an important skill in

(branch of science )

(career field)

(plural noun)

,” the professor continues, “and those of you who intend to enter into the field of should pay extra attention.” Everyone begins to put on their personal protective . My lab partner dons her safety goggles while I dig through my backpack, searching for

mine. I can’t find them, but I do manage to locate my lab

(article of clothing)

.

That’s good because safety sure is important!

UNIVERSITY OF PUGET SOUND | 41

Which Life Science Professor Are You?

BY ANNA MARCHAND

1.

How many cups of coffee do you drink per day? a. ∞ b. 6 c. 4 d. 1 e. 7 2.

What is your #1 pet-peeve? a. Excuses b.

Mixing up “less” and “fewer” c.

Being unprepared d.

Cocky attitudes e.

People who don’t pick up their dog’s poop, folks

who recline airplane seats (crushing the person

behind them), “whataboutism” (especially in

politics), big trucks that don’t pull over on a single

lane road to let cars pass them…

3.

Your dream car is a… a.

Doc Brown’s Time Traveling DeLorean b.

Self-driving, pollution free vehicle that also makes waffles c. Volvo d.

A hot air balloon e.

1958 Mercedes 300 SL Roadster convertible 4. a. b. c. d. e.

Your favorite song right now is…

“Shape of You” by Ed Sheeran “Lake Zurich” by Gorillaz “Wild Heart” by Bleachers “Soft Offering” by Hey Rosetta!

“Lucky One” by Alison Krauss

5. a. b. c. d. e.

Your favorite song in college was…

“Highway to Hell” by ACDC “Black” by Pearl Jam “Rez” by Underworld “Sweet Thing” by Van Morrison “Dancer on Thin Ice” by Dire Straits

A = “Doc” Martin, Biology, B = David Andresen, Neuroscience, C = Gregory Johnson, Biology, D = Carrie Woods, Biology, E = Sue Hannaford, Biology

42 | ELEMENTS

6.

What is the title of your critically acclaimed memoir? a.

Finding My Light in Microbiology b.

Do You Like My Pants? c. Hello d.

Searching for Medicine Man e.

I’m a little behind schedule, but…

7.

On a scale from 1-10, how much do you like

Organic Chemistry? (1 = I hate it; 10 = I love it) a. 5 b. 2 c. 7 d. 9 e. 5 8. a. b. c. d. e.

How would your friends describe you?

Too Markish, too often Pretty okay, I guess…

Thoughtful, honest, committed Happy, a good listener, funny, courageous, crazy Reasonably helpful but sarcastic

9.

Who is your celebrity crush? a. Adele b.

Tina Fey c.

Ryan Gosling d.

Ellen Page e.

Neil deGrasse Tyson 10.

Your dream vacation spot is… a.

New Zealand b.

A lake in the woods c. Hawaii d.

Tree house in Southeast Asian rainforest e.

Greek Isles 11.

What is your comfort food? a.

A nice steak with tater-tots b. Pizza c. Mexican d. Cereal e.

Crusty bread, cheese, and white wine

CITATIONS (When Goats Fly) 1.

7.

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2.

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(Scientific Genius)

Olympic Park Associates. 1995. An analysis of the mountain

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Mattson M. 2014. Superior pattern processing is the essence of the evolved human brain. Frontiers in Neuroscience 8(8):

Hutchins M, Stevens V. 1981. Olympic mountain goats.

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4.

Brooke J. 1991. Science and religion: some historical perspectives. Cambridge (UK): Cambridge University Press.

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Wisan, W.L. New Perspectives on Galileo. The University of

265-265.

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McHargue M. 2016. Finding God in the waves: how I lost my

Houston DB, Schreiner EG, Moorhead BB, editors. 1994.

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6.

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National Park Service. 2018. Mountain goat capture and

1.

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Caligula. In: Gods In Color: Painted Sculpture of Classical

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Humanities and Social Science 3, no. 17 (September 2013): 4.

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--

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Carroll D. 2008. Progress and prospects: zinc-finger

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