Issue 2

Elements The Scientific Magazine of the University of Puget Sound

Harned Hall ExposĂŠ How to Make BEER!

What Lives in Your Nalgene?

Issue 2, Fall 2006

Redistricting Utopia: Give the People Back Their Vote

Elements: The Scientific Magazine

Credits

Editor-in-Chief: Marissa Jones Managing Editor: Nick Kiest Copy Editors: Megan Dill-McFarland, Marissa Jones, Wren Williams, Emily Hoke, Matt Loewen Staff Photographers: Nick Kiest, Matt Loewen Layout: Nick Kiest, Megan Dill-McFarland, Matt Loewen, Marissa Jones, Wren Williams, Emily Hoke Image Editing: Nick Kiest Faculty Advisor: Mark Martin Front & Back Cover Photos: Nick Kiest and Matt Loewen Table of Contents Photo: Matt Loewen

Acknowledgments: Elements would like to thank ASUPS, private donors, the Biology Department, the Chemistry Department, the Geology Department, and the Physics Department for their generous donations and because, “All knowledge and wonder (which is the seed of knowledge) is an impression of pleasure in itself.” Well said, Francis Bacon!

We would also like to thank the Office of the President and the Admissions/Alumni Office for purchasing our magazine when they could have picked it up for free outside the SUB; the Media Board for working to get us the technology we need; Alan Thorndike for helping create the cover photo and for tirelessly answering our questions about Harned Hall; Ross Mulhausen for help with the cover photo; Mark Martin for advising and support; and our parents (we don’t mean this in the sappy “they raised us” sense, but in the “they copy edited and supported us on the phone while we went nuts” sense). Thank you, Wikipedia, for being a font of knowledge.

Lastly, we owe a tremendous debt of gratitude to Nick’s food, cookies and Haribo gummy bears, which sustained us throughout the production of this magazine.

Contact & Publishing: email: elements.ups@gmail.com

web: http://clubs.ups.edu/clubs/elements mail: ASUPS - Elements, University of Puget Sound, 1500 N Warner St. #1041, Tacoma, WA 98416 Published by Consolidated Press: 600 S. Spokane St., Seattle, WA 98134.

Letter From The Editor

W

elcome to Elements, the Scientific Magazine of the University of Puget Sound!

We produce this magazine in the hope of sharing science with the masses. This semester, however, the University seems to be doing our job for us.

Between the grand opening of Harned Hall, the addition of the Oppenheimer Café, and E. O. Wilson’s lecture, the science departments have been in the spotlight this fall. Also of particular interest have been the “Science on Display” features of the new science wing, which are designed to highlight and illustrate a few elements of scientific inquiry and discovery. The act of systematically assessing, distilling, and presenting observations as research is what defines science. As Jules Henri Poincaré, a French mathematician, said, “Just as houses are made of stone, so is science made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science.”

Science is constantly on display, be it in the hallways of Harned, the inner-workings of your cells, or in the physics of drinking a cup of coffee. Science is nothing more than the systematic analysis of everyday phenomena. With that in mind, our patron element for this issue is Earth. From breaking ground for Harned Hall, to watching our planet rotate relative to the new Foucault pendulum, Earth is pretty much were it’s at this term.

Sincerely, Marissa Jones Editor-In-Chief

  of the University of Puget Sound

Table of Contents

Credits & Acknowledgments Letter From The Editor Beer Making 101: Behind the Brew

2

Review: The Physics of Superheroes

7

Harned Hall: History and Mysteries

8

Lindsay Anderson

Madeline Gangnes

Elizabeth Becker and Matt Lonsdale

2 4

E. O. Wilson: My Science Hero

10

The Hottest Thing in Tacoma

12

The Science of Music

15

What Lives in Your Nalgene?

18

A Summer of Mapping

20

Redistricting Utopia

22

Biology’s Next Top Model

24

Altering Prey Behavior to Affect Predation Rate

28

Geologic Time, Or Lack Thereof

29

Match the Professor to The Cartoon on Their Door!

29

Marissa Jones Matt Loewen

Keaton Wilson Wren Williams

Michaela Hammer

Walker Lindley and Randy Bentson Will Baur

Wren Williams Matt Loewen

Crossword

30

Elements: The Scientific Magazine

Science in Contex t

Beer Making 101: Behind the Brew Please do not try this in your dorm Lindsay Anderson

A

hh, beer. The alcohol generally accepted as the college drink of choice, the staple of spectator sports everywhere, and as American as the hamburger. Beer is the bringer of good nights, bad mornings, and huge bellies. There is, however, another side to beer that is often overlooked in addition to all its recreational glory. The production and consumption of beer involves a fascinating interdisciplinary blend of organic chemistry, biology, physics, and even psychology. With a history spanning several thousand years, it is perhaps the world’s oldest biotechnology industry. For good or ill, the impact of beer on Western culture is undeniable. Because of this, it is important to pay tribute to the disciplines that brought it to us. This article is my toast to the science of beer.

The Ingredients All beers, ales, and lagers are brewed from the same four ingredients: Water, hops, barley, and yeast. United in the right proportions, these basic components create the magical flavor medley of each popular malted beverage. Each of the ingredients plays a crucial role in the beer making process and contributes to the color, consistency, flavor, and smell of the final product.

Water, the renowned universal solvent, fulfills its role in the beer making process by removing all of the necessary sugars, enzymes, and oils from their sources and suspending them in solution for consumption by yeast, our favorite eukaryotic microbe. Beer was used historically as a sterile substitute to water, because the acohol content prevents the growth of most pathogenic microbes. Ultimately, beer is nothing more than a mixture of plant-flavored, carbonated water and ethanol.

Barley acts as the source of the starches, enzymes, and sugars that are necessary for the fermentation process.

Before it is used in beer making, the barley is malted. This means that the barley seeds are allowed to partially germinate, in order for the seed to begin producing alpha- and beta- amylase. These enzymes are normally used to break down the starch stored in the barley seed to form glucose and other simple sugars. Beer making hijacks both of the enzymes and the starch stored in the seed to create a sugary sweet soup that is then fermented by the yeast. The seeds are heated and dried once partial germination has occurred. The temperature and duration of this process is responsible for both the intensity of the malt flavor and the color of the brew.

Hops, the female flowers of the hop vine, are members of the Cannabaceae family and provide the beer’s characteristic aroma, flavor, and bitter taste. Through boiling, the plant’s alpha acids and essential oils are removed and become part of the solution. The primary chemical components of hops are hydrogenated terpenes such as myrcene and b-pinene, as well as oxygenated compounds of alcohols such as linalool, geraniol, and esters such as geranyl isobutyrate and methyl dec-4-enoate. In the hot water, the alpha-acids isomerize. They change atomic structure, to form soluble iso-alpha-acids which provide the beer with its bitter flavor. As you may expect, the longer the hops are boiled, the more acid is extracted, and the stronger the bitter taste of the beer becomes. Exracting the flower’s essential oils is a bit tricky because of their volatile nature. Boiling is required to extract the oils, but it also causes them to evaporate out of the solution quickly. Therefore, “finishing hops” are added near the end of the brewing process in order to release the flavor and aroma in the oils without boiling them out of the solution.

Brewing Your Own Beer in a CoffeePot

Next, track down these ingredients:

First, find the following equipment:

1) 1.25 cups malted barley. You can use all “base malt,” such as 2-row or pilsner. Base malt provides the sugar content for fermentation. Or use 1 cup of base malt and 1/4 cup specialty malt(s), such as crystal or chocolate malt, which will provide added color and flavor.

Be warned! ELEMENTS has not attempted this recipe. If you are brave enough to test it, be safe and drink responsibly.

1) 2) 3) 4) 5) 6) 7) 8) 9)

An electric drip coffeemaker A warming plate A wooden rolling pin One coffee filter A saucepan, 4 quarts or larger 2 1-quart lidded canning jars 2 6-inch squares of cheesecloth Two rubber bands 1/2 gallon filtered water

2) 5 to 7 hop pellets, which are the cones of the hop plant compressed into little nuggets. Hops add bitterness to the flavor of beer, and help preserve it. The variety is your choice.

3) 1/2 packet of champagne or baker’s yeast.

of the University of Puget Sound Yeast, which produces the alcohol content and most of the carbonation found in beer, is the final component of the brewing process. There are two main species of yeast used in brewing. The first, Saccharomyces cerevisiae , is a top-brewing yeast that is widely used in ale brewing and baking. This yeast is highly aerobic, and thus ferments at the top of the beer where oxygen is more plentiful. In general, Saccharomyces cerevisiae produces sweeter, fruitier ales.

in a coffee pot, or as advanced as the breweries that produce thousands of gallons of beer a day all over the globe.

Consider the this before you begin:

3) Add 2 cups of filtered water to the coffee machine and turn it on. The temperatures of the water-heating chamber and hot plate- (170°F and 150°F respectively) are perfect for brewing! Let the coffeemaker percolate. It will keep the mix at a constant temperature for about an hour before it shuts off.

Matt Loewen

Step 1: The Mash – Making the Sugars

Mash production is the first step of the beer making process. The goal is to create fermentable sugars by extracting the starch and alpha- and beta- amylase from the malted barley. In comThe second species, Saccharomercial as well as home brewing, myces uvarum, is used in lager this process begins by crushing ale fermentation. S. uvarum is a the malted barley just enough microaerophilic bottom-fermentto allow the kernel to be broken ing yeast because that it only up, but not enough to destroy functions well around small the husks that act as filters. The quanities of oxygen. Since there crushed barley is then steeped is less oxygen at the bottom of in water at 150°F. This allows the brewing vat, this species of the alpha- and beta- amylase yeast metabolizes there. Sacenzymes to activate and begin charomyces uvarum produces a breaking down starch into fercrisp taste by fermenting more mentable sugars by cleaving the sugars than the S. cerevisiae. long polysaccharide chains into Both of these species of yeast glucose and other simple sugar metabolize glucose to form the molecules. Because alpha-amyethanol and carbon dioxide bylase is most active between products found in beer.

149°F and 153°F and beta-amylase is most active between The Science of Brewing 126°F and 144°F, the temperaBeer ture during mash production must be carefully monitored to The final product: a golden glass of beer.

So, how do you actually make ensure optimal glucose producbeer from these four common tion. At the end of this process, ingredients? The answer involves taking a bit of advice the result is a sticky sweet liquid that is filtered from the from Goldilocks and making sure you get the temperatures remaining crushed barley. “just right.” The science of brewing beer involves creating an optimal environment for the function of enzymes and Step 2: The Wort – Adding Flavors and the growth of yeast. In order to do this, brewers must Smells follow strict time and temperature guidelines to insure that everything goes right. Beyond these constraints, the brewing The next step in the brewing process is referred to as brewprocess can be as technologically simple as home brewing ing the wort. In this step, the mash extract is brought to

Cleanliness is a huge concern with brewers, because any unwanted microorganisms or residual chemicals can taint the beer. If you’re not careful, you’ll grow molds that will make you very, very sick. Make sure everything you are using is as sanitary as possible.

The twelve step program for home brewing: 1) Measure 1.25 cups of malted barley. Using the rolling pin, gently apply just enough pressure to the grains to crack them.

2) Place the cracked grains into the coffee pot.

4) Strain the liquid through the coffee filter, then place the filter full of grain into the filter basket.

5) Pour the strained liquid back into the water-heating chamber. Add 1 cup of water to the strained liquid in the chamber and turn the machine back on.

6) After the liquid percolates, pour it back into the heating chamber. Repeat this process five times, adding another cup of water each time. Keep a close eye to make sure it does not overflow.

Elements: The Scientific Magazine

a boil and hops are added to the mash. They are brought back to a boil and held there for 90 minutes in order to extract the alpha acids from the hops flowers to give the beer its bitter taste. Near the end of the 90 minutes, a second batch of hops is added to the mix to allow precipitation of the essential oils that give the beer its aroma and flavor.

Wikimedia Commons

The solids must then be removed from the mixture. In commercial brewing this is done by creating a cyclone in the brewing vat. This collects all of the solid particles in the center and causes them to settle to the bottom. The wort is then pumped off and allowed to cool to 68°F for ale brews and 48°F for lager brews.

Step 3: Fermentation – Creating Ethanol

Wikimedia Commons

The fermentation process can begin once the wort has cooled to the proper temperature. Initially the wort is added to a fermentation vat containing live yeast. This portion of the beer making process harnesses the fermentative metabolic capacity of the yeast to convert glucose into energy in the form of ATP and Pyruvate to release ethanol and carbon dioxide as by-products. The fermentation vat is sealed

Raw barley seeds before processing.

Brewing Beer in a Coffeepot, CON’ T. 7) This liquid and bring to ing, add 5 to minutes, then

is the wor t. Place it into the saucepan a rolling boil. Af ter 20 minutes of boil7 hops pellets. Boil for an additional 30 turn of f the burner.

8) Stir until you have a whirlpool. This will pull lef tover sediment into the center of the pot. Carefully empty the wor t into the canning jar, pouring down the side of the jar without splashing.

9) Nex t, you need to bring the temperature of the wor t down to a level where yeasts function well. Do this by setting the saucepan on a counter to cool.

Behold, hops on the vine. during this step to prevent contamination from unwanted microbes. To prevent the container from exploding, a small vent must be left to allow the escape of some of the carbon dioxide gasses released during the fermentation process.

The specific gravity of the wort is taken before fermentation begins and is used to determine when the beer has reached the proper alcohol concentration. This generally takes about two weeks for ales and six weeks for lagers. During this period, the temperature of the beer is carefully maintained at 68°F for ale brews and 48°F for lager brews. Once the proper specific gravity has been achieved, the vats are sealed and the beer is kept under pressure. The beer is cooled to approximately 32°F to insure that all of the yeast has settled to the bottom. Next, the beer is pumped into a different beer tank. Once bottling begins, extra sugar is added to the interior of each individual bottle to reactivate the yeast and produce new carbon dioxide to give the beer its final carbonation.

And now a toast … let us all raise our glasses in honor of one of science’s greatest contributions to Friday nights. To the shades of amber capped with foamy heads that make us lick our lips and say, “Ahh, that’s good stuff.” Here’s to beer!

10) Let it cool until the liquid reaches between 60°F and 70°F. Screw the top on the jar and shake vigorously. This aerates the wor t. Take the top of f the jar and add yeast.

11) The jar is now your fermentation tank. Place a piece of cheesecloth over the top of the jar and secure it with a rubber band. The cheesecloth will keep contaminants out, yet still allow carbon dioxide to escape.

12) Place the jar in a cool, dark place. The sweet liquor will become beer in f ive to seven days. It’s that easy!

of the University of Puget Sound Science in Contex t

Review: The Physics of Superheroes by James Kakalios Madeline Gangnes

ith what force would Superman need to push off of the ground to become airborne? What tensile strength must Spider-Man’s webbing have to support his weight while swinging? Could The Flash’s body support the friction created by the speed at which he runs? Answering these questions requires more than an active imagination and the suspension of one’s disbelief. This looks like a job for physics! With a few diagrams, some formulas, and a “super” professor, students at the University of Minnesota learned how to tackle these questions in a freshman seminar class.

Their professor attempted to make F=ma and all of its formulaic friends fun to learn about and easy to apply, and he seems to have succeeded. The class was structured to teach the fundamentals of physics using models from comic books rather than traditional examples involving masses, springs, and inclined planes. In The Physics of Superheroes, a book that compiles examples used in the seminar, Kakalios reports that the age-old question, “When am I ever going to use this stuff in my real life?” never surfaced in his class. Students were happier using fictional scenarios than concrete examples to explain physics principles.

In the midst of my struggle with Physics 111 last year, my father sent me a copy of The Physics of Superheroes. The book is organized in such a way that it is accessible to readers with little or no background in either physics or comic books. I found it to be extremely clear and engaging. Here are a few examples of how Kakalios explains principles of physics using comic book senarios: forces and

Matt Loewen

W

motion through Superman’s superhuman jumping abilities, gravity through an analysis of the supposed force of gravity on Krypton, impulse and momentum through Spider-Man’s failed rescue of Gwen Stacey, and friction, drag, and sound through the Flash’s super speed. The book is organized from the easiest physics concepts to more advanced ones, but there is a comprehensive index in the back for those in search of examples that reference a particular superhero or comic book.

Kakalios’ book is written with great approachability and humor. Relevant frames from famous comic books are interspersed throughout, and Kakalios provides a list of every comic book he references. He even takes time at the end to answer some frequently ßasked questions about the physics of super heroes. The book contains a short section with recommended related reading, as well as a complete list of all of the physics formulas he uses. Aside from being an extraordinary professor, Kakalios is also well-versed in the history of comic books, and The Physics of Superheroes contains a fascinating introduction detailing the major points of comic book history. There is also a foreword by Lawrence M. Krauss, author of The Physics of Star Trek, which is a similar work that might appeal to those who are Trekkies at heart.

Matt Loewen

Whether you have struggled with physics as much as I have, are a seasoned scientist who wants to see sound scientific principles at work explaining fun examples, or you just love comic books and have always wondered, “Could that happen in real life?,” I highly recommend The Physics of Superheroes. It is an easy, entertaining read by an intelligent scientist who believes that there are other effective methods of explaining physics besides impersonal models.

Madeline learned that even English majors can understand physics.

Note: You can hear an interview with James Kakalios about The Physics of Superheroes at www.npr.org. Search for the title of the book or for James Kakalios’ name. The Comic House will also be holding an event with this book Spring Semester, so keep an eye out if you’re interested!

Kakalios, J. The Physics of Superheroes. New York: Gotham Books; 2005. 384 p.

Elements: The Scientific Magazine

Harned Hall

Harned Hall: History and Mysteries Elizabeth Becker

W

and

Matt Lonsdale

hen Harned Hall was first approved for construction, professors from all departments came forth with plans to integrate science into the building’s structure. Biologists had a juvenile grey whale skeleton they had never found room to display in Thompson. Physicists wanted another chance at building a Foucault Pendulum after a disappointing attempt to hang one in the Thompson elevator shaft. Chemists designed the atomic orbits and protein structures that now adorn the façade, and the Mathematicians contributed the fractal patterns built into the brickwork of the courtyard. Geologists designed a crystal structure from glass that now sits in the courtyard’s center and houses a free trade café.

The whale has been at the university since March of 1973 when it was donated to the Slater Museum. The juvenile male grey whale washed ashore at the mouth of the Columbia River. Healing regions of bone on the lumbar vertebra may indicate that the cause of his death was spinal trauma.

He was 27 feet in length and weighed approximately six tons. Installation of the 270lb skeleton in the main entryway required piece by piece assembly onto steel suspension cables by a team of construction workers and UPS faculty, supervised by whale specialist Albert Shepard.

Matt Loewen

The generous gift of alumn H. C. “Joe” Harned officially turned these visions into reality on September 29, 2006 in the form of 64,788 bricks, 676,000 pounds of steel, and 9,625 square feet of windows. The structure is designed to meet the U.S. Green Building Council’s LEED Silver standards

by using sustainable materials and adhering to stringent environmental guidelines. The completion of this 51,000 square-foot building is the first phase in creating the final Science Center, which will include a renovated Thompson Hall. Due to its speedy constuction over the course of the summer, this treasure trove of science has appeared on campus grounds virtually overnight. Its sudden appearance left many students curious about the origins of Harned’s more memorable aspects.

The Penrose wooden tile base creates a dramatic backdrop for the rotation of the Foucault Pendulum.

Matt Loewen

Matt Loewen

The pendulum rotates above a Penrose tiled base. Thorndike enlisted the help of woodshop supervisor John Ratcliffe for its construction. Penrose, a British mathematician, discovered that two diamond shapes can be combined to completely cover the surface of a circle without leaving any gaps. Only very precise measurements will allow this mathematical pattern to arise on a three-dimensional surface.

Don’t forget to check out the intricate base of the pendulum the next time you drop by.

This mosaic tracks planetary orbits over the Northwest.

Thorndike also worked with James Evans to develop the vertical sundial in the main entrance hall. Called an analemma, this structure uses mirrors to track the position of the sun as a reflected image on a wall. Harned’s analemma faces opposite the pendulum and is visible from 11 a.m. to 1 p.m. every day. As the earth rotates around the sun each year, the angle at which the light strikes the wall changes due to the 23.5º tilt of Earth on its axis. This allows the analemma to show not only the time of day, but also the time of year. If the position of the light is recorded at the same time of day for a year, the resulting shape forms a figure eight, reflecting both the orbit and the rotation of the Earth through time.

A few other mathematical features are hidden in artistic displays throughout the building, particularly in the form of fractals — shapes which appear similar at all scales of magnification. One of the two-story mosaic murals is a nautilus constructed with 4-inch square tiles, which is also

This two-story mosaic depicts the “Golden Ratio.” a formulation of the ‘golden ratio,’ (a logarithmic spiral). A second mosaic depicts the solar system lying over a map of Puget Sound, with none other than our University at its center. The 10,000-square-foot courtyard contains a brick representation of Sierpinski’s Carpet, a fractal pattern which results from one square, divided into nine congruent squares in a 3-by-3 grid.

After the center square is removed, the formula is applied to the eight remaining squares and repeated infinitely.

The aesthetics of Harned Hall also extend to its exterior. At the request of our chemists, structural representations of elements are carved into stone medallions alongside a Greek key motif, found both in classical architecture and natural protein structures. The most significant feature of the new exterior, the entrance, extends far beyond pure aesthetics. The main entrance at Union Avenue features a Celtic representation of the Tree of Life, a symbol significant in nearly every studied culture. With its roots reaching deep into the earth and its branches stretching toward the sky, the Tree of Life dwells in three realms — hell, earth, and heaven — and is a link between the past, present, and future. Trees have long been a symbol of the most basic life-giving force: a renewable source of sustenance, shelter, and fuel. The second panel shows the celestial orbits of Earth and Venus intertwined to form a spirograph. This pattern is created when the relative motion of Earth and Venus are charted, and is called the Dance of the Planets. These depictions represent the desire of Harned’s contributors to unify all of the sciences taught within in a stunning and eye-opening environment, welcoming for every student.

Matt Loewen

Hanging adjacent to the whale within the spiral staircase is the Foucault pendulum, a brainchild of professor Allen Thorndike. The force of gravity and a system of magnets keeps the pendulum in motion after an initial push. Although to viewers the pendulum appears to rotate at 10 degrees an hour, it is actually the earth’s rotation itself that causes the changes. This is why the pendulum does not make a full circle every day. The closer the pendulum is to a pole of the Earth, the more complete the rotation. Despite the complicated physics concepts lying behind the pendulum’s construction, Thorndike says its purpose is simply to give us a spot to, “relax and watch a very soothing continual motion.” He also adds it is also for any “doubters” who may need “daily proof of the earth’s rotation.”

Matt Loewen

of the University of Puget Sound

The Tree of Life adorns the Union Ave. side of Harned Hall.

10

Elements: The Scientific Magazine

Science in Contex t

E. O. Wilson: My Science Hero Marissa Jones

I

n September, UPS was fortunate enough to host one of the most influential biologists of the century. Dr. Edward O. Wilson is the acclaimed author of numerous books, two of which earned him the Pulitzer Prize for General Non-Fiction.

He is also the distinguished recipient of many other prizes, all of which assert that he is pretty much the coolest nauralist of the modern era. Those of us who lined up in front of Schneebeck that night, one hour and fifteen minutes before his lecture began, knew: This was big.

tween social behavior and evolutionary history. The genetic leash defines a set of behaviors that have helped a species survive over time and therefore are genetically present in the current-day population.

Matt Loewen

While this theory was widely accepted as applicable to organisms such as ants, elephants, and chimpanzees, it did not go over so smoothly when applied to Homo sapiens.

In the last chapter of his book, Wilson extended his theory to human behavior, suggesting that genetics contributes to human nature. Today, this idea is widely embraced by both I was able to atbiologists and tend a freshmen psychologist s, seminar (don’t but at the time, we all miss it was hotly conthose days?) tested by both with Professor liberals and conDavid Groge servatives who who had invited preferred the Dr. Wilson to tabula rasa , or participate in blank slate, view a private quesof the human tion and answer mind. The Wilsession with his son opposition class. His admovement was vising seminar, spearheaded by Science and a “half dozen” Equality, invesof his Harvard tigates the ways colleagues who in which “public believed that debates regardone’s thoughts, ing the rights behavior, and and privileges efforts for surof African-Amervival are the E. O. Wilson, Pulitzer Prize winning author, speaks at the University of Puget Sound. icans and imresult of society migrant groups and personal have been influenced by scientific controversies regarding experience alone and are not innately influenced or defined group differences in intellectual and moral capacity.” In by a “genetic leash.” Wilson’s book gave some evidence on this class, Wilson did not discuss his books, The Future of behalf of “nature” in the time-honored debate of nature Life or The Creation, as he did in his lecture. Instead, he versus nurture, and the ensuing intellectual battle was one focused on observations he had made in the past. of the most heated of the century.

In 1971, Wilson published Sociobiology, a book that proposed evolutionary and genetic explanations for the social behavior of animals. Wilson described Sociobiology as his “magnum opus,” by which he means, “When dropped from a three-story building, it could kill a man.” Most of the book focused on ants and other colonial beings of the natural world that perform “altruistic” behavior, such as rearing another’s young or dividing labor tasks among individuals who do not directly benefit from the jobs. Wilson proposed that these behaviors benefit the colony or species as a whole and are therefore encouraged by natural selection and are more likely to continue in future generations. Wilson coined the term “genetic leash” to describe the relationship be-

It seems that the importance and success of a scientific theory is directly proportional to the amount of controversy it generates (case-in-point: evolution). In reaction to the last chapter of Sociobiology and the entire content of his Pulitzer Prize winning book, On Human Nature (1979), Wilson’s opponents accused him of racism, misogyny, and eugenics. At a conference in 1978, the International Committee Against Racism, which was associated with a socialist group called Science for the People, poured a pitcher of ice water over Wilson’s head, chanting, “Wilson, you’re all wet!”

Wilson informed us that he is possibly the only scientist who had been physically attacked over his ideas. “I’m rather proud of that,” he reflected.

of the University of Puget Sound Wait. Right now you might be a little skeptical about my choice of “Science Hero.” A racist? A misogynist? Well, during Professor Droge’s class, Wilson was able to address some of the issues he raised in Sociobiology.

Wilson explained that the racial extrapolations of sociobiology are “unfounded.” He asserted that there is no evidence for racial inferiority other than those due to presiding social restraints of a society. “If you kept someone in a mud hovel with no sanitation, they would show up with a lower IQ than someone raised in a middle class or upper middle class environment,” he explained. Wilson stated that, “The people who tried to expand biology into public policy were not qualified to do so.” He expressed the belief that biology and society should not be completely divided enterprises, but that the integration of the two must be done in a fair and delicate manner. He explained that, “What we need is a better definition of science: what it can do, how it relates in a particular time, what it is. The only way we can do this is in a democratic society.”

Another point of clarification is in the definition of both evolution and sociobiology. An individual organism does not evolve during its lifetime – populations evolve over the course of many generations. Sociobiology is based on evolution, and therefore would not explain why your roommate feels the need to stockpile top ramen in the closet, but might provide insight into the basis for the general human inclination to store food, which would have aided survival during times of famine. Sociobiology is a reflection of the modern biological inclination to look at a trait or a behavior and ask, “Hey, I wonder if that has evolutionary adaptive value?” The opponents of Wilson’s theory succeeded in giving the term “sociobiology” a sufficiently negative stigma when applied to humans, and so it is also referred to as Darwinian or evolutionary psychology, even though these terms are misleading.

During the seminar, Wilson provided a few examples of true sociobiology. For example, people generally agree that incest is wrong. Freud certainly had some interesting things to say on the subject, but he was not the only one. As it turns out, there are biological reasons to avoid copulating with siblings. Wilson explained that people are “bags of recessive traits” – every person is carrying approximately five debilitating to lethal disorders that remain dormant in their genome. The chance of encountering similar genetic liabilities when copulating with a brother or sister is sufficiently high to give such a union a “Darwinian disadvantage.” Not to mention, it is kind of creepy.

In order to empirically test whether there is a biological mechanism for preventing incest, researchers investigated families in India and China that purchased wives for their sons as infants and raised the girl as part of their family.

Research shows that exposure to one another during the first thirty months of life eliminates the possibility of sexual desire between the future husband and wife. This is true not only between similarly aged individuals, but for people of all ages. Therefore, we would expect that if Oedipus had

11 lived closely with his mother the first months of his life, the whole debacle would never have occurred.

Wilson recently dined with Bill and Melinda Gates at their home outside of Seattle. He pointed out that Gates’ home was an excellent example of what people look for in a living space. Their estate is on a hill overlooking the Sound on one side with open space on the other. He directed our imaginations back to the African savannah. Living in a high place allows the occupants to see around them, offering a better chance of seeing predators, warding off enemy attacks, and spotting prey. Open space offers the same visual security. A water source ensures that one’s clan is less susceptible to drought. A hill surrounded by open space and close to water was a pretty promising environment to our Pleistocene relatives. Now think back to the great palaces and castles of the middle ages, the modern ages, and even to some extent, this campus – the same trends appear. When you imagine where you would love to build a house, does it include these same elements?

Wilson’s theory suggests that, while these types of locations are culturally valued, they originated from the fact that they were evolutionary keys to security and success, and are somehow hardwired as a preference in our brains.

One of the hot topics for discussion in today’s society is the disparity between men and women’s involvement and performance in math and science. As a scientist, he could not say whether there is a difference between men and women and their capacities in the sciences since there was not sufficient evidence. He did, however, bring up two points: The first was that the gap between men and women who are involved in math and science is closing rapidly. The second was that we are seeing a divide, not in total numbers involved in math and science, but in the preferred fields of study for men and women. In general, we have seen a major increase in the number of female ecologists. Wilson explained that women seemed to prefer studying how a system works on its own, while men use a more reductivist approach, wondering instead what a particular system offers, how it can be changed, and what benefits it may afford. “It is not that women miss the point in studying particle physics and men miss the point in studying ecosystems,” Wilson explained, “The point is that we’re not getting all the talent that’s out there.”

Although my admiration of Dr. Wilson began with his work as an advocate for conservation (I fall into the camp of female ecologists he mentioned), what I admire most about Dr. Wilson is his understanding of the need to integrate society and science.

Sociobiology is the quintessential example of combining disciplines in a way that enhances our ability to interpret the world. As I understand it, this sort of amalgamation of subjects is a lot like stacking and compounding lenses in microscopes or telescopes, allowing people to observe common phenomena in new ways.

Whether you agree with sociobiology or would like to pour some ice water on Dr. Wilson’s head, these reactions are central to advancing our of understanding science and the world in which we live.

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Elements: The Scientific Magazine

Harned Hall

The Hottest Thing in Tacoma A review of the new science toys of Harned Hall Matt Loewen

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his fall Harned Hall opened its doors to the joy of all Thompson Hall occupants. Everyone admired the elegant corridors, three-story pendulum, brightly colored mosaics, gazebo, and other flashy accessories. Just a tad less noticeable than the signature “Science on Display” items are the new lab spaces complete with projectors, chairs, and unstained counters (at least for a little while). Unnoticed in all of these developments is the addition of several new instruments that have changed the way UPS faculty and students conduct research.

The most amazing thing about this process is the extreme temperature of the plasma: the ICP typically runs at temperatures of 6800-10,000K, which is 11,780-17,540°F! “At 7000K they’re [the atoms] excited. You’d be excited too,” explained Geology Professor Jeff Tepper, who operates the ICP and teaches environmental geochemistry. “It’s probably the hottest thing in Tacoma.” This is no exaggeration. No industrial processes in Tacoma need to heat things to such high temperatures, and neither PLU, UW Tacoma, nor TCC has such an instrument. Many people remark on how nice

Matt Loewen

The most notable additions include the Geology Department’s ICP-OES, the Chemistry Department’s NMR, and the Biology Department’s TEM. These new items are literally changing entire aspects of research at UPS, with increased efficiency, accuracy and new subjects accessible for exploration. Geology students no longer have to wait overnight for samples to churn slowly through the XRF. Nor must they patiently wait for the AA to examine one element at a time (if it even worked at all). Students in organic chemistry will no longer have to wait in long lines to use the elusive NMR, but instead will set up multiple samples and run them from the comfort of a computer at home. Biology students can enter the world of digital imagery and abandon the tedious work of darkroom photo development of electron micrographs.

The ICP-OES (Inductively Coupled Plasma-Optical Emission Spectrometer) is used to measure the abundances of different elements in water samples, dissolved rock samples (fused and dissolved in water), or any other material that can be put into solution. It can simultaneously measure over seventy elements, although analyzing more elements requires making up more complex standard solutions.

The instrument works by injecting the sample into superheated argon plasma and then recording the spectrum of light emitted. As the atoms in the sample are heated, they become excited, sending electrons to higher energy levels.

When these electrons drop back to their ground state, they emit photons of distinctive wavelengths. Detecting this emitted light can provide a fingerprint of the exact composition and abundance of different elements.

The ICP plasma flame analyzing trace elements in a water sample. The flame is approximately 7000 Kelvin.

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Matt Loewen

of the University of Puget Sound

The NMR autoinjector will now allow students to run spectra from any network computer.

Harned Hall looks, but few realize that it truly is the hottest thing in Tacoma.

For students in geochemistry, this instrument renders the AA (Atomic Absorption spectrometer) obsolete. This came just in time too, since last year the AA almost never worked, severely limiting Christian Manthei (class of 2006) in his senior thesis research on heavy metals in local lakes from the ASARCO smelter. Now he is back at UPS reexamining lake sediment cores to get better data.

The ICP has lower detection limits and can analyze more elements than the AA. This will allow students in the geochemistry class to pursue individual projects. In addition, students investigating rock chemistry will be able to run their samples on the ICP as well. Formerly rocks had to be melted into glass discs, which were then polished by hand for analysis with the XRF (X-Ray Fluorescence spectrometer).

This process took considerable time, usually running a set of samples took all night with the XRF spending an hour or more on each sample. Now students looking at rock chemistry can simply dissolve the glass in acid and run it through the ICP. This method is faster and detects lower element concentrations.

The ICP may be the hottest thing in Tacoma, but the chemistry department, not to be outdone, is making the laboratory three floors above the ICP one of the coldest spots in

Tacoma. Early in the semester tanks of liquid nitrogen lined the shiny new halls of Harned. The supercooled fluids were used to get the large superconducting magnets of the NMR (Nuclear Magnetic Resonance spectrometer) down to 92K, -293.8°F, but that was just the first step. Next, even colder liquid helium was added in order to cool the machine down to the required 4K for operation.

All that coolness delights the organic chemistry students, because they get to dive into a brand new NMR. This machine features vast improvements over the department’s old machine. Due to an increase in the magnetic field from 7 to 9.3 teslas, detection levels for photons increase from 300 MHz to 400 MHz. The magnet that produces this field weighs 1150 lbs. In addition to the gigantic magnet, the machine comes with pneumatically operated anti-vibration legs and a 9.5 foot long tripod boom to hold the machine during installation.

Installing the system proved quite the challenge. The NMR was first assembled in Massachusetts, disassembled, and then brought to UPS by a special moving crew. The tripod boom barely fit into Harned’s elevator, and only made it to the third floor through the efforts of some especially strong construction crew members. If the boom was just a few inches longer it would not have fit, and a crane would have had to lift it in through a knocked out window.

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Elements: The Scientific Magazine

Wayne Rickoll and Patrick Moyle

The resolution of the scope is quite shocking as well. It can image down to three angstroms. To visualize this, Rickoll explained that one angstrom is the change in water level of a 50 x 20 meter swimming pool caused by a fly landing on the water. To help keep this precision, the new building was especially designed for the scopes, with a separate foundation built for the University’s Scanning Electron Microscope and TEM.

An electron micrograph of the mombo virus. The yellow bar is 100nm long.

Even with all the flashy new hardware, what students will appreciate most is the increased ease of use. Gone are the days of students waiting in long lines late into the night for precious use of the slow moving NMR. Samples that took an hour to run on the old machine now only take 15 minutes.

Even more exciting, with new software students will not even need to be in Harned to run their samples. A 24-sample auto sampler can be remotely operated over the Internet from any computer. Now late at night students can casually click a button from the comfort of home and run samples.

The danger is that it will be easier for students to mess things up without close supervision.

If all that equipment was not enough, the department also has a new microtome, a device that cuts super thin sections to use in the TEM. The sections must be 70-90 nanometers to work in the machine. The new, better controlled microtome built by Leica is the “Mercedes of microtomes” as Rickoll explained. It is the second newest Leica model available.

Harned’s praises have been sung high and low throughout the fall as students and professors settle into the new space. These three major new pieces of equipment, however, are what truly change the capabilities of the UPS science departments. In the following years, Harned will become a well lived-in facility and walking down its halls will feel second nature. The data coming out of these machines, however, will continue to produce new and exciting research for years to come as professors, and students uncover some of the many mysteries of science.

The digital camera, with an array of 1024 x 1024 pixels, allows TEM users to take photos directly without a long darkroom developing process. For Rickoll’s course, he will no longer have to devote precious class time to teaching photo development, but instead can focus on the finer aspects of electron microscopy. Taking the pictures directly as digital files will also allow easier collaboration with researchers at other universities. This will be especially useful for Rickoll who collaborates with Dr. Dan Kiehart of Duke University on fruit fly development research.

Matt Loewen

Biology’s new prize of Harned Hall is not as flashy as a super cool or super hot machine, but it does take electron microscopy out of the dark ages, literally. With the old TEM (transmission electron microscope), photos were taken on film and developed in a darkroom in Thompson. The darkroom has moved to Harned, but the need for it has not. To seal the a deal, Professor Wayne Rickoll obtained a 15 year old TEM replacement for the department’s 25 year old TEM. With this machine, worth about $350,000, comes a $40,000 digital camera. All this, including installation, however, only cost the school about $55,000.

The tower of the transmission electron microscope.

of the University of Puget Sound

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Science in Contex t

The Science of Music What do Outkast’s Hey Ya, Futureman, and Ravel’s String Quartet in F Major have in common?

Keaton Wilson

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or many, listening to music is a relaxing activity, be it studying to Mozart, or setting the mood for a dinner party with some hot jazz. Music is what it makes us feel, what it makes us think, or the image of a particular lifestyle that it gives us. What many people do not consider is the science at work behind the music we hear. The experience of music is created by a complex amalgam of physics, mathematics, and biology.

Most simply defined, music is organized sound. The pitch of a single note is dependent on its frequency, or the spacing between the sound waves. A higher note has a higher frequency, and a lower note has a lower frequency, thus producing an almost infinite range of possible pitches, both within and outside the realm of human hearing. Humans hear within a range of 20 and 17,000 hertz, or the measure of how many waves go by in a second. Because of these near infinite possibilities of pitch, different tuning systems have arisen throughout history to define sets of these pitches as the “right” set.

Many people do not give a second thought to what they hear on the radio as being just one of many sets of pitches, which is due to our culture’s Western music bias. This is an interesting concept — what sounds “good” to our ears is merely a product of our musical and cultural conditioning, and not a function of any kind of system. Even within Western music there has been a discrepancy about the wrong and right ways of tuning systems.

the performer were playing incorrect notes, but it is just a system of pitch to which our ears are not accustomed.

Another tuning system is called Pythagorean tuning — named after the same man who described the well-known Pythagorean Theorem back in the 6th Century B.C. This is the oldest system of tuning, and is based on forming the pitches into perfect fifths, which have frequencies of 3:2. So, if you have a starting pitch of 300 hertz, then a fifth above that would have a frequency of 200 hertz, and so on. Consequently, this interval of a perfect fifth also sounds very stable, along with the octave previously discussed. This tuning system would also sound very dissonant to our equal tempered ears, and there are various harmonic problems that occur with this tuning because it does not break the octave into twelve equal parts. For more information on tuning, temperament, and the math involved, check out the flash animations on the helpful website, www.musemath.com.

However in tune we are with our standard Western system, there is one oddball that does not fit in with the traditional rules of tuning, and yet sounds completely resonant to our ears. A set of specific pitches within a tuning system is defined as a scale. One specific set of pitches, the blues scale, a series of seven notes, is found ingrained in almost all popular music today, but has very old roots. Although the true origin of this scale remains a mystery, it most likely traces its roots from a variety of cultures, including that of Africa, the Caribbean, and the Cajun Quarter of New Orleans, the birthplace

This is by no means the only tuning system, and not even the only type of equal temperament. Because equal temperament is defined as breaking an interval into equal frequency ratios, there are a multitude of options to explore.

In fact, some Arabian music is based on the same concept of dividing the octave, except that it is divided into 24 equal frequency ratios instead of 12. To a Western listener, this system would seem very different, and possibly even as if

Matt Loewen

The most common system of tuning in Western music is twelve-tone equal temperament, which divides a pitch and its octave (a pitch with a frequency of half of the original note) into equal frequency ratios. In the case of most Western music, we break this octave into twelve parts or intervals (the distance between two notes), with the baseline note being a pitch with a frequency of 440 hertz. This is the standard frequency that is used throughout the world today, and the system that we recognize intuitively as the “right” sound.

Piano scales use octaves that are divided into 12 intervals.

Elements: The Scientific Magazine

Matt Loewen

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of jazz. This scale sounds “good” to our ears, but has a large degree of inherent dissonance in it. Although the scale is replicable on instruments that cannot quickly modulate pitch (like a piano), its true form is best suited for the human voice, or another instrument which can change pitch in small degrees. The reason that this works is because the scale has what is known as a “blue third,” or scale degree that lies somewhere between the major third (with a pitch of a 5:4 ratio in frequency from the starting pitch), and the minor third (with a pitch of a 6:5 ratio in frequency from the starting pitch). This is a very strange phenomenon, but one that comes to the human voice quite naturally. This is another example of how “what sounds good” is a combination of mathematical differences and cultural conditioning.

Pitch is only one of the many aspects of music that draw from the sciences. Another crucial component of music is its temporal orientation, or the pattern in which music is repeated over time. We have all experienced the sensation of hearing music that makes us move in some way, be it tapping our feet, bobbing our heads, or even dancing, which is a instinctive manifestation of feeling the “beat.” A song that many people find so irresistible is a classic example of 4/4, one of the most common time signatures. This means that every bar of written music gets four beats to a measure, which divides the song into repeating patterns, and a quarter note (1/4 of the total four beats) gets one count. There are almost endless examples of songs in 4/4, but here are a few you might recognize: John Mayer’s No Such Thing, The Beatles’ She Loves You and Beck’s E-Pro. Try counting to four in repeating patterns along with the music, and you will feel how natural this sounds.

Of course, as music has progressed we have grown increasingly complex in our use of meter. Many pieces of music are arranged into odd groupings of beats which many times are completely baffling to listeners, but at times are almost unnoticeable to the untrained ear.

One great example of a meter that is obviously different is Dave Brubeck and Paul Desmond’s Take Five. Although the melody is catchy, if you try, you will find it very unnatural to try to tap your foot to this tune. This is because, as the name suggests, the song is in 5/4, with groupings of five quarter note beats per measure. Try counting to five the next time you listen to this song, and you will be surprised at how nicely it works out. Although 5/4 seems like a strange meter, it really is not a new meteric trick. The Impressionistic French composers Maurice Ravel and Claude Debussy both utilized this time signature. Ravel uses 5/4 in the fourth movement of his String Quartet in F Major and Debussy in his Prelude Les sons et les parfums tournent dans l’air du soir. The use of this asymmetrical time signature goes back even further into history. In fact, the earliest example of notated music of the Western world, The First Delphic Hymn, is notated in 5/8 (where there are five beats to a measure, but the eighth note instead of quarter note represents one beat), and dates back to approximately 138 B.C. There are many more modern examples of music in strange time signatures. One great illustration is Hey Ya by Outkast. On first listen, this song sounds just like any other type of infectious hip-hop tune. Strangely enough, however, the song is in 11/4, a time signature almost never used

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of the University of Puget Sound

There are a select few who try to combine the art of science and music into one cohesive sound. One such individual is Roy Wilfred Wooten, better known to the rest of the world simply as Futureman. Although Futureman has been involved in a variety of musical groups as well as solo exhibitions, his most well known foray has been with the technically powerful, sonically superb, boundry pushing jazz/fusion/bluegrass group Béla Fleck and the Flecktones.

Not only is the group full of musicians of the highest caliber, but they continue to bridge gaps in both the art of music, and the science of music.

While Béla Fleck and the Flecktones are known for their use of complex meters, like bars of 9/8 intermixed with bars of 4/4, it is Futureman who is pushing the boundaries of musical science. An inventor, composer, and general Renaissance man, Futureman has applied his skills to a variety of fields, including invention. Perhaps his best known creation, the SynthAxe Drumitar, is a truly one-of-a-kind instrument.

His creation is a homemade variant of a SynthAxe, which is a guitar-like instrument created in the ‘80s and based on a totally electronic concept of a guitar. Futureman rewired and modified the instrument to tie into a series of drum controllers, creating an electronic instrument never before seen, and a real wonder of modern music technology.

We have seen an increased use of technology in music with the rise of the electronic age. In 1983, “MIDI”, or Musical Instrument Data Interface was introduced to the world.

This technology allows sound and information specific to that sound to be transmitted between various devices electronically. MIDI is a complex system of messaging, which contains a variety of factors such a the velocity with which a note is struck (which normally controls the volume) and the time frame between when a note is struck and when it is released. Also, in some more complex instruments, the modifications made to the note during the time it is held down, (sometimes called aftertouch) are recorded. This entire signal is sent electronically to another device, and can be further modified, or even translated back into sound to be amplified and heard. In the case of Futureman, the SynthAxe Drumitar is just a controller connected to a series of five synthesizers, as well as a hard drive for an almost limitless array of sounds.

One of the lesser known instruments that Futureman has created is one that will be appreciated by chemists everywhere. Fondly dubbed the “RoyEl,” this instrument is based on the on the periodic table of elements. As shown on the Béla Fleck and the Flecktones DVD, Live at the Quick, the periodic table is laid out in a keyboard-like fashion, and the keys are labeled with each periodic symbol, producing a sound when they are struck. This invention is an amazing example of what a combination of music, math, electronics

and physics can do. To determine the pitch of each note, each element’s atomic number is multiplied by a power of the golden ratio until a value is reached that corresponds to a frequency that can be heard by human ears.

In this tuning system, intervals are broken into chunks represented by the golden ratio, an irrational number expressed as (1+√5)/2, instead of the traditional octave. The golden ratio is a concept that has been around for 2,400 years, and was first described in the mathematician Euclid’s Elements. It is described by Euclid as “sectioning a line in mean and extreme ratio, so as the whole line is to the greater segment, so is the greater to the less.” This ratio is a common mathematical theme that corresponds to many different fields and is expressed in art, sculpture, architecture, the human body, and music.

Futureman is a prime example of a new kind of musician in our modern world today — a pioneer who dabbles in both science and music and ties them together to produce a very unique, very personal expression of art. In many cases, we tend to think that the arts and science are two mutually exclusive fields, often at odds with each other. The truth is that in combining the two, both are better for it. Science has helped music develop into a global system of communication, as well as helped musicians continue to experiment and work their art. Music on the other hand, has helped science by giving a tactile example of physics and mathematics at work, as well as provide a laboratory for a variety of technological and acoustical systems to be worked out and experimented with. As we learn more about the nature of sound as a communication tool, we learn more interesting ways to adapt it, as well as a better understanding of the world around us — the goal of all science.

Matt Loewen

by recording artists of any genre, be it classical, jazz or hip-hop. Take a listen next time you pop The Love Below into your CD player. For a comprehensive list of songs in unusual time signatures, check out http://en.wikipedia.org/ wiki/List_of_works_in_irregular_time_signatures.

Basses are tuned to pitches in the Western Style.

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Elements: The Scientific Magazine

Research Repor t

What Lives in Your Nalgene?

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f you’ve ever heard someone justify not washing a cup or dish because “it just had water in it,” think again. From a microbiological perspective, there is nothing “just” about water at all. The students in Mark Martin’s Microbiology class recently realized this after taking swab samples of their Nalgenes. Based on the bacteria that grew on our agar plates that week, it is safe to say that most people have not been washing their water bottles.

“What is growing in my water,” you ask?

Well, it depends on what you had to eat that day, plus what is already dwelling in the warm, nutrient-rich environs of your mouth. Keep in mind that bacteria are always growing on you. In fact, your body contains more independent bacterial cells than the eukaryotic cells we identify as human tissues! Bacteria are essential to many of our bodily processes, such as nutrient uptake during digestion, so it should come as no great shock that you have your own personal ecosystem residing in your mouth. Plus, every time you eat, you ingest more miniscule beasties. Fresh veggies can be covered with all sorts of bacteria, and some of our foods are actually completely comprised of living bacterial colonies. Have you ever looked at a dab of Yoplait under a microscope? (In all honesty, I suggest you don’t.)

Long story short, there is plenty of life already present in your mouth. Depending on the source, water may be “just” water when you first pour it, but every time you take a sip your saliva deposits microbes and nutrients from your food into the container. Anyone who drinks out of a Nalgene during a meal is turning the water inside into a nutrient broth well-suited to bacterial growth. The wall of the container itself even plays a role. Bacteria in the “wild” (the highly scientific term for any area that cannot be considered an agar material) grow in “biofilms.” Biofilms are sheets of bacterial cells that grow on surfaces like countertops, tooth enamel, the surfaces of ponds, and the ring inside your Nalgene where liquid and air meet. Take a swab from that water line, culture it for a few days, and you can find out a lot about your diet and cleanliness habits.

Since it had gone missing in June, I did not bring my Nalgene to lab the day we took samples. Because of this, I could not see firsthand what was culturing inside. Even after learning what grew on other people’s plates, curiosity got the better of me. Professor Martin gave me the opportunity

to repeat the experiment on my own by providing me with some agar plates and sterile swabs. I quickly tracked down two bottles to test myself. The first bottle was my own, which I eventually found still half-full in the trunk of my car.

I decided to take a swab of the side to see if anything was left alive to culture after four months of disuse. The second was a Nalgene I grabbed out of the cabinet and drank from for a single day, making sure to take a few sips during each meal before leaving it to stew overnight. I took two swabs from each Nalgene and streaked them out onto two different types of agar. One, called LB, contains a lot of nutrients, and the second type, PPYE, contains very few. Since many bacteria prefer lownutrient environments in addition to those that enjoy resources in excess, this ensured that I would see growth of the majority of what was present on the sides of the water bottles. The bottles were both stored and used at room temperature, so an incubator would not be necessary to culture the bacteria within them. I left the plates to incubate in my china cabinet instead (much to the dismay of my housemates).

The car Nalgene plates were left to culture for five days. No visible growth was seen until day four. Luckily, by the morning of day five thirty-two small, translucent white colonies of a single type of mold were present on the PPYE agar, and more than fifty of the same kind were growing on the LB agar. There was also a faint “carpet” of bacteria present across the surface of both plates. I wasn’t very surprised to see growth, because many bacteria can “shut down” to survive times when food is scarce, and others can produce reproductive spores that remain dormant for a hundred years or more. With that in mind, a Nalgene I rarely washed that ended up spending four months stagnating in the back of my car is a comparatively mild environment. The organisms I cultured grew on both the high-nutrient and the low-nutrient plates, which indicates that they are capable of developing in a wide range of environments. It is likely that there were more specialized bacterial types present in the bottle when I first lost it that died off as nutrient levels dropped over time.

Matt Loewen

Wren Williams

The results of the fresh Nalgene were not at all what I expected. After four days of incubation, only three large greenish-brown colonies developed on the LB plate, and the PPYE plate remained completely blank. Even more interestingly, none of the growth was bacterial. All three colonies were molds, which means they were either in the bottle initially or from the cheese I had eaten that day, but not

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of the University of Puget Sound from my mouth (and that is certainly what I am going to continue to tell myself). According to these results, there was more life present in my old trunk-water than in a bottle I had freshly infused with food the night before swabbing.

After considering the information garnered from my quick observational study, I came to two conclusions. First, washing out water bottles regularly is effective, because bacteria are resilient and durable, yet take time to establish in a new environment. Second, I am never again going to use a dish that has been in my cabinet for a semester without rewashing it first, even if it was lidded the entire time.

For those of you who are horrified by this information and have already vowed to never use your Nalgenes again, stop worrying, because a little hygiene really does go a long way.

If you wash your Nalgene out occasionally, you’ll inhibit the growth of the biofilms inside, which will make it more difficult for bacteria to develop within. For the bacteria living in my mouth, at least, it seems to take more than a day of drinking to give them time to move in. Simply rinsing is ineffectual because bacteria are excellent at adhering to surfaces, and nothing short of a sponge and some soap is going to dislodge them in great quantities. Dishwashing is even more effective than hand-washing because the sustained levels of heat will kill off the bacteria that survive the soaping. Finally, if you’d rather stall their growth than actively remove them, refrigerate the bottle — the cold will slow the development of any microbes you have inoculated the water with while drinking.

If you have read my disclaimers that the majority of the bacteria in you, on you, and near you are benign, and yet are still staring at your water bottle with a crawly-skinned sense of distrust, I have one more thing for you to consider: I also took a swab from a water fountain in Harned Hall, and the molds I discovered growing on that spigot made my fungal car Nalgene seem like a water source of superior cleanliness. And at least if you are using your own personal water bottle, you know first-hand everyone who has been feeding and providing the bacteria within.

Mark Martin

Also keep in mind that the vast majority of microbes living on you are not going to make you sick. It is a common thought that all bacteria are bad, but in fact we owe a lot to

them. Cheeses are the result of bacterial processes, as are many other food items. Research has even been done using bacteria to create completely biodegradable plastics to replace the synthetics we currently use. Followers of the “probiotics” movement also assert that bacteria can be good for you. If every spot in your personal ecosystem is being occupied by non-harmful bacteria, there is no room for a potentially pathogenic species to step in (Ecology students refer to this as “niche exclusion”). This is exactly why many doctors remind people on strong antibiotics to eat plenty of yogurt; The lactic acid bacteria it contains are harmless to humans and will replace the benign bacteria within you that have been killed off by the meds. This re-supplying ensures that pathogens such as yeasts don’t get a chance to set up house in your mucous membranes. And finally, the body has its own natural barriers against bacteria. For example, the pH in your stomach is low enough to prevent the growth of all but a few highly specialized bacterial invaders. All in all, the worst thing most of the microbes you have been feeding and drinking are going to do is make you slightly more germaphobic, which is just going to get you to wash your dishes like you should be doing already.

These small, curved-rod bacteria were found living in four-month-old water.

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Elements: The Scientific Magazine

Research Repor t

A Summer of Mapping Explorations with a Wireless Robot Michaela Hammer

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hink your cell phone, laptop, and iPod automatically make you hip to the technological world? Gadgets and robots have long been a part of science fiction culture, but their current significance is largely overlooked. If your only idea of a robot is R2D2, you have two tasks: First, reassess your knowledge of the practical applications of technology.

Second, go have a chat with Ben Ahlvin.

This summer, Ahlvin took on the world of robotics with a University of Puget Sound Summer Research Grant. Ahlvin, a junior from Corvallis, Oregon, is now a member of the themed living program and resides in the Robot House. “I just think robots are really exciting,” he says, “It’s like all of my interests put together.” Ahlvin is currently double majoring in math and physics, and would love to minor in computer science if he finds the time. He says that robotics combines the physics of movement and localization with the mathematics of statistics and algorithmic programming, and, of course, computer science is incorporated with designing programs and organizing data.

The project was conceived during a computer science class last semester. Professor Andrew Nierman knew that Ahlvin lived in the robot house and had wanted to explore the capabilities of small robots for some time. Nierman had some extra cash from his personal research funds and was ready to invest in a little robot for research and instruction.

He invited Ahlvin to conduct a summer project under his supervision, and the plan grew from there.

Ahlvin and Nierman designed the venture with expansion in mind, but this summer they focused on creating a robot that could map its surroundings without an onboard computer. A couple of key tools were needed to accomplish the mission.

First task: Find a robot. Actually, make that a cheap, durable, small, and flexible robot. Luckily one is on the market, called the Khepera II. Manufactured by the K-Team Corporation, this little guy is only 3 cm tall and can sit in the palm of your hand. It is an adorable machine that comes with several advantages. Eight pre-installed infrared sensors give this robot a 10 cm range for detecting nearby objects that reflect light and the battery lasts for about an hour, allowing experiments around Thompson to run frequently during the long summer days.

Second task: Connect the robot to a computer. Since the Khepera II has no computational capabilities built in, Ahlvin had to establish a Bluetooth wireless connection to enable constant communication between the moving sensors and

a processor. Luckily, the Khepera II saved the day for this function since it came fitted with a modular extension for wireless contact. This extension gave the robot a 100 meter range in any direction from its computer source.

Beyond these basic resources, Ahlvin was left on his own to develop an accurate mapping system and put it to work.

He created a mapping algorithm based off of Pyro’s open source robot simulator. Modifying a known algorithm allowed him to not only test his software in an accurate system, but also compare his results with others derived from different sensors. No research can remain isolated from previous or future experiments, and Ahlvin took advantage of past experience and knowledge to establish his methods.

Conducting real tests with this robot was the meat of Ahlvin’s work. He constructed several small enclosures and let the robot loose to see how well it could map them.

Ahlvin’s favorite test area was a two by two foot walled-in region that had sharp corners and a few thin walls placed randomly inside. The goal was to see if the Khepera II could not only detect and navigate these obstacles, but also successfully relay their positions and sizes to a computer over a wireless connection. As you might imagine, the robot made a good map of the outer walls, but had trouble distinguishing the free-standing dividers.

Although these flaws may be corrected for in future studies, two things frequently compromised the accuracy of the maps in Ahlvin’s experiments. First, any sensor in the real world experiences “noise.” That is, the readings that it takes contain unavoidable flaws due to imperfect instruments, environmental conditions, and computational flaws.

When the Khepera II detects a nearby surface, its infrared sensors continually pick up inconsistent data even when it stands still. The robot translates this error with its eight independent sensors, all collecting information on a moving target, making the data slightly skewed over time. Designers now try to decrease the amount of noise an interactive robot experiences, but it is improbable that the noise error will ever be completely negated. The fact that noise is an unavoidable, common problem may or may not be a consolation for frustrated researchers like Ahlvin.

Second, the localization method used led to cumulative errors over the tests’ durations. Ahlvin used a localization method that calculated the Khepera II’s relative position 10 times per second based on how much each wheel had rotated since the last reading. If one wheel moved more than the others, this would translate into a turn. So, if the right wheel has moved 4 cm since the last reading (0.1 seconds ago), but the left wheel only moved 3 cm, the robot turned relatively left and can be located according to its prior po-

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of the University of Puget Sound

Other methods exist, but this was the most practical for Ahlvin’s study. He mentioned Monte Carlo Localization (MCL) as an alternative. It uses a method based on pre-determined points within the test area to keep track of the robot.

Although it is more advanced and almost eliminates cumulative errors from noise, it is unrealistic for unknown areas and was therefore inappropriate for this particular project.

A frustrating aspect of the localization method Ahlvin used was that wheel slippage prevented testing on various terrains. That is, his robot had the highest accuracy only when running on surfaces that prevented the wheels from overspinning. On wet or slippery ground, the Khepera II made many more errors in localization than when it ran on more frictional planes. It could not drive over bumpy, sandy, or very steep terrain either. Thus, Ahlvin and his robot were confined mostly to the floors of Thompson Hall.

Modest as it was, this goal took ten weeks of full-time work to realize. Robots designed for the real world are already in operation, but refining their technology and capabilities will take years.

One example of functional robotics comes from Carnegie Mellon University, where students designed a robot for exploring abandoned mine shafts, many of which are too dangerous for humans to enter. Their creation was a rugged four-wheeler with laser-range sensors. Ahlvin thought this laser technology would be a big improvement over his robot’s capabilities, since the sensors were its most problematic area. The robot at CMU, however, carried its computer onboard and was consequently heavier and more expensive.

Ahlvin chose to explore the possibility of wireless communication with a small, limited robot instead of packing on a computer, treaded wheels, and expensive sensors. Case-inpoint, he had to compromise versatility for size and cost.

Matt Loewen

sitions. This method works well over short periods of time and with relatively few directional changes, but for the long haul, tiny errors in position tend to become exaggerated.

This can eventually lead to a simulated map that appears to be crawling after a long interval of testing. Ahlvin did not see any gross miscalculations during his project, but he was swift to note that his small areas would contain such errors were they assessed over a prolonged period of time.

Keeping a computer onboard is necessary in many cases where wireless communication is limited or unrealistic, such as down a curvy, deep mine shaft. If a robot were fitted with a very far-reaching Bluetooth extension, however, it could complete its task without the burden of any computational elements on board. After offloading such cumbersome and expensive components to a remote computer, the robot can use its limited resources for other tasks.

This tiny robot is a modified Khepera II model.

The environment of the science building presented drawbacks in conjunction with convenience. Black surfaces went Semi-autonomous robots—armed with wireless connections unseen by the robot throughout the experiment because to offloaded computers—may one day be mapping the Mars they do not reflect any ambient infrared light to the sen- landscape, deep-sea landforms, or Antarctic ice fields. With sors. Ahlvin drolly described that he made this discovery the freedom of having no onboard computer, these maafter trying to test the 100 meter range of the Bluetooth chines can use their capabilities for what really counts: sensor. “[I decided] to set it loose down the hallways,” he acute sensors, accurate localization, and sample collection said. “I worked on the third floor this summer. It turned out and analysis. that all of the walls have a strip of trim on the bottom.

Unfortunately, it is made of black plastic.” So while provid- That is what we have to look forward to. For the moment, ing a steady surface for the wheels, Thompson Hall also mapping robots are most useful in collapsed or abandoned presented a significant complication for other parts of the buildings and old, toxic mine shafts. Ahlvin’s project and robotic system. In retrospect, he laughed, “It can detect others like it contribute to the body of knowledge that proeverything except black things… Ironically.” He found that vides exploratory teams with the tools to more efficiently the sensors also had trouble moving from areas of high to do their job. low ambient light.

This research was funded by the Summer Research Program Notwithstanding these minor problems, Ahlvin considers his in Science in Mathematics under Ahlvin’s advisor, Professor project a success. The Khepera II performed fantastically for Andrew Nierman. For more information about this project what it was designed to do, which was create an accurate and others, visit the display boards in Thompson 331A, map of an area without an onboard computational device. www.pyrorobotics.org, or www.k-team.com.

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Research Repor t

Redistricting Walker Lindley

W

and

Randy Bentson

Utopia

Many solutions to this problem have been proposed, such as instant run-off voting (IRV) and the removal of the electoral college. Drastic changes of this nature require not only major legal changes, but a complete reeducation of the American public. Furthermore, neither of these approaches necessarily do anything to deal with the problem of gerrymandering, a product of partisan politics that poses a grave threat to America today. Gerrymandering invovles drawing voting districts in such a way that one party is heavily favored over the other because of the region’s demographics.

Some states require that nonpartisan committees perform redistricting as a way to keep politicians out of the process.

It is difficult, however, to find a person who is completely unbiased when it comes to politics. If we can find a way to automate redistricting, then we can allow an impartial computer do do the work and assure a quality redistricting plan. For this, of course, we need to know what makes a district fair.

Most states have two primary requirements for people to follow when making a redistricting plan: apportionment and compactness. Apportionment is the principle of one person, one vote, and simply means that each voting district should have roughly the same population. It is trivial to calculate the population of each district given perfect apportionment and we can simply use the deviance from this as a measure of apportionment. Compactness is much harder to measure and no state defines what it means for a district to be compact. We propose to measure compactness as perimeter squared over area, we refer to this as the Gerrymander Factor (GF). Some of its important properties are the simplicity of its calculation and the fact that it is scale-invariant — a square will have the same GF regardless of its size. Given these two measures, we can assign a value to each district representing its quality. Conveniently, we want both of these values to be as low as possible, so we can combine them into a weighted sum that we will call a fitness value for reasons that will become apparent shortly.

Since we can assign a fitness value to every district, we simply need to optimize this value by finding the redistricting plan with the best (lowest) average fitness. We could

Wikimedia Commons

e face a problem today in America. Voter turnout is low and the 2000 and 2004 presidential elections have challenged the country’s faith in our democratic process.

Voting irregularities, confusing ballots, and a divisive political climate combine to make the electorate weary of politicians. All is not lost for our democracy. If we can restore the peoples’ faith in democracy and ease the tension caused by divisive politics, then we can bring our country back from the brink. To do this, we must first convince the populace that their votes do matter.

The original district described as a “Gerrymander” in this 1812 political cartoon. have tried all possibilities, but that would have taken far too long. Instead, we turned to a search technique from the field of Artificial Intelligence known as genetic algorithms.

This technique is based on evolution and requires that the solution to the problem be encoded as something similar to DNA. We will refer to an encoded solution as a genome.

Traditionally, a genome is a bit string, a sequence of 1’s and 0’s and, like DNA, these bit strings can be mixed together and mutated in a process analogous to reproduction. The final piece needed for a simulation of evolution is a way to implement survival of the fittest. For this we use the fitness function mentioned previously. This function allows us to give a numerical rating of quality to any genome.

Our implementation of the genetic algorithm was initialized with a starting population of 10,000 random genomes and was allowed to run for several days at a time, usually simulating hundreds of millions of generations. Each generation saw the removal of a genome with a poor fitness value (crucially not necessarily the worst fitness) and the generation of a new genome based on the reproduction of two genomes rated as having good fitness values (again, it is important that these are not necessarily the best two genomes). If we choose to remove the worst genome from the population every generation, we risk quickly losing important genetic material that may be necessary to move forward in the future. To solve this problem, we simply removed a genome from the worst 10% of the population.

While this does not eliminate the possibility of losing important genetic material, it means that the material is much

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of the University of Puget Sound

Crossover

Mutation

Parent 1: 11001010100101010111 Child: 11001010100110010101 Parent 2: 01011100010110010101 Mutated Child: 11011000101110011101 11001010100110010101 Child:

Genome added to population: 11011000101110011101 An example of how the process works. more likely to survive long enough to be included in future generations. Similarly, always reproducing with the best two solutions would quickly lead to a very homogeneous population, because there are a finite number of ways that two genomes can be combined. Homogeneous populations lead to stagnation and little improvement in the quality of the solutions we are creating. Again like the solution to the removal problem, we pick random genomes from the population for reproduction. This way we ensure that the full range of genetic material is incorporated into future generations, preventing the stagnation problem. After running for hundreds of millions of generations, it is reasonable to expect that the algorithm will have found good solutions and that is exactly what we saw in our results. Unfortunately, while we know the relative quality of the solutions we are finding, we do not know what the best solution is or even what its fitness value would be. Furthermore, the random nature of genetic algorithms means that we do not know when it will stop improving the fitness values of its solutions. Therefore the only thing we can do is simply let it simulate as many generations as time allows and hope for the best with a reasonable expectation that the solutions will get better over time.

Genetic algorithms provide a way to find good solutions in a large search space relatively quickly and the results from trials on synthetic data are promising. One of our better results had an average GF of 19.856 and an average apportionment deviation of 28.4 citizens. For the sake of comparison, the county council districts in King County, Washington have an average GF of 56.08. These data show that, on average, our algorithm produces districts that are nearly three times more compact than the districts created by humans. We are, however, comparing our algorithm run on synthetic data and humans’ efforts on actual data. Therefore, we need to attempt to apply our algorithm to the same data that humans work with, but two main obstacles stand in the way of that goal. The first problem is bodies of water and islands. This is a problem because our method of encoding solutions requires that precincts be adjacent to each other and there is no one, obvious way of determining adjacency across lakes, rivers, and other bodies of water. The second primary obstacle is the poor quality of the patchwork GIS data that is available. The data provided by the State of Washington was nothing more than a collection of the data provided by all of the counties. This is not necessarily a problem, but the counties did not seem to agree on their boundaries, so we were left with some areas that were in two or more counties (and therefore precincts) and some areas that were not in any counties at all.

This problem is not solvable by research and must be settled by the counties and the state working together to Synthetic precincts in color with black outlines defining five standardize and improve the districts created by our redistricting algorithm. Each district is quality of their GIS data. labeled with its GF value.

Walker Lindley

We now understand genetic algorithms and the fitness function that the redistricting problem uses, but we have yet to explain how a map of districts and precincts can be encoded as the bit string required for this algorithm.

Like computers, we can treat the 1’s and 0’s of a bit string as a sequence of true/false values, but we now need a set of objects that can each be represented with this single Boolean value. We solved this problem by assigning a true/false flag to each border between two precincts. This flag was set to true if the corresponding boundary was between

two precincts in the same district and set to false otherwise.

This led to an encoding that had between 2 and 3 bits per precinct. For instance, one map we generated with 100 precincts had a genome made up of 274 bits.

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Elements: The Scientific Magazine

Research Repor t

Biology’s Next Top Model

A panel discussion on the use of model organisms in biological research Will Baur

or nearly all forms of life, there is an organism that is commonly studied by biologists to understand a biological phenomenon not unique to that particular organism. Among insects, Drosophila melanogaster is king. Caenorhabditis elegans is chief among the nematodes. In the plant kingdom, Arabidopsis Thaliana is the preferred plant, depending on who you ask. Among the vertebrates, Danio rerio, Xenopus laevis, and mice represent their phylum well.

Scientists use these and other model organisms to provide insight on a great range of biological questions. Because so many genes and mechanisms essential for life have been conserved over the course of evolution, a discovery about a gene that controls eye development in a fruit fly can shed light on how that process works in a mammal or even a human. Many of the most important medical discoveries are based on work that began with a model organism.

Considering their great importance to biological research, I met with a group of UPS biology professors from a variety of different backgrounds to understand how one matches a research question with model organisms and whether some model organisms are more useful than others. Excerpts of that discussion are presented below: WB: How is the model organism you study useful in addressing your research question? What are its disadvantages?

Wayne Rickoll: Well obviously with Drosophila [fruit flies]…

Leslie Saucedo: (interrupting) I don’t want you to include me with your answer, please.

WR: It’s cheaper. That’s important.

LS: Yes, it’s obviously faster, but you can’t freeze the mothers, so you always have to keep the lines alive. Every other model organism that I can think of can do that.

Alyce DeMarais: I think Drosophila is a great model organism, but it is not a vertebrate and while the pathways are conserved, they have very different outcomes. I think you need a good vertebrate model to study. Even Christiane Nusslein-Volhard1 has seen the light and switched from Drosophila to zebrafish.

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WR: Well in that case bite me! (laughs)

LS: In other model organisms like the mouse you make the change the first day they’re born, but you might not look at it until three months later. In terms of cancer, a lot of other genetic changes can happen in that time, where as in the fly you can choose one tissue and change it and look at it three days later. It’s more reductionary that way.

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WR: Obviously, the advantage with Drosophila is bringing together genetics and molecular biology. You can turn on genes in specific locations, block gene functions in specific locations and see how that affects whatever processes you’re studying, in my case, morphogenesis. Initially, the big problem with Drosophila was its size. It was not ideal for traditional embryology, which involved surgery and transplantation. Our techniques have evolved so size is no longer an issue and the genetics and molecular biology are so fantastic that it makes Drosophila great organism to work with. Like most model systems, it has a lot more similarities with genetic function in mammals and humans than we ever expected. We used to do the old “wink, wink, nudge, nudge” when we talked about its application to humans and then all of a sudden we found it was true. The genes may have different outcomes, but the pathway will be the same for a human and a fruit fly.

Drosophila melanogaster

Danio rerio

of the University of Puget Sound

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AD: You can do some extrapolations from something like Drosophila or C. elegans,2 but if you really need to know how the genes are working in terms of developing the backbone you need to use a vertebrate.

WR: Let’s say you wanted to figure how the heart works.

Well, a fruit fly is not going to be a good model system.

There are some limitations. It has a dorsal vessel, but no heart.

AD: Zebrafish are perfect for studying genetics and molecular issues. Zebrafish embryos are clear and develop outside the womb. You can stick them under a microscope and take a look at them, activate genes, or turn them off. But then if you really want to study what is going on with mammals, you study mice.

WB: Which model organisms have scientists learned the most from and which model organism holds the most potential for future discoveries?

WR: Well, I’m biased for two reasons: I work on fruit flies and I am a developmental biologist. If I just stick to the area of developmental biology, I would have to say fruit flies. Fruit flies really put genetics on the map... What do I think of the future? It might be a toss up between zebrafish and mice.

Mice are just pretty dang expensive and take a long time to work with. It is almost hard to say just one organism. Yeast are great for some things, fruit flies are good for some things. Hell, even Xenopus3 is great for some things.

morphogenesis. Drosophila told you how the whole program works. I think that was as big of a question 20 years ago as cognition is now.

WB: What personal ethical/moral issues did you encounter when choosing a model organism?

WR: I started off working with rats... I had to learn how to kill a rat, or sacrifice it. It bothered me tremendously. I tried to do it on automatic pilot, so I could separate my emotions completely from the act. I separated them so well that when I got half-way through my stun-swing I let go of the tail of the rat. It hit the ceiling. It was a real mess. A month later I was working on Drosophila. I’ve also made antibodies in rabbits. At one point when I was at Duke, overseeing some biology labs, I had to sacrifice 8 or 10 rabbits in a week.

When it comes to dealing with vertebrates, I’m a wimp. A fly… (Wayne smacks the table)… not conscious.

AD: Really? I think you have to think about any organism you are dealing with — vertebrate or non-vertebrate.

WR: Emotionally, if you’re dealing with an organism that cries like a woman when you break its neck, that’s going to have more of an effect on you emotionally, believe me. Have you ever heard a rabbit scream?

AD: Well Wayne has already admitted his bias. I’ll step back.

WB: What kind of questions are hard to answer using model species?

WR: I think she is missing the point. Drosophila has told us the most important things about developmental biology: how genes control development pathways, embryogenesis,

LS: Anything about cognition.

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AD: I think Drosophila is important especially for genetics, but it’s not the most important even in terms of development. You have the sea urchin, chicken...

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WR: In terms of the hierarchy of genetic control, you never would have discovered that in anything other than Drosophila. The way sight genes work, internal effect genes...

Peter Hodum: I think gone are the days, and thankfully so, where you can do just about anything you wanted with any organism you wanted without really being accountable for it.

If you look at the literature, it’s scary what people were able to get away with and they were asking questions that were not necessarily visionary. It was mediocre research that involved sacrificing huge numbers of organisms. Although when you do the papers you grumble at it, it is well meant and necessary. It shouldn’t just be the charismatic mega fauna that get the attention. Anything that can really sense pain should be what we should be thinking about.

Caenorhabditis elegans

Mus musculus

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Elements: The Scientific Magazine

PH: A lot of ecological questions are because the natural world is so variable, and because ecology is trying to cover what is happening at the physiological level all the way up to ecosystems and bio-regions.

They have adapted to the local conditions over time and differ in key genes such as light regulation, stress avoidance etc. To study your gene of interest you can compare it to ecotypes from around the world.

At a later date, I interviewed Andreas Madlung about model plant species.

WB: What personal ethical/moral issues did you encounter when choosing a model organism?

WB: How is the model organism you study useful in addressing your research question? What are its disadvantages?

AM: None. I do mind killing animals, but I have no qualms with weeds.

Andreas Madlung: Arabidopsis was the first plant species to be fully sequenced. The first draft was completed in 2000.

However, A. thaliana has been a model plant long before that time. To be a useful genetic model a species should be easy to work with, have a short generation time, have lots of genetically variable offspring, and be easily mutated and transformed. Arabidopsis thaliana has all of these properties.

It grows from seed to seed in 6 weeks, produces thousands of seeds per plant, can be grown in minimal conditions: space, relatively low light, room temp. A particular boon is the fact that A. thaliana is a “selfer.” That means that it can self-fertilize. If you think about a genetic cross with an F1 hybrid for which you want F2 offspring you need to cross it to an identical sibling in order not to introduce confounding genetic variation. A self-fertilizing plant is ideal for that.

WB: Which model organisms have scientists learned the most from and which model organism holds the most the potential for future discoveries?

Arabidopsis thaliana is easily transformed by dipping the flowers into a solution of Agrobacterium carrying the desired sequence to be transformed. All you need to do is transform Agrobacterium which is as easy as transforming E. coli and you have done that in Bio. 111, remember?

Also, a good model organism should have genetic resources. What I mean with that is that it would be ideal to have a well-funded organization that collects and provides mutants to the community of researchers. For A. thaliana there are likely one hundred thousand or more mutants available. At least one in every gene. You can order them within days via the website www.arabidopsis.org. Also, to study gene function it is helpful to have plants that will express the gene of interest in specific tissues. For A. thaliana you can get promoters that are specific for almost any cell type you want. So you could splice your gene behind a tissue specific promoter and express it in the leaves for example. Also, marker genes are abundant. Take GFP [Green Florescence Protein] for example. Splice the native (normal) promoter and the gene of interest in front of GFP and you can see where the gene is normally expressed, maybe the roots or the stamens etc. For plants there are additional reporters apart from GFP. There are other genetic tools available for A. thaliana. To understand how they are used I would need more time but if you are interested you could look them up or ask me or take Plant Phys. They include enhancer-trap lines, recombinant inbred lines, and nearly isogenic lines, RNAi lines, genetic knock outs or knock downs just to name a few. One more terrific thing are the “ecotypes.” There exist more than 100 variants of A. thaliana collected from all over the world.

AM: ...Depends who you ask. Arabidopsis has of course enormous implications for agriculture. But for some cases it has been the model of choice for cancer research, too. RNAi (the winner of this year’s Nobel Prize) was first noticed, but not understood in plants (petunias, in fact). Arabidopsis has helped tremendously to figure out the use of RNAi as a remnant of cell defenses against invading viruses.

What conclusions can we draw from this distinguished panel of biologists? Simply put, there are several characteristics to a successful model species, but there isn’t one organism that has them all. The ability to perform precise genetic manipulation, the degree of relatedness to humans, the pace of development, the ease of maintaining the organism in lab, the quality of visualization permissible, and the amount of previous discoveries all go into making a great model organism. When choosing a model organism, one must match the strengths and weaknesses of their model organism to their research question, funding situation, and maybe most importantly, their own feeling towards the ethics of animal research. For those interested in biological research, choose your model organism wisely.

For more information about a particular professor’s research visit the biology department’s Field Guide to Research online at http://www2.ups.edu/biology/fieldguide.html.

1 Christiane Nusslein-Volhard shared the 1995 Nobel Prize in Physiology and Medicine for her work on the genetic control of development and embryonic growth she did using Drosophila. Shortly before receiving the Nobel Prize she made the switch to zebrafish and has influenced many to follow her example.

2 Caenorhabditis elegans is a nematode used as a model organism to study molecular and evolutionary biology.

Scientists have completely sequenced its genome and determined the fate of each of its approximately 1,000 somatic cells. The 2002 and 2006 Nobel Prizes were given to scientists who made their discoveries using this model organism.

3 Xenopus laevis is a frog native to Africa used as model organism in developmental biology. While it is more closely related to humans as an amphibian, the genetic techniques of Xenopus are not as well advanced as Drosophila, C. elegans, or zebrafish due to its tetraploid chromosome. The ease of cell transplantation experiments and the ability to grow Xenopus cells in culture are a couple important advantages of using Xenopus laevis.

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Welcome to The Allium

The following pages are works of satire.

28 The Allium

Altering Prey Behavior to Affect Predation Rates Wren Williams

H

ere at ELEMENTS, we strive to help our science students stand out. With that in mind, I am including an example of an independent project proposal I recently wrote for ecology. If your last proposal was less than exemplary, try modeling the structure, style, and citation of the following paper. Your next assignment is sure to be an attention-grabbing one!

INTRODUCTION

Elements: The Scientific Magazine and petted. During the training period we will be careful not to physically discipline any fleas that bite us to prevent accidental reduction of our sample size. After the fleas in all three tanks have reached adulthood, they will be taken out and handled together for a one-hour period. Each bite the handler receives will be recorded. Due to the discomfort caused by this method of data collection, we will need the help of another student who is willing to help us analyze flea response. We are currently looking for a volunteer handler for the love-negative tank.

To perform this experiment we will need sixty flea larvae. These can easily be obtained by flea combing our neighbor’s dog, where their populations seem to be flourishing. We may also need to rent sitcoms in case we run out of creative ways to compliment or insult our love-positive and love-negative fleas. The developing larvae will require a “flea diet” that consists mainly of dried blood. 2 This diet is cheap and can be ordered through the stockroom, though it is also possible for us to create the diet ourselves.

We plan to start gathering the flea larvae as soon as we have tanks though itchy, is not fatal. in which to put them.

The neighbor’s dog is readily accessible, and will allow us to harvest his crop at the cost of a few dog biscuits. It should take two to three weeks for the larvae to develop.

Larvae pupate for 7-14 days before reaching adulthood, so we will have some wait time before the experiment can be completed. Despite this, we are certain we can conclude the experiment by Thanksgiving.

MATERIALS AND METHODS

1

The Lion King [videocassette]. Mecchi I, writer. Walt Disney Video; 1995 Mar 3, 1 videocassette: 88 min, sound, color. Available from: http://disneyvideos.disney. go.com/moviefinder/products/3042003.html.

2

Flea [Internet]. Wikipedia [home page on the Internet].

Wikimedia Foundation, Inc. [modified 2006 Nov 9; cited 2006 Nov 10]. Available from: http://en.wikipedia. org/wiki/Flea

Fleas are an ideal specimen for this study, because they have always been avid predators of our species, but bites from a healthy flea are nonfatal. To test our hypothesis, we intend to take three sets of twenty fleas each and personally raise them from larvae to adulthood. Each tank will be treated in a different way. The control tank will be provided ample food, warmth, and humidity, and receive no further human interaction. The love-negative tank will be given the same ambient conditions as the control tank, but twice a day each larva will be taken out individually and insulted in various convincing and dramatic ways. The love-positive tank will be treated in a very different manner. Twice a day each larva will be individually serenaded, complimented,

Nick Kiest

Since listening to Professor Burnaford’s lectures this semester, my lab partner Sarah Korosec and I have become very interested in the topic of predation. For our independent project, we decided to determine what effect psychological manipulation at the hands of their prey has on predation rates of carnivorous species. We hypothesize that predators are less likely to consume a member of The bite of a healthy flea, a prey species that it has been raised to love. We know from previous research that predators raised by a species that would normally be considered its prey are less likely to consume them upon reaching maturity. For example, lions have been known to become insectivores due to the psychological influence of meerkats and warthogs.1 We intend to determine if this phenomenon also occurs in the insect world.

P.S. The time and effort required to write this lab proposal paid off — as soon as my professor read it, she asked me and my lab partner to come and meet with her to discuss it!

of the University of Puget Sound

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The Allium Geologic Time, Or Lack Thereof

Matt Loewen

T

he Geology Department of the University of Puget Sound is filled with many fascinating, exotic, and useful things. It has large machines that detect trace amounts of elements, furnaces that burn at a 1,000°C, and strange boxes intriguingly called “shatterboxes.” Rocks in all sorts of colors, including ones that fluoresce brilliant oranges and greens in ultraviolet light, are piled on and in every available space.

With all these objects, however, one common instrument essential to the pace of modern life is absent: the clock.

I set out to determine why so common an instrument should be lacking. What I found were conflicting answers.

One professor, whose specialty is in geochemistry and takes particular interest in radioactive isotopes, pointed to past experiences. Apparently, in the youth of the department, a full selection of clocks adorned the walls. These clocks possessed brilliant glow-in-the-dark paint on the numbers.

At that time such paints contained small amounts of radioactive material. Evidently, a nasty bout of cancer spread through the department after a decade of the clocks’ pres-

ence. The disease decimated the department’s population, and to this day it has not recovered.

A historical geology professor had a different explanation.

For him it was purely academic. “How could anyone in geology care about time, geologic time makes clocks irrelevant.”

What he refers to is the vast period of time with which geologists typically work, spanning the 4.5 billion years of earth’s history.

Many geology students have different opinions. One bitterly remarked that it was to keep “the revolution” from occurring. “I get here at 7:30 A.M., stay all day taking maybe one or two coffee breaks in the café. Next thing I know it’s midnight and I’m still here cutting rocks, staring at rocks, even eating rocks.”

Another student nearby agreed. “I gave up on living anywhere else. I put up a cot in one room, put some drinks in the fridge and turned a cabinet into my food cupboard. It’s great; I save on rent, wake up where I need to be, and don’t have to walk home in the rain late at night. I can even use the emergency showers in the chemistry labs.”

There seems to be no consensus on the lack of clocks in the Geology Department. We can only hope that with Thompson‘s renovation this is changed and geology students can quit aimlessly wandering through the eons of time.

Match the Professor to The Cartoon on Their Door!

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B

Wayne Rickoll Joyce Tamashiro Mike Spivey Ken Clark The Wizard Mike Valentine

Clueless? Take a stroll around Harned and Thompson to find out!

C

Answers: 1. A 2. F 3. B 4. D 5. E 6. C

D

E

30

Elements: The Scientific Magazine

Crossword 1

2

3

4

5

6

7

8 9

10

11

12

13

14

15 16 19

17

18

20

21 23

25

24

26 27

30

28

29

31

32 33

37

22

38

39

35

34

36

41

40

42

43 45

46 49 53

47 50

51

48

52

54 55

Across 1. Changing 5. Good for balloons 6. Pressure meas.

8. 114.82 fw 9. Sierra Nevada, Idaho, and Snoqualmie 13. Equals 1.01325 of 6 across 14. Good for the bones 15. Really big magnet and org. student’s joy 16. Sierpinski’s fractal 18. Honors the periodic table inventor 19. The exponent’s Mr. Hyde 22. [Xe] 6s2 5d 6 24. Translation of 1 down 25. Type of Funnel, abbr.

27. Geek gear extraordinaire 32. Shorter then 4 down 35. Harvey has his brain

44

56

37. Everyone’s favorite Gylcolysis enzyme!

43. Adversary of microbes everywhere 45. What you do to friendly polynomials 48. Bill! Bill! Bill! Bill!

49. The name itself is another France joke 51. You’d never date without it 53. Named for roses, frat style?

55. Atomic no. 21 56. Looking at light Down 1. Letters in the book of life 2. T-test, for a crowd 3. opp. opp./adj.

4. R.O.Y.G.B.I.V. 5. Angular momentum constant 6. 208.98 fw 7. Transcript of 1 down

9. Goodbye liquid, hello gas 10. Atomic no. 52 11. The hottest thing in Tacoma 12. Aloha from the mantle 14. Balls from space 15. Meters in a TEM image 17. Elemental in the E.R. 18. The new café 20. Close relative of 33 down 21. How molecules bite 23. Living subj.

26. Named for the continent of 49 across 28. Nasty weapon of WWI 29. Honors 35 across 30. Geologist tool OR Used for streaking 31. 10-12 33. Energ. currency of the cell

34. Earthy 36. Commonly mispronounced by Dubya 38. Latin for Copenhagen (abbr.)

39. Gladly accepts your roadkill 40. Bldg. of new labs 41. Expansion of polynom., high school style 42. Chaos!

44. 10-15 45. Has 100 protons 46. He coined alpha, beta, and gamma particles 47. Atoms on the outside of Harned 50. Makes watches glow 52. Enzyme suffix 54. Cold fusion of lead 208 and iron 58 (hint, add!)

For answers see: http://clubs.ups.edu/clubs/elements

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