Issue 1 by Elements Magazine

Elements The Scientific Magazine of the University of Puget Sound

Avian Flu:

Is It a Threat? The Ice Worm Man Cometh

Meet: The Stable Isotope Mafia

Bill Nye: Issue 1, Spring 2006

Where Is He Now?

Elements: The Scientific Magazine â&#x20AC;&#x2021;

AT TENTION all Nerds, Dorks, Dweebs, Brains, Whiz Kids, Einsteins, Artists, Literati, Pundits, Prodigies, Savants, Scholars and Geeks:

Are you TIRED of writing lab reports? Does science EXCITE you? Do you want to SHARE information with the uninformed masses? ELEMENTS is looking for writers, artists, designers and editors for 2006-2007. Think you have what it takes to write about science? Email elements@ups.edu for an application.

of the University of Puget Sound

Table of Contents Credits & Thanks

Credits

Editor-in-Chief: Marissa Jones

Letter From The Editor

3 Layout Editor: Nick Kiest 4 Business Manager: Marissa Jones

Letters To The Editor

5 Jones, Rebecca Radue, Alison Riveness, Will

Einstein’s brain after death

6 Kiest.

by Will Baur

Copy Editors: Megan Dill-McFarland, Marissa

Baur, Matt Loewen, Melanie Heisler and Debbie

Mars Shaped by Plate Tectonics

Divide By Zero

The Tragedy of Dr. Hwang

By Rebecca Radue by Erik Tollerud

by Eric Schneider

Staff Photographer: Nick Kiest Layout: Nick Kiest, Marissa Jones Image Editing: Nick Kiest Faculty Advisor: Mark Martin Front Cover Photo: Nick Kiest Back Cover Photo: Ross Mulhausen

Thanks To:

Admissions Department, Biology Department,

What Happened to Bill Nye the Physics Department, Math/CS Department, Science Guy? 10 Chemistry Department, Geology Department, by Lindsay Anderson

Private Donors, and the ASUPS Senate for funding this dream of ours.

Food Facts: Coffee Rings

The Stable Isotope Mafia

12 encouragement. Cathy Tollefson and Chuck

by Matt Loewen

Biology of the Flu: What You Don’t Know Might Kill You 14 by Rebecca Radue

H5N1 Poses Global Threat by Alison Riveness

CEDO: The Intercultural Center for the Study of Deserts and Oceans 19 by Keaton Wilson

Alyce

DeMarais

for

initial

support

and

Luce of Arches for valued advice and help with the title. Julie Reynolds in the Communications Office for help contacting printers. Nick Edwards, Editor of the Internationalist for encouragement, advice, and the reminder that students can make a magazine. The UPS Science Departments for endless hours of good, wholesome, sciencey fun. Tim “Wizard” Hoyt for lighting things on fire for us. Caffeine, for without you, elements would have never been finished!

Meet the Ice Worm Man: An Interview Thanks to our parents, and we don’t mean with Ben Lee 20 this in the sappy “they raised us” sense, but by Keaton Wilson

Sawmills, Sulfides, and Seagrasses: Eelgrass and Marine Ecology 24 by Marissa Jones

in the “they copy edited and supported us on the phone while we went nuts” sort.

Contact & Publishing:

Modeling Our World: Prof. Neshyba’s email: elements@ups.edu Research into the Composition and web: http://asups.ups.edu/clubs/elements/ Density of Arctic Clouds 28 website/default.htm by Safa Lohrasbi

Food Facts: Cheerios

Elements Personality Quiz

mail: elements, C/O Marissa Jones, University of Puget Sound, 1500 N Warner St. #1041 Tacoma, WA 98416-1041 Published by Consolidated Press: 600 S. Spokane St., Seattle, WA 98134.

Elements: The Scientific Magazine

Letter From The Editor

elcome to Elements, the new, student-run scientific journal for the University of Puget Sound! You may be wondering what this is and where it came from. Well, I must admit, it started out as a joke. It was just one of those ideas you toss around until you get distracted by assignments and obligations. Ali Riveness, Keaton Wilson and I were in biology lab during our freshman year, measuring the rate of oxygen consumption in germinating and dry peas. Our experimental setup and sampling equipment were not the soundest, and as a result, the glass beads we used as a control appeared to “breathe” more air than either set of peas. “Headline news!” we joked, “A scientific marvel! Glass beads show signs of cellular respiration!” Perhaps it was only in contrast to the riveting cellular activities of germinating peas, but this seemed pretty funny at the time. We decided to make a mock scientific journal to publish the most amusing lab mishaps of the year. And then it dawned on us: why not make a real scientific journal for UPS? Scientists do not always present their data in the most reader-friendly manner, at least as far as the average student at a liberal arts university is concerned. In general, the number of people who understand scientific research is inversely proportional to the amount of time a researcher spends preparing it. We don’t feel that this is the way things ought to be. Wouldn’t it be great if, as research delved further into the realm of the strange and bizarre, more effort was put into explaining it to a general audience? We think so. Elements may not be a scientific journal in the traditional sense – the research we discuss is not presented formally or subjected to peer review – but the topics we discuss were chosen by students who were interested in a particular topic and qualified enough in the field to understand and explain it to others. So what is Elements, exactly? The periodic table is made of elements. There are the classical elements of earth, air, fire, and water. There are elements of style, elements of presentation, and elements of society. Whether classical, periodic or otherwise, elements are the fundamental building blocks of the natural world. When you break it down, this is what science is all about: looking at the world, recognizing its mindboggling complexity, and trying to catch a glimpse of the pieces to see how it all works together. In terms of this magazine, we looked into Thompson, admired the posters on the walls and the students in the halls, and asked, “Hey you, Thompson, what makes you so cool?” We have distilled and purified a few of the elements of scientific research at UPS, as well as some samples we have collected from the larger scientific community, and done our best to present the facts accurately and engagingly.

As you can see from the cover, our patron element for this issue is fire. One might say this embodies the spontaneous, spirited, dare I say, exothermic nature of this publication. Elements: Hot off the press. Drop it like it’s hot. Come on baby, light my fire. Not to mention, the Wizard set some neat chemicals aflame so we could get the cover photo. And it all fell into place. I invite you to peruse the pages of this journal. Let us know what you think and what you want to know. After all, we wrote this magazine for you. Sincerely, Marissa Jones Editor-In-Chief

Nothing says, “I love you,” like Carbon, but don’t let the emblem of your love fade with the millennia. A diamond, however brilliant, cannot withstand the true test of time. Instead, offer her carbon’s most stable allotrope – After all, Graphite is Forever…

of the University of Puget Sound

Letters To The Editor My informal plea: Labs are required in science courses at UPS. They are very time consuming but excellent opportunities to learn first hand the techniques used in today’s modern science research. Knowledge of these techniques is essential for further research. Lab also validates in many ways the theoretical concepts we learn all day in science classes. It’s great blah, blah, blah. I spend 4 hours (more like 6, lately) in the chemistry lab itself each week. Add 2 hours of pre-lab preparations, 4-5 more hours of analysis, interpretation, and lab “writeup” and we are looking at about from 10-11 hours of lab related work per week. This is only my chemistry course. Biology is not as intense (less theoretical so not as necessary to validate in excess) and I get 4 hours in lab and 3 hours of pre-lab and analysis and there goes another 7 hours of my week. We have a grand total of about 17-18 hours working on lab related work in my science classes per week. In summary that is a tremendous amount of time yet it is only about ¼ to 1/3 of my grade in these courses. I want some credit for all this work! Most Universities throughout America award units for classes, the most time consuming courses (like the sciences) being 4 units, less time consuming courses less. They also receive separate units for labs, 2 units for the more time consuming and 1 unit for less. Here at UPS we receive 1 credit for every course offered here as if they all require equal amounts of time consumption. Now, I’m not going to argue that the material taught in science classes is harder then the humanities courses, business courses, etc. (we all know the truth), but I am hoping to get some credit for the 17-18 hours of diligent lab work that those of us in the sciences (including the professors) put in each week for no credits. If we examine, for example, the typical business major’s load of classes we are looking at 12-14 (roughly 4 classes ᙮ 3 hours) a week of in class time. I on the other hand put in 11 hours of in class time a week (I’m only taking three classes), in addition to 17-18 hours of lab. All I am asking for is a measly .25 credit for lab. I would ask for more but I don’t want to risk it. I know this is a liberal arts college but the lab work load is taking away from my liberal education by limiting me to less time consuming elective courses to compensate. I did some calculations: currently right now if you’re a biology major (the most credit demanding major in the sciences) you get 9 elective courses outside of overlapping cores and bio requirements. If you add in the .25 more for each lab course you take within the bio major you still get 5 elective courses. That’s “liberal” enough for me.

If you think I’m right and want to see a change just send me an email. If enough of you show interest I will take one for the team, pull another all nighter, and actually take this in front of the curriculum committee and try to make some changes. Thank You and Good Night Barton Bodrian bbodrian@ups.edu

Letters Wanted: Elements wants your thoughts and comments! Email us at elements@ups. edu with letters to the editor, guest articles, cool science-y photographs, or anything else you want to get out there.

End of the Year Department Picnics: From all your favorite sciences! Math/Computer Science, May 3rd, 4pm, in Trimble Forum. Biology, May 3rd, Xpm, in Trimble Forum. Geology, xx , Xpm, in Somewhere. Chemistry, xx , Xpm, in X. Physics, xx , Xpm, in X.

Where Are They Now?

Einstein’s brain after death by Will Baur

instein died from an aortic aneurysm on April 18 th, 1955 after refusing a potentially life extending surgery. Dr. Thomas S. Harvey, a pathologist at Princeton Hospital, was responsible for performing the autopsy on the world’s most famous scientist. Before Einstein died, he said he wanted his brain to be saved so that it could be studied. He explained, “My brain ought to be studied, so that if anyone has a question, it can be answered”. Harvey claimed that Einstein’s family gave him permission to perform the autopsy, but they were still upset that Harvey removed the brain. Harvey was in good standing with the executor of Einstein’s estate Otto Nathan, however, who wanted the brain studied to explain Einstein’s genius. In the final step of the autopsy, Harvey removed the brain in the presence of Nathan. The brain was weighed, photographed, and preserved in formaldehyde. The rest of Einstein’s body was cremated later in the afternoon. A day later Harvey talked to Albert Einstein’s son Hans Albert, who was wary of the how the brain would be handled. Harvey stated, “I told him I would take good care of it, that I would not exploit it or expose it to publicity. I promised it would only be used for scientific study and that reports about it would appear only in scientific journals”. Regardless of these facts, Harvey has had to protect his reputation from those who believe that he was something of an unqualified, opportunistic grave robber. Soon after preservation, Harvey sent the brain to the University of Pennsylvania to have large portions of it thinly sliced, stained, and put onto microscope slides. Harvey then sent these slides to a few neuroscientists he knew, but they did not find anything unique about it. Some in the field even questioned the purpose of studying the brain. At the time, research was focused on understanding neurological disorders and general brain functions. As a result, studies of Einstein’s brain were not the first priority of the neuroscientists who received Einstein’s brain. Harvey explains, “I couldn’t pay researchers to study it, and they all had their own work to do.” He did not even hear back from most of them. “I had distributed most of the slides that I had to leading neuropathologists in the country, hoping they would come up with something, and they hadn’t, and I thought if these people couldn’t, then I certainly wouldn’t be

Elements: The Scientific Magazine able to...” he explained. In 1960, Harvey was fired from his job as a pathologist at Princeton hospital, but he retained possession of the brain. Several years later, he moved to Kansas and taking the brain with him. He was then working as supervisor for a biomedical laboratory. In addition, he volunteered as a pathologist for a local hospital, keeping Harvey and the Brain himself extremely busy with work. Einstein’s brain was left unstudied in the basement of his house, but Harvey continued to take precautions to ensure that the brain remained well-preserved. After the initial media attention following Einstein’s death, people lost track of Harvey and the brain. It was not until 1978 that Harvey and Einstein’s brain were rediscovered by Steven Levy, a young journalist on an exhaustive search to find them. Levy found the brain in two mason jars beneath a beer cooler. This news brought Einstein’s brain to the attention of scientists again. An Arcticle on the whereabouts of Einstein’s brain caught the interest of Marian Diamond, a neurobiologist at the University of California: Berkeley. She became the first person to publish a study on Einstein’s brain. Before Diamond asked Harvey for permission to study Einstein’s brain, she had found evidence of anatomical differences between rats raised in different environments. Rats that lived in enriched environments had a higher ratio of glial cells to neuron cells. Glial cells provide metabolic and structural support to neurons. The rats that lived in the enriched environments needed more glial cells to support the very active neurons in their cerebral cortex. After calling Harvey every six months for over three years, Diamond received the sections of brain tissue she wanted, four sections of Einstein’s brain: one section from both sides of the inferior parietal lobe and both sides of the prefrontal cortex. These areas of the brain take information from other parts of the brain and try to make sense of it. More specifically, the section of the inferior parietal lobe studied is thought to be important for planning behavior, attention, and memory. The area of the prefrontal cortex studied is thought to be important in language and other complex functions. In 1985, thirty years after Einstein’s death, Diamond published the first study on Einstein’s brain in Experimental Neurology. Diamond found that Einstein’s brain

of the University of Puget Sound had a higher glial cell to neuron cell ratio than eleven “normal” brains, but only the tissue from the left parietal lobe had a statistically significant difference. These results may indicate that Einstein’s neurons required and used more energy than neurons in a normal brain. His brain had a greater amount of glial cells, and these provided more structural and metabolic support than in normal brains. Diamond’s results and conclusions have been criticized, because her study only counted neurons and glial cells on one section from each of the four areas of Einstein’s brain Some researchers are also against the very idea of studying Einstein’s brain because of the difficulty of correlating brain anatomy to intelligence. Diamond’s paper is important, because it was the first study that found that the anatomy of Einstein’s brain was significantly different than other brains previously studied. Another paper, published in 1996, showed that Einstein had a greater density of neurons in his cerebral cortex than the control brains studied. A third paper published in 1999 found anatomical differences in regions of Einstein’s brain that are thought to be important in mathematical and spatial reasoning. No one knows if other great mathematicians or physicists share the same anatomical characteristics as Einstein. Studies on Einstein’s brain have yet to give a definitive anatomical explanation of his unique mental abilities. In 1996, Harvey brought the remaining pieces of Einstein’s brain to Dr. Elliot Krauss, chief pathologist at Princeton Hospital. “I was getting more and more requests for interviews and for tissue and I thought I’d better turn this over to some younger people,” Harvey said. Krauss loans the brain to scientists to conduct research and it is returned to him once the study is complete. Current research is looking for signs of Alzheimer’s disease in Einstein’s brain and another study is again counting glial cells in unstudied areas of the brain. Anderson, B. and Harvey T. (1996). Alterations in cortical thickness and neuronal density in the frontal cortex of Albert Einstein. Neuroscience Letters, 210, 161-164. Diamond, M.C., Scheibel, A.B., Murphy, G.M., Jr. and Harvey, T. (1985). On the brain of a scientist: Albert Einstein, Experimental Neurology, 88, 198204. Witelson, Sandra F., Kigar, D.L. and Harvey, T. (1999). The Exceptional Brain of Albert Einstein. The Lancet 353(9170), 2149-2153. Diamond, M. (1999, January) Why Einstein’s Brain. from http://www.newhorizons.org/neuro/diamond_einstein.htm. Abraham, C. (2002). Possessing Genius: The Bizarre Odyssey of Einstein’s Brain. New York: St. Martin’s Press. Paterniti, M. (2000). Driving Mr. Albert: A Trip Across America with Einstein’s brain. New York: Dial Press.

News in Brief

Mars Shaped by Plate Tectonics By Rebecca Radue

ASA scientists have presented new evidence that Mars was once shaped by plate tectonics, much like Earth today. In 1999, scientists were able to map a small portion of Mars’ magnetic field using the Mars Global Surveyor’s magnetometer, and discovered “stripes” of alternating magnetic polarity in the planet’s crust, similar to those observed on Earth. When molten rock rises to the surface between two plates and cools, it aligns in the direction of the Earth’s strong global magnetic field. The Earth’s magnetic field reverses its polarity several times every million years, creating an alternating magnetic pattern in the new rock.

While the 1999 evidence was only for a small portion of the planet’s surface, a highly detailed map of the entire planet’s magnetic field, built over the course of four years of constant orbit, was released in early October. This map shows that the striping phenomena repeated itself in other regions of the planet, and also indicates that transform faults (where two plates slip past each other, characterized by shifts in the magnetic field pattern) were once present. The discovery of past plate tectonic activity explains many of the geological features of the red planet. For example, the Valles Marineris, a canyon six times as long and eight times as deep as Earth’s Grand Canyon, looks very similar to rifts formed on Earth by diverging plates. The orientation of the canyon also happens to match the magnetic patterns on the new map. “It’s certainly not an exhaustive geologic analysis,” said Dr. Mario Acuña, a principal investigator for the Mars Global Surveyor magnetic field investigation at Goddard Space Flight Center, “But plate tectonics does give us an explanation of some of the most prominent features on Mars.”

Research Report

Divide By Zero by Erik Tollerud

ath is full of rules. Crack open any advanced math textbook, and you cannot help but notice that nearly every section includes a variety of theorems and propositions proved over the subsequent pages. While these mathematical rules are often complicated, there are many commonly accepted by everyone. For example, everyone knows you cannot divide by zero – that is a basic rule, right? Your fifth grade teacher told you that, and you have known it ever since. After all, it just does not make any sense to divide something into zero parts. Yet Austin Roberts, UPS class of 2006, set out in the summer of 2005 to do just that. On an Adam S. Goodman Research Scholarship, Austin began to develop the basics of a mathematical framework necessary to make sense of what “dividing by zero” could really mean.

Elements: The Scientific Magazine ducted in Wales, Austin completed most of the work at his house in Tacoma. His work, however, was uncharted ground for Austin and he could not help but note, “Math research has got to be one of the most bizarre things ever. It’s all in your head. … There was always the possibility that I would find an inconsistency and everything would go away in an instant. I did a lot of research into others’ work before and during, but ultimately I was out in left field so there weren’t any authors I could lean on.” The process was unfamiliar, and there was always the possibility that it would also be unrewarding in the end. Yet in the end, there was a result. The fundamental principle Austin used was the fact that division can be represented as multiplication by a negative power. i.e 1/2 = 1 × 2-1. Using this, division by zero is simply multiplication by zero to a power. So 3 / 0 = 3 × 0-1. The traditional “number line” is converted into a “number plane” of the form:

While this contains all the same numbers used in traditional arithmetic, the inclusion of powers of zero to this number plane allows for division by zero, but also creates further complexity. In fact, in this system, addition is neither commutative, nor associative; 1 + 2 ≠ 2 + 1 and (1 + 2) + 3 ≠ 1 + (2 + 3). In Austin’s final report, he laid the formal mathematical groundwork for this system, and proved some of its basic properties.

Austin Roberts When asked what prompted this line of thought, Austin explained, “In math there are all of these theorems with disclaimers at the bottom saying ‘as long as such and such isn’t zero’. It just seemed kind of ridiculous. One day in advanced calculus I started asking questions about why, and I started to wonder if I could find a way around it. A lot of math has come out of doing things that others just assume you shouldn’t do, so I thought I’d give it a try. Plus I’m a bit neurotic.” While neurosis is a topic of study in psychology, it is also one of the driving forces behind math. Hence, Austin applied for a UPS Summer Research award while in Wales, where he was studying abroad, and through judicious use of e-mail and the internet, he was granted the award without ever setting foot on campus. While the first few stages of his research were con-

But what good is all this? Many mathematicians would say that “pure” math requires no application to be worthwhile. Whether or not you believe this to be true, division by zero holds the potential for a number of useful applications in science and other disciplines of math. In physics and introductory calculus classes, there is a rough sense of what division by zero results in – infinity (or more precisely, dividing by very small numbers results in very large ones… so just extend it as far as you want). But this approach only works so as to give a rough idea of simple situations. It does not allow for arithmetic with such quantities. For example, ∞ - ∞ + 1 = 1, but ∞ - (∞ + 1) = 0. The traditional stance is that this just does not make any sense; you cannot use infinity this way. Yet a consistent means of dividing by zero provides a way to perform such arithmetic, or at the very least, keep track of what such arithmetic means. Another possible application lies in the field of error analysis. Because many very small quantities are treated mostly as zero, understanding division by zero may help to improve the understanding of how to treat such physical quan-

of the University of Puget Sound

tities. Ultimately, an idea this new has plenty of time to develop applications. The field of complex analysis (involving a similar extension to the number line), for example, saw some of its applications appear decades after the underpinning math was investigated. Without these applications of complex analysis, crucial for quantum mechanics and electrical engineering, computers could not exist, and neither could the world as we know it.

stem cells could potentially be used to regenerate nervous tissue for many purposes, including treating Alzheimer’s and spinal chord injuries. Hwang’s final achievement was published in Nature in August 2005. He announced the viability of a puppy he cloned using a similar technique to the one he used to create human embryonic stem cells. This was an especially great achievement, because dogs had been pArcticularly hard to clone compared to other animals.

Whether useful beyond academic curiosity or not, Austin’s research and conclusions are the sort that would interest any scholar – small enough to fit in a paper, yet open enough to allow for further work, should the desire arise. There are a number of related investigations and branches of research yet to be explored. Only time will tell if Austin’s research grows to be well known in the field, but in any event, it is a fascinating look into an example of UPS summer research.

These achievements as well as the praise of many American stem cell researchers who visited Hwang’s lab in Seoul, South Korea gave Hwang credibility in the stem cell research community, making him a world leader in biotechnology. This praise was also echoed at home, where Hwang was seen as a national hero who would lead South Korea into future world prominence in science. He was given extensive government funding, had fan websites, and even had a stamp made in his image. Hwang’s credibility led several prominent scientists to co-author his important papers without actually seeing the results themselves. Hwang was able to publish most of his Arcticles with little criticism until one of his research partners and co-author of the July 2005 Arcticle, Gerald P. Schatten, severed their twenty month collaboration because Hwang’s supplier of eggs had paid women to donate their eggs. Two junior scientists in Hwang’s lab had also donated eggs, begging the question of whether they donated of their own accord or to gain favor with upper level scientists in the lab.

Science Ethics

The Tragedy of Dr. Hwang by Eric Schneider

n November 2005, TIME Magazine published its Most Amazing Inventions issue and began the section with an unconventional invention of the year. Rather than pick some new advance in robotics or microchips, they chose the cloning of a dog by Dr. Hwang Woo Suk, a South Korean veterinarian. This is just one example of the publicity and acclaim that Hwang enjoyed until late November when young Korean scientists became skeptical of his work. By the following January he had lost his prestige and credibility in a series of scandals that rocked the public and scientific community. In 1999, Hwang became popular in South Korea for cloning a cow, thereby establishing himself as the leading Korean scientist in biotechnology. In 2004 and 2005 he published, along with other prominent Korean and American scientists, four major achievements in cloning and stem cell technology. The first, published Science in February 2004, announced Hwang’s success in producing human embryonic stem cells from an adult nucleus. In the second, Hwang introduced a more efficient method of transferring the nucleus into donor eggs, greatly decreasing the number of eggs needed to create an embryonic stem cell. Hwang’s third Arcticle, published in Science in July 2005, announced the development of embryonic stem cell colonies from eleven different patients. These studies were greeted with enthusiasm from the scientific community, because colonies of embryonic

It is unclear whether doubt about the morality of Dr. Hwang’s work led directly to further investigation by young Korean scientists, but less than a month later Korean scientists began questioning whether Hwang’s stem cell colonies ever existed. A battle of whistle blowing and denial ensued until a panel at Seoul National University finished its investigation. They concluded that Hwang had not created any successful lines of stem cells, but he had successfully cloned a dog. Hwang faces a pending governmental investigation of his misconduct and fraud and his previous papers about stem cell research have been removed from Science. Hwang has become an embarrassment to the Korean people who believed that he could help to establish Korean scientific prominence after the 1997 Asian financial crisis. He has also sparked questions about the amount of raw data evidence that journals should require from scientists before they publish new findings. Fraudulent discoveries like Hwang’s embryonic stem cell lines and cold fusion help to discredit the scientific community in the eyes of the public and make other scientists doubt the integrity of their colleagues. It is extremely important that ethics are upheld within the scientific community so that new discoveries can be built upon credible information.

10 Where are they Now?

Elements: The Scientific Magazine

What Happened to Bill Nye the Science Guy? by Lindsay Anderson DID YOU KNOW THAT…when you mix one skinny scientist bedecked in a goofy bow-tie and white lab-coat with some zany humor, you get a hit kids show loved by children and adults alike?…NOW YOU KNOW.

ost of us remember factoids like this booming from the mouth of an announcer as he interjected warnings and tantalizing bits of scientific knowledge on the popular TV show, “Bill Nye the Science Guy.” This funny and fast-paced kids’ show mixed do-it-athome experiments with corny jokes and over-the-top sound effects, helping a generation of kids get excited about science. So where did that cool cat, that hip guy, that super science stud go after the final episode of Bill Nye the Science Guy? Why, on to more scientific adventures of course! As it turns out, Bill Nye actually is a real scientist. Okay, so he is an engineer, but close enough. Before his national TV début as “The Science Guy,” he worked for Boeing and designed the hydraulic pressure resonance suppressor currently used on 747s. (It is comforting to know that every time you fly, Bill Nye is keeping things from getting too loud at 6,500 ft). With such a promising career at Boeing, you must now be wondering what could have possessed Nye to go into the very inaccurate (and un-engineer like) field of show business. Well, it was actually Nye’s co-workers at Boeing who gave him his start. They encouraged

ACID ATTACK: Nye Labs Home Demo #10 New rocks constantly form inside the Earth and get pushed up by earthquakes, volcanoes, and the constant shifting of tectonic plates. Erosion is the natural process that wears down these rocks, constantly changing the face of planet Earth. Erosion and mountain building have gone on since the Earth was born. When carbon dioxide in the atmosphere dissolves into raindrops, it causes the rain to become a natural acid. It can dissolve and erode rocks: it’s acid rain. Here’s an experiment to see how chemical erosion works. What you need:

Bill Nye with trademark bow tie him to enter a Steve Martin look-alike contest at a Seattle comedy club. From there, Nye’s showbiz career took off, transforming a part-time standup comic into a full time performer on the Seattle comedy show “Almost Live!” In the early 90’s, Nye left “Almost Live” to develop “Bill Nye the Science Guy.” The show ran for six year, from 1992-1998, as part of PBS’s after school educational programming along side shows like the “Magic School Bus.” With the show Bill Nye did what he has always done best: mixed science, education, and entertainment. Since the end of “Bill Nye the Science Guy,” Nye has spent his time consulting for movies, designing and 1. Lemon juice 2. Vinegar 3. Three pieces of regular white chalk What you do: 1. Place one piece of chalk in a glass of lemon juice. Note: for each glass, the chalk should be about three-fourths submerged in the liquid. 2. Place the other piece of chalk in a glass of vinegar. 3. Place the last piece in a glass of plain tap water. 4. Check back on the glasses over the next few days.

of the University of Puget Sound patenting educational products, building flight control systems for aircrafts, and designing micrometer and tooling calibration instruments. Nye has been working as a consulting engineer for the likes of the Department of Justice, Disney, and most recently, NASA. Nye teamed up with NASA on the 2003 mars rover, Athena, by designing and implementing two sundials used for color and time calibration. The idea was inspired by his father’s love for sundials and acts as a sort of monument to the evolution of technology and space travel.

On his first show, however, Bill Nye gave science a universal appeal by relating it to everyday life. He introduced audiences both young and old to earth science, physics, ecology, astronomy, and environmental science on an interactive and engaging level. The Science Guy encouraged audiences to go out and “do” science instead of just reading about it. And now it’s your turn! Try this really cool experiment courtesy of Bill Nye’s website www.nyelabs.com.

Nye is currently teaching at Cornell University where he was appointed as the Frank H.T. Rhodes Class of ’56 University Professor in 2001. He has also been developing a new show called “The Eyes of Nye” which is aimed at more mature audiences and addresses topics like over population, cloning, and sex. The show débuted in limited release in November of 2005.

Coffee Ring

Why does it do that? Food Facts:

Why do coffee stains form a ring when they dry? Bill Nye’s new program, Eyes of Nye

What’s happening? Lemon juice and vinegar are acids. Chalk is made of rock called limestone, which contains a chemical called calcium carbonate, which chemists write as CaCO3. Acids react quickly with the limestone, breaking apart the calcium (Ca) and the carbonate (CO3) to form calcium and carbon dioxide gas (CO2). Acid rain is a much weaker acid than vinegar or lemon juice. But since acid rain falls week after week, year after year, it can eat away at rocks, eroding them. By the way, when humans burn coal with sulfur in it, rain makes the smoke turn into powerful sulfuric acid. This human-made acid rain can be very tough on a forest.

In 1997, researchers at the University of Chicago discovered that the “ring phenomenon” is caused by a previously unexplained principle of capillary flow. Imagine you spill coffee on your shirt. In the name of science, you don’t wipe it up. The solvent (water) evaporates, leaving the solute (coffee residue) behind. Liquid, when it is in direct contact with air, so evaporation occurs fastest around the edge of the drop where there is the most surface area. The adhesion between water molecules “pulls” water from the center of the drop to replenish the outside, where more solvent evaporates. The water transports solute pArcticles to the edge of the drop and leaves them there, depositing the coffee residue in a ring on your shirt. So next time you spill, don’t rinse it out – instead, tell your friends about this awesome property of capillary action. Want to know more? We found the answer to this question at http://mrsec.uchicago.edu/Nuggets/Coffee/.

12 Research Report

The Stable Mafia by Matt Loewen

Elements: The Scientific Magazine

Isotope

n the lower halls of Thompson, rumors of strange activity have been circulating. The only concrete sign of these happenings may be the new “powder room” tag put over the X-Ray Florescence room. Whispers abound, however, about strange screams coming out of the Geology wing’s hall late at night, suspicious charred human-like bone fragments leftover in the furnace, and mysterious use of the department’s boats in the Sound late at night coinciding with discoveries of bodies attached to cement blocks at the bottom of the Sound. These stories originate from the strange concurrence of three geology major’s theses this year. Ben Johnson, Doug Phelps, and Dave Eiriksson, all advised by Professor Travis Horton, have earned the ominous reputation as “The Stable Isotope Mafia.” All three have thesis projects involving stable isotope measurements. To add to this, the Al Capone of the group, Travis Horton, presented a two-part lecture on the stable isotope subject as part of the Thompson Hall Science and Math Seminar. Does this mean the mafia controls the lower halls of Thompson hall? Perhaps not, but it does highlight a significant scientific technique that can be used for research on a variety of scientific questions. Hired just last year, Professor Travis Horton planted the seed of this sudden interest in stable isotopes. Horton’s doctoral thesis involved using the stable isotope ratios of meteoric water trapped in rocks to determine past elevation changes in the Basin, Range provinces and Sierra Nevada mountains of California and Nevada. Doug Phelps’ thesis continues upon Horton’s, focusing on the Colorado uplift. In interviews and during his two-part lecture last November, Horton explained some of the history, basic concepts, and future expansions of stable isotope research. Stable isotopes, unlike more popular radioactive isotopes, do not decay over time. They are the same elements, but with different numbers of neutrons, and therefore different molecular weights. This tiny yet important weight difference causes the different isotopes to fractionate when undergoing different processes that are weight dependent, such as evaporation and respiration. The most important elements in this research are CHON: carbon, hydrogen, oxygen, and nitrogen. The important carbon isotopes are C13/C14, which are in-

volved in photosynthesis, the plant respiration cycle. Carbon dioxide made up of heavier C14 is not able to move through leaf pores as easily as C13. This is an example of the kinetic fractionation of isotopes: the different weighted isotopes of carbon move at different speeds, and therefore separate. Nitrogen isotopes are involved in a different process of respiration fractionation. Organisms take in atmospheric ratios of nitrogen, but retain more of the N15 than N14. This result is amplified up the food chain, as animals higher on the food chain absorb steadily higher ratios of N15/N14. Oxygen isotope fractionation occurs through the water cycle. Rain water loses more O18 than O16 at lower elevations. As a result, higher elevations have lower ratios of O16/O18 .

Doug Phelps explores the Colorado Plateau Both Horton and Phelps have used the properties of oxygen isotopes in the hydrologic cycle to determine the historical uplift of mountain ranges. Phleps is trying to determine the paleotopography (historical elevations) of the Colorado Transition Zone. The geologic community generally agrees that the Colorado plateau has uplifted in the past, the problem lies in the lack of any obvious tectonic trigger for this rise. By investigating isotopic changes in the stratigraphy (a vertical column) of sediments in the region, Phelps is constructing a timeline that can pinpoint the exact time of the uplift. The limitations of the isotope technique, however, are large. The use of ratios to determine elevations only works on scales in the kilometer range. Different minerals effect the water composition, not to mention the many processes that can alter the water composition in rocks as they sit over millions of years. Results can, however, indicate at least the general time period of uplifts. The second member of the mafia, Ben Johnson, worked in a similar area of research, but did not examine elevation changes. Instead, Johnson is working more as a detective on the scene of a murder. He wants to reveal the mysterious burial environment of a terrestrial fossil dinosaur (Therizinosaur) discovered

of the University of Puget Sound

Ben Johnson investigates the circumstances surrounding this dinosaurs death. around an assortment of aquatic fossils. Adding to the mystery, the coastline at the time of the dinosaur’s life is estimated to be sixty miles away. The previous explanation for the location was that the dinosaur died and was washed out to sea before sinking and being buried. This explanation seems unlikely considering how complete and well preserved the fossil is. Something washed sixty miles out to sea would most likely be picked apart before sinking. Johnson is looking for evidence to make a more educated guess as to what might have been at work. There is a possibility that the area was a purely marine region, in which case this fossil could be a freak floater, and more terrestrial fossils in the area are highly unlikely. Another possibility is that the area was a broad, flat, marginal marine environment in which terrestrial animals could walk. If this hypothesis is true, more terrestrial fossils may lie hidden in the area. Ben is specifically investigating the oxygen, as well as hydrogen, isotope ratios in the sediments to determine if the area was a freshwater, saltwater, or transitional region. Results from his study have shown that indeed, this area was some sort of marginal marine/freshwater environment.

13 The final member of the mafia, Dave Eiriksson, is working on what Horton describes as an “awesome, awesome, project.” He is looking at rare tufa deposits from the Mono Lake Tufa Towers in Barstow, California. Tufas are rare rock deposits from coldwater lakes. They are very similar to deposits in Yellowstone National Park at Mammoth Hot Springs called Travertines. Travertines, however, are deposited from hot water sources. Eiriksson first wants to determine if these are indeed true cold-water tufas. If they are, he will look at the isotope data to create a high-resolution paleoclimate record for the area. Current detailed climate records come from ice cores, but only work for approximately the last 100,000 years. Deep-sea drilling cores give older data, but do not provide much detail. The tufas, at 14.8 million years old, could give a highresolution snapshot of short-term climate changes. They act in a similar way to tree rings, by depositing a new layer each year. Isotope data from each band shows chronological changes over short time periods. Seeing detailed climate changes from millions of years ago could have implications as the world deals with today’s rapidly changing temperatures. Professor Horton, the head honcho of the mafia, is expanding his use of stable isotopes to include ecological pathways. Currently, Horton is working with fur from polar bears. By analyzing the isotope ratios of carbon and nitrogen in fur samples, he can determine the diet of the bears. Bears in zoos for instance, eat cows that are lower on the food chain (only eating grass) and therefore have lower N15 values then wild bears that eat seals that are higher on the food chain (eating fish that eat plankton, etc.). This technique does not determine the exact content of the polar bear’s diet, but a general idea is obtained without using more invasive techniques such as dissecting stomachs. Also, historical samples of fur can be analyzed to determine past diets. Horton has already started looking at older pre-1950 samples, and hopes to get some modern samples from Churchill, Canada to determine how, if at all, bears’ diets have changed, especially in response to global climate changes. If current trends continue with ice melting, in the next one-hundred years bears will not be able to hunt for seals on sea ice and will have to adapt to eating other animals lower on the food chain or else the species will go extinct. This research may help determine to what extent the highly specialized polar bear can change its diet. The rumors of the stable isotope mafia may be exaggerated, but the technique is certainly a valuable tool currently used by many UPS geology students, and will almost certainly expand into other fields of scientific investigation in years to come.

Dave Eiriksson’s Tufa Towers at Mono Lake

14 Science in Context

Biology of the Flu: What You Don’t Know Might Kill You by Rebecca Radue

ometime during the course of Tacoma’s wet winter season, you may be shocked find yourself coming down with a case of the sniffles. Having nearly suffocated in piles of tissues while floating through strange, Nyquil-induced dreams after making a midnight run to Bartell’s for cough drops myself, I can sympathize. While most of us will visit CHWS and leave feeling lame, some of us may actually get to tell their professors that they can’t come to class because the have “the flu”, or the scarier-sounding “influenza”. The flu is not just for old people, you know, and an influenza infection can be very serious. According to the Centers for Disease Control, 5-20% of the U.S. population gets the flu each season, with 200,000 hospitalizations and 36,000 deaths on average. With these alarming statistics in mind, and with recent reports about the infection of humans with avian flu, the threat posed by influenza becomes all too clear. There are three types of influenza virus: A, B, and C. Influenza C usually causes only minor respiratory illness, and influenza B infection is fairly mild as well, though it does pose a threat in residential communities such as nursing homes. Influenza A is the most infamous of the three, and causes the widespread

Elements: The Scientific Magazine flu outbreaks that occur almost every winter season. Influenza A is so insidious due to its ability to widely affect humans, domestic animals, and wild birds. Viral A strains can “jump” from one species to another through a few small mutations, and be able to combat their new host’s immune system quite effectively. Recent reports of avian flu outbreaks among humans, and news that the 1918 Spanish influenza virus probably came directly from birds, are indications of just how great a threat influenza A poses. This October, scientists announced that the virus that had caused the 1918 Spanish influenza pandemic had been fully sequenced, and that it appeared to have been an avian strain that moved directly to humans. This discovery is both frightening and neat, with all this talk about avian flu, especially considering that the 1918 pandemic killed an estimated 50 million people worldwide, and infected 30% of the world’s population. The 1918 strain was exceptionally virulent, and highly lethal in comparison to other strains. While the recent avian flu infections in humans have had high mortality rates, they haven’t proved very transmissible. This is good news for now, but the initial infection of a few humans can spell the beginning of an epidemic. When a cell is infected with two types of influenza A virus, the viruses can exchange genetic material that change their surface proteins. This phenomenon is known as antigenic shift, and leads to the creation of new viruses. A person can be infected with an avian flu strain and a human flu strain, and they can recombine to create a transmissible human strain with avian surface proteins. These surface proteins can be unrecognizable to the human immune system, and

Influenza A virus. The bar represents 100 nm. Micrograph courtesy Dr. Hans Ackermann.

of the University of Puget Sound provide the potential for a worldwide pandemic. The results of a recent study could help scientists by explaining the virulence of the 1918 virus. The severity of infection with the strain may have been due to the immune response elicited by its hemagglutinin surface protein. Scientists at the University of Wisconsin engineered an influenza strain with the 1918 hemagglutinin gene, and observed the immune response in mice. The 1918 hemagglutinin protein activated a class of immunologic molecules called pro-inflammatory cytokines, which attract white blood cells, called neutrophils, into the air sacs of the lungs. In their attempt to combat the invading viral cells, the neutrophils attacked infected lung tissue, causing severe to lethal lung damage. The immune response triggered by the 1918 strain may have been what made the virus so lethal. This would also explain why the virus seemed to affect the young and healthy, those with strong immune systems and therefore a stronger immune response, more so than the old and very young. Surface proteins hemagglutinin and neuraminidase are important to study because they’re necessary for viral infection of host cells. Influenza A can’t infect host cells unless hemagglutinin binds to sialic acid receptor sites on the cell surface. But if left unchecked, hemagglutinin will bind all around the cell and prevent the replicated virus from leaving and spreading the infection. This is where neuraminidase comes in, removing some sialic acid binding sites so that the new viral pArcticles can bud out of the host cell and spread the infection. Scientists are able to use their understanding of the influenza proteins to develop effective anti-viral medications. Humans have one line of defense against influenza A: anti-viral medications. There are two classes of medications used to combat the virus. The newest drugs are NA inhibitors. These medications include zanamivir (Relenza®) and oseltamivir (Tamiflu®), and were recently recommended as the only medications to be used against the primary flu strains of the season. NA inhibitors prevent neuraminidase from removing the sialic acid binding sites on the host cell, allowing hemagglutinin to bind to the cell and prevent the escape of new viral pArcticles. FYI, in a 2002 study conducted by Dr. Terrence M. Tumpey of the CDC and colleagues, both of these medications proved 90% effective in preventing the deaths of mice infected with recombinant virus containing the 1918 HA and NA genes. Another class of influenza anti-virals, M2 ion-channel inhibitors, also proved effective at preventing lethal infection, though the CDC recently advised that they are ineffective for this season’s strain. These medications work by deactivating the M2 matrix protein within the virus. The M2 protein forms an ion channel that is believed to help remove the viral coat, allowing the virus to replicate in the host cells. M2 ion-channel inhibitors

15 keep the virus from fully removing its coat, preventing replication of the virus. The inhibitors can also change the acidity within the host cells, which can hinder some influenza A strains. The two most famous M2 inhibitors are amantadine and rimantadine. Vaccination can prevent influenza infection in humans. The flu vaccinations that are currently offered are effective against influenzas A and B. Three strains are used to make the vaccinations: two A (H1N1 and H2N3), and one B. The specific strains are chosen each year for maximum effectiveness against the season’s emerging strains. There are two types of flu vaccinations that are commonly used. The first is the “flu shot”, which contains inactivated (dead) virus. The second is a nasal-spray vaccine that contains living virus, known as the LAIV, for Live Attenuated Influenza Vaccine. The virus used in the vaccine is attenuated, meaning that it has been weakened, but still causes the body to produce antibodies against it. In order to remain protected, a person should be revaccinated each year with either type. So, if you haven’t been buried in a mountain of Kleenex, or drowned your sorrows in a cup of Theraflu by this point in time, you’ll have learned more than you ever wanted to know about the flu. Hopefully you’ll be able to better understand the reports coming in about vaccine shortages and avian flu and all things influenza. Maybe next year you’ll get a flu shot. Oh, and I hope you get well soon. Kolata, G. and Harris G. (2005, Oct 6). Experts unlock clues to spread of 1918 flu virus. The New York Times, p. A1. Smith, T. (2003). The creation of Relenza for the treatment of influenza. from http://www.omedon. co.uk/influenza/influenza. Taubenberger, J.K., et al. (1997). Initial genetic characterization of the 1918 “Spanish” influenza virus. Science 275, 793-1796. Taubenberger, J.K., A. Reid, and T. Fanning. (2000). The 1918 influenza virus: A killer comes into view. Virology 274, 241-245. Taubenberger, J.K., et al. (2005). Characterization of the 1918 influenza virus polymerase genes. Nature 437, 889-893. Traynor, K. (2006 Jan 17). M2 inhibitors ineffective against flu this season. American Society of Health System Pharmacists. from http://www. ashp.org/news/ShowArcticle.cfm?id=13877. Tumpey, T.M., et al. (2002). Existing antivirals are effective against influenza viruses with genes from the 1918 pandemic virus. Proceedings of the National Academy of Science of the United States of America 99, 13849-13854. Tumpey, T.M., et al. (2004). Pathogenicity and immunogenicity of influenza viruses with genes from the 1918 pandemic virus. Proceedings of the National Academy of Science of the United States of America 101, 3166-3171. von Bubnoff, A. (2005). The 1918 flu virus is resurrected. Nature 437, 794-795.

16 Science in Context

Elements: The Scientific Magazine

H5N1 Poses Global Threat by Alison Riveness

among avian species, humans have no immunity to it and are therefore more susceptible to health problems upon contracting the virus, such as pneumonia and organ failure1.

e have all heard about the so-called “bird flu” infecting humans in East Asia, but to many the threat of it reaching the U.S. seems distant and unlikely. The danger of a pandemic, however, is more menacing than one may imagine. It is therefore important to understand the avian influenza and its implications.

Who Has Been Affected By H5N1? Thus far, the cases of H5N1 among humans have only resulted from direct contact with infected birds. Many of the cases reported in humans have been among previously young and healthy individuals and more than half of the cases have been fatal1. Most of the individuals that contracted the virus had kept domestic birds in their home and had come in contact with bird feces or with their bodily fluid during careless food handling1. No cases have yet been reported of transmission of the disease between humans1.

What is the Bird Flu? Bird flu, or avian influenza, is a contagious virus that usually infects birds but is occasionally transmitted to mammals1. Avian influenzas usually originate in wild waterfowl and then spread to domestic birds such as chickens, turkeys, and ducks that come in contact with the secretions of bodily fluid or excrement of infected birds1. There are two types of avian influenzas, differing in their severity. The symptoms of the less pathogenic influenza include ruffled feathers and a decrease in egg production1. It usually only mutates into the more virulent strain once it infects a domestic avian population1. The highly pathogenic influenza is fatal and can spread quickly within a domestic bird population, usually causing a 100% death rate within 48 hours1.

The virus has so far been most prevalent in East Asia although it has now begun spreading throughout Europe1. Unlike other avian influenzas, H5N1 has affected multiple countries simultaneously. The infection of H5N1 in avian species has been reported in Africa, East Asia and the Pacific, South Asia, the Near East, and Europe and Eurasia. Laboratory-confirmed human cases have been confirmed in Cambodia, China, Vietnam, Indonesia, Thailand, Turkey, Iraq, and most recently in Azerbaijan.

What Makes H5N1 Threatening?

Will There Be a Pandemic?

The avian influenza currently in circulation, H5N1, is of great concern to the global community. The H5N1 virus is unique because its more pathogenic form can infect not only domestic birds, but migratory waterfowl as well, accelerating the spread of the virus, especially in the Eastern Hemisphere where five main migration routes connect Central Asia with Africa and Europe1, 2.

Since the virus still lacks an efficient means of transmission between humans, the threat for a pandemic, or worldwide outbreak of the virus, is ranked at a level three threat out of six according to the World Health Organization (WHO)1. At this stage, WHO recommends that countries with outbreaks of the influenza should remain open for travel but that travelers should stay clear of regions of the country where instances of the influenza have been reported1.

In addition, the virus is unusual because it can penetrate the human cell directly without an intermediate mammalian host1. Because the disease originated

Number of Confirmed Human Cases of Avian Influenza A/H5N1 Reported to WHO as of April 6th, 2006 Country

2003

cases

deaths

2004 cases

deaths

2005 cases

deaths

2006 cases

deaths

Total cases

deaths

Azerbaijan

Cambodia

China

Egypt

Indonesia

Iraq

Thailand

Turkey

Viet Nam

Total

192

109

of the University of Puget Sound

Although the current threat is limited because the virus does not yet spread between humans, worldrenowned epidemiologist, Michael Osterholm, claims that a pandemic is inevitable and all that can be done is to prepare5. He says it is likely that the virus will mix genes with human influenza viruses to lead to an “entirely new viral strain, capable of sustained human-to-human transmission”5. Because of the increasing numbers of mammalian infections due to bird flu, Osterholm maintains that whether caused by H5N1 or some other strain, a pandemic flu will almost certainly appear within the next ten years5.

Is There Treatment for H5N1 in Humans? Currently, the global community is not prepared to combat a pandemic spread of H5N1. Since the strain may mutate multiple times before spreading across the globe, researchers must wait to see which form the virus will take before creating a vaccine for humans1. Therefore, development and production of a vaccine would only come after a time lag of at least six months6. The two antiviral drugs, commercially known as Tamiflu and Relenza could possibly slow or stop the progression of the influenza if taken within 48 hours of the first sign of symptoms1. Unfortunately, the production of Tamiflu and Relenza is complicated and costly1. There are few producers and a low supply, and as a consequence, third world countries would probably not be able to afford the drugs1. As part of its strategy for combating a pandemic, WHO has stockpiled antiviral drugs to ad-

minister to the region where the first signs of rapid spread occur1. They hope to concentrate the drug at the source of the pandemic so as to either impede or slow its spread1. If WHO’s strategy is successful, chances are that the mortality rate would be reduced as compared to past pandemics such as the Spanish influenza (1918), the Asian influenza (1957), and the Hong Kong influenza (1968) 6. The Spanish influenza was considered to be one of the most dangerous outbreaks of influenza in human history, resulting in 40 to 50 million deaths worldwide6. The Asian influenza and Hong Kong influenza were less severe, causing 2 million and 1 million deaths respectively6. The Center for Disease Control and Prevention estimates that if a H5N1 pandemic resembled the severity of the Asian and Hong Kong influenzas, 209,000 deaths could be expected in the U.S.6. If it were more like the Spanish influenza, the U.S. would probably experience approximately 1,903,000 deaths6.

What would be the consequences of a Global Outbreak? According to Michael Osterhom, a pandemic flu would have many far-reaching effects on society and the economy5. Schools and businesses would likely shut down and there would be a shortage of hospital personnel and supplies5. Borders would close in order to inhibit the spread of the disease, making trade with other nations virtually impossible, and causing in a shortage of goods and services from foreign markets5.

Elements: The Scientific Magazine â&#x20AC;&#x2021; the Washington Department of Health would operate an Emergency Operations Center and distribute stockpiled medications7.

How Can Individuals Prepare For a Pandemic?

Nations With Confirmed Cases of H5N1 Avian Influenza as of April 6, 2006 Tourism, a major source of revenue for numerous countries, would also be at a standstill5. Moreover, if the government failed to respond in an efficient manner, it would lose credibility5.

How is the Pandemic?

U.S.

Preparing

for

The U.S. has formed its own plan for combating a global influenza outbreak. As part of its strategy, the government created the International Partnership on Avian and Pandemic Influenza to cooperate with countries from all over the world to monitor and contain the virus6. The U.S. also allocated $350 million to stockpile medications, expand early-warning systems, and fund state and local preparedness initiatives6. A total of $100 million of that money went toward state and local preparedness6. Each state and territory was given a minimum of $500,000 with extra funds based on relative population 6. In addition, the Department of Health and Human Services is making preparations for the creation and distribution of a vaccine6.

How is Washington State Preparing for a Pandemic? A total of $1,990,994 of the federal funds went to the state of Washington to use for pandemic preparation7. Currently, the Washington Department of Health is working with all levels of government to create a preparedness plan and to educate the public about the avian influenza7. If there were to be instances of human-to-human transmission outside the U.S., the Washington Department of Health would stockpile antiviral drugs for those who needed them most, reassign staff in the agency to more effectively prepare for a domestic outbreak, work with the federal government to screen travelers coming from infected areas, identify alternative healthcare options, and increase education efforts7. If the pandemic were to spread to the U.S.,

In the case of a pandemic, individuals could the expect closings of businesses and schools, and a shortage of medical equipment and staff 6. The Center for Disease Control and Prevention recommends that in preparation for a potential pandemic, individuals should store food, water, prescription, and non-prescription drugs6. It is also important to remember basic health precautions such as washing hands, covering sneezes and coughs with tissues, and staying away from public places if sick in order to hinder the spread of influenza6.

Epidemic and Pandemic Alert and Response (EPR). (2006). World Health Organization Web site: http://www.who.int/csr/disease/avian_influenza/ en. Wild Birds and Avian Influenza. (2005). Food and Agriculture Organization of the United Nations Web site: http://www.fao.org/ag/againfo/subjects/en/health/diseases-cards/avian_HPAIrisk. html. French, Howard W. (2005, Decemer 2). Bird by Bird, China Tackles Vast Flu Task. The New York Times, p. A1. Rosenthal, Elisabeth. (2006, January 13). With Flu in Turkey, Close Neighbors and Europeans Go On Alert. The New York Times, p. A5. Michael T. Osterholm. (2005). Preparing for the Next Pandemic [Electronic Version]. Foreign Affairs, 84(4), 24-37. Avian Influenza (Bird Flu). (2006). Centers for Disease Control and Prevention Web site: http:// www.cdc.gov/flu/avian. Pandemic Influenza Planning Overview (2006). Washington State Department of Health Web site: http://www.doh.wa.gov/panflu/plansummary.htm.

continued from page 19

CEDO does all that a good conservation organization should do: it combines education, entertainment and research to cover all aspects of helping restore or conserve a natural place. CEDO has grown since its beginning, and if it continues to stay true to its motto of sharing knowledge and promoting conservation, it will only continue to do so. Other groups need only to look at CEDO as a model for their own systems, and natural habitats everywhere could be better preserved and protected.

of the University of Puget Sound Science in Context

C E D O : The Intercultural Center for the Study of Deserts and Oceans

by Keaton Wilson

s a child, I spent many days along the coasts of Baja, Mexico. It was the ideal spot for a family roadtrip – close to the border and easily accessible. My mom still tells stories of hauling me in the backseat, before I could walk, down to the sun-baked, backwaters of the Mexican peninsula on the Sea of Cortez. At the time, it was a small, undeveloped region, full of locals and the occasional tourist looking for an outof-the-way vacation; coincidentally, this is exactly the kind of adventure my parents were looking for. It was here that my love affair with the ocean began. The numerous beaches of Baja were where I first discovered the alien beauty of the sea among the tide pools of Rocky Point, so named because of the tides that drag the sea out, exposing expansive tide pools. I remember being enthralled for hours out in the tide pools, looking at all the strange animals. It was so exciting when the kids next door caught an octopus, and I was even more thrilled when I made a catch of my own – a small fish, which I promptly named Barney, and kept in a bright red bucket for the remainder of our trip. Barney, (although I have no idea what kind of fish he was) was the precursor to my strange love of the ocean, which would grow as I grew, and manifest itself in new ways. As the years passed, I snorkeled as much as possible, took every class my small high school had to offer on aquaculture and eventually became a certified scuba diver, which is the ultimate aquatic experience. Nothing brings you closer to fish than “breathing” underwater. Now I begin to realize the magic of what I had experienced in Baja during my youth. Progress is occurring everywhere. Condominiums, hotels and resorts fill what was once pristine beach. Animals that were once common are now decreasing in number. This is a common occurrence in many parts of the world. People want to experience the wilderness without experiencing the wild. The desire is to be comfortable and observe nature from a safe distance. With this “progress” comes a cost – the natural state of a place. In many such cases of “progress” there are organizations attempting to lessen the impact of human construction that are either entirely inadequate or altogether non-existent. Luckily, Baja has neither of these. What it has is an organization committed to educating the public about the Baja peninsula as well as promoting conservation

19 and sustainability. CEDO, the Intercultural Center for the Study of Deserts and Oceans, is located in Puerto Penasco, Mexico. The organization existed even when I visited in my youth, and is still thriving today. CEDO offers a multitude of services aimed at educating the public. In addition to a newsletter outlining their current work, they sponsor lectures on Upper California Gulf History, Estuary Life, Intertidal Life, the Pinicate Volcanic Region, Marine Mammals, and Biosphere Reserves and Conservation in the Upper Gulf of California. CEDO also provides guided tours of the surrounding areas including excursions to Estero Morua, a local estuary, the Cholla Bay Mud Flats, and a Dune Discovery trip to North America’s only Sand Sea. These programs are open to both students and tourists, educating a diverse group of people about issues that threaten the vital habitat of the gulf coast. Besides being involved heavily in education, CEDO is a dominant force in conservation in Baja. Currently, they are involved in several research projects. In addition to reports on species diversity and bird surveys in local estuaries, CEDO is also doing important research on local marine mammals. Of pArcticular interest is the vaquita, Phocoena sinus, an endangered cetacean (from the same family as whales and dolphins) living in the waters surrounding Puerto Penasco. The Vaquita, also called the Gulf of California harbor porpoise, weighs in at around 55 kg, and is 1.2-1.5 meters in length. This makes it the smallest of all the cetaceans. Research completed in 1997 indicated that the entire population in the Gulf of California, which is the only place the vaquita lives, totaled 567 individuals. CEDO addressed the decline of the Vaquita in their hallmark style – education. By educating local fisherman through both classes and published reference guides, they helped local fisherman see the importance of the vaquita, and the destruction to the vaquita population caused by such fishing practices as gill netting. This garnered a positive response, and work continues today to improve the fishing practices by reducing gill netting and trawling, and establishing adequate regulation. The activities put on by CEDO are not only about conservation. There are also recreational programs that help fund CEDO and serve to both educate the public and provide an opportunity for tourists to see the surrounding flora and fauna of Baja. CEDO has a series of what they call Eco-Adventures, ranging from Kayaking tours of the estuaries to trips out to a local, uninhabited island. These programs undoubtedly spark the imagination of countless people, old or young, today. continued on page 18

20 Research Report

Meet the Ice Worm Man: An Interview with Ben Lee by Keaton Wilson

icture an organism that can survive in the icy glaciers of Mt. Rainer or the Olympics. It is so well adapted to its climate that when brought back to normal temperatures, it dies. The ice worm, which seems at first to be closer to science fiction than science, is UPS senior Ben Lee’s animal of expertise. The mystery surrounding this creature has recently drawn the attention of many researchers. Ben Lee and his research were featured in the February 21, 2006 issue of the Seattle Times, as well as in several other news sources around the country. Luckily, I was able to snag a chance to sit down with Lee and separate the mystery and the science of the ice worm, from a student working on the cutting edge of research on these organisms.

Elements: The Scientific Magazine BL: They eat glacial algae and other organic material that gets blown on top of the glacier. EL: Is it circulated underneath the ice so they can reach it or do they come up and get it? BL: They come up. The food stays on the surface, where there is light so the algae can grow. The worms burrow through the ice – we think it’s through the tiny cracks between the ice crystals. They come up every night an hour or two before sunset, when direct sunlight is off the ice. They stay up all night, feeding and crawling around; presumably reproduce during this time as well. Then, about an hour or two after sunrise, after the direct sun hits the glacier, they will burrow back in. They’ll do that every night. EL: There were several presumptions there - I take it that not much is known about the ice worm? BL: Yeah, they don’t know anything about their reproduction. They don’t know how that’s done; they’ve never seen it in the wild. They don’t know anything about the life span; they don’t know how long they live. The other guy who is working on them, Professor Dan Shane out at Rutgers University, keeps them in the lab alive. He has kept them up to two years without them dying. Also, we don’t know much about what they do in the winter. They haven’t really been studied because conditions are so tough, there is so much snow, and it’s hard to find them and get up to the glaciers in the winter time. EL: So they didn’t reproduce in captivity? BL: I don’t know. I don’t know if he has seen that or not. EL: So what exactly are you looking at in the ice worms? What does your study consist of?

The reknowned Ice Worm Elements: What exactly are Ice Worms? Ben Lee: They are worms in the Annelid phylum, which means they are segmented, like regular earthworms you see out there. Except that these ice worms are, as opposed to earth worms, darkly pigmented – dark brown to black in color. The worms in the cascades and Olympics are about 1.5 – 2 centimeters long. They have to live in glacial ice. If they aren’t on the ice, they won’t survive because of the temperature range and also because of the lack of a food source. EL: What is their food source?

BL: I’m looking at population genetics. They’ve done a study to show that the worms’ geographic range is from northern Oregon: from the three sisters range up to southeastern Alaska, along the coastal belt of mountains. They have done a study of the genetic relationship of these worms throughout the range, looking at genetic divergence to kind of classify how they’ve changed over time. What they found out is that there are two sub-species of ice worms. What I’m doing is checking out the Olympic Mountains, because they’ve never been studied up there. I’m taking a certain section of a certain gene, and I’m sequencing that section and then comparing it to that same section in worms from the cascades, Alaska, and British Columbia. I’m seeing how the Olympic worms kind of fit into that population structure. On top of that, I’m looking at variation and differences inside the Olympic mountain ranges. Because they are totally dependent on ice, there are separate populations that can’t reproduce with each other, totally cut off from the other populations.

of the University of Puget Sound

Ben Lee Out on Blue Glacier EL: So is there the potential here to discover a new species or sub-species of iceworm? BL: Well, potentially. I mean, I don’t want to go out and say anything, but the first few worms I found from my first trip were white, unpigmented, which is really unusual because everything I read and everyone I talked to said that these worms were dark brown. The first worms I found were white, so I’ve got sequences back from my first two worms, which are white, and when I put them into a phylogenetic tree, compared to the dark worms of the cascades, they came out on a separate branch, which suggests [these worms are] something different. So right now, I don’t know if they come out on a different branch because they are from the Olympics and of a different subgroup, or if they come out different because they are white, and they are just totally different. Another possibility is that they are completely different, and just a snow worm. There are other types of worms that live part of their life-cycle on the ice. The Ice worm is the only worm that lives its entire life on and within the ice. EL: You talk about the subspecies around here in the northwest, but do different species exist in glacial ice say in Asia, or….? BL: You know, there have been stories about Ice Worms in Siberia and Greenland, but nothing confirmed yet by any scientists. There is a guy up at UW, he went to Siberia and Greenland, and couldn’t find any, so nothing confirmed yet.

EL: It sounds pretty wide open, really. BL: Yeah, yeah. EL: How did all this start? What year were you, how did all this come about? BL: It was my junior year. I was in the Biology Colloquium, which is a class you sit in and every week, a different professor comes in and gives a presentation on the research they are working on. The theory behind this is that you watch the professors, and you get excited about one of these presentations/fields of study, and you want to pursue that in summer research, and then the next semester, you go on and write a grant proposal for the research done over the summer, and then you work with the professor on the project. I was in that class and they were talking about cool stuff, but none of it really inspired me, none of them got me really going. So I just started looking on the internet to try and find something I liked. I wanted to try and combine my love for little critters, and my love for the outdoors. So initially, I just started searching “high altitude life” and “glacial life” and after a few days, I ran into these things and found out there isn’t a lot known about them, and there are a lot of gaps in the knowledge. One pArcticular gap was that the Olympic worms had never been studied in this genetic relationship, or even at all, which just left it wide open – a perfect project for an undergraduate, and right in my backyard. I talked to that guy out East, Dan Shane, who was all for it, really excited about it. He was really supportive throughout the whole thing. I was a little worried

Elements: The Scientific Magazine

about calling him and asking him about his work on it, because well, you know…invading on his turf or whatnot. He was really helpful though, and thought it was a great idea, and it just kind of spawned from that.

EL: And that’s all in the Olympics?

EL: Did you have help as far as equipment goes from UPS faculty as well?

EL: Anything exciting happen on these trips? Interesting stories? I would imagine up on the glacier, there has got to be…

BL: Like the lab equipment? EL: Yeah. BL: Yeah. My advisor here was Peter Wimberger and he was really great throughout the whole thing. He was the first one I really talked to about it. I knew he was doing genetic testing and DNA sequencing in mussels in Puget Sound. He was the evolutionary biologist so he was the perfect one to talk to about it. He was really helpful, and thought it was a great idea. From the getgo, was just like “yeah, lets do it!”, and I was in his lab all summer using all his equipment. His other student in his lab, Ryan Coon, got a McCormick Grant, which offers a lot more money as far as project costs. EL: How many times have you collected worms? BL: I went on about six or seven trips; to about 10 different glaciers.

BL: There was one trip up to Vancouver Island, and I just did one this winter to Rainer.

BL: The first trip I was on, we got up there and we got up to the glacier and there was still a bunch of snow on the glacier, and then we had to dig through it to get to the worms. I was just digging through the snow with my ice-axe, and we were sifting through all this snow looking for dark worms. Finally, my assistant saw something moving, and it was just this little white worm. We spent like two and a half hours sifting through shards of little ice, and we found just like three worms. On that same trip down, she ended up breaking her ankle, but she didn’t know it until a good month afterwards – she didn’t get it checked out. When we were up at Rainer looking for worms, we went to this spot that a guy had told us would be a likely spot for ice worms. We went up there and starting digging through the snow, trying to get to the glacier’s surface where all the food would be. We ended up digging thirteen feet down. It was just wild! We ended up

Ben Lee on the Comox

of the University of Puget Sound digging for about two hours…two of us were digging, and we only found two worms there. EL: When you’re doing this, when there isn’t snow, do you try and time it so you get there when they are feeding at night? BL: Yeah, it’s a lot easier at night, when they are on the surface. We have spent nights camping near the glacier and then you go up at nine or ten at night when it’s dark, and they are fairly easy to find when you’re out on a healthy glacier that has a good population. There was a night that I went out with my advisor, Peter, and we were out at about eleven at night because it was a bit of a hike up the glacier. This was mid-august, and it was during the meteor shower at the time. We were up there for a good two hours, and there were meteors coming down, just in the beautiful valley. We ended up staying until about one or two in the morning. So yeah, that was cool. But most of the collection was at night.

well, they really just thrive at colder temperatures. EL: You’re getting ready to graduate, is this something you’re going to keep going with? What’s the plan? BL: Yeah, I’m not really sure right now. Dan Shane, offered me a spot at Rutgers, to do graduate work and stuff. For the moment, I declined though. I want to do other stuff; I don’t want go to school right away. But I told him to keep me in mind, for a couple years down the line. It’s something that is a great opportunity – I love doing it, it gives me a chance to get out there in the mountains. It’s a possibility to keep going with it. EL: Like you said, it’s so great because it’s undiscovered territory. Nobody really knows. BL: The big thing that he is working on right now is that he just got a big grant from NASA on a study about how they cope with the cold. EL: Oh really?

EL: Is there any indication of what purpose the worms have in glacial systems?

BL: Yeah, that is just a start. They may look more in depth into how the anti-freeze protein works.

BL: In an ecological sense?

EL: So, utilitarian uses of it, right?

EL: Yeah, or is not enough known yet?

BL: Yeah, they are looking for extremophiles, animals that live in extreme conditions. This gives a hint of how an organism could live on another planet, like some moon of Jupiter, or something, because it has similar cold climates.

BL: I don’t know. One thing that they do, they process all that algae…eating it, keeping it in check. I don’t know what that does downstream for the melt. As far as I know, they aren’t primary prey for anything. I know that snow buntings will go out and eat these worms once in a while, they have been seen doing that anyway. Really, they are just kind of hanging out, as far as I know. EL: I guess the obvious question is how these worms stay in such a cold environment. BL: So one thing… they’ve got… I don’t know if they have done a paper on this or not, but I think they have these anti-freeze proteins or enzymes in their bodies that keep them from freezing at zero degrees or below. They can survive down to negative six degrees Celsius. Usually though, they are hanging out on the surface, right on the ice where it’s zero. In the winter the snow falls and kind of insulates the surface, keeping it at about zero degrees, and so it’s not a very dynamic system as far as temperature is concerned. They don’t have to deal with those wide ranges of temperatures, whereas some desert animals do. But, another thing, it doesn’t apply to how they survive in the cold, but they have noticed in the lab that when they are exposed to the cold, their adenolite levels increase, which is contrary to most other animals. Usually, when you shock an animal with cold temperatures, their adenolite levels will just drop, will drop off the charts. And then when you raise the temperature, the adenolite levels will increase. It’s the exact opposite for ice worms though. Really, really interesting. They have become adapted so

EL: So you’re just not sure yet? BL: No, not at all. EL: Is there anything else that you’ve thought about as far other things you would like to pursue or study? It seems that through all of this, and through maybe the colloquium, you would have come across some other stuff that interested you? BL: Well… the one thing that got me into biology in the first place; the thing that changed me from a physics major to a biology major was this study of Peruvian dragonflies. There is a professor who retired a few years ago who worked on these Peruvian dragonflies. It’s not stuff I’m pArcticularly interested in, but it’s just stuff that brings you to a cool spot, or brings you places that you wouldn’t get a chance to go normally. I mean, I’m always excited about stuff like that – that can give you an adventure, give you a reason to go on an adventure. I think there are lots of opportunities like that. EL: Thank you for your time Ben. BL: That’s great. Thank you.

24 Research Report

Sawmills, Sulfides, and Seagrasses: Eelgrass and Marine Ecology by Marissa Jones

Elements: The Scientific Magazine ment. Elliott’s organism of interest in his project is eelgrass, or Zostera marina. Unlike algae, eelgrass is a true plant, complete with flowers, roots, and seeds. Audubon magazine describes eelgrass as “a veritable underwater ark,” due to the vast web of aquatic life it supports.1 Eelgrass has been found to carry up to twice its mass in “hangers-on,” as well as providing structural habitat for juvenile chum salmon, pipefish, clams, young Dungeness crabs, sea stars, and many more.1

p until about 150 years ago, Commencement Bay stood as it had for centuries: trees filling Vashon and Fox Islands to capacity, standing on the edge of the land, marking the abrupt junction from island to water, austere and impassive and seemingly endless. Beneath the surface of the water lay a similar landscape: fields of eelgrass extended throughout the shallow regions of Commencement Bay like underwater equivalents to the Douglas fir trees that covered the land.

Along the Ruston Way waterfront, where restaurants like Shenanigans and Katie Down’s are today, there once stood as many as thirty saw mills processing lumber for the West Coast. 2 The mills were constructed on wood pilings in the bay, many of which can still be seen today. The constant presence of paper mills resulted in the accumulation of large amounts of wood debris in an area that had previously been host to sandy beach and rocky shore.

As America grew, westward expansion and industrialization mandated the use of Washington’s natural resources. Puget Sound became the Port of Tacoma, the wildly abundant Douglas firs became the nation’s supply of lumber, and the abrupt edge between Sound and land became home to a bounty of saw mills sprung up to accommodate the nation’s growing need for paper. This is the point in history when Tacoma started to smell like cabbage.

While no one knows exactly how much wood waste is decomposing along the shores of Commencement Bay, its presence is undeniable. When wood decomposes, it releases compounds containing sulfur, which contribute that familiar whiff of eau de rotten eggs to our favorite Tacoma Aroma. Sulfur reacts with water to form hydrogen sulfide, a neurotoxic compound that can be fatal to humans in high doses. If you troop out to Commencement Bay at low tide and poke about along the rocky shore, your nose will probably be affronted by the telltale smell of sulfur, noticeably stronger in some areas than in others. Wood waste left over from the Tacoma paper mills has since been covered with sand, rocks and detritus. In some places, the ground is springy from several cubic meters of water-logged sawdust either protruding from or resting just below the sand and rocks. At high tide, the wood absorbs water like a sponge; during low tide, the sulfide-rich water is expelled in streams that well up from the sand like acidic springs.

We have all heard this story before. Progress took its toll on the nation’s seemingly endless supply of resources, significantly altering ecological systems. But what does it all mean and what, if anything, are we supposed to do about it? Here at UPS, Dr. Joel Elliott, Professor of Marine Biology, is guiding an assortment of research projects designed to investigate the lasting effect these historic saw mills have had on the marine environ-

Photograph of Puget Creek gulch from the end of the E.J. Mcneeley and Company dock, in early 1900’s. Photo Courtesy of Puget Creek Restoration Society.

of the University of Puget Sound

dance of underwater organisms, so Spear and Elliott modified this process in order to take a quantitative look at eelgrass in Commencement Bay. UPS has a research boat, currently nameless, and from this, Spear and Elliott towed an underwater camera that recorded pictures of the substrate. The camera was hooked up to a GPS unit that linked the exact latitude and longitude to the images on the screen. They later analyzed the images at one-second intervals to map out the distribution of eelgrass and Beggiatoa.

Beggiatoa and Thiothrix coat rocks in the intertidal with hairlike white filaments These hydrogen sulfide streams provide habitat for multiple species of sulfur-oxidizing bacteria, including Beggiatoa and Thiothrix, which form white bacterial mats along the ground. The bacteria cover all available surfaces, including not only rocks and sand, but also the bodies of the organisms that live there. The bacterium is classified as “filamentous” due to the hair-like structures it forms, making crabs, rocks, barnacles, and all other surfaces appear as if they had sprouted slimy, white fur. In the subtidal zone, the shallow region past the lowest low tide level, the saga continues as sawdust deposited in varying amounts and at different depths decomposes. This creates patchwork densities of hydrogen sulfide and the associated bacteria along the sea floor. The subtidal zone is also home to eelgrass, which covers an estimated 43% of Puget Sound’s 2,496-mile shore.1 While eelgrass still makes up a large portion of subtidal life in the Sound, its population has dramatically decreased in the last century. This has greatly affected the entire marine community since eelgrass is what ecologist call a “linchpin” species, meaning that it holds an ecosystem together.1 “The ultimate goal is restoration,” Elliott explained, but the first step is a detailed assessment of the situation. Elliott, in collaboration with Erin Spear ’05, designed an experiment to survey the abundance and distribution of eelgrass along the Ruston Way waterfront. Other researchers had described a method for using an underwater video camera to map out the abun-

As you can imagine, however, the boat was lurching back and forth, the camera was swaying in the water, and the ground was deeper in some places than in others, so the amount of substrate that actually appeared in the video screen varied significantly from one moment to the next. In order to keep some semblance of scale while recording underwater images, they attached two lasers to the camera, which cast beams of light at a constant distance on the ground. In this fashion, they trolled a camera along the shore of Ruston Way, slowly uncovering the composition of the to bay floor in much the same manner as scratching off the top layer of an instant-win lottery ticket: not so much that you see the entire picture, but enough to give you an idea of whether or not you hit the jackpot. Over the summer, Spear and Elliott analyzed the video one second at a time. In order to summarize the composition of the bay floor, they assigned a point system to the varying abundance of Z. marina. If the frame contained only a few eelgrass shoots, it received 1 point; if it contained 100% eelgrass, they gave it a 4. They also recorded either the presence or absence of Beggiatoa, which was visible in white mats along the substrate. They mapped out the “big picture” by trolling along the entirety of the Ruston Way waterfront, as well as making a detailed analysis of the area near Katie Down’s, where Puget Creek empties into Commencement Bay. This site is pArcticularly important because the Puget Creek Restoration Society is working to restore salmon to the creek and the eelgrass bed serves as a nursery for salmon spawn. Spear and Elliott wanted to see if there was in fact a correlation between increased sulfide levels and the presence of bacteria. They took core samples of ground sediment in select areas in which eelgrass, bacteria, and sand were present. The coring apparatus, which they borrowed from the geology depart-

Video Analysis of Eelgrass density

Elements: The Scientific Magazine

ment, was jammed forcibly into the ground and used to pull up a section of the ground with the layers intact. They took these plugs from the ground back to the lab and measured the concentration of sulfide on the surface, at 15 cm, and at 35 – 45 cm by inserting a syringe into the cylinder. Elliott explained that they often had trouble getting a deep sample, because the corer hit a cache of water-logged sawdust right below the surface and bounced off as uselessly as if they had shoved it onto cork. They weighed the core samples and then burned off all the organic material in an oven. They looked at the difference in volume after burning in order to determine the amount of total volatile solids (in this case, primarily saw dust and other wood waste) that was incorporated into the substrate in each area. In order to present a substantial argument to the scientific community, Spear and Elliott prepared a sort of logical proof to assess and verify the effects of sulfide on the marine environment. From their painstaking analysis of the underwater videos, Spear and Elliott found that there was in fact less eelgrass in areas where historically there were mills. Also, they generally did not find eelgrass where they found bacterial mats. Spear and Elliott determined that core samples taken from Beggiatoa mats had higher levels of total volatile solids than those taken from sandy areas or eelgrass

beds. These measurements let them classify sites as “impacted” or “unimpacted” according to the level of wood waste in each area. Based on pore water samples (water contained in the pores of soil) impacted sites contained 150 times more sulfide than unimpacted sites on average. Pore water taken from cores under Beggiatoa mats showed sulfide concentrations that were about ten times higher than those taken from underneath patches of Z. marina and about six times higher than those from sandy sites. All of these results were found to be statistically significant, meaning that the range of error in each group of data did not overlap with that of any other group. One of the main implications of Spear and Elliott’s study is the potential to use sulfur-oxidizing bacterial mats as an indicator species for assessing the “health,” or degree of negative impact, in a pArcticular area. Since they found that Beggiatoa mats corresponded with increased amounts of wood in the seabed, increased sulfide levels, and a lower abundance of Z. marina, it appears that using bacteria as an indicator of how impacted an area has become is indeed a viable application. Other researchers discovered that sulfide-oxidizing Beggiatoa often appears in the substrate without forming the visible white mats. This is more often the case when sulfide concentrations are comparatively lower than those found in highly im-

Exposed Eelgrass Beds during an extreme low tide at Puget Creek

of the University of Puget Sound pacted sites. 3 Studies performed in Shelton and Port Angeles Harbor in 1999 and 2000 by the Washington Department of Ecology showed similar bacterial mats in marine environments that contained wood debris.4,5 In 1995, researchers noted that Beggiatoa may not always be present on the surface, as it is known to perform diurnal, or daily, migrations, appearing on the substrate at night more often than during the day or during periods of intense light, and it may also be removed by wave action.6 To summarize Spear and Elliott’s study, if Beggiatoa is present, the area is most likely to be impacted. But the absence of the bacteria does not prove that an area is unaffected since the bacteria a) may be present but not visible, b) may have migrated below the surface of the seabed, or c) may have been removed by waves. What affect does sulfide have on seagrass? Aside from the relationship between presence of bacteria and absence of Z. marina that Spear and Elliott discovered, Goodman et. al. found that even small increases in sulfide concentration can make it difficult for Z. marina to photosynthesize. Sulfide concentrations of 100 – 1000 µM inhibited Z. marina by damaging the meristematic tissue, which is involved in plant growth.7 For comparison, Spear and Elliott recorded pore water sulfide levels as high as 12,348 µM, levels drastically higher than those necessary to decrease the functioning capacity of eelgrass. Sulfide may not be as detrimental to eelgrass as it sounds. If you were to look really closely at the roots and rhizomes of seagrasses, you would find what’s called an oxygen microzone, or oxic microshield, that is created by the release of oxygen during photosynthesis. This thin layer of oxygen may protect Z. marina from sulfide damage by oxidizing sulfide to form sulfate, a harmless compound. Spear and Elliott noticed that Z. marina was not abundant in the intertidal zone. One potential explanation for this is that the physiological stresses in this area decrease the rate of photosynthesis and therefore deplete the oxic microshield surrounding the roots and rhizomes, making plants more susceptible to sulfide damage. Although Beggiatoa is closely associated with the increased wood debris, sulfide concentration, and general bad news for seagrasses, the bacterium itself is not actually harmful and may in fact be beneficial to Z. marina in this unique environment. Since the bacterium oxidizes sulfide, its effect may be similar to that of the oxic microshield, protecting roots and rhizomes by converting phytotoxic sulfide to harmless sulfate, and making it easier for eelgrass and other organisms to tolerate extreme sulfide levels. 3 Spear and Elliott observed filamentous sulfide oxidizing bacteria within Z. marina rhizomes, which supports the idea that the bacteria may be ameliorating the toxic effects of sul-

fide on sensitive areas of the plant. With the paper mills closed and environmental awareness spreading, we have embarked on the next stage in this transformation of the great Northwest: restoration. Erin Spear graduated last spring, but Joel Elliott and other students are continuing research on eelgrass and the highly impacted marine environment along Ruston Way. Spear and Elliott determined that sulfide has a negative effect on eelgrass, opening the door to many questions and insights into this unique system.

1. Solomon, Christopher. (2003). An Underwater Arc. Audubon. from http://magazine.audubon. org/truenature/truenature0309.html. 2. Elliott J, Spear E, Wyllie-Echeverria S. (in review) Visible mats of Beggiatoa reveal that organic pollution from historic lumber mills inhibits the growth of Zostera marina. 3. Mußmann M. et. al. (2003). Phylogeny and distribution of nitrate-storing Beggiatoa spp. In coastal marine sediments. Environmental Microbiology. 5(6), 523-533. 4. Norton D, et. al. (2000). Reconnaissance Survery of Inner Shelton Harbor Sediments: Chemical Screening of Nearshore Sites and Evaluation of Wood Waste Distribution. Prepares for Washington State Department of Ecology, Publication No. 00-03-014. 5. Port Angeles Harbor Wood Waste Study, Port Angeles, WA . (1999). Science Applications International Corporation. Prepared for the Washington Department of Ecology. 6. Fenchel T, Bernard C. (1995). Mats of colourless sulphur bacteria. I. Major microbial processes. Marine Ecology Progress Series. 178, 161-170. 7. Holmer M, Bondgaard E.J. (2001). Photosynthetic and growth response of eelgrass to low oxygen and high sulfide concentrations during hypotoxic events. Aquatic Botany. 50, 37-47.

The Unnamed Boat

This boat does not have a name. Elements feels that this is a travesty on the part of the university and should be remedied immediately. If you have suggestions for names, email us at elements@ups.edu!

28 Research Report

Elements: The Scientific Magazine

Modeling Our World: Prof. Neshyba’s Research into the Composition and Density of Arctic Clouds

by Safa Lohrasbi

hen creating models of the Earth, the Arctic is especially important, because it has an enormous capacity to affect the world’s climate. Even the smallest changes can lead to positive feedback loops that result in massive glacial melts, which in turn cause sea levels to rise, affecting the entire world. Clouds are essential to understanding the fragility of the Arctic environment. In the Arctic winter, when no sun shines for several months, polar stratospheric clouds provide surface area for chemical reactions that speed the destruction of ozone molecules, contributing to global warming. They also act as an insulating layer for the temperature of the glaciers below. Over the past ten years, Professor Steven Neshyba has done extensive research into the properties of Arctic clouds. He is currently involved with several ongoing experiments concerned with the close examination of stratospheric ice crystals as well as determining a way to incorporate Arctic cloud density into global climate models. His research has taken him to such remote locations as Barrow, the northernmost city in Alaska, and to places all over the continental United States, from Washington to Massachusetts. In pursuing his research he has also had to overcome various environmental and technological obstacles, including finding an instrument sensitive enough to distinguish cloud density at a level where patterns are detectable and dealing with the logistical problems of running complicated machinery at extremely cold temperatures. In most global models, Arctic clouds are oversimplified as flat, uniformly dense slabs. While it is true that Arctic cloud formation consists of long, thin clouds, they are not homogeneously thick. Failing to account for this crucial variable leads to enormous errors when trying to calculate the heat of the land beneath the clouds, because a cloud’s ability to insulate depends on its density. This is especially important in models designed to understand the effects of global warming. This insulating property allowed Neshyba to measure the thickness of Arctic clouds. By monitoring rates of thermal radiation released downward from Arctic clouds, he was able to gauge their relative density in the hopes of finding a pattern. The task, however, was not as easy as it sounds. Of the few ways to measure thermal radiation, only some are sensitive enough to detect very thin cloud formations.

One of the billions of crystals that make up a polar stratospheric cloud In order to get as high of a degree of sensitivity as possible, Neshyba obtained his results from a Fourier Transform Spectrometer (FTIR) instead of a Microwave Radiometer (MWR), the instrument usually used in calculating cloud density. Incorporating technology used in radio telescopes, the MWR measures microwave emissions of vapor and liquid water molecules in the atmosphere at specific frequencies. Unfortunately, MWRs can only detect fairly pronounced cloud densities, leaving many questions unanswered. FTIR, which collects infrared spectra, is advantageous, because it is much more sensitive to slight changes in concentration and is capable of taking a full spectrum of readings both quickly and simultaneously. The FTIR is still relatively new technology, and thus not deeply understood. In order to use the FTIR data, Neshyba first had to establish an algorithmic way to interpret FTIR spectra. With the assistance of several UPS undergraduate students, Neshyba spent six weeks aboard the Arctic icebreaker, Laureat, taking FTIR spectra of individual clouds while simultaneously monitoring the temperature and density of the sky via weather balloons. From this data, Neshyba was able to construct a high resolution FTIR that displayed the different trends visible when taken in various weather conditions and different angles. While aboard the Laureat, Neshyba had a stroke of luck that opened the door to the next phase of his research. Towards the end of the voyage, the Laureat docked with its sister ship, The Groseillers, and the captain made a proposal to Neshyba that he could not refuse. The Groseillers was to take part in the Surface Heat Budget of the Arctic Ocean (SHEBA), where it would be frozen into the perennial ice and left to collect scientific data for a year. Having gathered the data necessary to establish FTIR’s ability to monitor cloud density, the next logical step in creating a model for Arctic clouds was to use FTIR to assemble horizon-wide assays of the Arctic sky. The SHEBA project allowed Neshyba to do this and amass a substantial amount of data. Neshyba readily agreed to transfer the FTIR.

of the University of Puget Sound

29 Due to the large variability of ice crystal shapes found in any given cloud, they are often represented by spheres in climate models. Spheres are geometrically simple structures and this makes them easy to work with. Numerous studies have shown that they can also be incredibly inaccurate. In the past, viable models included spheres with equal volume or area to the actual ice crystals, but as large errors in these models became apparent, they lost credibility. Neshyba’s team sought to identify a more accurate ice crystal model. In contrast to past models, they chose to represent ice crystals as spheres with equivalent volume to area ratios (A/V), creating a model that can simultaneously characterize what prior models were only able to embody singularly: volume-based absorption readings and surface area-dependant scattering patterns.

Visual distribution of cloud density and homogeneity for the months of March (dark circles) and September (light circles) from 1999-2001 at Barrow, Alaska. Notice the Gamma distributions of the compounded data. The final deployment of the FTIR occurred at Barrow, Alaska in 1999, and lasted for four years. Having overcome the challenge of transporting delicate equipment hundreds of miles by boat in cold temperatures, Neshyba collected extensive FTIR data while using the remote research village as a base of operations. Working in association with the Atmosphere Radiation Measurement program (ARM), Neshyba collected large amounts of data while spending the majority of his time in Tacoma. After obtaining a sufficient amount of data to begin modeling, Neshyba graphed the relative cloud densities. This temporal arrangement of the data yielded an interesting pattern. While the relative concentrations of cloud density and intensity varied significantly, they did so in a way reminiscent of a Gamma distribution. Since publishing his results in the 2003 Journal of Geophysical Research with colleague Carsten Rathke, Neshyba has expanded his studies of Arctic clouds. While continuing his involvement in researching viable cloud models by supervising the undergraduate studies of Laura Reed, currently studying why Arctic cloud formations match the Gamma distribution so closely, Neshyba has shifted his focus from an all encompassing view of cloud patterning to the properties of the tiny water crystals that make up stratospheric clouds. Neshyba’s initial forays into crystal modeling began in 2001 when he spent his sabbatical at the University of Washington working with several distinguished professors. These professors, Thomas C. Grenfell and Stephen G. Warren, each brought their own specialized expertise to the search for viable ice pArcticle models. Warren had an especially extensive background in the intricacies of global climate, while Grenfell was a celebrated and accomplished mathematician. Neshyba himself brought a mastery of computer programming to the group.

The discovery that ice crystals were hollow (Walden et. al 2003) also contributed to Neshyba’s experiments in modeling. Not only hollowness, but also the shape of the ice crystal itself affects the surface area and number of equivalent A/V spheres. This relationship is the subject of Neshyba’s most recent paper, which deals directly with the A/V sphere’s ability to anticipate and accommodate these structural differences. While the A/V sphere does indeed perform better than its equal volume or area counterparts, it continues to be far from an accurate ice crystal model, primarily because the exact nature of the hollows inside the hexagon (and thus the total surface area) is unknown. Since publishing his results in Grenfell et. al in 2005, Neshyba’s current project revolves around discovering the character of these hollows. Working with Tim Guasco ’06, he has grown ice crystals in the laboratory similar to those found in stratospheric clouds, and is currently attempting to identify what governs the shape of the hollow when ice crystals have formed. Another unexpected development occurred upon taking Low Temperature Scanning Electron Microscope (LTSEM) pictures of ice crystals at the University of Massachusetts. He discovered that the surface of ice crystals, earlier thought of as smooth planes, were in fact rough. Proving this anomaly to be more than just an artifact of the LTSEM process also occupies his time. As global conditions worsen, Neshyba’s research becomes more and more pertinent to the world’s peoples. When he first started investigating cloud density ten years ago, global warming was not a prominent issue. Today it consumes the thoughts of scientists and civilians alike. Through global modeling, scientists seek to comprehend the fate of our world, but an adequate understanding can only be obtained through an accurate model. By expanding upon the true nature of Arctic Clouds, Neshyba seeks to make this understanding just a little bit clearer.

Elements: The Scientific Magazine

Why does it do that? Elements Personality Food Facts: Quiz Why do Cheerios stick together in milk?

Which Periodic Element Are You?

When a Cheerio rests on the surface of milk, its weight displaces some of the liquid, creating a small depression in the otherwise smooth liquid surface. When one Cheerio drifts close to another, the two cheerios slide down the slope of the other’s indentation. This makes it appear as though the Cheerios are drawn to one another by forces mysterious, when in fact, their movements are determined by gravity and the geometry of a liquid surface.

1. You head to the SUB to grab some food before your next class. You: a. Sit by yourself and pretend to read the Tattler. b. Are intercepted by 13 people who want to talk to you before you even leave the salad bar. So much for a quick bite and some homework… c. Call your friends to see if anyone will eat with you. No one can make it so, moderately peeved, you decide to come back later. d. Never eat alone. You’re always accompanied by your closest atoms – I mean, friends… e. Run into a friend and sit with her until she has to go to class, at which point you pull out a book and do some reading.

Want to know more? Believe it or not, there are entire websites devoted to “Cereal Science.” We found the answer to this question at www.livescience.com.

2. Someone spills tea on you in the café and apologizes profusely. You: a. Explode. b. Don’t really notice. You’re pretty dense. c. Run and grab some paper towels. You introduce yourself to the tea spiller and help clean up. Before long you’re engaged in conversation. d. Smile and tell them not to worry about it. e. Accept their apology with dignity and get on with your day. 3. a. b. c. d. e.

How many friends do you have at UPS? 6.022 x 1023 60 20 5 Friends?

4. Your calculus exam promises to be a real doozie. To prepare, you: a. Study with a few friends before the exam. b. Review by yourself – you’d only ask for help if you were very, very desperate. c. Get a study group together, but only after you’ve looked over it on your own. d. Can’t make sense of it by yourself so you call up your friend the math major to get some help. e. Head to the library and before you know it you’re studying with a large group of friends. 5. You are watching a real tear-jerker with some friends. You: a. Grab a box of tissues and prepare for the waterworks. b. Don’t see what the big deal is, and you certainly don’t cry during movies. c. Sniffle slightly, but only because everyone else is doing it… d. Sink low in your chair. You’re crying before the

of the University of Puget Sound movie even starts. e. Start to cry. Your friends are surprised because they didn’t suspect you were so soft-hearted. 6. You attend a friend’s pool party. When you jump in the water you: a. Immediately sink to the bottom. b. Are suspended by your water-wings. c. Swim underwater with your snorkel. d. Don’t even break the surface of the water. e. Water?! It burns! 7. When you get hot under the collar you: a. Step outside to smoke to escape the high pressure environment b. Still keep your cool; people can push your buttons all day and you never let off any steam. c. Remind yourself that it’s just a phase (change). d. Seek more personal space. e. Start bouncing off the walls. You can be pretty high-strung. 8. What kind of music do you like most? a. Heavy metal. b. Classical music. You have a taste for noble music. c. Soft rock. d. Electronica. You’re very conductive. e. You don’t like music. You’re not very radio-active. Now, add up your points. The number of points you got tells you what element you are:

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

a a a a a a a a

= = = = = = = =

1, 4, 5, 2, 5, 1, 3, 2,

b b b b b b b b

= = = = = = = =

Li Be

Na Mg lllB lVB VB VlB VllB

Key: c = c = c = c = c = c = c = c =

4, 5, 3, 3, 3, 3, 4, 3,

d d d d d d d d

= = = = = = = =

Periodic Table of the Elements

llA

5, 2, 4, 1, 2, 5, 2, 1,

K Ca Sc Ti

Vll

llB

2, 3, 2, 4, 1, 2, 1, 4,

e e e e e e e e

= = = = = = = =

3. 1. 1. 5. 4. 4. 5. 5.

131.29

15 - 20: Tungsten: The name for this transition metal comes from the Swedish words for “heavy stone” and they sure weren’t exaggerating… a specific gravity of 19,600 is enough to make lead look like pumice! Tungsten is rarely found in its pure elemental form, instead is it usually in the earth’s crust bumming around with oxygen and nitrogen. Sure, you may be a little dense, but at least you have friends.

183.84

21 - 27: Carbon: Stable, versatile… is there anything carbon can’t do? Your tetravalent electron shell enables you to form allotropes as diverse as diamond, graphite, and even buckminsterfullerane! You’re fine being alone, and also ready to react. Let’s face it, carbon’s got it going on.

12.01 11

22.99

lllA lVA VA VlA VllA

F Ne

Al Si

S Cl Ar

V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr

Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te

Cs Ba *La Hf Ta W Re Os Ir Pt Au Hg TI Pb Bi Po At Rn

Fr Ra +Ac Rf Ha Sg Ns Hs Mt 110 111 112 113

Lanthanide

Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu

Series

Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr

* Series + Actinide

28 - 33: Sodium: This soft-hearted metal reacts instantly with air and violently in water as a pure element, so it’s no surprise you’re most comfortable when accompanied by your best friend, chloride. As an ionic compound, you may shatter easily, but with melting points around X degrees Celsius, you can certainly take the heat! O

8 - 14: Xenon: Ah… The noble gas. Perhaps you’ve noticed a distinct lack of interest in bonding? It’s because you’ve got it all! With a full valence shell, other molecules don’t really have anything to offer you. But if the lonely plight of a noble gas starts to wear on you, don’t despair! Aside from the occasional reaction with a fellow noble gas, Xenon has been known to form tetra- and hexafluoride compounds under extreme conditions!

34 - 40: Fluorine: The trouble with fluorine is that it’s so darn electronegative… This greenish-yellow, poisonous, corrosive and penetrating gas might not sound too attractive, but you’d be surprised! Nearly all compounds can be decomposed by fluorine to form fluorides that are among the most stable of all chemical compounds. Your remarkable knack for reacting lends you many friends and you’ve always been the only one to ruffle the haughty noble gases.

19.00