Issue 12 by Elements Magazine

Elements The Scientific Magazine of the University of Puget Sound

Perfect! President Thomas Fits the

GOLDEN RATIO of Beauty

Discover the Benefits of Forest Bathing

Microbes & Chocolate How Divine!

Issue 12, Fall 2012University of Puget Sound

Evolution Quiz: Find your Humanity 1

Letter From The Editor

ight now, I’m sitting in a room littered with ButterfinR ger wrappers, old magazines, and several UPS students with their closed backpacks cast to the side. We are debat-

Credits

Editor-in-Chief: Claire Simon Content Manager: Mel Kohler Head Layout Editor: Kira Thurman Head Copy Editor: Chelsea Clark Staff: Maggie Shanahan & Jay Goldberg Front Cover Photo: Provided by President Thomas Back Cover Photo: Dylan Witwicki Table of Contents Photo: Matt Sklar Allium Cover: Mel Kohler CosmoNerd: Spencer Gordon CosmoNerd Photo: Chris Putnam CosmoNerd Layout: Mel Kohler

Acknowledgments We would like to thank the following organizations and individuals: the ASUPS Media Board for welcoming Elements as an official ‘campus media’ this year, Tamanawas for loaning us their computers and software, and UPS Photo Services for curbing our Wikimedia usage!

Contact & Publishing

e-mail: elements@pugetsound.edu web: http://clubs.ups.edu/clubs/elements mail: ASUPS - Elements, University of Puget Sound, 1500 N Warner St. #1017, Tacoma, WA 98416 Published by QC Graphics LLC 1819 Central Avenue S, Suite 80, Kent, WA 98032 This issue was published on paper from well-managed forests, controlled sources and recycled wood or fiber. Recent science discoveries got you excited?

There’s a place for you here at Puget Sound. Elements wants writers, editors, media designers, and photographers interested in producing a scientific magazine once a semester. Make like margarine and support the spread of science! What’s it gonna be, the red pill or the blue pill?

Express your interest at elements@pugetsound.edu

ing whether or not the mode of transportation for a Neanderthal would include mammoths (see the Evolution Quiz, pg 29) Did I mention it’s a Saturday night? A snapshot of this moment reflects many truths about Elements Magazine and this issue in particular. For one, we are extremely unhealthy and need to stop stress eating candy. A deeper meaning extracted from these symbols is necessary to address, mainly the closed backpacks, which are like the accepted elephant in the room. It’s amazing that the staff (myself included) put the time, energy, and creativity into Elements, usually above all other homework and other school obligations. This week of editing has been particularly heavy—filled with microbiology exams, biochemical lab reports, analytical chemistry lab reports, molecular lab reports, and maybe some reading for a non-science class (but that was neglected long before Elements required it). Working on Elements is fun, and while our LCD-burned eyes, frayed hair, and aching fingers show the stress we all feel, we not-so-secretly love it (right, guys?). This issue is amazing. We have thought outside the cell wall with microscopic focus, specifically on visuals. Presenting science in a visually pleasing and accessible format is half the battle. Thanks to a consultation with Arches Magazine, we have adopted them as our unofficial media mentor (they don’t know this yet) and learned googols of tools that will make Elements surpass its previous issues and appeal to a more general audience. Look out National Geographic— you’ve got some serious competition. What can one expect in the pages of Issue 12? (Twelve? Wow, it’s like our annual issue). You might be surprised to learn that microbes swarm in the savory squares of your chocolate bar. Your brain might explode as you try to conceptualize the number of zeroes in a googolplex (but don’t worry, it happens even to the smartest of physicists who do this for a living—even Carl Sagan). Oh yeah, and you can read about why the president of our university, Ronald Thomas (aka Ron Thom), has lines drawn all over his face on our cover (it has to do with beauty, of course). We also get to hear from previous editors who clearly still follow and love to read Elements Magazine. They are proud of how far it has come and that it still captures the interest of UPS students who love to keep it alive. We’re running low on Butterfingers and chocolate-covered blueberries, so I better wrap (pun intended) this up before the room erupts into chaos and eventually, the staff’s crazyeyed, sugar-fueled energy snaps. We hope the greater UPS community finds our magazine amusing and interesting. We hope it convinces at least four new business or religion majors to Wikepedia (this might as well be a real verb) the mathematic ratios of flowers or the chemical composition of fungi. We’d love to see the sexy Cosmonerd posted on an English major’s dorm room wall (who needs Jake Gyllenhaal when you can have Spencer Gordon?). Lastly, we’d like to get more participation from campus. Write to us about what you like, don’t like, crazy questions you want explained (like what is the Higgs Boson? Why does wax repel water?). Also, write more Au’s; they’ll be in a pipette tip box in Oppenheimer next semester. Thanks to Photoservices for dealing with our ambiguous and strange photo requests, support from the lovely Media Board, Spencer Gordon for taking his shirt off on that chilly Saturday morning, President Ron Thomas, and all the writers and staff. You guys are the rarest and most prized of the elements. Think twice when you bite into that melty chocolate dessert over the holidays and try using a googolplex in a sentence. Thanks for reading! Sincerely, Claire Simon, Editor-in-Chief

Elements Magazine

Table of Contents Letters From the Former Editors

A Tale of Two Forests: How Tree-Kangaroos Came to Be

â&#x2C6;&#x17E;+1: Numbers Beyond Comprehension

Marissa Jones, Tanya Rogers, Chelsea Corser-Jensen Jay Goldberg

Mitch Benning

Tree Hugging: Itâ&#x20AC;&#x2122;s Not Just for Hippies

You Snooze you...Win?: Sleep Science Puts the Dreamer in Charge

Sugar, Spice, & Microbial Nice: Microbes and the Flavor of Chocolate

Golden Ratio: The Truth Behind Beauty

Focus on the Fungi

Your Favorite Animals: Exposed

Introducing New Science Professors: Welcome to The Puge

THE ALLIUM Au!

Google Translate

Periodic Humor

Justin Roberts Marisa Lopez

Jessica Wong Becca Long

Jay Goldberg & Claire Simon Kathryn Papoulias Jason Blanks

Stew Dants

Kira Thurman

Angelica Kong

Microbial Mixology

NEW Biology Course 2013: Evolution Lab Syllabus

Citations CosmoNerd

30 31

Jason Blanks

Daniel Guilak & Maggie Shanahan

University of Puget Sound

fr o m

Letters to the Editors lements has an impressive legacy of staff and editors. When we followed up with their accomplishments after graduation from University of Puget Sound, we found that not only had they continued with science, but they’ve found some interesting niches in the real world. We asked previous editors-in-chief to write about their post-graduation journey and their current sciencefilled life. They are on their way to great discoveries and careers. Hopefully prospective scientists and soon-to-be graduates will find their stories and perspectives useful. Nerds for life. Want to hear more? If you would like to connect with one of our Elements alumni, email elements@pugetsound.edu for their contact info.

Marissa Jones ‘08 Editor-in-Chief #1 Grad Student: Salmon Evolutionary Genetics

Photo by Marissa Jones

I am a graduate student in the School of Aquatic and Fishery Sciences at the University of Washington studying salmon evolutionary genetics. Although I have never been what one might call a “fish person,” the decision to study salmon and trout was an easy one. I am not an avid angler; I had previously only studied things that lack backbones and never show up on postcards. At UPS I studied intertidal invertebrates with Joel Elliott and, after studying abroad in Costa Rica, I was hugely obsessed Climbing the career ladder with strangler figs and their pollinating wasps. My home was with the understudied and the underappreciated. But this perspective evolved when I worked for the Washington State Department of Ecology after I graduated from UPS in 2008. Peter Wimberger forwarded me the job posting, and my marine biology experience working with Joel Elliott was instrumental in landing me the job. I owe them a huge thank you; working in the Marine Monitoring Unit was extremely gratifying. I maintained moored water quality sensors around Puget Sound and the coastal estuaries, performed oceanography via float plane, and played with mud on the sediment monitoring program. I liked that my work met the goals of Washington State, but I missed studying ecology and evolution. I decided that the best way forward would be to study something that was topical to Washington State management or conservation, but also rooted in ecology and evolution.

The answer: salmon. Iconic, economically valuable, imperiled, and with a fascinating life history variation to boot… It was the perfect crime – er, study species. Right now I’m trying to understand the genomic basis for adaptive evolution. Specifically, I’m studying domestication that takes place in fish hatcheries and adaptive trade-offs between hatchery and wild fish. Graduate school seems to be largely as advertised – expect to not know what you’re doing, to make mistakes, to struggle, but also to be part of a vibrant community, to learn, and to accomplish things. It also helps to have activities outside of school. I enjoy cooking, running, and volunteering with Seattle Audubon’s high school progam. Reflecting back on my experiences, it occurs to me that many of them sound much more glamorous than they actually were. If you’re serious about science, expect to spend most of your time in front of a computer, either writing or analyzing data. Don’t shy away from either. I recommend learning a statistical program like R; it’s free (so you can be sure they’re not paying me to say this), open source, and extremely powerful for just about any field of study. Expect to have giddy moments of “I can’t believe I get paid to do this!” and exasperated moments of “I can’t believe I get paid to do this!” If you’re interested in graduate school, I recommend the book Getting What You Came For: the Smart Student’s Guide to Earning a Masters or PhD by Robert L. Peters. The book is written by a biologist, but applicable to students of all disciplines. Much of it seems like common sense, but it can be helpful and reassuring to review it when navigating grad school applications and beyond. And last of all, have fun out there.

Tanya Rogers ’10 Editor-in-Chief #2 Research Tech.: Ecology Since graduating from Puget Sound, I have been working as a research technician at Florida State University for a lab which studies the community ecology of oyster reefs, salt marshes, and other coastal ecosystems. My job is to turn project ideas from my superviSunny day at the office sor, the Primary Investigator, into realities and to make sure everything happening in the lab runs smoothly. What I do on a daily basis is always changing, which I greatly enjoy. I spend a lot of time in field, traveling to sites across the state, kayaking or boating out to reefs, deploying experiments, and collecting data and samples. In the lab, I measure invertebrates, process water and sediment samples, and design and construct predator-exclusion cages. In the office, I enter and organize data,

Elements Magazine

Photo by Tayna Rogets

^fo r m e r

coordinate logistics and scheduling, and write protocols. I also train and guide undergraduates with their research projects. I’ve gotten to work in some amazing places, see some amazing things, and be involved in many fascinating ecological research projects. This isn’t to say there aren’t downsides to field ecology (crazy-deep mud, billions of biting insects, backbreaking physical labor, weather conditions that no sane person would venture outdoors in), but I could not see myself happier in any other line of work. I am currently applying to graduate schools, as my goal is to get a PhD in Ecology and to eventually direct my own research. What was most useful in getting me to where I am today was obtaining research experience as an undergraduate, both on and off campus. This was valuable not only in terms solidifying my interest in research and providing skills and experience, but the connections you make doing research are absolute gold in terms of finding and obtaining a job and/or a graduate advisor after college. If you are interested in scientific research, I would encourage you to volunteer for professors, to look into the summer undergraduate research grants, and to investigate off-campus opportunities such as any of the NSF Research Experience for Undergraduates (REU) internships. I would also recommend taking time off and working in science before applying to grad schools (although fair warning, the job market is extremely competitive), because this is the best way figure out what you really want to commit to, and the insight and advantage you gain will be huge whatever you ultimately pursue. For more information about my lab, visit our outreach blog: In the Grass On the Reef at http://wfsu.org/blog-coastal-health/. Search “Tanya Rogers” to see my contributions.

Photo by Chelsea Corser-Jensen

Chelsea Corser-Jensen ‘12 Co-Editor in Chief #3 Grad Student: Neuroscience

Chelsea’s version of small talk

Where am I now? Well, right now at 9:30 p.m. I am hovered over my laptop at a funky Denver coffee shop, taking a break from working on my presentation for tomorrow’s lab meeting, analyzing endless rows of data from rat MRI brain scans, and reviewing lecture notes from my course, “Special Topics in Neuroscience: Physics of Light and Microscopy.” In the summer of 2011 I moved from Tacoma to Denver and

started as one of six graduate students in the Neuroscience PhD program at the University of Colorado Denver, Anschutz Medical Campus. The past year has been a grueling combination of first-year biomedical science and specialized neuroscience courses, three rotations in different labs, weekly neuroscience seminars, student journal clubs, and lunches with invited speakers. After passing my preliminary examination in June, I officially joined the lab of Dr. Kim Heidenreich, which is focused on studying early inflammatory events after traumatic brain injury that contribute to long-term impairments in memory and cognition. The best, and sometimes worst, part about being a graduate student is that I take control of designing my experiments, setting my own deadlines, and troubleshooting when something doesn’t work as expected. This means that every day is different, I don’t have set hours and sometimes work long, seven-day weeks in lab, but I wouldn’t do it if I didn’t absolutely love it. I am surrounded by people who are passionate about their research, collaborate with other labs and physicians from the hospitals on campus, and go out of their way to help students. The atmosphere here is just like that in Thompson and Harned Halls, just with a more specific, biomedical focus—I am on a first-name basis with all of my professors, my neuroscience classes involve a combination of lecture, paper discussions, and take-home exams. The key to success in graduate school is being able to effectively communicate ideas in writing and in presentations, which also requires being able to think on your feet. This was my biggest advantage over my fellow graduate students who came from big research universities. It’s easy to learn a specific research technique— it’s much harder to learn how to stand in front of a lecture hall full of professors and students and explain my research project, convince them that the experimental approach I’m taking is the best for my particular project goals, and answer questions that I may or may not actually know the answer to. Although I came straight from UPS to UC Denver, I don’t think that direct path is right for everyone. It was challenging in the fall of my senior year to be applying to graduate programs on top of taking classes, working as a TA for two different labs and as a co-editor of Elements, and enjoying my last few months in Tacoma. I am the youngest of the six students in my graduate class and only three months older than the youngest student in the new first-year class, so most students take at least one year off to work in a lab before making the decision to apply to graduate school. Despite the vast spectrum of ages, we are a close-knit group of graduate students and make sure to get out of our labs as much as possible to go to concerts, hike, camp and ski in the Rocky Mountains, and sneak out to happy hour early on Fridays. Despite the long road ahead of me before I receive my PhD in neuroscience, I cannot imagine doing anything else right now. I think about my experiments while I’m brushing my teeth and driving to school in the mornings. I read at least one new journal article before I go to bed at night. I rack my brain over failed experiments or unexpected results and celebrate when a p-value of significance is less than 0.05. I have not yet decided on which career path I will take after graduating. For now, I’ll stick to maintaining my steady influx of caffeine—one of the other skills I acquired in my four years at Puget Sound that have prepared me for graduate school.

University of Puget Sound

A Tale of Two Forests

Photo by Jay Goldberg

How Tree-Kangaroos Came To Be

J ay G oldberg

Photo by Sigrid Heise-Pavlov

Top: Lumholtz’s Tree-Kangaroo Bottom: Yellow-Footed Rock Wallabies

Meet the adorable treekangaroos. They are members of the family Macropodidae (big feet in Latin), which means that they are “true” kangaroos. As their name suggests, these kangaroos live in the trees and love to eat leaves, unlike their terrestrial cousins that prefer the open terrain and grasses of the Australian outback. There are roughly twelve tree-kangaroo species inhabiting the tropical forests of New Guinea and Northern Queensland, Australia.4 The tree-kangaroos are one of the more recent additions to life on Earth.1 They hit the scene around the turn of the Holocene, about the same time that modern humans began standing on two legs and dispersing throughout the globe. This is their evolutionary story, in essence, how they came to be.

Elements Magazine

P h oto s by W i k i m ed i a C o m m o n s

Photos by Jay Goldberg

Our tale begins with a possum, not unlike the Green Ringtail Possums that inhabit modern Australia. These primitive possums lived in the ancient rainforests of Gondwana (the supercontinent that Australia, South America, and Antarctica once comprised). During this time, the Gondwanan continent was warm, wet, and covered in a dense forest so large it could dwarf the Amazon.2 This was the perfect place to be if you were a treeloving marsupial like the possum.

Top: Green Ringtail Possum Left: Red-legged Pademelon

The possums, being treedwellers, moved about the tree-tops slowly and carefully, walking on all four limbs. Eventually some possum-like creatures began making the move to the ground. Over time they became more and more adapted to life on the ground and began doing something truly unique: they started hopping.4 Hopping allowed these marsupials to cover more ground to search for food and escape the frightening predators that roamed the ancient Gondwanan continent. Many of the critters that became especially proficient hoppers began taking on a more upright posture.1 The transition from ground-hugging walkers to upright hoppers is especially apparent when one takes a look at some of the current residents of Australian rainforests, such as hypsies, bettongs, and pademelons. The pademelons are particularly important to our tale as they were the first creatures that took on the iconic kangaroo appearance.

Left: Rufus Bettong, Right: Hypsie , AKA: Musky Rat-Kangaroo

Such a wonderful thing as the lush Gondwanan rainforest could not last forever. The continents drifted apart, and the majority of the once-lush forests all but dried up (or, in Antarctica’s case, froze over). This forced the marsupials of ancient Australia to leave their beloved forests and make a new life in the vast desert that was quickly swallowing their former home. The pademelons, with their exceptional hopping abilities, had little trouble adapting to the new open terrain. They simply grew bigger and faster, eventually becom-

Rosy

ing the kangaroos and wallabies that are the modern icons of life “down under.”2 Some wallaby species developed a love of rock climbing, and this prepared them for what was to come next. Eons of drifting north brought the Australian continent closer and closer to Asia. Eventually it drifted close enough for some critters to cross the sea from Asia and colonize the unfamiliar Australian landscape. Rats, reptiles, bats, and birds were all quick to make a new home in Australia, and many plants hitched a ride on their flying, seed-dispersing friends.2 Over time this caused the Asiatic forests to take root in the northern reaches of Australia. While the forest plants were able to migrate to Australia, many of the animals that inhabited the Asian forests were unable to make the journey.1 This left the forest incomplete, as it needed the animals to live there and fill its myriad ecological niches. One of the first Australian critters to colonize the Asiatic forests were the rock climbing (and creatively named) rock wallabies, who had no trouble switching from climbing barren rock fields to scaling the trees of lush, food-filled, forests.3 They filled the niche left by monkeys, who lived in the treetops eating leaves and other foliage. Over the years, the rock wallabies became more and more specialized for living in the trees. Eventually, the rock wallabies lost their love of the ground and lived solely in the trees, evolving into the now-extinct bohra. The bohra retained some of the traits of their terrestrial cousins, such as the huge feet that gave them their familial name, but over time their enormous kickers became smaller and nimbler to suit an arboreal life.6 The tree-kangaroos of today did not begin appearing until the ice ages of the Pleistocene caused populations of bohra to become isolated from one another. While the ice never reached as far as Australia or New Guinea, the colder climate forced the tropical forests to retreat into small, isolated fragments.5 Each fragment harbored a single population of bohra and over time one of these populations developed into the tree-kangaroos of today. Now this is where the adorable tree-kangaroos came from, but what’s next? For these critters it could be extinction. Years of hunting by indigenous peoples had reduced populations of treekangaroos to a fraction of what they once were, even before the British began using Australia as a prison. With the arrival of European settlers, logging and the introduction of invasive species destroyed much of the treekangaroos’ natural habitat. Today, the agile wallaby the particular forest type preferred by Lumholtz’s tree-kangaroo, known as the Mabi forest (Mabi is the indigenous Australian word for tree-kangaroo), is an endangered ecosystem.1 As such, the unique evolutionary story of the tree-kangaroos may soon come to an end once and for all. Few people know that these wonderful creatures even exist, so spreading their story may be the only way to save them.

University of Puget Sound

1 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 by itch enning 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000 000000000

â&#x2C6;&#x17E; +1

Numbers beyond comprehension M

t some point in life, everyone has wondered how to quantify â&#x20AC;&#x2DC;bigâ&#x20AC;&#x2122; and has pondered the existence of something that is bigger than everything else. Even children play little games naming bigger numbers than the other kids (oh yeah? Well, infinity + 2!). But what is the biggest meaningful number? Some of the biggest well-known numbers are the very famous googol (10^100) and googolplex (10^googol). While googol falls somewhere in the real world significance section, googolplex is so incomprehensibly large that it is physically impossible to write down all of the zeroes in a googolplex because there is not enough room in the universe.1 To explain the size of the universe is beyond Elements. Seek the wisdom of Carl Sagan.

This is a big number:

Since googolplex is much too large to represent anything in the real world, we should start with relatively small numbers and build up to larger numbers. To begin with, there are about 2,500 students at the University of Puget Sound and approximately 200,000 people living in Tacoma. These numbers are trivialized by the 7,000,000,000 or so people who live on earth. However, just inside of each of our bodies, there are about 25 trillion cells, which makes the population on earth look small.

and these are really, really big numbers... Googol: 10^100

Googolplex 10^Googol

= =

1 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 1 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000

Elements Magazine

0000000000 0000000000 0000000000 0000000000 0000000000 0000000000

When we expand our thought beyond this planet, what we consider as “big,” really begins to dwarf in comparison. Our own universe is huge. Consider the number of particles that make up our universe, estimated to be 10^80.1 And what if our universe is not alone? What if there are other universes out there? Recent developments have led to the multiverse idea, which states that the Big Bang actually produced many different universes, not just one. Theorists estimate that there may be 10^10^10^7 universes in our multiverse.2 It is easy for us to comprehend things that we can actually see or visualize, but these large numbers, like googol, googolplex, or the number of universes in a multiverse, are so incredibly large that our brains can literally not comprehend them. Numbers are abstract, and although we think of them as taking up physical space, they really don’t. And although it is disconcerting to not be able to visualize something that takes up no space, now you know a nice ‘little’ number or two to whip out next time you’re talking with somebody about just how big things can get.

∞

Mind Bender: Grains of Sand^

# of grains per cubic cm...

...in a handful

...in a playground/ beach/ dune

0000000000 0000000000 0000000000 0000000000 ...in a planet, galaxy, universe...do we 0000000000 0000000000 0000000000 0000000000 dare go on? 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 0000000000 (to be continued for the next 10^Googol issues)

University of Puget Sound

A l l p h oto s by W i k i m ed i a C o m m o n s

{

Looking up at a Chinese light festival. Even though we cannot comprehend large numbers, we are still mesmerized by them.

P h oto by W i k i m ed i a C o m m o n s

Elements Magazine

Tree Hugging: Itâ&#x20AC;&#x2122;s not just for hippies By Justin Roberts

he once-favorite pastime of many of our parents may be on the rebound thanks to support from an unlikely source: science! While no studies have come to light that actually examine tree hugging as a health practice, an even goofier practice has received much recent attention in Japan: forest bathing. While it may sound like some hocus-pocus health fad, the benefits of forest bathing, or â&#x20AC;&#x153;shinrinyoku,â&#x20AC;? appear to be supported by cold, hard science.

University of Puget Sound

P h oto by C h r i s P u t n a m

If you’re ready to test the waters, go out and smell some wood chips. Many trees and other plants produce chemicals called phytoncides that serve to protect themselves from infections or destruction from microbes, fungi, and insects. Phytoncides also seem to have a beneficial effect on some human physiological functions.4 Participants in a Japanese study showed a marked decrease in systolic blood pressure (the maximum pressure during a heart Be sustainable and bathe in beat) and decreased prethe forest! frontal brain activity after smelling cedar wood chips, indicating a “relaxed physiological state.”3 The cause of this physiological response is not entirely clear, though it seems likely due to connections between the body’s olfactory system (smell) and the limbic system (associated with emotion and memory) rather than direct chemical absorption into the blood.3

P h oto by W i k i m ed i a C o m m o n s

Forest bathing consists of not just smell but rather a whole mess of potentially influential sense-variables, such as sight, sound, and touch. Researchers employed various strategies, such as cerebral hemodynamics, to measure the effects of all of these variables. Cerebral hemodynamics, which measures brain activity by tracking blood use in the brain, was used to indicate stress. Higher levels of activity in the prefrontal area of the brain, for example, indicate higher levels of stress. They also measured the secretion of salivary amylase, the enzyme in our spit that breaks starches down into sugars, as an indicator of mental stress.3

Three separate field studies in Japan found significant evidence to support forest bathing as a legitimate health practice. Two of the studies compared stress indicators for people who spent time walking in the forest relative to people who walked in an urban area. One study which measured prefrontal brain activity and salivary amylase found that subjects who walked in a forested area for twenty minutes showed lower levels of both stress indicators compared to those that walked in the urban environment.3 In a similar study, forest bathers showed a decrease in systolic blood pressure, pulse rate, cortisol levels, and sympathetic nervous activity, as well as an increase in parasympathetic nervous activity.3 Unlike the parasympathetic nervous system, which is associated with low-stress activities, the sympathetic nervous system is stress-activated and induces the “fight or flight” response, so its reduction signifies reduced stress.2 Another study focused on how forest bathing might affect the immune system by examining “natural killer” cell activity. Natural killer cells, though they sound a bit frightening, are actually on your side; they help the body fight off tumors and viruses.1 Separate studies examining male and female production of natural killer cells found that after staying in a forest environment for three days and two nights, both men and women experienced a significant increase in natural killer cell activity, which lasted for more than seven days following the trip. A similar trip to an urban area did not have this effect.3 While all of this evidence seems to suggest a fundamental connection between human health and nature, and to provide a compelling incentive to get out of cities and into the woods, it also begs us to reconsider the divide we have created between the urban world and the natural. If the mere sight, smell, sound, and feel of nature an reduce our stress levels, improve our immune system functioning, and calm our hectic minds, why should we be content with cities largely devoid of plants and wildlife? Why not plant the roofs and the walls of buildings and put value on urban green space? Perhaps one day urbanites will even be able to forest-bathe as they walk to work.

Cascading rooftop gardens in Japan bring nature and beauty to the city and to modern architecture.

Elements Magazine

P h otos by W i k i m ed i a C o m m o n s I l l u s t r at i o n s by M a g g i e S h a n a h a n

You Snooze you...Win? by

sleep science puts the dreamer in charge

M arisa L opez

he concept of controlling your dreams seems far-fetched and ridiculous, but in reality it is more plausible than you think. Lucid dreaming is a type of natural dream state in which you are consciously aware that you are dreaming. With this awareness, people are able to control their dreams at night and enter a world in which they are no longer constrained by the laws of physics or society and are free to use their imagination to construct a different reality. For centuries, many people regarded this conscious dreaming to be nonsense, because it seemed impossible to determine when a person was actually lucid dreaming. Within the last fifty years, however, scientist have discovered a way to collect empirical evidence. Because eye muscle movement is not paralyzed during the rapid eye movement (REM) cycle, scientists have been able to determine when a dreamer is in a lucid state. When the dreamer enters a lucid state, they signal to the observer through a specific

pattern of eye movements.1 This allows a method for scientists to collect empirical evidence of lucid dreaming. Not only did this breakthrough allow scientists to conclude that lucid dreaming arises during REM cycle, but evidence also suggests that time perception during lucid dreaming nearly matches real-time. Although lucid dreams vary in length, perception of time within the lucid dream closely matches that of reality.2 According to leading expert Stephen LaBerge, some physiological processes such as breathing and heart rate can fluctuate in relation to activities in the lucid dream. For example, LaBerge observed an increase in heart rate when lucid dreamers were dream running.3 Using electroencephalography (EEG) to measure electrical activity along the scalp, scientist have recently concluded that lucid dreaming is a hybrid state of consciousness in brain activity. This hybrid state of consciousness exhibits REM-like fre-

University of Puget Sound

...ZZZZZZZZzzzzzzZZZZZzzzzzzZZZZ!

Want to lucid dream? Here’s how!

...Title Page: No relation to Robert Downy Jr., this Fe Man is an original dream work.

quencies but is unique due to an increased 40-Hz frequency band which is especially strong in the frontolateral portion of the brain. The 40-Hz frequency band indicates neural activity in the frontal sites of the brain and is hypothesized to correspond to the control of conscious awareness across different conscious states.4 Although lucid dreaming seems like a relatively rare experience, studies indicate that about 20% of the population report having lucid dreams naturally at least once a month.5 As a result, much research has been focused on determining what provokes these lucid states. Astonishingly, research has indicated that lucid dreaming is in fact a learnable skill that through various mind exercises can be voluntarily induced. Many strategies to induce lucid dreaming have been devised, but probably the best known is Mnemonic Induction of Lucid Dreaming, or MILD.6 In this strategy, lucid dreaming can be induced by waking yourself up early from a dream and engaging in a brief activity before returning to bed. The key is to remember your previous dream, so when you return to sleep you repeat the dream you just woke from, now aware that it is a dream.1 Another lucid dream approach is based on performing reality tests. With this approach you pick text or symbols that you memorize and focus on periodically throughout the day. If while focusing on these letters or symbols they begin to change then you are most likely dreaming! Conversely, if you witness no change in these indicators, then you are still in reality. This approach is based on the idea that thoughts and ideas that you experience throughout the day often end up influencing your dreams at night.7 Uncovering this learnable skill has proven beneficial for its possible application in therapeutic treatment for people who have lost mobility. The neural pathways involved in imagining movements and conducting real movement are similar. So when individuals are unable to conduct movements in real life, movements in lucid dreams may have an effect on the neural network of real movement; this can be very beneficial in rehabilitation.8 In addition to medical uses, lucid dreaming has also proven useful for professional athletes who use this dream state to rehearse their performance. This is one of the many possible practical applications that are likely to develop from lucid dream research. Although there is much to be learned about this dreaming phenomenon, anyone can try lucid dreaming for themselves using a few simple steps.

The MILD method was developed by Dr. LaBerge and was used in many of his studies to achieve lucid dreaming at will. Although many people have found this method to be successful, the speed at which you develop this ability is largely dependent on how good you are at dream recall.7

First Step: Developing dream recall One of the most important skills for learning to lucid dream is developing effective dream recall. Keep a dream journal, in which every morning you record at least one dream as completely as you can.

Second Step: Focusing intent

Set your alarm early to disrupt one of your dreams. Immediately try to recall your dream completely. Briefly engage in some activity (i.e. reading, going to the bathroom, getting something to drink). Upon returning to sleep, concentrate on recalling your previous dream with the intention of recognizing that you’re dreaming. LeBerge stresses to repeatedly tell yourself “Next time I’m dreaming, I will remember I’m dreaming”. Stay focused on this intent; don’t let your mind wander.

Third Step: Visualize yourself

becoming lucid While focusing on recalling and recognizing your dream, begin to imagine that you are back in that dream. This time imagine that you recognize that you are dreaming. Set a dreamsign. For example, imagine you are flying in your lucid dream. If you see your dreamsign, you will automatically know you are dreaming.

Fourth Step: Repetition

Repeat steps 2 and 3, making sure this intent is the last time thing in your mind before falling asleep.

Elements Magazine

Sugar, Spice, & Microbial Nice:

Microbes and the Flavor of Chocolate By Jessica Wong

takes place during fermentation. The initial acidity of the pulp (pH 3.6) due to citric acid and low oxygen levels allows an early predominance of yeasts. As yeast populations decline over time, lactic acid bacteria take over, which are then succeeded by acetic acid bacteria. Acetic acid bacteria are responsible for the oxidation of ethanol (produced earlier by the yeasts) to acetic acid. This results in the formation of metabolites that trigger a series of biochemical and enzymatic reactions in the seed, which then produce the precursor compounds of chocolate flavor. The diversity of microbes involved in fermentation can vary depending on the origin of the cacao beans and the processing method used. Climatic conditions can sometimes influence the order of microbial succession. Scientists are working to determine how each species contributes to fermentation and the quality of chocolate produced. Ongoing projects are attempting to improve the fermentation process, increase health benefits, and produce more diverse flavors of chocolate.

he generic name for the cacao tree is Theobroma, Friends of this flu mimeaning “food of the gods.” It’s crobe will satisfy those no wonder, for from this tree we get the midnight cravings. main ingredient for one of the world’s best desserts—chocolate. If you’re a chocolate-lover like me, you know what I mean when I say that I live for that rush of endorphins when biting into a sweet, delicious piece of chocolate. But guess what makes chocolate, well, chocolate? It’s not just the milk or sugar or spices, but microbes! Microbial fermentation of cacao beans is the first step in making chocolate, and it is the most important for developing its distinct flavor. Each cacao bean consists of a sweet, white pulp that provides a rich medium for microbial growth. The pulp becomes “contaminated” with microbes when workers expose it by slicing open the pods of the cacao tree; many of the microbes that aid in fermentation come from workers’ hands, knives, and the baskets in which the seeds are transported. Don’t be alarmed, though— fermentation creates a very hot, acidic environment and the beans are then roasted at 100°C, which makes it difficult for contamination by E.coli or Salmonella to occur. The key to chocolate flavor is the microbial succession that

University of Puget Sound

P h oto s by W i k i m ed i a C o m m o n s

So, without microbes, chocolate just wouldn’t taste like chocolate. The next time you bite into a chocolate bar, thank our tiny friends for laying the foundation for that chocolate flavor you’ve been craving!

Golden Ratio

The truth behind beauty

B y B ecca L ong

Nature’s perfect number for beauty is integrated into the natural world and has served as the backbone for art and architecture throughout history. This number, called phi, is universally recognized as ideal and is usually rounded to 1.618. Phi geometry is based on the Fibonacci sequence. The Fibonacci sequence is named after Leonardo of Pisa, who was known as Fibonacci. Although the sequence had been described earlier in Indian mathematics, Fibonacci introduced it to Western European mathematics. The Fibonacci sequence is a pattern of numbers where each number is the sum of the preceding two numbers, for example: 144, 233, 377, 610, 987, 1597, 2584, 4181, 6765, 10946, 17711. As you travel further down the Fibonacci sequence, dividing a number by the number that precedes it, the product approaches 1.618. The resulting golden ratio, 1:1.618 is reflected in nature’s symmetry. This ratio is closely linked to the proportions of the human body and the ‘ideal’ face. The idea is that the closer an object’s proportions are to the golden ratio, the more beautiful it appears. But

The sunflower is an expample of the golden ratio in nature.

can our perception of beauty really be reduced to such a simple mathematical formula? Dr. Stephen Marquardt, of the University of Southern California, has studied human beauty for years in his practice of oral and maxillofacial surgery. In cross-cultural surveys on beauty, Dr. Marquardt found that all groups had the same perceptions of facial beauty. He also analyzed the human face from ancient times to modern day. Through his research, he discovered that what people perceive to be beauty is not only related to phi, but can be generalized across genders and for most races and cultures.1 Marquardt developed a mask

P h oto s by C h r i s 7 3/ W i k i m ed i a C o m m o n s & W i k i m ed i a C o m m o n s

“The golden ratio had graced architecture long before it was deemed a beauty detector.”

Nature

a. Nautilus Shell b. Orchid petals c. Aeonium tabuliforme (a succulent plant)

Elements Magazine

using pentagons and decagons as its foundation, which embodies phi in all its dimensions. Symmetry is another factor that determines a face’s attractiveness. Dr. Kendra Schmid, an assistant professor of biostatistics at the University of Nebraska Medical Center, says that the equation for a “pretty” face, the golden ratio, strongly relies on symmetry. However, plastic surgeons and scientists weren’t the first ones to discover the power of the golden ratio. The golden ratio had graced the pages of history in art and architecture far before it was deemed a beauty detector. Da Vinci himself used it when he drew the perfect human male body in his famous work, the Vitruvian Man. He used the ratio in many of his works, including his most famous piece, the Mona Lisa. Even the Egyptians used the ratio to construct the pyramids of Giza. But the golden ratio emerged way before humans took up tools or a paintbrush; the natural world is riddled with the fingerprints of the golden ratio. 2

Elements Writer: Jason Blanks Golden ratio between outer edges of lips and upper ridges of lips

P h otos by P h oto S e r v i ce s/ M i c h ae l V i l l a s e n o r

Phi represents some remarkable relationships between the proportions of patterns of living plants and animals. The contour spirals of shells, such as the chambered nautilus, reveal growth patterns that are related to the golden ratio as all the chambers reflect the 1:1.618 ratio. Even sunflower seeds and pine cones grow in accordance to the Fibonacci sequence. The growth pattern and space between tree branches and the length of your bones also reflect the ratio.2 Before you start matching your nose shape and eye length to a number, consider the exceptions that defy these golden proportions. They are often as beautiful, or even more spectacular than those that fit them perfectly. After all, beauty isn’t always in the phi of the beholder.

Faces

Elements Staff: Mel Kohler Golden ratio between eyes, mouth and chin

The Mona Lisa was painted using the golden ratio as a guide. This is just one of the many mysteries associaed with this painting.

Elements Writer: Mitch Benning Golden ratio between width of eye and with of iris (right) Golden ratio between outer and inner edge of eye and center of nose (left)

University of Puget Sound

Focus on Fungi B y C l aire S imon

and

J ay G oldberg

ushrooms resemble brains, jelly, teeth, flowers, and rotting flesh. They are used to clean up oil spills and are eaten on a Friday night stuffed with mozzarella and bread crumbs.8 Enough generalities, find out for yourself how cool, alien, and beautiful fungi are. After this, you may want to buy a photographic book of mushrooms--it’s perfect for a coffee table.

Lycoperdon perlatum

Note: Don’t use this as a guide when hunting for mushrooms; picking edible mushrooms is risky. Unless you are an expert with years of field experience (or our Cosmonerd), use extreme caution. One can either have the best meal of their lives, the strangest hallucination, or a long and terrible death.

Lactarius indigo

Commonly known as the “puff ball” or “devil’s snuff-box”, this commonly-found fungi produces a diverse population of useful compounds. It has antimicrobial activity against harmful bacteria like E.coli, the pigment melanin, and cinnamic acid--an organic acid usually found in cinnamon with potential for cancer intervention.11, 1, 6 Ironically, it also contains compounds with antifungal activity.10

A rarity in nature, this fungi is a naturally a beautiful indigo blue. When the tissue is cut, it willl ooze a milky blue substance called latex that turns green after exposure to air. Surprise! It is edible.5

Clavaria zollingeri

Aseroë rubra

This Australian fungus is aptly named the “anenome stinkhorn”. It covers itself with a thick layer of slime that emits a powerful odor resembling the smell of rotting flesh.4

This coral fungus can range in color from deep violets to bright shades of red. It lives just about everywhere from Ireland to Australia. In Ireland, it is used as an indicator of fungal diversity and grassland health.7,8 P h otos by W i k i m ed i a C o m m o n s

Elements Magazine

Amanita muscaria

Amanita muscaria, also known as “fly agaric”, with its bright red cap and tall white stem, is the quintessential toadstool. While they may look like the mushrooms in a game of Mario, eating them won’t make you double in height. They live just about everywhere in the world, and are generally regarded as being poisonous, but not everyone who eats A. muscaria ends up dead (although their cousin the Death Angel, Amanita ocreata, is a different story). Some people report having visions of flying reindeer after having eaten them, and now there’s a growing community of people who believe that these mushrooms might be behind the legend of Santa Claus.2

Tremella mesenterica

Epichloë tiphyna

Nicknamed the “fly wranglin’ fungus”, this orange fungus “talks” to flies by chemo-attractants in the air (aka smell). Just as flowers attract bees, fungis attract flies to facilitate reproduction. Once the flies are swooned, the fungus loads the fly bodies up with gametes, just like a flower covering a bee with pollen. The fly then spreads the fungi’s gametes around, helping it disperse its population.1,2

The best part about this fungi? Its common names. This slimy glob goes by the name of “yellow brain”, “golden jelly fungus”, “yellow trembler”, and “witches’ butter.” Although visually unappealing and tasteless, this fungi is edible and is sometimes used to texture soups. Take a stroll through the president’s woods and pick up some witches’ butter for a homemade winter soup, because this fungi grows in the Northwest.3

University of Puget Sound

Your Favorite Animals by

K athryn Papoulias

e all know mammals can be pretty cute – just one look at a fluffy, adorable kitten and pretty much everyone will melt. But just like we humans are capable of some pretty disgusting and not-so-precious things (I’m looking at you, nose-pickers-andflickers), so too are those cute, cuddly animals. Here we focus on four commonly oohed-and ahhed over mammals.

Photo by Jay Goldberg

Koalas The koala – cute, cuddly, and… cacophonous? Those adorable koalas you see relaxing in eucalyptus trees are significantly less charming when they’re bellowing at the top of their lungs during mating season. Male koalas have specially designed larynxes that allow them to make loud, deep, resonant calls that are comparable to those of bison. Specifically, their larynxes are descended, which means they are lower in the throat and therefore leave more room for an extended vocal tract.1 Larger males have longer vocal tracts, making them more desirable to females. Males also have scent glands on their chests which they rub against trees during mating season, leaving behind a very musky odor; but don’t worry, when it’s not mating season they don’t smell like musk, only urine. Much better. But wait, that’s not all. Koalas looking to mate in Queensland need to watch out – currently, at least 50% of koalas in Queensland have chlamydia.2 It’s not the same strain that is found in humans, and no one is quite sure how the koalas picked it up, but it’s decimating populations. It’s easily transmitted through mating and birth (and possibly fighting), and can cause blindness, urinary tract infections, respiratory problems, and infertility – all of which can lead to death over time.

Dwarf Sperm Whale Hides from ca mer our a s!

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Whales – the enigmatic ambassadors of the open ocean. They’re beautiful, serene, and (who would have guessed?) they produce clouds of feces as defense! Dwarf sperm whales (particularly mother and calf pairs) have been observed releasing clouds of feces when they feel threatened. The whales fan it out with their tails and then hide inside the cloud for defense.3 The cloud of poop. You’re welcome.

Slow Loris The slow loris has become an internet phenomenon ever since a certain YouTube video hit the mainstream (search “tickling the slow loris” if you haven’t seen it yet). And who can blame the general public? The slow loris is adorable – it’s a small primate that has absurdly huge eyes, a bemused expression, and of course, it is really slow. But before you rush out to buy your own slow loris to tickle, you should know that they might be the world’s only venomous primate (research is ongoing). Slow lorises have sharp, needlelike teeth on their lower jaw called dental combs. When startled or threatened, slow lorises lick a gland near their elbow, swish the sweat-turned-toxin around in their mouth, and bite with their nowvenomous teeth.4 So why would anyone ever want one as a pet if they bite when uncomfortable? In order to make them safe for your average ill-informed citizen looking for an exotic pet, illegal pet traders cut or rip out slow loris teeth before they’re sold, making it hard for the loris to bite . . . and eat (they often die from poor nutrition and infection).5 They’re also nocturnal, so those cute videos filmed during the day are actually blinding the slow loris. So next time you see an adorable picture or video about a slow loris, remember that they might not make the most suitable pets. Look out for Big-Eyed Needle-Tooth! Its mouth may be toxic.

Sea Otter

Photo by Wikimedia Commons

And now, the grand finale: sea otters. The sea otter is arguably the cutest, most beloved animal of all time. If all world leaders played with sea otter pups together, we would probably achieve world peace in roughly five minutes. But knowing how those cute sea otter pups are made? Well, it’s terrifying. During mating, male otters often hold the female underwater and bite their noses for grip, leaving them bloodied and scarred. In fact, you can usually identify otters in the wild as male or female by the presence of scars on their nose.6 Because these encounters are so violent, they can prove fatal for the female. But it gets worse – for currently unknown reasons, female sea otters are declining in number, leaving males without mating opportunities. Sea otter social structure Is that an urchin or what’s left of his mate’s head? is based on dominant males having a harem of females and excluding weaker males, so the falling numbers of females in sea otter populations are leaving many male otters without mates. In Monterey, California males that are denied mating opportunities have been seen aggressively copulating with harbor seals, almost always leading to the seal’s death.6

“...why would anyone ever want one as a pet...”

This concludes our tour of the darker side of some of our most adored mammals. Next time someone gushes to you about how much he wants to hold a koala, or how she would love to swim with a whale, feel free to point out that the koala probably has chlamydia and that dwarf sperm whale could engulf you in a cloud of poop. You’ll definitely make that animal all the more memorable for them.

University of Puget Sound

Introducing new Science Professors Welcome to the Puge! By Jason Blanks

Siddharth Ramakrishnan Assistant Professor, Biology, Jennie M. Caruthers Chair in Neuroscience Siddarth Ramakrishnan joined the Puget Sound community this year as the first ever Jennie M. Caruthers Chair in Neuroscience. With experience in computer science, artificial intelligence, developmental neurology, and media arts, Siddarth brings a diverse academic background to this growing interdisciplinary program. Can you tell me a little about your background and about how you ended up at Puget Sound. I was born in South East India. In India you have to decide what you want to do around sixteen or seventeen. I was doing biology in high school and was very fascinated by biology. My dad was a doctor, my older brother was a doctor, but I didn’t want to be a medical doctor. But a PhD is kind of looked down upon. In India they say, “If you can’t do anything else you get a PhD.” I went to a great liberal arts college for a computer science degree. I then went to Chicago for my Masters in Artificial Intelligence. I had expected it to be very interesting, but all we did was optimize algorithms—very bland and boring. There was nothing intelligent about it at all. I decided to quit my Masters and did a PhD in neuroscience, where I could model animal brains. Then I moved to New York where I worked at Columbia in the Electrical Engineering department, while also teaching at Parson’s School of Design (where Project Runway is hosted). After two years in New York, I was hired to be the Neuroscience chair here at Puget Sound.

What are your plans for the neuroscience department? What classes and/or programs can a student interested in neuroscience expect in the next few years? Neuroscience is going to remain an emphasis. Maybe down the line it will become a minor, but we feel neuroscience is a very interdisciplinary field. In terms of classes, we plan to continue with the core introductory Neuro 201 class but begin introducing pilot labs. Next semester, the capstone seminar will be on neuroendocrinology.

Siddharth feeling at home in the labs of Puget Sound

What we’re planning for the program itself is a little ambitious. We want to start having podcasts where students interview neuroscience professors and researchers. I also want students to ask lay people what they know about neuroscience. One of main problems I feel is that universities are becoming closed spaces and the knowledge is not flowing out into the community, and I hope that this will help university people reach out to the community.

What research can students expect to see in your lab? I’m still in the process of purchasing equipment for my lab, but ultimately I will have an electrophysiology lab where we record nerve potentials from snail and fish neurons. Neurophysiology, as a technique, takes a lot of time, not just to learn, but the actual experiments required constant attention for at least three hours. Therefore, this technique is much more feasible over the summer as a research grant.

If you could teach any class, what class would be most excited to teach? Puget Sound has been great about letting me teach the classes I’m interested in. They are letting me teach Art and Science in the Spring as well as nanobiology next fall.

What was your third grade Halloween costume? We don’t have Halloween, but we do have fancy dress competitions, and I was a fairy in a white dress with wings. My older brother won by dressing up as a famous Hindi spiritual leader and giving a speech, but I was still happy as a fairy!

Weapon of choice in a food fight? Food fights are not common in India, but I’d use curry powder. I’d definitely win; no one would want to get hit by napalms of curry powder.

Elements Magazine

Luc Boisvert Assistant Professor Chemistry After 32 years of teaching Organic Chemistry, Professor William Dasher retired, leaving the Chemistry Department in need of a laid-back Organic Chemist with great taste in music. This position was aptly filled by Luc Boisvert (pronounce Luke Buā-vēr), an easygoing Organic Chemist from Canada with a love for jazz, blues, and classic rock (he openly claims that “While My Guitar Gently Weeps” is the greatest rock song ever written).

Luc (right) and Dasher (left) share a laugh at the annual Chemistry Club Cider Squeeze

Can you tell me a little about your background and about how you ended up at Puget Sound, obviously you are not originally from the US? I see you are detecting my accent. I was born in Canada in the province of Quebec called Abitibi, more specifically the city of Amos. When I was nine years old I moved closer to Montreal, which is the biggest city in Quebec, and did my undergraduate studies at Sherbrook University in Sherbrook. Where I come from it is much more common to do your undergraduate and your graduate work in the same place so I did my PhD at Sherbrook University as well. And between my undergraduate and my graduate studies I worked for about a year and a half in a pharmaceutical company. After my PhD I moved to Seattle where I did my Post-Doctoral work at the University of Washington. Then I was a visiting professor at Reed College in Portland for two years and now I am here at Puget Sound, hopefully for a long time.

Was it a hard decision to switch to the chemistry track, you were obviously very interested in history and literature?

Most dangerous thing that has happened in a lab you’ve taught? I was co-teaching an Organic Chemistry lab and at some point I hear a scream and run to the other side of lab to see a student with a Pasteur pipet right through her hand, squirting blood everywhere! I’ve seen fires, explosions, implosions, but having a Pasteur pipet through the hand, how do you react to this? And as the instructor you have to be calm and find a solution, but on the inside I was freaking out!

If you could teach any class, what would you teach?

I think I would teach Jazz history. I am not a musician, but I love music and I always listen to music, especially jazz and blues. I could never teach music theory or performance but Jazz History would be really fun.

Favorite Element?

I’d have to say Carbon. If it wasn’t, I’d be in the wrong area of research.

Who’d win in a fight? Le Chatelier or Heisenberg?

My approach was actually very rational. I knew that I needed liter- Well to fight Heisenberg you have to get your hands on him, right? ature and history in my life and I knew also, that I needed science. You know in which direction he is going but you don’t know where I needed equations, I needed equalities: this plus this equals that. I he is really. So because of his fleeting nature, I think Heisenberg needed that very Cartesian way and I needed the other part. Then would win. when it came down deciding which I was going to chose, for me Third grade Halloween costume? it was very rational. If I go into I was probably Superman or a pirate. I was very into pirates science as a profession I can do the rest, read about literature, “I knew that I needed litera- even when I got older. read about history. But if you’re Weapon of choice in a food fight? in history or literature how are ture and history in my life... you going to get your science also, that I needed science.” I’m guessing the goal is not to hurt but to splash. Both for its quality of fight and its quality of splashing it would have fix? You can’t do it at home can to be something like spaghetti with red sauce. It has the you? There’s not much you can density to fly and it’s going to SPLOOSH very nicely. do that is very advanced. So I picked Chemistry; easy as that.

University of Puget Sound

THE ALLIUM We’ve done the golden calculations. It turns out the onion is perfectly proportioned, so visually pleasing that it burns your eyes when you get too close. but careful with this dangerous beauty! Like haircuts, ogres, and other layered things, the allium should be approached with caution. When you peel this onion, things may get dicey... Meaning, articles in this section aren’t perfectly serious, take them at face value with little to no calculation.

P h oto by W i k i m ed i a C o m m o n s

WARNING: This is Elements’ comedic section. You may laugh so hard you cry. Or, you may just cry.... It is an onion after all.

2424

Elements Magazine

Au!

The “Hey You” for science majors Feelin’ nerdy? Submit your Au’s to the box in Oppenheimer or email elements@pugetsound.edu Au! Roses are 630 nm

Au! Why is your flagella the size

Au! What is yellow and black that of a microbe? That is too small to

enter my pore. helps create the majority of the food we eat on this planet? The honey bee, silly. Au! Lab partner, can’t you feel the chemistry between us... on TuesAu! Wolbachia is my friend. day nights... from 6-10?

Au! You activate all my heat sen- Au! Bio sucks! Kiss a chemist! sitive pathways!

Au! I said I have chlamydomonas, Au! Tonight let’s get to equilib-

not the clap. Violets are 450 nm When I see all your colors I think your spectrum’s quite nifty Au! Le Chatelier had it right, as soon as we were added together equilibrium shifted towards the Au! Persian hottie. You’re as hot reaction coming to completion. as the inductively coupled plasma (ion) torch – And I’ll be your nebAu! … and it only took as long as ulized sample. a bond vibration.

rium together.

Au! If we were a software design,

with my geo prof. next semester.

we’d suck since we’re so tightly Au! Housemates, those gasses

Au! Cute girl in Thompson, I like the way you move electrons. Let’s overlap orbitals sometime.

Au! Chemistry is Boron! Biology has more life!

Au! I’m excited to get my rocks off

you’re making don’t smell very Au! Boy who wears shorts, I don’t noble... need a physics lab to tell me there’s friction between us! Au! Be my stalagmite and grow mighty in my cave. Au! Sometimes I think that coupled!

chemical spill wasn’t an accident, Au! I’ve evolved for millions of Au! I wish I could be adenine so and you just wanted to see me in years to make your caramel macthe emergency shower. that I could be paired with U. chiato, you sweet thing.

Au! I have a solution that will Au! I want to be your derivative help us bond favorably. so I can lie tangent to your curves.

an electric pickle at are the way you are due to incomthe Chemistry magic plete penetrance. show.

Au! Hottie in geology, you make me quake as you walk by.

University of Puget Sound

P h oto by K i r a T h u r m a n

Au! Sometimes I wonder if you Au! Rock me like

From: Scientific After extensive research

I skimmed an article

By Kira Thurman

In this experiment

Once Twice…maybe three times

Case after case As shown by careful calculations

I spilled my lunch on my work and am NOT doing it again

Measured to a high degree of precision and accuracy

I could not remember the difference between precision and accuracy

It is generally known that…

My professor told us in class

The data is satisfactory

Maybe if you tilt your head and squint your eyes… maybe

Additional research is required

I still don’t get it

A trend is evident in the following graph

I don’t see one, but my professor told us it was there

P h oto by W i k i m ed i a C o m m o n s

A possible source of error

I messed up

Periodic Humor

A ngelica K ong

Some (highly sophisticated) jokes to lighten the mood! Although the answers have been provided, they still need to be decoded! Find the numbered element on the periodic table and use the letter symbols reveal the answer. [Example: 56 27 7 spells “BaCoN”] 1: What do pirates do at sea? A: 74 13 19 , 15 57 7 6 19 16 , 6 8 7 16 73 7 81 39

4: What if I told you 15 was my favorite number? A: 90 85 16 , 15 75 15 67 16 15 67 44 16

2: What is the answer to this question? A: 56 14 6 , 16 8 71 22 8 7

5: What do you call an impulsive pack of kleenex? A: 7 68 23 8 92 16 , 22 16 16 92 99

1: WAlK PLaNCKS CONSTaNTlY 2: BaSiC SOLuTiON 3: NoThIn ThErEs No ArTiCuLaTiON 4: ThAtS PRePHoSPHoRuS 5: NErVOUS TiSSUEs

3: What did the humerus say to the femur? A: 102 90 49 , 90 68 99 , 102 , 18 22 29 57 22 8 7

Elements Magazine

P h oto by W i k i m ed i a C o m m o n s

To: English

WARNING! Over 21, For Your Legal Eyes Only! *These contain alcohol and dangerous bacteria

Microbial Mixology

“‘Jello’ Bacillus Shot”

fter a long day in lab where, let face it, none of your experiments worked, nothing remedies your despondency like a few shots of alcohol. But why spend $4 at a bar for a Lemon Drop when you can use material in lab that your PI’s grant pays for? Here are a few shot recipes created from everyday bacterial culture reagents to get you through the hard time (i.e. lab dayl). I mean if it’s good enough for E. coli, it’s good enough for you!

In a shaker add: 2.0g Peptone 0.4 Yeast Extract .6g agar 0.1 g NaCl 20ml Blue Curacao 20ml Malibu Rum, 60ml Blue Kool-Aid

P h otos by J a s o n B l a n k s

“Lysogeny Drop” In a shaker add: 4g Sucrose 1.2g Yeast Extract 2.4g Peptone 60ml Vodka 40ml DI water Juice of a lemon

Heat agar in the Kool-Aid (sterile) for 30sec in microwave. Add other ingredients, shake and pour. Let sit in the fridge until jello-like!

Shots!

Coat rim of each shot glass in Sucrose then pour in the drink. Garnish with a Lemon Wedge Gut bacteria like E. coli love high nutrient medias with lots of sugars and proteins, making the Lysogny Drop excellent fodder for our microbial friends. And with over 1kg of bacteria in the gut alone, the more Lysogeny Drops you drop, the happier your microbiota will be. Talk about probiotics in action!

Shots!

“Jose Halo” In shaker add: 1.2g Yeast Extract 2.4g Peptone 80ml Tequila 20ml DI water .5ml 2M NaCl

B y Jason B lanks

You don’t need agarase to enjoy these maritime beverages. Of course a little HGT between Pseudomonas atlantica and your gut bacteroides wouldn’t hurt. Just be careful; drink too many of these and you’ll be nuder that a nudibranch!

“Thermophile’s Delight” Add 15ml of Grenadine to a shot glass In a shaker add: 2g Dextrose 1.2g Yeast Nitrogen Base 1.2g Peptone 60ml Fireball Whisky Layer 20ml of the Whisky mixture over the Grenadine with a 1ml pipet then add 5ml 151 rum and ignite!

Coat rim with Pink Sea Salt. Add party hat! Don’t be fooled by the cute hat; this shot is only meant for the most extreme muchachos. This adventurous mix of tequila and salt is strong enough to awaken your palate and any halophile. So put on your sombrero and get ready for a night you’ll never remember.

University of Puget Sound

If you can’t handle the heat, get out of the incubator. This fiery drink is a breeding ground for Thermophiles and steamy nights out on the town! Drink enough of these and you’ll feel like Hudson Freeze (discoverer of Thermus aquaticus)!

Shots! 27

Elements Sneak Preview-NEW biology course for Spring 2013:

Bio 360:AB

Evolution Lab Syllabus

I nstructor : The I llustrious and I mmortal D r . P e t er W imberger CA s : M aggie S hanahan and D aniel G uil ak Offices: Dinosaur Shelter 6, Pangaea Seer’s Hut/Communal Outhouse, Mesopotamia, Fertile Crescent Thompson Hall Room 295, University of Puget Sound Credits: 13.75 ± 0.11 billion years = roughly 1.562 x 1020 credit hours Prerequisites: Approximately 2 billion years of prokaryote development, or Biology 111 Course Materials: Philosopher’s stone; TARDIS, Magic School Bus, or 1981 DeLorean DMC-12 with flux capacitor (no less than 1.21 gigawatt power output, please).

Course description: A lab on an evolutionary time scale is a significant time commitment -- with the odd schedule it’s not exactly the natural selection for a course. Observations will likely take millions of years, and most experiments will fail (see ammonites, trilobites, Hallucigenia, mammoths, dodo birds, and Passenger Pigeons although there will be unexpected successes (see coelacanth).

Class policies: Late assignments will be marked down 10% per millenium. In the event of mass extinction or unexpected rifts in

the space-time continuum, papers may be submitted via email. Always come to lab prepared. For labs taking place in early atmospheric conditions, students will be expected to bring their own oxygen.

Important dates: 650 million years ago: Snowball Earth (winter break) 545 million years ago: the Cambrian explosion, or “midterms,” which include a 70-80 million year period where evolution accelerates by an order of magnitude. 250 million years ago: mid-term exams returned in time for the Permian mass extinction. 3.85 million years ago: evening seminar with guest grunter, Lucy. 1662: Dodo bird conservation in Mauritius: practice experimental troubleshooting (birds in trouble; no shooting.) 1820s: Panel discussion - Lamarck and Darwin go neck ‘n (giraffe) neck on the function of acquired characteristics. 1856: Pea-planting with guest lecturer Gregor Mendel 1925: Scoping out the monkey trials

Final Project: GMOs and homeobox genes - make your own species (bonus points for new limbs, vestigial structures will be marked down)

Lab Practical: Successfully create complex life on Mars Class will reconvene post-apocalypse on December 21, 2012 at The Restaurant at the End of the Universe for appetizers and desserts.

Elements Magazine

Human Evolution Quiz What kind of human are you? By Maggie Shanahan and Jay Goldberg

What is your favorite food? a) tree bark (1) b) pop-tarts (4) c) berries (2) d) giant sloth steak (3) Your best friend is cornered by a saber-toothed cat. How would you go about helping him/her? a) hit the cat with your wooden club (2) b) throw your homemade spear at it (3) c) punch it in the tooth (1) d) coax him/her out from under the museum display (4) Time for dinner. How do you get there? a) fly there with my jetpack (4) b) walk (1) c) drive there in a foot-powered car (3) d) hitch a ride on my wooly mammoth (2) What size hat do you wear? a) my head is so big I can’t find a hat that fits(2) b) what’s a hat? (1) c) bigger than a grapefruit but smaller than a bread box (4) d) armadillo only comes in one size (3) What is your dream home? a) I’ll stick with my cave, man (2) b) tree house (1) c) space station (4) d) I’ll carry mine with me, thank you (3)

0-5 Australopithicus afarensis You have strong arms and curved fingers well-suited for climbing trees. Your face is quite ape-like, but you are able to walk upright. You have an aunt named Lucy.

5-10 Homo habilis Your name is Latin for “handy-man,” as you learned how to make tools out of stone before any other species. Small wonder, since your brain is about 50% larger than your Australopithicine ancestors.

10-15 Homo neanderthalensis You are more evolved than people give you credit for. You were the first species to speak a language, bury your dead, and behave symbolically. Your body is specially adapted for cold, glacial climates.

Scoring

Sample Cave Calculation:

15-20 Homo sapiens Congratulations! You are a modern, civilized human being. Your species evolved roughly 200,000 years ago, and had spread across the globe by 100,000 years ago.

University of Puget Sound

CITATIONS TREE KANGAROOS

1. Martin, Roger William (July 2005). Tree-kangaroos of Australia and New Guinea. CSIRO. ISBN 978-0-643-09072-9. 2. Archer, Mike (1991). Riversleigh: The Story of Animals in Ancient Rainforest of Inland Australia. Bangowlah, NSW: Reed Books. 3. Tuft, K. D.; Crowther, M.S.; McArthur, C. (2011). “Multiple scales of diet selection of brush-tailed rock-wallabies (Petrogale penicillata)”. Australian Mammalogy 33: 169–180. 4. Flannery, Timothy; Martin, Roger; Szalay, Alexandra (1996). Treekangaroos: A Curious Natural History. Melbourne VIC: Reed Books. pp. 68–72. ISBN 978-0-7301-0492-6. 5. Hopkins, M. S.; J. Ash, A. W. Graham, J. Head, and R. K. Hewitt (1993). “Charcoal evidence of the spatial extent of the Eucalyptus woodland expansions and rainforest contractions in North Queensland during the late Pleistocene”. Journal of Biogeography 20: 357–372. 6. Prideaux, G. J., Warburton, N.M. (2010). Macropods. Collingwood, VIC: CSIRO. pp. 137–151. 7. Flannery, T. (1995). Mammals of New Guinea. Reed Books. ISBN 0-7301-0411-7.

GOLDEN RATIO

1. Marquardt, S. . Golden Decagon and Human Facial Beauty. Journal of Clinical Orthodontics. 2012. 2. Livio, M. The Golden Ratio: The Story of Phi, the World’s Most Astonishing Number. New York. Broadway Books. 2002. 3. Dunlap, R. The Golden Ratio and Fibonacci Numbers. Singapore. World Scientific. 1997.

FOREST BATHING

1. Science Daily contributors. Natural Killer Cell [Internet]. Science Daily, your source for the latest research news; [cited 2012 Oct 29] Available from: http://www.sciencedaily.com/articles/n/natural_killer_cell.htm 2. Science Daily contributors. Sympathetic Nervous System [Internet]. Science Daily, your source for the latest research news. Available from: www.sciencedaily.com/articles/s/sympathetic_nervous_system. htm 3. Tsunetsugu, Y., Park, B.-J. & Miyazaki, Y. Trends in research related to ‘Shinrin-yoku’ (taking in the forest atmosphere or forest bathing) in Japan. Environmental Health and Preventive Medicine. 2010: 15(1): 27–37 4. Wikipedia contributors. Phytoncide [Internet]. Wikipedia, The Free Encyclopedia; 2012 Sept 28, 12:50 UTC Available from: http://en.wikipedia.org/wiki/Phytoncide

LUCID DREAMING

1. Blackmore, Susan. “Dreams that do what the’yre told: Most of us are deceived by dreams, manipulated while asleep. It doesn’t have to be like that - lucid dreaming can put you back in control.” New Scientist. 06 1990: n. page. Print. 2. LaBerge, Stephen. “ Lucid dreaming: Evidence that REM sleep can support unimpaired cognitive function and a methodology for studying the psychophysiology of dreaming” Behavioral and Brain Sciences. 23. (2000): n. page. Web. 20 Oct. 2012. 3. LaBerge, Stephen, Lynne Levitan, and William Dement. “Journal of Mind and Behavior.” Journal of Mind and Behavior. 7. (1986): 251258. Web. 20 Oct. 2012. 4. Voss, Ursula, Romain Holzmann, et al. “ Lucid Dreaming: A State of Consciousness with Features of Both Waking and Non-Lucid Dreaming.” Sleep. 32. (2009): 1191-1200. Web. 20 Oct. 2012. 5. Snyder, THOMAS J., and J. A. Y. N. E. Gackenbach. “Individual differences associated with lucid dreaming.” Conscious mind, sleeping

brain: Perspectives on lucid dreaming (1988): 221-259. 6. STEPHEN P. LABERGE (1980) LUCID DREAMING AS A LEARNABLE SKILL: A CASE STUDY. Perceptual and Motor Skills: Volume 51, Issue , pp. 1039-1042. 7. LaBerge, S. & Levitan, L. (2004). Lucid Dreaming FAQ. Version 2.3, January 16, 2003 http://lucidity.com/LucidDreamingFAQ.html 8. Hamzelou, Jessica. “Hijack your own dreams to improve your skills.” New Scientist. 20 2011: n. page. Web. 20 Oct. 2012.

FAVORITE ANIMALS EXPOSED

1. Welsh J. Koalas bellow out their size during mating season. Live Science. 2011 Sept: 29. 2. Barrow K. Squeezed into smaller spaces, koalas now face deadly disease. New York Times (National Ed.). 2012 Feb 21: Sect. D:3. 3. Scott MD, Cordaro JG. Behavioral observations of the dwarf sperm whale, Kogia simus. Mar Mamm Sci. 1987: 3, 353-354. 4. Kalimullah EA, Schmidt SM, Schmidt MJ, Lu JJ. Beware the pygmy slow loris? Clinical Toxicology. 2008: 46, 602. 5. Sherwin A. YouTube sensation fuelling trade in an endangered species. The Independent. 2011 Mar 22. 6. Mulvaney K. The other side of otters. Discovery News. 2011 Mar 21.

BIG NUMBERS

1. Wilkins, A. These are the biggest numbers in the universe. io9. 2011. 2. Physicists Calculated Number of Universes in the Multiverse. The Physics arXiv blog. 2009.

FUNGI

1. Almendros G, Martín F, González-Vila FJ, Martínez AT. (1987). “Melanins and lipids inLycoperdon perlatum fruit bodies”. Transactions of the British Mycological Society 89(4): 533–7. doi:10.1016/ S0007-1536(87)80087-6. 2. “Amanita muscaria.” Wikipedia. Accessed 17 Nov. 2012. URL: a.org/ wikipedia/commons/a/a9/Epichlo%C3%AB_tiphyna.JPG 3. Davidson JL, Davidson A, Saberi H, Jaine T. (2006). The Oxford Companion to Food. Oxford [Oxfordshire]: Oxford University Press. p. 420. ISBN 0-19-280681-5. 4. Grey P (2005). Fungi Down Under:the Fungimap Guide to Australian Fungi. Melbourne: Royal Botanic Gardens. p. 95. ISBN 0-64644674-6. 5. “Lactarius Indigo.” Wikipedia. Accessed 17 Nov. 2012. URL: http:// en.wikipedia.org/wiki/Lactarius_indigo 6. Liu L, Hudgins WR, Shack S, MQ Yin, Samid D. (1995). “Cinnamic acid: a natural product with potential use in cancer intervention.” Int J Cancer 62 (3): 345-50. 7. McHugh R, Mitchel D, Wright M, Anderson R. (2001). “The Fungi of Irish Grasslands and their value for nature conservation”. Biology and Environment: Proceedings of the Royal Irish Academy 101B (3): 225–42 8. Petersen RH. (1978). “Genus Clavaria in southeastern Australia”. Australian Journal of Botany 26 (3): 415–24. 9. “Petroleum-Eating Mushrooms.” Science Daily: Science News. 30 Nov. 2011. Accessed: 17 Nov. 2012. URL http://www.sciencedaily. com/releases/2011/11/111130125412.htm. 10. Pujol V, Seux V, Villard J. (1990). “Research of antifungal substances produced by higher fungi in culture”. Annales Pharmaceutiques Françaises 48 (1): 17–22.ISSN 0003-4509. 11. Ramesh C, Pattar MG. (2010). “Antimicrobial properties, antioxidant activity and bioactive compounds from six wild edible mushrooms of western ghats of Karnataka, India”. Pharmacognosy Research 2 (2): 107–12. doi:10.4103/0974-8490.62953.PMC 3140106. PMID 21808550. 12. Steinebrunner, F., Twele, R., et al. Role of odour compounds in the attraction of gamete vectors in endophytic Epichloë fungi. 2008. New Phytologist 178: 401-411 P h oto by M at t S k l a r

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University of Puget Sound

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