Issue 13

University of Puget Sound 1Issue 13, Spring 2013

The Scientific Magazine of the University of Puget Sound

Digging DeepReveals a

Naked Mystery

Where WillCuriosity Take Us?

Good Vibrations:The Physics of Guitar Sound

Status Updatefrom The Allium

See Back Cover!

Elements Magazine2

CreditsEditor-in-Chief: Claire SimonHead Copy Editor: Chelsea Clark Head Layout Editor: Kira ThurmanStaff Editors: Maggie Shanahan & Jay GoldbergFront Cover Illustration: Mary Wexman Table of Contents Photo: Marisa LopezAllium Cover: Claire SimonCosmoNerds: Rachel Edgar and Daniel GuilakCosmoNerd Photo/Layout: Chris Putnam/Mel Kohler

AcknowledgmentsWe would like to thank the following organizations and individuals: the ASUPS Media Board, Tamanawas for loaning us their computers and software, and UPS Photo Services for curbing our Wikimedia usage!

Contact & Publishinge-mail: [email protected]: http://clubs.ups.edu/clubs/elementsmail: ASUPS - Elements, University of Puget Sound, 1500 N Warner St. #1017, Tacoma, WA 98416Published by QC Graphics LLC1819 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.

Letter From The EditorPart I: Unconventional Introduction

Welcome to Elements Magazine from UPS!Now on number thirteen,With handmade illustrations, intriguing articles, and student pho-tos,This issue is the best I’ve ever seen.

The creativity from fellow students is amazing.It shows how science and art readily combine,It has inspired this unusual form of a letter And compelled me to make parts of it rhyme.

Part II. Ode to Issue 13, We Went BOLDIn this issue, we break the boundaries of topsoilAnd explore the tunnels of peculiar semi-naked creatures.While underground, be sure to examine the roots, Beneficial microbes and fungi dwell in those plant features.

Curiosity on Mars breaks the boundary of our planet,Student research expands our understanding of pain,And a tiny organism also known as a “water bear”Can survive in outer space conditions, it’s insane!

Part III: Elements of ElementsStepping away from the rhyme for a moment, I want to highlight this spring issue in a broader perspective. At Elements, a magazine that roots itself in balancing presentation, accuracy, as well as acces-sibility, it is challenging to strike the right pitch. Deciding when to simplify or add complexity in science writing seems to pit readability against accuracy within every paragraph. For images, which are worth a thousand words, things get propor-tionally more complicated. In a textbook or scientific publication, figures are a manifestation of a particular concept, yet in a magazine they must also be visually pleasing and accessible to our readers. For example, a photo of a perfect snowflake may give insight into the beauty of crystallization while at the same time deceive the viewer--these “perfect” snowflakes rarely occur in nature. One should par-ticularly notice the diverse display of images in this issue. There are hand-drawn illustrations, computer generated figures, and a plethora of student photos. We hope this issue challenges your per-ception of any image or figure you encounter in a text book, article, or magazine. Not every line, shape, or blade of grass is exactly as it seems. We also hope it adds to your appreciation of the hard work and effort behind what appears to be an effortlessly great photo. For some, this takes a lifetime. For us at Elements, it takes one hard-working semester. So it figures, we are awesome.

Part IV. Rhyming Again for the Final GoodbyeIt is most of the staff’s and my final year at UPS and Elements Mag-azine.This is an attempt to condense the greatness of our experience to-getherOf deadlines, weekly meetings, challenges, friendships, Fun, growth, and way, way too much fruit leather.

Huge appreciation to everyone involved in this and every issue!Your participation, dedication, and enthusiasm is inspiringThat means you, math nerds smeared with pie, dangling photogra-phers, Everyday supporters, and all the editors who work without tiring.

As Elements and I go on to new and separate adventuresI will surely keep in touch.All I can say is that I will miss this.Everyone at Elements, it has been clutch.

Enjoy our hard-work and this amazing spread!

Sincerely,Claire (aka “Rhymin’”) SimonEditor-in-Chief

“Mad Lab” Elements Staff

Front: Chelsea Clark, Claire Simon, Kira Thur-man

Back: Maggie Shanahan, Jay Goldberg

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Front Cover Species Plant/Fungi Identification Key (from left to right):Oregon grape, Sword Fern, Western Trillium, Horsetail-Western Trillium, Amanitas, brown mushroom 1, Blue Gum (Eucalyptus), shelf shroom (top), light brown mushroom 2

University of Puget Sound 3University of Puget Sound 3

Table of ContentsNaked Mole-Rats Bare it All: Stories from Underground 4Katie Moran My Love Affair with the Eastern Newt 6Michaela AldenMission to Mars: Getting the Best of our Curiosity 8Kira ThurmanDefining Science: It’s an Asteroid… It’s a Meteor… It’s a Meteorite 9David SantillanFriends with Benefits: Symbiotic Relationship Between Plants, Bcteria, and Fungi 10Spencer GordonPhysics and the Fretboard: Getting in Tune with Your Guitar 12 Angelica KongDelayed Effects of Stress: The Relationship Between Stress and Headaches 14Chelsea ClarkPB & A: Peanut Butter and Antibotics Fill Stomachs, Fight Infections 16Becca Long Gossiping Gardens: What do the Trees Have to Say? 17Jay GoldbergBack from the Brink: Researchers identify proteins that allow tardigrades to enter “reversible death” 19Michaela AldenTHE ALLIUM 21Mad Labs 22Maggie Shanahan and Chelsea ClarkPointed Observations 23Mary Wexman“I’m Just Too Viscous, Mr. Bowen” 24Lauren FellowsThey Said WHAT?: Little known sayings from widely known scientists 25Kira Thurman and David SantillanCosmoNerd 26 Citations 27FLIP!Back Cover: Contest Winner, Sharon StyerPhoto Contest Winners 31Honorable Mentions: Staff favorites 30Ode to the Images in Science 29Claire Simon

FLIP!

Elements Magazine4

Contrary to their name, naked mole-rats (Heterocephalus glaber) are not moles, rats, or even naked. You probably recognize these little guys from childhood visits to the

zoo, or because they make great sidekicks for teenage secret agents like Kim Possible. They are known for their giant teeth and excel-lent digging skills, and they have been known to periodically yell things such as, “Booya!” ...or maybe that was just in the cartoon. Naked mole-rats are small rodents that live in extensive under-ground tunnels in Eastern Africa. They are in the same order as rats (Rodentia) but belong to a distinct family (Bathyergidae) of mole-rats including the blind mole-rat, cape mole-rat, star-nosed mole-rat, and common mole-rat. These rodents are not truly na-ked because they have special sensory hairs that stick out from their body to help them navigate their dark tunnels, much like the whiskers of a cat.

Naked mole-rats are like professors: the more you learn about them the more interesting they become, and they look really weird when they’re not in their natural habitat. Perhaps part of the reason they live underground is because they are so strange in appearance. Their eyes are beady and useless, their ears are covered over with skin to

Naked Mole-Rats Bare it All Stories from underground

by Katie Moran

keep the dirt out, and their skin is the color of a nude crayon. But looks aren’t everything.

The fascinating story of the naked mole-rat begins with their unique lifestyle. The mole-rats live in a community of about 80 individuals who share communal living spaces as well as differ-ent jobs that make the colony run smoothly.` They are eusocial animals, meaning they have a queen and distinctive social roles within their colony such as workers, breeders, and diggers. Euso-ciality is more typically seen in insects, such as bees, and the only other mammals that live this way are African Mole-Rats.2

Workers, who go out digging in search of tubers and roots in the ground for food, are the smaller individuals. Some of the larger in-dividuals act as guards, remaining in the nest to defend the colony from predators. Though unconfirmed, there is some speculation that there is a special job for a select few naked mole-rats that do nothing all day but eat so that they will be large enough to plug

Mole-Rat Manor: extensive tunnels house colonies of up to 80 individuals. Diggers, sweepers, and volcanoers excavate the tunnel system while other naked mole-rats forage for food, care for offspring, and guard the nest.

Wikimedia CommonsA naked mole-rat aka “sand puppy” eating

University of Puget Sound 5

up the tunnels in the case of a flood. Other mole-rats, both male and female, share the responsibility of caring for the young.1

The queen of the naked mole-rats is the female in charge of populat-ing the whole colony with the help of a harem, a small selection of males that provide the best genes. She is the only reproductively ac-tive female in the colony. Her presence represses the sexual maturity of her subjects, so that the queen truly is the only one who can re-produce.3 She is more aggressive than the other mole-rats, and larger since she must carry litters of almost 30 offspring!2 To make room for the fetuses, the queen’s vertebrae lengthens by 32% so that she gets longer instead of wider, giving her the ability to continue roaming the tunnels even while she is pregnant. The queen’s presence in the tunnels is important for pro-moting the order in the colony; her smell alone can instill fear in the workers, mak-ing them dig more efficiently. Evidence of this comes from studies that record the amount of digging an individual does in the presence or absence of the queen’s odor.3 The queen also bar-rels through the tun-nels, trampling some of her subordinates as she goes about her daily business. This trampling is not physically detrimen-tal, but it shows the queen’s dominant role in the colony.

The complex set of tunnels the naked mole-rats inhabit is another fas-cinating aspect of their lifestyle. Tunnels can extend up to two miles long and are almost completely excluded from the world above, with all of the tunnels closed off from the surface. Naked mole-rats live in an almost completely hypoxic environment. They can survive with extremely low levels of oxygen, which is abnormal for most mammals. Within the tunnels there are special chambers for communal sleep-ing, eating, and pooping, and there is even a special ‘daycare’ chamber where the babies are raised.4

This mammal’s ability to survive in such unique conditions is interest-ing to many medical researchers. For researchers who focus on brain injury after strokes or heart attacks, the hypoxic survival mechanisms of the naked mole-rat are of interest because it may help us to under-stand or improve the treatment of human brains. Unlike the brains of naked mole-rat, human brains cannot survive long with low levels of oxygen. It is believed that naked mole-rats can survive these poor living conditions because their brains remain in an immature state, similar to a fetal brain, as levels of oxygen available in utero are low.5 It is not surprising that brains are very different before birth, but it is interesting to consider that they are changing in response to oxy-gen. Understanding more about the brain’s response to oxygen after birth may provide useful in developing ways to prevent or treat brain

injury.

Additionally, naked mole-rats have an extremely long life span in com-parison to other animals of similar size and livelihood. Naked mole-rats can live to be upwards of 30 years old whereas a typical mouse only lives for about a year.6 This is a huge discrepancy and many labs are studying naked mole-rats to learn more about how they are able to remain physically and neurologically healthy for such a long time. For one, naked mole-rats do not go through normal senescence, or cellular aging mechanisms. In contrast to the typical aging processes that oc-cur in most mammals, naked mole-rats show few signs of age-related mortality until very late in life.8 This unique aging process is accompa-nied by an ability to reproduce well into the third decade of their lives.

Another thing that keeps them living for a long time is that they do not get cancer. Even when researchers try to force c a n c e r o u s growth in naked mole-rats (by ge-n e t i c a l l y m o d i f y i n g them to have predisposi-tions to can-cer or by mu-tating their cells in vitro), they do not see the same

scale of cancer growth that is observed in other model organisms. Mutations to the p53 and pRB pathways almost always lead to cancer in mouse cells, but do not cause cancer in naked mole-rats.7 Researchers are looking into the cellular mechanisms that provide this apparent cancer immu-nity. One such mechanism is the contact inhibition pathway in naked mole-rats, which is distinct from the one found in humans (see figure above). Naked mole-rat cells do not form tumors in part because they cease proliferation when they get too crowded. This process, called contact inhibition, occurs earlier in naked mole-rats compared to other mammalian cells, and it could contribute to the prevention of cancerous tumor growth in this species.8

To us, it seems like naked mole-rats would have a hard life. Humans spend time, energy, and even hire professionals to secure an environ-ment sunny and wide open to breathe fresh (oxygenated) air; an en-vironment that is quite opposite of the dark naked mole-rat tunnels. Humans also strive to clothe themselves sufficiently, soak up sunlight, revel in high-excitement and high-stress situations, and in many cases revolt against the absolute rule of a monarch. Though these human characteristics are not necessarily a direct cause for cancer, the dark, non-stressful, and immortal story of the naked mole-rat might have a lot to tell us about our own health.

Naked Mole-Rats and No Cancer:

Contact inhibition is the process by which cells stop growing and dividing when they come in contact with other cells. For example, normal cells will stop proliferating once they fill up the bottom of a culture dish with a single layer of cells. However, cancer cells do not exhibit proper contact inhibition processes and thus continue to proliferate, resulting in many layers as the cells grow on top of each other. Ultimately, this leads to the formation of tumors. Humans exhibit single level contact inhibition, meaning that the signals to stop dividing only occur once, when crowding has reached a threshold. Naked mole-rat cells, on the other hand, have two levels of contact inhibition, includ-ing a contact inhibition process occurring at very low cell density, which has been termed “early contact inhibition.” As a result, naked mole-rat cells do not even form the dense single-layer of cells that human cells do, but halt growth before this point. The extra level of contact inhibition may be a large contributing factor in suppressing tumor growth and thus preventing cancer in naked mole-rats.7

Figure by Chelsea Clark and Claire Simon

A naked mole-rat aka “sand puppy” eating

Elements Magazine6

My Love AffAir with the eAstern newtby Michaela alden

Every summer in the Adirondacks, I observe all kinds of wildlife, but the highlight of my trip is always the tiny, mellow, unbelievably or-

ange Eastern Newt (Notophthalmus viridescens). These newts are part of the family Salamandridae and can be found in deciduous and conifer-ous forests throughout the eastern United States and adjacent parts of Canada.

Photos by Michaela Alden


The Eastern Newt has a unique life cycle. An individ-ual begins life in an aquatic larval stage, develops into the familiar terrestrial form known as a “red eft,” then returns to the water as an adult. The red eft stage lasts for 2-7 years and makes up about half of the life span.

During its red eft stage, the newt is nocturnal and may be found wan-dering through leaf litter on rainy nights, snacking on small inverte-brates. In fact, they are thought to play an important role in controlling the populations of small insects like mosquitoes.

When they develop into adults and re-sume life underwater, they lose the reddish-orange coloration and turn yellow-olive, though their bright red spots remain (see below). As adults, they can grow up to five inches in length.

Although the number of Eastern Newts has declined due to habitat degradation, they are still so abun-

dant in their range that they are not considered to be threatened. This means that they are

easy to find if you know when and where to look.

If you want to pick up a newt, be sure to keep it moist, handle it gently, and put it back close to where you found it. It’s best to keep handling to a mini-mum and wash your hands afterward because, as bright coloration often in-

dicates, the newts secrete toxins from their skin when threatened. This is a

defense mechanism that makes them un-palatable to predators like birds, mammals,

and fish.

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What sets Curiosity and MSL apart from the other rovers is the sophisticated instruments on board. While Spirit and Oppor-tunity are still roving on Mars, despite the fact they were only scheduled to be operational for a year, Curiosity is larger, more so-phisticated, and has more tools. Before it could analyze anything, Curiosity had to travel to and land on Mars.1

Going to Mars

Curiosity’s space journey started on November 26, 2011 at 7:02 a.m. PST. The rover was launched in an Atlas V-541 rocket as Curiosity is twice as heavy as Spirit and Opportunity and is three times larger. The Atlas V-541 rocket was chosen due to its ability to lift the heavy rover, The 541 signifies the diameter of the nose cone (payload, where Curiosity is housed), the number of solid rocket boosters and the number of engines respectively. Thus, the diameter of the nose cone is five meters, there are four solid rocket boosters and one engine.1

The timing had to be perfect to allow for safe passage for the rover. If the launch was not timed out properly, the rover would not be able to reach Mars and would be lost in space forever. The launch window for Curiosity was from November 25- December 18, 2011. The launch window is calculated for when Earth is the closest to Mars. This allows for the least amount of space travel, reduces the amount of fuel required to propel the spacecraft, and creates a less costly mission.1

Due to its size, when Curiosity reached Mars, it employed a new landing technique, rather than the “bouncing” technique em-ployed by both Spirit and Opportunity. Because Curiosity is so much larger, both in mass and in volume, this “bouncing” tech-nique was not a good option. Instead, using new precision-landing

techniques, Curiosity successfully landed on August 5, 2012 at 10:32 p.m. PDT.1,2

The first stage of this new landing technique was guided entry where small rockets were used to guide though Martian atmosphere. An on board system steered the rover to the pre-de-termined landing sight. Next a parachute (see figure) was deployed to slow the spacecraft down. Parachutes were used with previous

missions, however, this one had to be much larger. During a pow-

Why Mars?

Since NASA’s first glimpse of Mars in 1965 with the Mariner 3 flyby mission, the Red Planet has been a mystery. While strangely resembling Earth in composition, the surface of

Mars is similar to the moon, pockmarked with craters created by space debris crashing into the surface. Mars is also similar to Earth in that it has polar ice caps, an atmosphere (while it is extremely thin), and a slight tilt, causing seasons. Many scientists want to explore Mars, as they believe it could explain the history of climate change, which could be useful for Earthly applications. As human beings we are naturally curious and want to find more about this strange planet that could have once resembled Earth.

Past and present missions

Over the years, NASA has sent numerous missions to Mars. From Mariner 3, where we learned the surface of Mars is not covered in liquid water, to now, with rovers and orbiting satellites, we con-tinue to learn more about this mysterious Red Planet.

The rovers are perhaps the most iconic and well-known missions to Mars. Since 2003 Spirit and Opportunity have been searching the Red Planet. The newest Martian mission, the Mars Science Laboratory (MSL) mission, housed in the Curiosity rover, now joins these two rovers on the surface of Mars. They are tasked with

finding out more information about Mars and re-laying that information

back to Earth.1

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Mission to Mars Getting the Best of our Curiosityby Kira thurMan


ered descent, mini thrusters guided the spacecraft to nearly zero velocity and stabilized the spacecraft. Finally a sky crane lowered Curiosity by tethers to the surface. The mobility system turned on so Curiosity could essentially rove as soon as its wheels hit the ground. Once the on board system sensed touchdown, the tethers were cut and the sky crane flew away where it crashed at full force safely away from the rover.1,2,3

Gadgets and Gismos

The MSL has many nifty gadgets and gismos on board. Many of these were gifts from other agencies around the world. The Russian Federal Space Agency donated a neutron-based hydrogen water detector, the Spanish Ministry of Education and Science donated a meteorological package and the Canadian Space Agency donated a spectrometer. All of the gifts from different agencies are important because, although the USA and NASA are the ones responsible for Curiosity, MSL, and the mission, it is still a mission that will benefit all of us on Earth.1

The rover has many parts. The 6 wheels and camera mounted on a mast (like Spirit and Opportunity) allow Curiosity to rove and take pictures. A laser vaporizes thin layers of surface rock to al-low it to analyze the underlying elemental composition. Onboard chemical testing chambers also analyze rock and soil samples. A suite of other scientific instruments analyzes organic molecules, in particular looking for life supporting elements (Nitrogen, Phos-phorus, Sulfur, and Oxygen). The rover is powered by the radioac-tive decay of Plutonium.1,4

Self portrait of Curiosity on Mars

Research

The first rock touched by Curiosity had an unexpected composi-tion that was different from rocks found on previous missions. This rock is more varied in composition and resembles rocks found in volcanic regions on Earth. Analysis of soil samples show the Mar-tian soil composition to be similar to basaltic soils from Hawaii’s volcanoes. Another milestone and something for the history books is that on February 20, 2013, Curiosity became the first instrument to drill into the interior of a rock beyond Earth. This rock was named “John Klein” after the first deputy project manager of MSL, who passed away in 2011.5,6,7

The Curiosity mission has not been without its setbacks. In late February, Curiosity suffered from a memory glitch. Because there are two computers on board, the rover was still able to function during this problem. The source of the glitch has yet to be deter-mined but, Curiosity recovered in early March.8

In mid-March, the MSL team reported that Curiosity found “evi-dence of water-bearing minerals in rocks near where it had already found clay minerals inside a drilled rock.” 9

While there is not yet evidence of little green men on Mars, Cu-riosity still has much to find. Curiosity’s power sources will last at least a Martian year (about 687 Earth days) hopefully enough time for the mission to demystify Red Planet.10

it’s An Asteroid… it’s A Meteor… it’s A Meteorite

by david Santillan

There is a haze of confusion over the differences between an asteroid, meteor, and meteorite; in reality these outer space rocks have very few differences and a lot in com-

mon. An asteroid is a small, inactive body of rock, which orbits the sun. A meteor is a fragment of an asteroid that is absorbed in the Earth’s atmosphere, also known as a shooting star. The only distinction between a meteor and a meteorite is that a meteorite is a meteor that has safely passed the Earth’s atmosphere and has come to impact the Earth’s surface. There is constant fascination with the different rocks our galaxy has to offer; now you have the tools necessary to decide whether or not it is actually a meteor or a meteorite . . . or perhaps it is truly Superman.

Defining Science

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Elements Magazine10

Plants allow all of us to survive on our earth, and they are a vital part of almost every land-based ecosystem. Most people don’t know that plants are dependent on their un-

derground buddies, mycorrhizal fungi, as well as bacteria. My-corrhizal fungi only grow with plant roots, and more than 80% of plants depend on them.1 Bacteria act as important mediators of this symbiotic relationship.

Mycorrhizal fungi have an arrangement with plants so that they share resources and rely on each other completely for certain dietary needs. The fungus helps the plant acquire the necessary amount of water and nutrients each day. As humans, we need our daily vitamins, which we get through eating certain foods that we buy at the grocery store. The fungus does all of the shopping the plant needs in exchange for a fee, which is typi-cally carbohydrates. However, different fungi can charge differ-ent fees. Plants have evolved with fungi for the entirety of their existence and over those generations have developed relation-

ships with specific fungi. In some cases, a fungal strain that is symbiotic with one plant could even be parasitic to another.1,2

Mycorrhizal fungi enter the root cells of plants and, through that intimate connection, exchange carbohydrates and other

Friends with Benefits

Symbiotic Relationships Between Plants, Bacteria, and Fungi

by Spencer Gordon

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The totally hot threesome beneath our feet

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as a way to farm the fungus for food. Certain bacteria have been labeled as biodegraders due to their ability to break down fallen trees, leaf fall, and many other compostable substances.2

Some bacteria also have the ability to regulate plant growth and possibly whether or not the plant will accept the fungus as a guest. Bacteria share multiple hormones with plants and thus have a very strong influence on how these plants behave. The mechanisms for the transmission and cellular communication occurring in this relationship have yet to be fully explored. Giv-en the crucial role of bacteria-fungus symbiosis in the growth of some crop species, manipulation and application of these sym-bionts may potentially increase both crop yields and tolerance to many different kinds of natural and man-made problems.1,2

Mycorrhizal fungi extend structures called mycelia into the root cells of plants, and bacteria inhabiting myce-lia facilitate the exchange of carbohydrates and other nutrients.

nutrients. Mycorrhizae can also grow through the soil to con-nect multiple plants, creating an underground highway for nu-trients. Generally, when people think of fungi, they think of a single mushroom sticking up from the ground or coming out of an old stump, but there is more to them than meets the eye. These structures sticking up from the ground are just where the fungi produce spores for reproduction, and they make up just the tip of the iceberg. Most of their biomass is underneath the ground in an extensive, web-like network of mycelia.1,2

Single-celled organisms called bacteria have been discovered as integral players in this symbiotic relationship. Bacteria have been observed living inside certain kinds of mycorrhizal fungi and play a very significant role in fungal growth and structure. Through scanning electron microscopy, bacteria have been seen digesting the outer layer of some fungi, while other studies have found bacteria to be required for fungal spore germination. The bacteria could be using their ability to germinate fungal spores

11University of Puget Sound

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C#. Continuing this pattern (D, D#, E, F, etc), we eventually arrive back at C, this time an octave higher. In the end, what we have is a whole octave equally divided into twelve different notes. Basically, the frequency of a sound wave determines the tone that is produced. A higher frequency results in a higher pitch, while low frequencies result in lower pitches. We find that the frequency ratio between the sound waves a half-step apart is an interval of 1.05946. In other words, if we play a note and then multiply its sound wave frequency by 1.05946, we get a note a half-step higher. For example, we could play the note C,multiply the note’s frequency by this interval, and then we would end up with a C#. Since middle C has a frequency of 261.6 Hz,2 mul-tiplying 261.6 by 1.05946 equals a new frequency of 277.15 Hz, and the corresponding note C#.

This is where the guitar design called the “rule of eighteen” comes from. It turns out that 1.05946 happens to be extremely close to the fraction 18/17, and so the total distance from the start of the fretboard to the bridge is divided equally into eighteen. The

first fret is placed at 1/18 of the total distance. The remaining distance is again divided into eighteen equal portions, and the second fret is placed 1/18 of this distance. The process repeats, and as a result, the fret spacing decreases as you move up the fretboard.1

Harmonics

Most people identify harmon-ics as a light ringing sound, but what exactly are harmon-ics and how does that sound occur? In fact, the harmonics are part of the overtone se-ries.3 Suppose we have a note created by natural means (by using instruments, as opposed to computers and electronic music). We hear not only the sound wave of the desired note, or fundamental pitch, but also the overtones. Over-tones occur at frequencies other than the fundamen-tal pitch and are only heard subtly, but they contribute to the overall sound produced when a string is strummed.3 Playing harmonics all comes

One of the most popular instruments in Western culture is the guitar, and it has been a huge influence on the pop culture of music. While it’s safe to say that many

people could identify the sound and appearance of this instru-ment, fewer are familiar with the physical aspects of the guitar. Little do some guitar players know that they are really playing with math and science! Fret spacing, harmonics and instrumen-tal tuning can be explained by physics.

Fret Spacing

Frets are the little metal bars on a guitar’s fretboard that mark where a string can be held down to produce a certain note. The number of frets a guitar has varies depending on whether it is electric, acoustic, classical, etc, but what’s important is the spac-ing between each fret, which is essentially the same on every guitar.

The distance between each fret is a half-step.1 If holding down a certain fret gives the note C, moving up one fret will play a

Physics and the Fretboard Getting in tune with your guitarby angelica Kong

Guitar In Action! Holding down a fret decreases the length of the string, producing a different sound wave frequency and creating a different note.

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down to isolating these overtones. If you visualize these sound waves as a sine graph, there are several nodes along the graph where the waves intersect with the x-axis.4 Now if you imagine the x-axis as the guitar string, then these nodes are the places along the string where you can strum harmonics.

When you play a guitar string without compress-ing the string at any frets, you hear the fundamen-tal pitch, in addition to all of its overtones. By find-ing a place along the guitar where there is a node and lightly damping the string in that spot, most of the sound waves that result are muted, except for the ones that intersect the node.2 As a result, the waves that intersect the node become isolated and are the only sound waves that can be heard, creat-ing a light ringing tone called harmonics.

Tuning

If two sounds of different frequencies are played at the same time, their vibrations will interfere with one another. This causes a pulsation, called a beat, between the two tones.4 Pulsations can be heard as long as the two different tones are continuing to sound together. However, the pulsations will disap-pear when the two frequencies of the notes match a harmonic ratio. Therefore, this method of paying attention to the beats can be used to tune instru-ments. For example, as long as the desired note is being played in the background, a violinist can start to play a string and adjust the pitch to match the original note until the beats disappear. At that point, the two frequencies being played sound in pure unison, and there is no more interference be-tween the two matching wave frequencies.3 This method of tuning can be quite effective. In most cases though, it’s not so effective for tuning guitars. In order to hear the beat pulsations between the frequencies of two sounds, the sounds have to be sustained for several seconds. When a guitar string is played, though, the note diminishes fairly quick-ly, which doesn’t provide enough enough time to listen for beats.

Luckily, with the help of modern technology, there may be a way we can hear beats on a guitar after all! Using an amplifier with an electric guitar might allow us to sustain the notes long enough to hear these beats. If that’s not really your style though, there is always the invention of electric tuners! It’s up to you. But the moral of the story is, do try this at home.

The 5th, 7th, and 12th frets are where three nodes are located on the guitar

string, and where harmonics can distinctly be heard.

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Headache pain affects a large portion of the population and can be very disabling for those who experience it. Headache consultations constitute about 4% of gen-

eral practioner visits in the medical field, and one of the most common reasons for referral to a neurologist is headache pain.1

‘Primary headaches’ refers to headache disorders for which no other cause can be attributed.2 ‘Secondary headaches’ are caused by some other condition, and they often produce very extreme, even life-threatening acute pain. However, the pain from pri-mary headaches should not be overlooked – primary headaches often greatly reduce quality of life and result in significant long-term disability.

In general, most headache patients experience fluctuations in headache pain intensity, duration, and frequency. There are many known factors that influence this variability. For example, many foods can serve as triggers, and alcohol, weather, exercise, and

stress can also have an effect.2,3

Over the past year, I worked with Dr. Roger Allen in the Physi-cal Therapy Department at Puget Sound to study the impact of stress on fluctuations in headache pain. Stress is known to be a contributing factor in many headache disorders.2,3,4-8 The body responds to various environmental conditions with a stress response, which activates the hypothalamic-pituitary axis to pro-tect the body. When this stress response is chronically activated, the body can be worn down, eventually resulting in disease.4

Stress can affect headaches in many ways. It may in some cases trigger fluctuations in pain, or it may be a predisposing factor to having headaches. Frequent headaches can also play a role in creating more stress for a patient, potentially resulting in negative feedback loops. In particular, stress can be one of the components causing infrequent, episodic headaches to become a chronic problem.9 The exact relationship between stress and

Delayed Effects of StressThe relationship between stress and headachesStudent reSearch by chelSea clarK

A plausible mechanism for the ten-day delay in pain onset following a stressful event shows the release of thyroxine by the hypothalamic-pituitary-thyroid (HPT) axis.

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headache pain is poorly understood, but stress likely directly influences the processes that produce and modulate pain.4 Al-though the mechanisms may not yet be clearly understood, it is clear that stress is an important factor in the mediation of headache pain.

Previous studies have found a ten-day delay in the onset of pain flares following a stressful event in patients with other chronic pain disorders, including fibromyalgia syndrome (FS) and com-plex regional pain syndrome (CRPS).10-13 Using serial lag corre-lations, these studies reported low correlations between stressful events and same day pain but high correlations between stressful events and perceived pain intensity occurring ten days later.

The delay in pain onset was also shown to correlate with the release of a thyroid hormone called thyroxine.13 When an in-dividual experiences stress, the hypothalamic-pituitary-thyroid (HPT) axis is activated, ultimately stimulating the thyroid gland to release thyroxine (T4) and triiodothyrodine (T3).4 Thyroxine is immediately bound and inactivated by thyroxine-binding globu-lins (TBGs) for ten days following release by the thyroid.14,15

This means that when the HPT is activated by stress, thyroxine is released but does not become active in the body until ten days after the stressful event. High thyroxine levels can lead to in-creased anxiety as well as increased nerve excitability, which can both contribute to an increase in perceived pain levels.16

My study aimed to build off of this information and to expand the research to headache pain. My project investigated the rela-tionship between headache pain and stress to see if the results describing the ten-day delay in pain onset for other chronic pain disorders (FS and CRPS) also apply to chronic headache pain.

Two subjects completed the study. The subjects were given a daily paper and pencil questionnaire for a period of 10 weeks, which was completed in the evening before the patients went to sleep. This questionnaire was used to assess the average level of stress throughout the day, pain at its worst during the day, and level of functioning.

Our results varied widely between the two subjects studied. For Subject 1, the results were consistent with previous work on FS

and CRPS showing a ten-day delay in pain following a stressful event. This subject showed high correlations between stress and headache pain levels ten days later. This suggests that stress may impact chronic headache pain in a similar way that it does other chronic pain syndromes, such as FS and CRPS.

However, the data from Subject 2 did not follow the same trend as Subject 1. A strong negative correlation was found, meaning that high levels of stress led to a decrease in pain ten days later, instead of an increase in pain as seen before. This suggests a dif-ferent mechanism for pain modulation in response to stress for Subject 1 compared to Subject 2. As we still see a strong correla-tion for a ten-day lag, it is possible that for this patient, increased stress leads to a decrease in HPT activity, causing less thyroxine to be produced. If less thyroxine is being produced, we would expect to see a decrease in free thyroxine levels ten days later, and thus decreased pain perception.

There is some debate over whether stress leads to an increase or decrease in thyroid hormone release. For example, in a review of the HPT axis responses to stress, Selye concludes that thy-roid hormone release can either increase or decrease, depending on the species and type of stressor.15 The findings of my study show differences in the body’s reaction to stress. The root cause of these differences has yet to be determined, but it is worth investigating in the future.

The findings of this study have many implications for headache patients and their therapists, as well as other healthcare provid-ers. For patients, it is often frustrating to manage seemingly random fluctuations in headache pain. The results of this study suggest that highly stressful events may lead to elevated pain perception ten days later, or decreased pain perception ten days later, depending on the individual. Healthcare providers may be able to help patients to determine if their pain fluctuations fol-low this trend, which will allow them to better understand their individual pain and thus manage treatment accordingly.

Research Advisor: Dr. Roger Allen, PhD, PT at University of Puget Sound

Correlations between daily stress and pain levels 0-14 days later. Subject 1 (left) showed a strong positive correla-tion for stress and pain ten days later, while Subject 2 (right) showed a strong negative correlation (Clark, unpublished data).

Elements Magazine16

In 1928, Sir Alexander Fleming discovered penicillin, the first recognized antibiotic, which became a go-to cure for many maladies.1 After the discovery of this medical marvel,

antibiotics became extremely popular. In general, an antibiotic is a substance produced by a microorganism that is aggressive to the growth of other mi-croorganisms when used in high concentrations. These microorganisms destroy infections and can cure dis-eases, but the story is not that simple. When humans consume antibiotics, some bacteria survive the initial kill-off, and natural selec-tion favors bacteria that are resistant to the drug.

Ironically, the increasing use of antibiotics leads to mutated “super-bugs,” which are resistant to the antibiotics manufactured to kill them. These emerging su-per-bugs are often deadly. There are 16 million cases of antibiotic

resistant Tuberculosis around the world.2 Super-bugs are also becoming a huge problem in hospitals where sick patients liv-ing in close proximity have an increased risk of acquiring infec-tions.3 The super-bugs are stubborn, and it seems that the only way to kill them is more drugs. Though the dangers of antibiotic

use have caused heated debate, not all antibiotics are evil. They may even help combat malnutrition.

A group of doctors from Wash-ington University in St. Louis studied malnourishment in “Project Peanut Butter,” which showed doctors that food wasn’t enough to cure malnutrition.1

Studies conducted in Malawi revealed that severe malnutrition may involve more complicated

damage to the stomach, which can lead to infections. Therefore improving diet may not provide adequate treatment for malnourished individuals.

Project Peanut Butter focuses on areas with intense poverty, like Malawi, where individuals suffer from a form of malnutrition called kwashi-orkor. Kwashiorkor is caused by se-vere lack of protein, but diets rich in protein and fat are not enough to heal the damage done by malnutri-tion.4 The team from Washington University in St. Louis learned that supplementing peanut butter with high doses of amoxicillin helps fight stomach infections. So as the protein in the peanut butter combats the ef-fects of kwashiorkor, the antibiotics tackle the infections in the stomach. This double trouble team of medicine and nourishment is proving to be a literal lifesaver for children in devel-oping countries.

As hospitals became breeding grounds for super-bugs and the use of antibiotics in food increases, it’s hard not to wonder if antibiotic use should be limited. But antibiotics do serve a noble purpose today, just like they did when they first appeared in Sir Fleming’s laboratory: to kill and to cure.

PB & A: Peanut Butter and Antibiotics

Fill Stomachs, Fight Infectionsby becca long

This double trouble team of medicine and nourishment

is proving to be a literal lifesaver for children in developing countries.

Innovative antibiotics: Using pills and peanuts a research team supplements pea-nut butter with amoxicilin to treat stomach infections and malnutrition in Malawi.

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While talking trees may seem like something out of the mind of J.R.R. Tolkien, they are a very real phenomenon. Many plant species are able to com-

municate with their community members, be them plants or insects, friends or enemies. Unlike the Ents of Middle Earth, real plants do not communicate with a spoken language, but a vastly more complex one composed of chemicals. Simply put, they communicate with odor.

The odors of plants are composed of a wide range of vola-tile (gaseous) compounds.1 Some of these chemicals, such as nicotine and methanol, are familiar. However, the majority of these substances are frequently unknown outside the field of odor science, despite their relative ubiquity in the natu-ral world. One such substance is caryophyllene, a chemical found in the odor of oregano,2 clove,3 basil,4 hops,5 hemp,6 and many other plants.

Just as people change the tone of their voice or the choice of their words depending on their physical or emotional state, plants too can vary the chemicals they produce and thus the messages they send to their surroundings. Plants produce certain volatile chemicals in response to various stresses such as light, heat, and herbivory. The chemicals produced in re-sponse to feeding by herbivores are known as herbivory in-duced plant volatiles, or HIPVs.1

HIPVs can send a diverse array of information to a plant’s neighbors. Even a single chemical released by a plant can say different things to different organisms. Some components of HIPVs send a cry for help, recruiting predatory insects to feed on the plant’s attackers.1 A class of HIPVs known as green leaf volatiles are produced by a plethora of plants when under attack by herbivores. While you might not be familiar with green leaf volatiles by name, you most likely know the smell of freshly mown grass, for which they are responsible. Since these chemicals are often indicative of damaged plants, herbivores can eavesdrop on their scent, following a trail of green leaf volatiles to an easy meal.

Distressed plants release yet another HIPV, methyl jasmonate, alerting nearby plants to prepare defenses for the coming at-tack.7 Methyl jasmonate is able to accomplish this because it is derived from a plant hormone, jasmonic acid,

Gossiping Gardens

What do trees have to say?

by Jay goldberg

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This tobacco leaf (Nicotiana attenuata) called a preda-tory Geocoris bug (brown) to remove the herbivorious

Manduca catepillars (green) eating it.

Elements Magazine18

which regulates the plant’s defenses. Once a plant receives methyl jasmonate it is quickly converted into jasmonic acid, thus promot-ing the production of anti-herbivory defenses. Many scientists question whether or not this is an altruistic act on the part of the plant. It is believed that it may actually be the plant’s way of quickly signalling to distant sections of its own body, as volatiles can disperse across long distances much faster than internal messenger molecules. Still, the neighbors manage to also get the message and benefit from it.

The blend of chemicals released varies de-pending on the part of the plant in question. The odors of leaves, flowers, stems, and roots will vary according to what the plant needs to say. Many flowers have a specialized scent to attract pollinators, whereas the scent of roots can promote the growth of beneficial microbes while suppressing the growth of harmful ones.8

Some root volatiles have even been suggested to function in attracting animals that feed upon pathogenic fungi and microorganisms.9

As humans, we are unable to hear the constant chatter of the plants around us. Next time you sniff a flower, pick a berry, or mow your lawn, try to listen with your nose. Many ants have symbiotic relationships with plants and are espe-

cially attune to the smell of their voices.

While this slug is munching away on a leaf, the plant has already produced signals called herbivory induced plant volatiles (HIPVs) to send a cry for help.

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Tardigrades, also known as “water bears,” are the ultimate polyextremophiles. They are able to withstand extreme temperatures, high pressure, ionizing radiation, and low

levels of oxygen. These tiny invertebrates, about a millimeter in length, are the only multicellular organisms known to tolerate the radiation and vacuum of outer space.1 Their near-indestructibil-ity at every stage of development has allowed them to colonize a variety of extreme habitats including deserts, high mountains, and polar regions, although they are most commonly found in moss.2 There are over 900 species of tardigrades and they consti-tute their own phylum in the superphylum Ecdysozoa.2

One of the extreme conditions tolerated by tardigrades is ex-treme water loss, also known as desiccation. They endure this by entering a state called anhydrobiosis (meaning life without water). During anyhdrobiosis, a tardigrade curls up into a form called a “tun,” halting its metabolism, reproduction, and develop-ment for as long as harsh conditions persist. As long as water is replenished within about four years, they reanimate and resume normal function.2

Anhydrobiosis occurs in a variety of bacteria, protists, metazoans and plants. The ability of anhydrobiotic organisms to tolerate a loss of up to 95% body water is interesting to biologists because water makes up the bulk of all living cells and normally

BAck froM the Brink

Researchers identify proteins that allow tardigrades to enter “reversible death”

by Michaela alden

Elements Magazine20

protects macromolecules from damage. There are many prac-tical reasons to investigate the mechanisms that prevent and repair this damage; research in this area has implications in vaccinology, cryogenics, organ storage, agriculture, and astro-biology.3,4

How is it possible for cells to survive in such harsh conditions? A study carried out by Yamaguchi and colleagues (2012) ap-proached the question using proteomics, the branch of mo-lecular biology dealing with determining the proteome (the entire complement of proteins ex-pressed by the DNA of a cell, tis-sue, or organism).5 The researchers knew that many anhydrobiotic or-ganisms express high levels of Late Embryogenesis Abundant (LEA) proteins in response to desiccation. According to the water replace-ment hypothesis, LEA proteins expand to stabilize membranes and shield DNA from damage when water is scarce. Thinking that tardi-grades may employ similar proteins, Yamaguchi and colleagues looked for heat-soluble proteins in the an-hydrobiotic tardigrade Ramazzot-tius varieomatus, a species known for high desiccation tolerance.

The proteins of interest were those that remain folded and functional after exposure to heat, like LEA proteins do. To isolate such proteins, the researchers collected a “pre-heat”’ protein fraction from 500 individuals using centrifugation, heated the sample to 95°C, then collected the fraction of proteins that were still intact with another round of centrifugation. These re-maining heat-soluble proteins were analyzed using gel electrophoresis, a technique that separates proteins according to size. The proteins were then separated into their amino acid components with the help of trypsin, a protein-di-gesting enzyme found in the digestive system. Mass spectros-copy, which detects elements based on their signature emission wavelengths, was used to determine the types and amounts of amino acids present in each protein. A computer program compared these amino acids against the genome of R. varieo-matus and traced each protein back to its DNA sequence.

With this technique, the researchers did not find LEA pro-teins—but they did discover five new proteins that had never been described before. Two of them are similar to mamma-lian fatty acid binding proteins (FABPs), but lack enough key features of FABPs that they are considered new proteins. This two-protein set was named the Secretory Abundant Heat Sol-uble (SAHS) protein family. Three other heat-soluble proteins

did not resemble any known proteins and were dubbed the Cytoplasmic Abundant Heat Soluble (CAHS) protein family. When faced with dehydrated conditions, these proteins change structure in a way similar to LEA proteins.

How did these new protein families get their names? After dis-covering the presence of these proteins, the researchers inves-tigated their locations within cells. To do this, they tagged the proteins with green fluorescent protein (GFP) and observed the fluorescence under a microscope to see where the proteins

were located. They found that CAHS proteins existed mostly in the cytoplasm (ambient cel-lular fluid), while most SAHS proteins showed up outside of the cell, an indication that they had been secreted. These dis-coveries led to the identification of CAHS as ‘cytoplasmic’ and SAHS as ‘secretory.’ Because of the proteins’ locations, the re-searchers speculate that CAHS proteins contribute to protec-tion of cytoplasmic components, while SAHS proteins contribute to protection of secretory organ-elles such as the Golgi appara-tus.

Finally, the researchers compared the abundance of these proteins in hydrated and dehydrated tardigrades. They found no sig-nificant difference in abundance, which suggests that these pro-teins are constitutive—meaning that they are continuously ex-pressed regardless of whether or not the tardigrade is under environmental stress. DNA da-tabase searches showed that the DNA encoding these five novel

proteins is conserved among tar-digrades, but not in other anhydrobiotic invertebrates like ar-thropods, nematodes, and rotifers. It is thought that tardigrades evolved these genes independently from other phyla.

This study represents important progress in understanding the amazing survival tactics of these unique animals. The mecha-nisms of anhydrobiosis and other forms of cryptobiosis are still not well understood, so there are many possible directions for continued research. We could learn a lot from our tiny, inde-structible friends.

Scanning Electron Microscope image of a tardigrade, also known as a “water bear”

Check out this time-lapse video of a tardigrade converting itself into a tun and re-emerging (by YouTube user ddhorikawa):

www.tinyurl.com/bbqn73a

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The Allium Update Info Activity Log

Timeline About Photos 705 MoreFriends 3

#makingpeoplecry Onions making puns: punions. Onions on youtube: http://www.youtube.com/watch?v=CD-q-PKKbyE

Photos PlaceStatus

The Allium, you’re the best comedic section and bff a grown bulb like me could ask for. Last weekend was the best weekend of my life. Funions 4 eva!! Promise not to take the following section seriously? Tomo let’s go sit on a bleu cheese burger in The Sub. <3 <3

Pearl The Allium22 hours ago

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Life Event

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About

Studies at University of Puget Sound

Lives in Every Grocery Store

From The Dirt

21University of Puget Sound

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By Maggie Shanahan and Chelsea Clark

ABSTRACT (1) (2) are indigenous to (3) but they have spread throughout (4). In their native habitat, this species forages for (5). However, expansion to new habitats could lead to dietary changes. This study was done to explain the effects of novel diets on the behavior of wild (1). Specimens were collected from the (6), and kept in a (7) environment for (8) days. Specimens were divided into two groups. The control group was fed (5) and the treatment group was fed (9). Immediately after eat-ing (9), the treatment group began to (10). The control group remained (11) throughout the experi-ment. Due to human error, (12) of the subjects escaped. The p value was found to be (13), so we consider these results to be significant. The results corroborate the (14) phenomenon, in which (15) (16) on (17), suggesting that (18) diets induce a (19) neural response in (1). Future studies should consider the effects of (9) on closely related species such as (20), in order to deepen our understanding of the (14) phenomenon.

Unknown Breakthrough Ecological Phenomenon By Dr.________(Your last name), Ph.D.**University of Puget Sound

1. Animal (plural) ___________ 2. Latin-sounding name _______ 3. Country ___________ 4. Country ___________5. Food ___________ 6. Destination __________ 7. Adjective __________ 8. Number __________ 9. Food __________ 10. Verb ____________11. Adjective____________12. Percent____________ 13. Decimal less than 1 _________ 14. Someone in the room_______ 15. Noun (plural) _________ 16. Verb__________17. Noun__________ 18. Adjective__________19. Adjective__________20. Animal__________

Fill in the Blank:

Elements Magazine


Pointed

Observations

Comics by Mary Wexman

1. Animal (plural) ___________ 2. Latin-sounding name _______ 3. Country ___________ 4. Country ___________5. Food ___________ 6. Destination __________ 7. Adjective __________ 8. Number __________ 9. Food __________ 10. Verb ____________11. Adjective____________12. Percent____________ 13. Decimal less than 1 _________ 14. Someone in the room_______ 15. Noun (plural) _________ 16. Verb__________17. Noun__________ 18. Adjective__________19. Adjective__________20. Animal__________

Elements Magazine24

I’ll never get these crystals growin’I’m just too viscous, Mr. Bowen.”

Bowen rubbed his chin in thought“My theories can’t all be for naught.”“Have you tried it with low pressure?

Have you tried it… with a tape measure?”

“Now you’re talking,” Obsidian replied,“Take out the pressure, and you might findThat over many years, (you’ll have to wait)

Fine-grained crystals will start to take shape.

“But that’s far too much work,” Obsidian adds,“A lazy rock like me is much better off glass.”

Bowen considered, and pondered, and asked“You say that you are happy as glass

But say we add water, at low pressure too,Wouldn’t those conditions be better for you?”

Obsidian thought about this for a bitBefore replying with a rock’s impeccable wit:

“But those crystals, too, take a while to be made,You’ll be long dead by then, I’m afraid.”

Bowen laughed, “Of course, how silly of me!That these things take time is geologists’ creed!

You seem quite happy as you are nowOne day you’ll grow crystals--it won’t matter

how.”

And so Bowen wished Obsidian “have a good day!”

Put it down, tipped his hat, and went on his wayAnd thought to himself how wonderful it must be

To be as patient as a flow with high viscosity.

Ageologist named Bowen went out for a walkAnd on his stroll came across a unique rock

With a glassy surface that seemed almost newAnd was black as pitch the whole way through

“Obsidian,” he said with much dismay,Please tell me how you got this way.”And even without a mouth or teeth

Obsidian hm-hhm’d and began to speak

“I can’t form crystals,” came its reply“They’re far too much work for one such as I”

And Bowen pondered this, and thought“He has to crystallize someway, he ought.”

Bowen smiled, for a suggestion he knew,And asked Obsidian these questions two:

“Have you tried it in a pluton?”“Have you tried it… on a futon?”

Obsidian’s resent its stoic surface beliedGrumpily it gathered its words and replied:

“I will not crystallize in a plutonI will not crystallize on a futon

I’ll never get these crystals growin’I’m just too viscous, Mr. Bowen.”

“Well then,” thought Bowen, “what have we here?A rock that won’t crystallize? How very queer!”As Bowen thought, more suggestions he foundHe picked the obsidian up from the ground.

“Have you tried it with more water?Have you tried it… with an otter?”

“I will not crystallize with more waterI will not crystallize with an otter

“I’m Just Too Viscous, Mr. Bowen”A geology rhyme

By Lauren Fellows

Elements Magazine24


One point for each correct answer

Undergrad: 1-2 points. Try again in a couple of years.

Graduate student: 3-5 points. You still have much to learn.

PhD student: 6-9 points You think you know everything, but you do not.

Professor: 10-13 points Congradulations, you know every-thing!

Scoring

Answers:1-D 2-M 3-F 4-H 5-A 6-K 7-G 8-C 9-J 10-L 11-B 12-I 13-E

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1. 2. 3. 4. 5. 6. 7.

8. 9. 10.

11. 13.

1. Albert Einstein2. Carl Sagan3. Richard Dawkins4. Erwin Schrodinger5. Charles Darwin6. Isaac Newton 7. Sigmund Freud8. Louis Pasteur 9. J. Robert Oppenheimer 10. Marie Curie11. Jane Goodall12. Rosalind Franklin 13. Barbara McClintock

They Said WHAT? Little known sayings from widely known scientistsby Kira thurMan and david Santillan

A. “A man who dares to waste one hour of time has not discovered the value of life.”

B. “Certainly, if you look at human behavior around the world, you have to admit that we can be very aggressive.”

C. “Chance favors the prepared mind.”

D. “Insanity: doing the same thing over and over again and expect-ing different results.”

E. “Every time I walk on grass, I feel sorry because I know the grass is screaming at me.”

F. “By all means let’s be open-minded, but not so open-minded that our brains drop out.”

G. “Time spent with cats is never wasted.”

H. “The scientist only imposes two things, namely truth and sincer-ity, imposes them upon himself and upon other scientists.”

I. “Science and everyday life cannot and should not be separated .”

J. “I am become death, the destroyer of worlds.”

K. “If I have seen further than others, it is by standing upon the shoulders of giants.”

L. “I was taught that the way of progress was neither swift nor easy.”

M. “If you wish to make an apple pie from scratch, you must first invent the universe.”

12.


Elements Magazine26


CITATIONSNAKED MOLE-RATS BARE IT ALL1. Borst, D., and Deyo, C. The Naked Mole Rat. N.p., 4 Dec. 2006. Web. 18 Apr. 2013.2. Kutsukake N., Inada M., Sakamoto S.H., Okanoya K. A Distinct Role of the Queen in Coordinated Workload and Soil Distribution in Eusocial Naked Mole-Rats. PLoS ONE. 2012: 7(9), e44584. 3. Kutsukake N., Inada M., Sakamoto S.H., Okanoya K. A Distinct Role of the Queen in Coordinated Workload and Soil Distribution in Eusocial Naked Mole-Rats. PLoS ONE. 2012: 7(9), e44584. 4. Doug, Borst, and Deyo Christine. “The Naked Mole Rat.” Last modified De-cember 04, 2006. Accessed April 18, 2013.5. Larson J, Park TJ. Extreme hypoxia tolerance of naked mole-rat brain. Neu-roreport. 2009: 20(18), 1634-7.6. Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011: 479(7372), 223-7.7. Azpurura, J., Seluanov, A. “Long-lived cancer-resistant rodents as new model species for cancer research” Frontiers in Genetics. 2013: 3, 3198. Seluanov, A., Hine, C., Azpurura, J., Feigenson, M., Bozzella, M., Mao, Z., Cata-nia, K.C., Gorbunova, V., “Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat” PNAS. 2009: 106(46), 19,352-19,357.

MY LOVE AFFAIR WITH THE EASTERN NEWT1. Hammerson, G. Notophthalmus viridescens. IUCN Red List of Threatened Species, version 2012.2. 20042. Riemland, S. “Notophthalmus viridescens.” Animal Diversity Web. 2000. <http://animaldiversity.ummz.umich.edu/>

MISSION TO MARS1. Mars Science Laboratory [Internet]. Washington DC: NASA; 2012. Mars Sci-ence Laboratory; [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa.gov/programmissions/missions/present/msl/.2. Mars Science Laboratory [Internet]. Washington DC: NASA; 2012. Entry, De-scent, and Landing; [cited 2012 Oct. 01]; Available from: http://mars.jpl.nasa.gov/msl/mission/timeline/edl/.3. Mars Science Laboratory [Internet]. Washington DC: NASA. Sky Crane [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa.gov/msl/mission/technol-ogy/insituexploration/edl/skycrane/.4. Mars Science Laboratory [Internet]. Washington DC: NASA; c2012. Launch Windows; [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa.gov/msl/mission/timeline/launch/launchwindow/5. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet]. Wash-ington DC: NASA; c2012. Mars Rock Touched by NASA Curiosity Has Sur-prises; [Cited 2012 Oct. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/whatsnew/index.cfm?FuseAction=ShowNews&NewsID=13756. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet]. Wash-ington DC: NASA; c2013. NASA Rover Confirms First Drilled Mars Rock Sam-ple; [Cited 2013 Mar. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/whatsnew/index.cfm?FuseAction=ShowNews&NewsID=14277. Webster, Guy, Dwayne Brown, and Rachel Hoover. Mars Science Laboratory [Internet]. Washington DC: NASA; c2012. NASA Rover’s First Soil Studies Help Fingerprint Martian Minerals; [Cited 2012 Nov 3]; Available from: http://mars.jpl.nasa.gov/msl/news/whatsnew/index.cfm?FuseAction=ShowNews&NewsID=13858. Agle, DC. NASA Jet Propulsion Laboratory [Internet]. Pasadena, CA: NASA; c2013. Curiosity Rover’s Recovery Moving Forward; [Cited 2013 Mar. 20]; Avail-able from: http://www.jpl.nasa.gov/news/news.php?release=2013-0919. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet].The Woodlands, TX: NASA; c2013. Curiosity Mars Rover Sees Trend in Water Pres-ence; [Cited 2013 Mar. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/whatsnew/index.cfm?FuseAction=ShowNews&NewsID=144610. NASA. 2012. Jet Propulsion Laboratory [Internet]. Washington DC: Discovery Guide: Mars Rover Curiosity [Cited 2012 Oct. 01]; Available from: http://www.jpl.nasa.gov/education/marsrover.cfm

DEFINING SCIENCE1. 2013 Feb 27 [Cited 2013 Apr 7]. What is the difference between an astroid, comet, meteoroid, meteor and meteorite? AeroSpaceGuide [Internet]. Available from <http://www.aerospaceguide.net/whatisanastroid.htm>

FRIENDS WITH BENIFITS1. Smith S.E., Read D.J. Mycorrhizal Symbiosis. New York:academic. 3rd ed. 2008.2. Bonfante, P., Anca, I., Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions. Annual Review of Microbiology. 2009: 63, 363-383.

PHYSICS AND THE FRETBOARD1. Rossing, T. D., Moore, F. R., and Wheeler, P. A. The Science of Sound: Third Edition. San Francisco. Addison Wesley. 2002.2. McNab, R. J., Smith, L. A., Witten, I. H., Henderson, C. L., & Cunningham, S. J. Towards the digital music library: tune retrieval from acoustic input. 1996. In DL’96. Retrieved from http://dl.acm.org/citation.cfm?id=2269343. Duffin, R. W. How Equal Temperament Ruined Harmony (and Why You Should Care). New York. W. W. Norton & Company. 2007.4. Davis, M. “Guitar strings as standing waves: a demonstration.” Journal of Chemical Educa ion, 2007: 84(8), 1287-1289.

DELAYED EFFECTS ON STRESS1. Kristoffersen, E.S., Grande, R.B., Aaseth, K., Lundqvist, C., Russel, M.B., Man-agement of primary chronic headache in the general population: the Akershus study of chronic headache. The Journal of Headache Pain. 2012: 13(2), 113-120.2. Goadsby, P.J. Headaches. Bonica’s Management of Pain. Philadelphia: Lip-pincott Williams Wilkins. 2010.3. Rasmussen, B.K. Migraine and tension-type headache in general population: precipitating factors, female hormones, sleep pattern and relation to lifestyle. Pain 1993: 53(1), 65-72.4. Nash, J.M. and Thebarge, R.W. Understanding Pyschological Stress, Its Bio-

logical Processes, and Impact on Primary Headache. Headache: The Journal of Head and Face Pain. 2006: 46(9), 1377-1386.5. D’Amico, D., Libro, G., Prudenzano, M.P., Peccarisi, C., Guazzelli, M., Relija, G., Puca, F., Genco, S., Meggioni, F., et al. Stress and chronic headache. The Journal of Headache and Pain. 2000: 1(1), S49-S52.6. Nadoaka, T., Kanda, H., Oiji, A., Morioka, Y., Kashiwakura, M., Totsuka, S. Headache and Stress in a Group of Nurses and Government Administrators in Japan. Headache: The ournal of Head and Face Pain. 1997: 37(6), 386-391.7. Sexton-Radek, K. The nature of recurrent tension-type headache and stress experiences. Psychotherapy in Private Practice. 1994: 13(3), 63-72.8. White, K.S., Farrell, A.D. Anxiety and Psychosocial Stress as Predictors of Headache and Abdominal Pain in Urban Early Adolescents. Journal of Pediatric Psychology. 2006: 31(6), 582-596.9. Houle, T., Nash, J.M. Stress and Headache Chronification. Headache: The Journal of Head and Face Pain. 2008: 48(1), 40-44.10. Allen R.J., Hulten J.M., Roelofson M.J., Martin T.G., McCormack S.A. Delayed pain reactions due to stress in patients with complex regional pain syndrome. Physiother. 2007: 93, S293.11. Harlow, L.M., Kumiji, K.T., Allen, T.L., Allen, R.J. Effect of perceived psycho-genic stress on pain intensity and timing of increased pain episodes in patients with fibromyalgia syndrome. J Orthop Sport Phys. 2005: 35(1), A17.12. Hulten, J.M., Martin, T.G., McCormick, S.M., Roelofsen, M.J., Allen, R.J. Influ-ence of perceived stress on delayed onset pain episodes and related functional changes in complex regional pain syndrome patients. Neurol Rep. 2002: 26(4), 190-191.13. Allen. R.J., McCann, C.J., Higa K.G. Relationship between delayed episodic pain flares and release of stress-related thryoxine in a patient with complex regional pain syndrome- a case report. J. Phys Ther. 2011: 32-42.14. Pyle, C.W., Moe, A.S., Terao, M.M., Luppino, E.R., Athing, C.R., Allen, R.J. Stress-related latency in sensory and affective dimensions of reported pain in patients with fibromyalgia syndrome. Eur J Pain. 2009: 13, S147.15. Seyle, H. Stress in health and disease. Boston, MA: Butterworths; 1976.16. Guyton, A.C., Hall, J.E. Textbook of medical physiology. 10th ed. Philadel-phia, PA: Saunders. 2000.

PB & A1. Johnson, A.E. “Antibiotics”. The American Journal of Nursing. Vol. 50, No. 11 (1950), pp. 688-6902. Dye, C. and Marcos, A. “Will Tuberculosis Become Resistant to All Antibiot-ics?” Espinal Proceedings: Biological Sciences, Vol. 268, No. 1462 (2001), pp. 45-52.3. Lipsitch, M., Bergstrom, C. T. and Levin, B. R. “The Epidemiology of Antibi-otic Resistance in Hospitals: Paradoxes and Prescriptions.” Proceedings of the National Academy of Sciences of the United States of America. Vol. 97, No. 4 (2000), pp. 1938-19434. Trehan, I. et al. “Antibiotics as Part of the Management of Severe Acute Malnutrition”. New England Journal of Medicine, 2013: 368, 425-435

GARDEN GOSSIP1. Dicke, M., Baldwin, I. The evolutionary context for herbivore induced plant volatiles: beyond the cry for help. Trends in Plant Science. 2012.2. Harvala C., Menounos P., Argyriadou N. “Essential Oil from Origanum dictam-nus”. Planta Med. 1987: 53(1), 107–9’3.Ghelardini C., Galeotti N., Di Cesare Mannelli L., Mazzanti G., Bartolini A. “Local anaesthetic activity of beta-caryophyllene”. Farmaco. 2001: 56(5–7), 387–9.4.Zheljazkov V.D., Cantrell C.L., Tekwani B., Khan S.I. “Content, composition, and bioactivity of the essential oils of three basil genotypes as a function of harvesting”. J. Agric. Food Chem. 2008: 56(2), 380–5.5.Wang G., Tian L., Aziz N., et al. “Terpene Biosynthesis in Glandular Trichomes of Hop”. Plant Physiol. 2008: 148(3), 1254–66.6.Gertsch J, Leonti M, Raduner S, et al. “Beta-caryophyllene is a dietary can-nabinoid”. Proceedings of the National Academy of Sciences of the United States of America. 2008: 105(26), 9099–1047. Farmer, E., Ryan, C., Interplant communication: airborne methyl jasmonate induces synthesis of proteinase inhibitors in plant leaves. PNAS. 1990: 87, 7713-7716.8. Jurgens, A., Witt, T., Gottsberger, G. Flower scent composition in Dianthus and Saponaria species (Caryophyllaceae) and its relevance for pollination biol-ogy and taxonomy. Biochemical Systematics and Ecology 2003: 31, 345-3579. Wenke, K., Kai, M., Piechulla, B. Belowground volatiles facilitate interactions between plant roots and soil organisms. Planata. 2010: 231, 499-506

BACK FROM THE BRINK1. Jönsson, K.I., Rabbow, E., Schill, R.O., Harms-Ringdahl, M., and Rettberg, P.. Tardigrades survive exposure to space in low Earth orbit. Current Biology. 2008: 18, R729-R731.2. Rebecchi, L., Guidetti, R., Borsari, S., Altiero, T., and Bertolani, R. Dynamics of long-term anhydrobiotic survival of lichen-dwelling tardigrades. Hydrobiologia. 2006: 558, 23-30.3. Garcia, A.H. Anhydrobiosis in bacteria: from physiology to applications. J. Biosci. 2011: 36, 939-950.4. Pereira, T.C. and Lopes-Cendes, I.Cryptic anhydrobiotic potential in man: implications in medicine. Medical Hypotheses. 2009: 73, 506-507.5. Yamaguchi, A, Tanaka, S., Yamaguchi, S., Kuwahara, H., Takamura, C., Imajoh-Ohmi, S., Horikawa, D.D., Toyoda, A., Katayama, T., Arakawa, K., Fujiyama, A., Kubo, T., and Kunieda, T. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade. PLoS ONE. 2012: 7,e44209.

THEY SAID WHAT?1. 2013 [Cited 2013 Apr 7]. Barbara McClintock Quotes. Today in Science His-tory [Internet]. Available from <http://todayinsci.com/M/McClintock_Barbara/McClintockBarbara-Quotations.htm>2. 2013 [Cited 2013 Apr 7]. BrainyQuote [Internt]. Available from <http://www.brainyquotes.com/>3. 2013 [Cited 2013 Apr 7]. Rosalind Franklin Quotes. Good Reads [Inter-net]. Available from <http://www.goodreads.com/author/quotes/232917.Rosa-lind_Franklin>

ODE TO THE IMAGE IN SCINECE1. Tercedor-Sanchez, MI. 2005 The Role of Images in the Translation of Techni-cal and Scientific Texts. URI http://www.erudit.org/apropos/utilisation.html

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Elements Magazine28

Ode to the Images in Science By Claire Simon

Scientists will spend the majority of their lives in search of that perfect image, which depending on the goal, can vary. The right image can illuminate the beauty of an object and inspire public awareness and involvement or it can shed light on a life process. Through submitted

photos and illustrations in Elements, we bring attention to the importance of an image in science. The lengths that the passionate will go to get accuracy, beauty, symmetry, and perfection can take hours or a lifetime. Here is an ode to the photographer...

In the mid-late 1880’s, Wilson Bentley began his life-long endeavor to photograph snowflakes. Since his subject melted upon contact with skin or the slightest blip of heat, he had to move quickly, catching the snow flakes on black velvet with thick gloves. While not breathing, he arranged the snowflake under a microscope that was jerry-rigged with a film camera without breaking them. His patience and careful technique paid off; to reveal the first stunning images of this crystallization process.

Karl Blossfeldt was another scientist photographer from Germany who took close-up photos of plants and seedlings. His images portrayed the beauty and intricacy of plant life

as well as provided sci-ence with information on their processes and growth development.

Figures must communicate a concept from the depths of one mind to another. In order to promote growth of knowledge and establish

theories, one person’s understanding must be accessible and translatable to a variety of logical minds. A figure must face the challenge of appeal-ing to a specific audience while remaining true to its original concept.

As a soon-to-be graduated molecular biologist I immersed myself in the study of cells, bacteria, and molecules, aka the realm of figurative images and invisible subjects. In molecular research, the subject of study (usually proteins and DNA) are invisible until the scientist has used creative techniques just so an image can be taken. The only way we can “see” these molecules is by staining them with dye or linking them to a glowing molecule ( Fig 1. Protein B). From there, we get images in lab that look like dark gray bars or glowing green dots and nothing like our text books. Of these microscopic entities, some are blue circles in one text book ( Fig 1. Protein C), squiggles in another (Fig 1. Protein A), or glowing green dots in the figure of a research article. In this discipline, it wouldn’t be surprising if a student didn’t really know what a protein was until their senior year of college even after succeeding on multiple exams and passing several science classes (I may or may not have been one of those students...).

It is the duty and a challenge of the scientist to convert those pret-ty green dots into a conceptual understanding of molecular structure, chemical behavior, and role in cellular operations.

The Photo:

The Figure:

Protein A is quantum mechanically cal-cualated by a computer to show atomic accuracy and detail. The different colors correspond to different subunits of the protein, the round bulges are atomic masses, and the colored space in be-tween them represent electron charge distribution.

Protein C is simplified to a blue oval “enzyme” with shapes cut out of it to depict a structure that specifically binds to the other “substrate” protein drawn as basic orange shapes.

A

C

B Protein(s) B are fluorescently “tagged” proteins extracted from a cell that glow from a special molecule attached to the amino acid chain. In each lane of this “gel”, smaller proteins are dragged far-ther down this porous gel by an electric current. When compared to a standard, the size and identify of a protein can be determined.

Figure 1. Confunding Figures, 3 Depictions of a Protein

Ask Yourself: Particularly in a scientific context, is photo manipulation justified to achieve a desired purpose, or does that lead to misguided inferences

and decrease the image integrity?

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Honorable Mention: Staff FavoritesWe were impresssed with the great response to this contest with over 35 submissions from several University of Puget Sound students. We wanted to publish them all-this is our attempt. Keep taking photos and keep Elements in the loop because we want to publish them!

Sincerely, Elements Staff

Top: Lexy Woods

Left: Martyn ReifTitled “Stay Awhile”

Taken in the Enchant-ments, Alpine Lake Wilderness, WA

Top: Bryce Bunn

Left: Abby Mattson


Elements Magazine30

2nd PlaceTouching on Sensitivity | By Kathryn Papoulias The Golden Orb spider, Nephila clavipes, use their legs to pluck their asym-metrical webs and feel everywhere in the web for prey. This is the largest (female) neotropical orb-weaving species of spider.

Kathryn’s image captures a spider’s delicate touch. We love this depition of a sensa-tional element.

Photo Contest Winners: Elements, however you interpret it...

Most Creative Interpretations of the Theme Feeling Out of Our Element | By Shana Murraywolf

Two girls on a bridge in Amsterdam. This photo is unique r for this theme and an abstract representation of a common human expe-rience.


Photo Contest Winners: Elements, however you interpret it...

3rd PlaceElement of Fear | By Erin Jamroz

Climbing Mt. Rainier and walking across an icy chasm.

We love the immediate gut reaction of fear to this photo. Taken from the photographer’s perspective, you are put in his shoes (or wooden planks?) to imagine the experience of cross-ing a deep, icy chasm. What happens if you fall? His gear is also in focus, which adds anoth-er dimension to the experiemce.

Two girls on a bridge in Amsterdam. This photo is unique r for this theme and an abstract representation of a common human expe-rience.

Elements to me mean the natural things in life, materials we see everyday but end up taking for granted or forgetting | By Diedre McNally

This was taken last summer on my birth-day in Port-land, Oregon.

We love this perspective of appreciating the small things around you.

Elements Magazine32

Element/Earth|By Sharon Styer“This photo was taken last Fall at Terry’s Berries in Puyallup. Bee, whose feet these are, had just returned from a workshop on making outdoor ovens. She learned how to use her feet to mix mud with straw and create building material for the ovens. Combining the mud, straw, and other organic matter actually takes quite a bit of physical strength and energy to bring the mix to the right consistency.”

Not only was this photo artistic, but we also immediately thought of Elements Magazine and how many ways it fit the contest theme, “your inter-pretation of elements”. The feet are squished in the earth that is squirming with organic matter, microbes, roots, and the life-supporting nutrients. It invokes a feeling of human connection with earth and all its wonderful elements.

ElementsThe Scientific Magazine of the University of Puget Sound

Issue 13, FLIP SIDE, Spring 2013

Photo Contest Winner! more contest winners inside...

Issue 13

Documents

Transcript of Issue 13