Issue 20

ELEMENTS A MAGAZINE FOR SCIENCE AT THE UNIVERSITY OF PUGET SOUND

ISSUE 20 - SPRING 2017

EVOLVABILITY - ENVIRONMENT

NEUTRINOS - PUBLISHING

“The most important thing in science is not so much to obtain new facts as to discover new ways of thinking about them.”

-SIR WILLIAM BRAGG, 1862-1942

FROM THE EDITOR theme taps into what curiosity and imagination can bring to science, considering what it’s like to publish research as an undergrad and simply having fun in our lighter “Allium” section. We hope you’ll learn something in this issue, or perhaps be inspired to continue supporting and engaging with science both at the local level of the Puget Sound campus and in the broader context of the Tacoma community, our nation, and the globe.

Before you jump into the magazine, I’d like to take a moment to sincerely thank the Elements staff team for all the work they have put into the making of this issue, as well as all our writers and artists who have contributed their valuable thoughts and insight. I extend my gratitude to Megan Schowalter for being willing to represent the STS department on our CosmoNerd cover this semester. Special thanks also goes to Marta Cady, Kyle Chong and the ASUPS Media Heads for being a supportive, always listening group of peers at our weekly meetings.

Finally, a note that Elements is always aiming to offer itself as a platform for all voices and topics concerning science, education, and the environment. If you are interested in writing and article, creating art for Elements, or working on the Elements staff team for the 2017-18 academic year, reach out to us at elements@pugetsound.edu. Thanks goes to you, reader - we hope you enjoy this issue and come out asking some new questions.

Welcome back to Elements, the Science Magazine of the University of Puget Sound. At Elements, we showcase student writings and creative content that aims to make knowledge accessible and engaging to all. This semester, we’ve noticed several ties between our articles and arranged the issue thematically. We begin with the concept of evolution, debunking some common misconceptions and exploring evolvability’s broader implications for developing fields such as biomimic engineering. Evolution gives us a view of the world that is dynamic and ever-changing.

However, one thing that will always be here, and that we will be leaving with future generations, is the earth. Our second theme focuses on the environment. We interview Professor Hodum on the future of the EPA under the current political climate, and turn to a poetic perspective to reflect on human and non-human relationships to the seasons.

Our third section on genetic discoveries also explores what can be gained through engaging with variegated perspectives, with several articles that compare how recent research in genetics is presented in academic journals and the popular press. Our fourth section, “The Big and the Small,” applies the power of perspective to science as a whole, with articles moving from the smallest of subatomic particles, to the ecology and life history of the Prickly Forest Skink, to infinities we can conceptualize only by sets and functions. Indeed, as humans we are but one pinprick on a vast spectrum of time and space, but within that we have the power to unleash a special human creativity. Our final

Megan Reich

STAFF Megan Reich EDITOR IN CHIEF

Caroline Ronveaux DESIGN EDITOR

Cover photo by Megan Reich

Hannah Floren COPY EDITOR

Shreeti Patel ASSOCIATE EDITOR

Kaitlyn Finlayson

Melody Saysana

ASSOCIATE EDITOR

ASSOCIATE EDITOR

The production of Elements Magazine is possible due to the funding and support of the Associated Students of the University of Puget Sound. We thank ASUPS and, by extension, the student body for making this publication a reality. This magazine was printing by Digital Print Services (Kent, WA) using FSC certified paper sourced from wellmanaged forests, controlled sources, and recycled fiber.

In this issue Evolution 6

Modern Misconceptions: What Does the Word “Evolution” Really Mean? - Anna Marchand

8

Evolvability: What Is It and How Do We Get It? - Matthew Moreno

Environment 13

State of the EPA: An Interview with Prof. Peter Hodum - Melody Saysana

19

23 ½ Degrees - Curtis Mraz

Genetics This Month 20

Genetic Meltdown in the Woolly Mammoth - Megan Reich

23

Tsimane’s Benefits from the Alzheimer’s Gene Mutation - Morgan Eddolls

The Big and the Small 25

What the Heck is ∞? The Theorems of Georg Cantor - Jesse Jenks

28

No Skink No Crumble! - Gabrielle Genhart-Stiehler

31

All About Neutrinos - Megan Reich

Creativity 33

Is Publishing Possible as an Undergraduate? - Hannah Floren

35

The Allium

41

Works Cited

Modern Misconceptions: What Does the Word “Evolution” Really Mean?

BY ANNA MARCHAND

THEME 1: EVOLUTION There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

“Evolution” is one of the most controversial words in human history, and over the course of that history the word has taken on many different meanings. Several of these meanings are misleading, as they do not accurately reflect evolution as a scientific theory. Why are these inaccurate definitions so popular? We are uncomfortable with the full implications of evolution, and what those implications mean for our place in the animal kingdom.

Evolution has several definitions that are not scientifically accurate, yet still are used today, such as linear innovation and improvement. These definitions are often used by companies in advertising and marketing. What kinds of associations do consumers have with the word “evolution? What does it imply to them about the product? It implies that the product is the newest, the best, and the last in a line of prototypes. With just one word the company can tell their customers, “This product is the future.

All others are inferior, lower on the evolutionary ladder.” However, the “ladder” or “linear improvement over time” definition of evolution that is so favored

- Charles Darwin, On the Origin of Species, 1859 ABOVE: A “ladder” evolutionary model. Photo: Wikimedia Commons

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by marketers is a misconception. The concept of natural selection making things “better” is key to the marketing plans of the companies that use evolution for their own purposes, but this is not how the force of natural selection works. The ladder theory implies that each new version of a species is better than the last. However, natural selection, the mechanism of evolution, is not a conscious force. Natural selection pushes organisms to adapt to the current environment, which is subject to change at any time. When the environment does change, natural selection will reverse itself and push organisms in a different direction. Therefore, selection doesn’t make things “better” or “worse”—these words are purely subjective.

Another similar misconception about evolution is that organisms evolve from “simple” to “complex” forms over time. While this version of evolution is a legitimate definition in a non-scientific setting (Google dictionary defines evolution as “the gradual development of something, especially from a simple to a more complex form”), it is still not scientifically accurate. Unfortunately, this definition is still applied to evolution, and is generally referred to as the “cone model” misconception. One of the things the cone model fails to account for is that there are countless species that went extinct in the past. Including these species would warp the cone-shaped tree into a much wider shape. Another fallacy of the cone theory is that it assumes that all current species developed from a single base species, which is not always the case.

A third issue with defining evolution on a simpleto-complex scale is that it fails to recognize the fact that species that developed further back in time are no less complex than species today. For example, the older, smaller version of the horse, which had more toes and smaller teeth than the horses we see today, was no less complex (1).

There is a third definition of evolution: descent with modification through natural selection, which works through four simple steps. Natural selection begins with variation. Variation between individuals in a species may be small, but these small differences can have a big impact on the future of the species.

The variable traits between individuals must also be heritable. The next necessity of natural selection is that in each generation, more offspring are produced than can survive. Therefore, individuals with certain traits are more likely to survive and reproduce than

others. Evolution by natural selection occurs when heritable variation in individuals leads to variation in reproductive success. This reproductive success is defined as “fitness,” and a heritable trait that increases fitness is called an “adaptation.” It is this definition of evolution that leads scientists to accept that “Life is a copiously branching bush, continually pruned by the grim reaper of extinction, not a ladder of predictable progress” (1).

So why do so many people cling to inaccurate definitions of natural selection? Simply put, because the discovery that humans were not necessarily placed on earth to rule over the other species has been an affront to the largest ego in the animal kingdom: ours. Though much scientific evidence is available for the true definition of evolution, people continue to avoid or deny the facts because “we are forced to pay an almost intolerable price for a major gain in knowledge and power—the psychological cost of progressive dethronement from the center of things, and increasing marginality in an uncaring universe” (1). If the world had a “reset” button, and that button was pushed, it is very unlikely that human life would exist again as we see it today. However, though we may despair at how insignificant humanity seems, one has equal opportunity to rejoice over the sheer privilege of being alive in our current, self-aware, form.

ABOVE: A phylogenetic tree. Darwin sketched a similar tree in his ‘B’ notebook of 1837, implying the idea that all species arose from a single common ancestor.

Photo: Wikimedia Commons

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Evolvability: What Is It and How Do We Get It?

BY MATTHEW MORENO

The impressive matching of form to function in biological systems has long been admired by engineers, giving rise to the field of biomimicry, where design elements generated by the evolutionary process are employed in technological applications.

Examples of biomimicry include legged locomotion in robotics that provides both efficiency and maneuverability (5), nanotextures mimicking shark skin on boats that discourage barnacle growth while simultaneously decreasing water drag on the vessel (17), and tire treads inspired by the wet-adhesive properties of tree frog toe pads [Persson, 2007]. Soon after the advent of modern computing, researchers began experimenting with biomimicry at a higher level of abstraction. Instead of mimicking the particular phenotypic forms generated through evolution, they harnessed the evolutionary process — repeated cycles of selection on random variation — to generate novel solutions to a wide array of problems. This approach has since blossomed into the field of evolutionary algorithm (EA) design (10). Language used to discuss EA reflects the biological metaphor on which the algorithm is predicated.

Evolutionary algorithms operate on candidate solutions to a problem, which in the biological metaphor are equivalent to individuals. The aptitude of candidate solutions to solving a target problem is used to determine the candidate solution’s fitness, the amount of offspring it generates. Evolutionary algorithms traditionally begin with a population of randomlygenerated candidate solutions. Then, through a series of successive generations, the population is regenerated through recombination of fit candidate solutions, so selection is performed for candidate solutions that better satisfy the target problem. In biological evolution, a distinction is drawn between the phenotype of an individual — the physical characteristics which govern its interaction with the environment, its morphological, physiological, chemical, and molecular characteristics — and the genotype of an individual — the heritable

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information that influences the phenotype displayed by the individual, i.e. the ordered sequence of base pairs in its DNA. This distinction can become blurred in the realm of evolutionary algorithms, where the phenotypic characteristics of an individual might be directly encoded in the genotype. We will return to this idea later on.

The desired outcome of the evolutionary algorithm is, as generations elapse, to observe candidate solutions that provide an increasingly satisfactory solution to the target problem that was used to determine their fitness.

Once a predefined stopping criterion is met, usually after a specific number of generations or at a threshold fitness score, the evolutionary algorithm halts. Researchers and engineers have widely demonstrated the ability of EAs to attack labor-intensive optimization problems and to discover novel solutions beyond the reach of human ingenuity (15). For example, evolutionary methods have been successfully applied to evolve communication antenna designs to satisfy the demanding specifications necessary for use in miniaturized spacecraft (6). Figure 1 depicts an evolved antenna design from that project.

Although its form appears alien to traditional human approaches to design, it is nonetheless effective.

While biological phenotypic adaptation is indeed spectacular, another marvel of biology lurks just below the parade of phenotypes well-suited to their respective environments. It is hypothesized that biological organisms exhibit adaptation to the evolutionary process itself, not just to their environment over the course of their lifespans. That is, biological organisms are thought to possess traits that facilitate successful evolutionary search. The term evolvability was coined to describe such traits. A general consensus exists in the literature that evolvability stems from traits that facilitate the generation of heritable phenotypic variation that is viable.1 Breaking the concept down, evolvability stems from:

Why does evolvability manifest (i.e. what ultimate mechanistic forces endow biological organisms with traits that promote evolvability)? Addressing these two questions gives us a shot at tackling a third: how can evolvability be promoted in evolutionary algorithms? We will proceed to explore these questions but let’s begin by priming our intuition for evolvability by considering an artificial selection experiment performed on Drosophila melangoster, common fruit flies.

ABOVE: Figure 1 - A spacecraft antenna design generated using evolutionary methods. Photo: Kirschner and Gerhart 2005 (8)

1. the amount of novel, heritable phenotypic variation among offspring, 2. the degree to which heritable phenotypic variation among offspring is viable [2], The dependence of evolution on these capacities is straightforward. Without any heritable variation, evolution would have no raw material to select from and would stagnate. Without any viable variation, evolution would select against all novelty and again stagnate.

Hence, systematic evolutionary change depends the production of heritable, novel phenotypic variation, some of which must not be severely deleterious. We have established plausible traits that might facilitate evolution, but several important questions remain unanswered. How does evolvability manifest in biological organisms (i.e. what traits of biological organisms provide proximate explanations for the presence of viable heritable variation among offspring)?

These experiments, performed by Tuinstra et al.

(1990) and Coyne (1987), revealed that bilaterally asymmetric phenotypic traits, such as different-sized eyes, could not be induced through artificial selection.

In contrast, other artificial selection criteria, such as overall smaller eyes, yielded observable phenotypic changes over the course of a number of generations.

The success of artificial selection for most traits on Drosophila demonstrates the existence of a good amount of heritable phenotypic variation for those traits. It is hypothesized that the negative result in artificial selection for bilaterally asymmetric phenotypic traits is due to a lack of bilateral symmetry-breaking information during the embryological development of Drosophila.

In other words, the very nature of the developmental process constrains the nature of phenotypic variation that can be observed in offspring, in this case curtailing the abundance of offspring that lack bilateral symmetry.

As Tuinstra et al. (1990) phrase it, “the developmental system does not seem to allow this type of variation.” In the life of a fly, buzzing about in search of food and sex, bilateral symmetry is usually more fit than asymmetry.

In this way, the distribution of phenotypic diversity in offspring is biased away from a particular type of deleterious variation, asymmetry. The results from these artificial selection experiments can be cast in terms of evolvability: the distribution of phenotypic outcomes of mutation is not entirely arbitrary. Drosophila melangoster more readily exhibits heritable phenotypic variation for certain traits — overall eye size, for example — than for other traits, such as bilateral asymmetry.

Armed with this cursory introduction to evolvability, let us continue our discussion of evolvability by focusing in on each of its two components separately: promotion of heritable phenotypic variation (Section 1) and bias against deleterious phenotypic variation

[1] This statement does not suggest that mutation is nonrandom, a controversial and widely discredited theory referred to biologists as adaptive mutation. Instead, it is predicated on the notion that the internal configuration of a biological system (i.e. the developmental process, modularity, degeneracy, etc.) constrains the outcomes of arbitrary perturbations to that system. It is hypothesized that biological organisms possess traits that influence the distribution of phenotypic effects of random mutation.

[2] This can be thought of in terms of the frequency at which lethal or otherwise severely harmful mutational outcomes are observed.

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(Section 2). In Section 3, we will conclude by examining how evolvability fits into contemporary activity in the fields evolutionary biology and evolutionary algorithm design.

1. Promotion of Heritable Variation In discussing the generation of heritable variation, an important theoretical distinction can be made between individual evolvability and population evolvability.

Individual evolvability refers to the potential of an individual to generate a diverse set of offspring (9). In individuals with high individual evolvability, phenotypic form is less stable under genetic mutation. That is, mutations tend to yield more dramatic phenotypic change more frequently (19). In contrast, population evolvability refers to total amount of phenotypic diversity among potential offspring of a population as a whole (19). Although individual and population evolvability might be correlated to some extent, a direct relationship does not exist between the two. In the context of this paper, we will focus on discussion of individual evolvability.

Discussion of individual evolvability is predicated on the notion that biological organisms can possess qualities that facilitate heritable variation for a phenotypic trait. The regulatory action of hormonal signals such as somatotropin exemplifies such a quality.

This compound, also known as growth hormone, is well known for its widespread anabolic effects on tissues throughout the body. Mutations affecting the regulatory pathways that regulate somatotropin production and release, receptors and cell signaling components that mediate cellular response to somatotropin, and the protein itself all provide avenues for significant heritable variation in body size (3).[3] The presence of such hormonal signaling pathways could be viewed as increasing the range of heritable phenotypic variation that can be realized, increasing individual evolvabiltiy.

Dog breeds, which exhibit a range of body weights nearly spanning an entire order of magnitude, evidence the accessibility of heritable variation for body size in animals. Among certain groups of dogs, much of this variation can be explained by just six genes, several of which are associated with pathways somatotropin

participates in (16).

Variation in environmental conditions over evolutionary time is thought to promote individual evolvability. This idea is motivated in part by the fact that biological organisms do not evolve in a static environment. Instead, their environment changes over evolutionary time. These changes might be due to abiotic factors, such as changes in the climate or the geological composition of an area. These changes might also be due to biotic interactions with other organisms, such as competition for resources. Thus, criteria that determine fitness — which strategies for survival and reproduction are viable in a particular environment — are temporally varying.

Discussing a hypothetical example will help provide intuition for the concept of temporally varying fitness criteria and its consequences. Consider a hypothetical population of finches, which feed on a particular type of seed. Suppose that in order to successfully feed, finch beak widths must be matched with to the size of the seeds they feed on – beaks can be neither too wide nor too narrow or the finch will be unable to feed effectively.

Suppose that the sizes of the seeds that the hummingbird depends on were to be systematically manipulated over evolutionary time, proceeding through cycles of gradual increase and decrease. Under this regimen, individuals that are predisposed to yielding variable offspring are advantaged over individuals that are not. Although much of that phenotypic variation is likely to be deleterious, it is likely at least some will prove adaptive. Thus, a subset of the offspring from individuals with high individual evolvability tend to outcompete the offspring from individuals with low individual evolvability that lack fresh adaptation to changing environmental conditions.

As Wilder, et al. (2015) put it, “if selection sets a moving target, individuals will be more likely to introduce variation in their offspring to adapt to an uncertain future.”

Gradually shifting fitness criteria is thought to induce evolutionary pressure for individual evolvability, essentially providing a means of selecting for it.

Evolutionary simulations have confirmed that gradual changes to the environment — that is, a temporally

[3] Recent research implicates somatotropin in a number of processes unrelated to its classical association with metabolism and growth.

Although the phenotypic consequences of mutations affecting somatotropin pathways are not exclusively limited to body size, somatotropin response nonetheless provides an avenue for heritable phenotypic variation in that regard.

varying fitness function — can promote individual evolvability (7, 19). By inducing a selective pressure for individuals with phenotypic variation among their offspring, some of which will track changing environmental conditions, temporally varying goals promote traits that facilitate the generation of heritable variation.

2. Bias towards Viable Variation In biology, the genetic information of an organism, its DNA, strongly influences the organism’s phenotype via a developmental process.

Hence, the genetic encoding is said to be indirect. This indirect genetic encoding provides a good example of a biological mechanism that promotes viable phenotypic variation; indirect encoding is hypothesized to exert an innate bias towards viable variation by promoting phenotypic regularity. Informally, regularity can be used to describe repetition of phenotypic form.

Repetitive form might manifest as symmetry and/or recurring modular substructures. Formally, regularity refers to how much information is required to describe a structure (2). Indirect encodings tend to be biased towards phenotypic regularity because a large amount of phenotypic information is generated from a smaller amount of genetic information via a developmental process; these processes may favor regularity because each piece of genetic information determines many pieces of phenotypic information — otherwise independent phenotypic characteristics are specified in a more coordinated fashion (2).

This bias towards regularity in phenotypic form tends to translate to a bias towards viable variation. That is, in aggregate, regular phenotypes tend to outperform highly irregular phenotypes in most situations. The superior viability of regular phenotypes, of course, depends on the demands of the environment that the phenotype inhabits. Phenotypic regularity tends to be useful in more regular environments (that is, environments that exhibit regular characteristics), which are commonplace in the natural world (4). Many domains of interest to EA researchers are also highly regular (3). Thus, digital and biological organisms often benefit from the bias towards regularity inherent to the indirect encoding of phenotypic characteristics in the genotype.

Figure 2, taken from Cheney et al., 2013, nicely illustrates the impact of indirect encodings on regularity.

The figure compares two virtual soft robots, which are composed of an arrangement of small colored voxels with each color representing a unique tissue type. Each of the differentiated tissues has a distinct set of physical properties. This arrangement of voxels – the organism’s phenotype – determines the fitness of the individual in its environment. In this case, fitness is determined by the individual’s ability to walk on a simulated flat surface. The leftmost individual was generated via evolutionary search using a direct genetic encoding; the tissue type of each and every voxel was directly encoded in the individual’s genome. In contrast, the rightmost individual was generated via evolutionary search using an indirect genetic encoding. Unlike its counterpart,

ABOVE: Figure 2 - Representative examples of soft robots evolved with direct (left) and indirect (right) representations Photo: Cheney et al. 2013 (1).

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the genetic information of this individual is encoded as a Compositional Pattern Producing Network (CPPN), a mathematical formula that translates threedimensional spatial coordinates into tissue types. The phenotype of this individual, the spatial arrangement of tissue voxels, is determined by the output of its genome, the CPPN. A striking visual contrast exists between the two soft robots. The indirect encoded individual is highly regular with large patches of uniform tissue type while the direct encoded individual is a jumble of differentcolored voxels. As one might expect, the solution found by evolutionary search with indirect encoding, which likely shuffles along with a motion vaguely resembling an animal gait, moves faster than the solution found by evolutionary search with direct encoding, which likely moves at a slow crawl by vibration. In this particular virtual environment, a correlation between phenotypic regularity and fitness (i.e. the ability to move) biases the evolutionary search with the indirect encoding towards higher-fitness solutions. Indeed, evolutionary search in this soft robot locomotion domain with indirect genetic encoding was experimentally shown to vastly outperform search with direct genetic encoding (1).

3. Evolvability in a Broader Context Evolvability is a topic of active discussion among elements of the evolutionary biology community (14).

The concept falls under the umbrella of a broader effort to expand the theoretical framework of evolution called the extended evolutionary synthesis (14). Compared to the EA community, however, the concept of evolvability has been slower to gain traction. As Kirschner and Gerhart, a pair of evolutionary biologists known for their theory of facilitated variation, comment, “Many evolutionary biologists do not see a need to connect somatic adaptability to the generation of variation, and some see a need to keep them separate.

For them, it is sufficient to say that random mutation is required and that the phenotypic variation arises haphazardly from it as random damage; the organism’s current phenotype does not matter for the variation produced, and the output of variation is nearly random [Kirschner and Gerhart, 2005, p 219].”

Perhaps, in part, evolutionary biologists are less predisposed to interest in evolvability because they are not so directly stymied its absence. Success in attempts

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to emulate the evolutionary process to generate designs for sophisticated systems such as artificial neural networks or robotic bodies hinges on the ability of the evolutionary algorithm to generate viable, heritable variation. This development of this capability has been a major hurdle in EA research, especially in the field’s early years. The intense and ubiquitous interest in evolvability among the EA community should therefore come as no surprise.

EAs have yielded interesting and useful results, but have not yet come close to replicating the intricacy or scale of biological systems (18). In classical EAs, a directly or trivially indirectly encoded population evolves against a static fitness function. Fitness gains are typically realized for a period of several hundred generations before innovation stagnates and the population settles out at an equilibrium. This approach, predicated on a fundamentally accurate but extremely simplistic view of evolution, yields limited results. The stunted effectiveness of early EAs might be cast as a reflection of the limitations innate to the theory on which the algorithms are built. Mirroring activity among elements of the evolutionary biology community, there has been a fruitful thrust to build algorithms that incorporate a broader array of theoretical factors that may influence evolution, such as varying fitness functions and phenotypic plasticity (4, 7, 11).

At present, it seems likely that evolvability stems from a large and diffuse web of cooperating mechanisms. The establishment — or rejection — of empirical evidence for causal links between factors such as plasticity or the developmental process and evolvability must be a key research goal in the field of evolutionary algorithm design. Such results will directly support efforts to refine the evolutionary algorithm and realize performance more closely akin to that of its biological counterpart.

This line of inquiry raises and addresses questions of interest to the evolutionary biology community, especially in light of controversy surrounding the extended evolutionary synthesis. It will help determine which theoretical elaborations are necessary to account for evolution as observed in biology. It is hoped that further research in this vein — both in silico and in vivo — and, especially, continued exchange between EA and evolutionary biology researchers will yield both biological insight and more powerful digital engineering techniques.

State of the EPA: An Interview with Prof. Peter Hodum

BY MELODY SAYSANA

Melody: We’d like to get your take on the current state of the EPA under the Trump administration and other current events as well as background information, especially because I don’t think that everyone is able to keep up with the recent new cycles.

THEME 2: ENVIRONMENT It is a curious situation that the sea, from which life first arose should now be threatened by the activities of one form of that life. But the sea, though changed in a sinister way, will continue to exist ; the threat is rather to life itself.

- Rachel Carson, The Sea Around Us, 1951

Professor Peter Hodum: Yes (laughs), it’s impossible to keep up with so many things happening. It’s almost every day that there’s a new crisis or new concern. From my perspective, there are two major concerns with the EPA. Scott Pruitt, who was appointed to head the EPA, and the threatened budget cuts. [Pruitt’s] appointment is worrying for multiple reasons. One, his close association with the petrochemical industry in the past. Two, his long history of litigation against the U.S. EPA and his lack of support for existing regulations as the attorney general of Oklahoma. He brought a number of lawsuits against the EPA, against clean air standards and so forth. And three, his position as a climate change denier and his dismissiveness of the well-established science that is foundational to climate change models and predictions.

I think that he is a classic example of a cynical political figure who selectively uses science, where he accepts science when and only when it fits his worldview and his agenda. When the science is problematic, he discards it and attempts to discredit it by using the commonly applied argument that there’s no consensus and that we don’t know enough to make conclusions about whether or not climate change is happening and, if so, whether or not humans are a significant contributing factor to it.

Melody: Pruitt recently did the same thing, not discrediting science but saying that more research needs to be done on the pesticide chlorpyrifos - are you familiar with this chemical?

Prof. Hodum: Yes, [I heard of it] just last week actually when it emerged as an issue that needed to be decided because of an imminent deadline. I hadn’t heard anything about it [before], and I guess in part because it’s a decade long

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issue that has been in the courts and then in the EPA’s hands. From what I understand, there was a deadline on Friday [March 31, 2017] by when the EPA needed to make a decision as to whether or not they were going to ban the use of chlorpyrifos federally. From the little that I’ve read, Pruitt’s decision went against the recommendation of the EPA’s own professional research scientists. That said, there have been other recent studies that have not completely dismissed [chlorpyrifos] the health concerns raised by the EPA studies but have said ‘it may not be as clear as that’. And that doubt is what he [Pruitt] based his decision on - outside reviews by independent scientists.

The EPA scientists, who are not an activist group by any means, came out quite strongly and stated unequivocally that this is a pesticide that we need to ban...it’s a dangerous chemical. It’s Pruitt’s decision, but he chose to disregard the conclusions and recommendations of his agency’s staff in favor of outside opinions - which again, to be fair, were produced by professional research scientists. There certainly was no precautionary principle applied in this decision-making process.

Melody: So do you think that this means there will be more relaxed laws concerning chemical use in the future, or at least for the EPA under Scott Pruitt?

ABOVE: A view from the Nisqually National Wildlife Refuge, operated by the United States Fish and Wildlife Service. Photo

by Megan Reich

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Prof. Hodum: That certainly seems to be the precedent that he is beginning to establish. His communication and a key part of President Trump’s platform all along has been about minimizing regulations, cutting government oversight, making it easier for businesses to do business. I think that the positionality of President Trump coupled with the position that Pruitt has taken suggests that, yes, it will be increasingly difficult, at least over the course of this administration, to get substances that are potentially dangerous, banned. It does make me question whether or not EPA scientists are going to be shackled in terms of what they are authorized to communicate about findings related to decisions on chemical use.

Melody: In general I know some popular views of the EPA are that they don’t do enough or people want to see the EPA doing more. What is your stance on that?

Prof. Hodum: It cycles. There are permanent staff at the EPA. There are scientists and policy experts who are not in elected positions and so that provides continuity. But the direction of the EPA is really driven by the administrator, and the people under that administrator are appointed. So the EPA is a needle that swings as a function of who’s in the White House.

Under President Obama, [the Obama administration’s] EPA took on a much more visible role and definitely moved a number of issues forward that had stalled for quite a long time. President Obama saw the EPA as a vehicle to advance some of his agenda, including clean air and climate change initiatives. And I think they’ve done it in a clever way - not in a manipulative way - where they considered CO2 emissions as a contaminant, a source of pollution because of the impacts of climate change. So there was creativity brought to the process of engaging the EPA in climate change regulations, and I think that leveraged the EPA’s position to allow the country to move forward with the Clean Power Plan and regulating emissions in a way that had never been done before. One way to think about it is that the EPA is a tool, and it’s a matter of how you choose to use it and if you choose to use it. It’s kind of a multi-tool - you can use it for different things, if you choose to open the tool at all. And thus far, at least from what President Trump has signaled, he’s going to keep that tool firmly closed.

Melody: Scott Pruitt has expressed that he is somewhat skeptical of the Paris Agreement. What kind of effects do you think this would have on America and the general world if we were to withdraw from this agreement?

Prof. Hodum: Nationally, it’s problematic on so many levels, I think. One is that a number of public utilities, power companies, and major corporations are already moving towards renewable energies, because they see where the future is. They have to plan on with longer time horizons in mind. Energy infrastructure such as power plants have multi-decadal time scales, in contrast with the time scales of the electoral cycle in the US. This is exemplified with the issue of coal. Days after President Trump was inaugurated there were a series of interviews with CEOs of power utilities in various parts of the country and the general response from these folks was, ‘Coal’s got no future…. We’ve moved beyond coal. We’re using natural gas, we’re looking at renewables’ and so forth. In some respects, I think - not because of political whims, but because it makes the best business sense these corporations and utilities are saying it doesn’t matter what is happening in terms of federal policy.

It’s actually quite a complicated situation, and that’s where I don’t know what will spin out of a decision to withdraw from the Paris Agreement. I think at a global level, countries are going to move forward. Europe has committed to doing so, and so has China. It may be weaker without us, and some countries might [question it]. If we withdraw, it weakens our standing globally, and morally. Climate change is ultimately a very moral issue because a lot of people in this world are going to suffer unless climate change impacts are mitigated. And less developed and low-lying countries are going to be affected disproportionately. And again, if we abdicate our leadership role on this issue, what does that say about us as a country? As someone who takes the role of the US as a global citizen seriously, I think we really lose a tremendous amount of credibility and standing.

Melody: It is reassuring to hear that the direction is already towards sustainable energy, because I know Trump has

ABOVE: Prof. Hodum conducting a survey for Tufted Puffins off Protection Island, WA. Photo: Peter Hodum

expressed that he wants to put more funding into coal mining jobs, which is another thing that makes it feel like we’re going backwards.

Prof. Hodum: Right. And that’s his intention, but the jobs aren’t going to be there. And the ones that they’re able to generate because of the relaxation of these rules aren’t going to be there for that long because the demand no longer exists and cannot be recreated. And if the demand isn’t there, what do you do? In fact, there are a number of people in those communities that have recognized this reality. People from coal-mining regions who are Trump supporters have said there’s no future in this, that this is not how we are going to save communities in the long term. Sure, we may get a few hundred jobs here and there and that’s going to help in the short term, but it is not helping us transition as a community and region to an economy that’s actually viable in the medium to long-term.

Melody: So, going back to what the EPA does, how important of a role do you think that the agency itself plays in the daily life of an American?

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hope - believe in climate change. But to the average American who might not have the same resources as us, do you think that that could be really concerning or detrimental to people’s opinions about climate change and how they choose to live their lives in relation to the environment?

Prof. Hodum:

ABOVE: Mason Gluch, Tacoma, where Prof.

Hodum’s Conservation Biology class has been partaking in a survey/restoration project. Photo

by Megan Reich

Prof. Hodum: It’s pretty fundamentally important. I think it’s understated - you only hear about it when there’s a controversy, but in terms of regulating contaminants and pollutants and chemicals, on that level its presence is pervasive in our lives. Any sort of product that you have in your house, including items that are made of plastic those are all things that have been assessed and deemed acceptable by the EPA. In terms of our daily health and what we’re exposed to - in our homes, where we work, in school, in our vehicles - those are all products and materials that the EPA is attempting to regulate. Clean air, clean water - these are so fundamental to our lives.

They’re ecosystem services that are administered and supposedly regulated, at least in part, by the EPA.

Melody: How concerning is it to have a climate change denier’s opinions so openly publicized to the media? At this school I think we’re all very lucky to - I 16 | ELEMENTS

I think any time you have any influential person publically providing an opinion, regardless of their position, there is consequence...I think it is very damaging, and it sets the conversation back. Instead of moving it forward, right now we’re fighting to maintain a position in the country with respect to public opinion about climate change. And the needle moves on it, and it definitely moves as a function of who’s in power and what messages are being communicated. It’s unfortunate when really strong science is politicized so badly, but that’s what has happened with this issue.

And it’s understandable why, because there are huge economic implications. The people who have benefited from the status quo, again, irrespective of the issue, are the last people you want making decisions about whether to depart from that status quo. And yet, those are the people who are making those very decisions. And that’s broader than the Trump administration. I think that’s a troubling issue with our society in general. It’s definitely going to make the task of moving forward on climate change issues and mitigation much tougher, not just from a policy and legal standpoint, but from the perspective of public support.

Melody: How have you been talking to your students about political changes that have been happening in relation to the EPA? Prof. Hodum: It’s hard to try and bring it to a neutral point to discuss it. I want students to take positions on issues and articulate their positionality, but I also want them to think about the complexity and nuance. I think in general that we don’t do ourselves a favor if we get up and sermonize and moralize. These are really complicated social issues with multiple layers of context. We may

fundamentally disagree with someone on a position, but unless you understand their positionality and why they’re there, no one’s going to make any progress. It’s really easy to demonize the ‘other’. Especially when you perceive that there’s so much of significance at risk.

I definitely recognize that I have at least some authority as a faculty member. And I try to be very mindful of that. I don’t want any of my students leaving my classes parroting something like ‘oh Peter said this, I guess that’s what I should say.’ No, that’s the last thing I want you to do. So I try not to insert too much of myself in these discussions, because I want the students to have the space to do the critical work of assessing their own positionality. But also, I want them to know that I’m not dispassionate about it.

There are very real consequences to policies that are being disassembled and assembled. Whether it’s climate change or something else, it comes back to showing up, engaging, participating, and recognizing that the things that you do, do have consequences. And not doing anything - that has a consequence, too. Not doing anything is also an action.

Issues important to you may be pushed back, but you need to continue to just work towards advancing them. You can’t let setbacks and changes in the political winds define you or absolutely discourage you. When I was an undergraduate, Conservation Biology as a discipline was just beginning, and now, you can major in it, you can get a graduate degree in it, you can become a professor - that’s my position here, as a conservation biologist. And that didn’t exist less than thirty years ago. If you think about the regulations that we now have – are they enough? Absolutely not. But - if I look at where we were versus where we are now, we’ve moved.

That needle has moved. And it may get pegged back a little bit, but it’s not going to go all the way back. And we can mitigate the damage that’s done if we get out there and really participate.

Melody: According to The Washington Post, there are proposed budget cuts to the EPA to 25% of employees and 56 programs that involve “pesticide safety, water runoff control, and environmental cooperation with Mexico and Canada under the North American Free Trade Agreement” (1). What do these proposed budget cuts mean for young adults who hope to work and research in the realm of environmental policy?

Prof. Hodum: I think in the short term it’s going to have a very real impact. I honestly don’t think that over the long term the setbacks will be particularly significant ...However, over the next few years, absolutely. There are going to be fewer jobs. There are going to be fewer jobs in the US Fish and Wildlife Service, in the USGS, EPA, NOAA-they are all going to be hit to some degree. The good thing is that what Trump has proposed is the ‘skinny budget’.

That’s not actually mandate. That budget proposal is going to be discussed, and ultimately has to be approved,

by Congress. So hopefully it will not be as severe as is proposed, at least for some of the agencies. I think we can all confidently say that there’s going to be less funding. But, encouragingly, there are enough people on both sides of the aisle that are looking a little bit more critically at what the implications of such cuts would be and are not necessarily following strict party lines. We still have to see. We don’t know how severe those cuts are going to be. We have known this is what Trump wants, but Congress weighs in on that and has a very significant say as to whether or not they support the budget.

It’s short–sighted and it’s discouraging and disheartening. These are agencies that arguably are underfunded for the work and for their mission already.

The Fish and Wildlife Service doesn’t even have enough staff to keep up with the petitions for endangered species listing. With respect to jobs, there may be more opportunities with NGOs. There are [also] state agencies where more opportunities may exist, although some of their funding is derived from federal sources.

RIGHT: Prof. Hodum with his daughter.

Photo: Peter Hodum

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Melody: What can we as individuals who care about the environment do in this situation?

Prof. Hodum: I think multiple things. We’re not going to “save the world,” but our actions do matter. Again, it comes back to engaging and participating - making sure you’re communicating with your legislators, become active with that. That communication can be phone calls, emails, letters. Although you’re not going to be the only one and you’re going to get a standard template reply, those count - legislators or their staff look at what they get. Also just continuing to be intentional about how you live your life. You living according to your values and beliefs is important not only for yourself but also allows you to be a role model. Other people notice the way you live, and you may unwittingly model behavior for a lot of other people. It [also] depends on what your personality is and what you’re comfortable with. If you’re comfortable going to protests, go to protests. If you’re not, maybe you’re more of a researcher or a letter writer. There is space for everyone, but we each need to decide for ourselves to become involved. Do research that addresses some of the concerns that are emerging. Rather than prescribing specific actions, it’s more a case of encouraging people to be self-reflective, and to ask themselves “How do I feel comfortable contributing?” Decide on what you feel you can do effectively, and do it.

Melody: Anything else you would like to comment on?

Prof. Hodum: One of the things I’ve been thinking about over the past several months - and it’s something we talk about explicitly in conservation - is the tension that exists between science, advocacy and activism. You have this valuesdriven discipline in a supposedly valueless scientific world - which again, values inform all of our science – but the inclusion of values is intentional, as opposed to inadvertent. How do science, advocacy, and activism fit?

Can you be a credible scientist while being an advocate?

Can you still be a credible scientist while being an activist?

Does that compromise your ability to do good, rigorous science and portray it in a way that’s appropriate? And the reason I mention that here is because I think that when we look at recent developments like the idea of a “March for Science” - scientists don’t “march,” that’s so antithetical to our traditional vision of what science is. I think the last few months have been a huge reality check for the scientific community. And some of the concerns may be overblown, at least from my perspective. But we don’t know, and those uncertainties with the Trump Administration and their relationship with science are troubling. But I do think it’s going to be interesting over the next several years to see how the scientific community engages with this pretty profound challenge, because a lot of scientists due to the type of research that they conduct, haven’t really needed to engage with broader communities. I wonder if the challenges that the current political environment have generated are going to produce a level of reflection about engaging more intentionally with the rest of the world, beyond the ivory tower, beyond the research community itself. Will the scientific community respond to these challenges with a greater commitment to broader societal engagement? If so, maybe that’s a good thing that can come out of this.

We would like to thank Peter Hodum for his time, knowledge, and insight on these important issues.

ABOVE: Prof. Hodum’s Spring 2017 Ornithology class. Photo: Peter Hodum

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23 1/2 Degrees A POEM BY CURTIS MRAZ

Small, misplaced detail Earth tilted just right Nudged out of balance Ever so slight Gives rise to winter Gives rise to flight Perfect tilt Brings sun and snow melt Smell of spring sings Honey bees stretch wings Take to the air Earth spins on its axis Not seeming to care June, July, August Some of the hottest Welcomed with flowers Sheer honey bee power Thirty thousand per hive Summer must be alive Blossoms die Leaves change color Earth’s perfect angle Reveals branches in a tangle Autumn has arrived Beekeepers No time for bribes Stealing honey Sweet crops turn money First frosts come quick Spinning on a seasonal spit Honey bees return home Resources tight Not enough for males to take a bite Useless drones dragged out by the knees Never knowing it’s because 23 and a half degrees UNIVERSITY OF PUGET SOUND | 19

Genetic Meltdown in the Woolly Mammoth

BY MEGAN REICH

THEME 3: GENETICS THIS MONTH “We seem to arrive at the ridiculous conclusion that the clue to the understanding of life is that it is based on a pure mechanism. ...But please, do not accuse me of calling the chro mosome fibres just the cog of an organic machine.”

Erwin Shrödinger, What is Life, 1944

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This semester, Prof. Alyce DeMarais assigned the students of her Genetics class to write a “Genetics This Month” paper, a mixture of a short paper and opinion piece. Two of these papers are featured here. Students were asked to find a story form the popular press related to a recent finding in the field of genetics, and then compare that article to a research paper from the primary literature that addresses the same topic.

On March 2nd, Rebekah L. Rogers and Montgomery Slatkin published a study in PLOS Genetics entitled “Excess of genomic defects in a woolly mammoth on Wrangel island,” which compared mutations between recently sequenced genomes of two species of extinct woolly mammoths. One of the species was sequenced from a 45,000 year-old specimen found in mainland Siberia, when mammoth populations were still relatively high. The second genome, however, came from an isolated population only 4,300 years old from Wrangel Island north of Siberia, one of the last remaining mammoth refuges. The 43-fold reduction in population size between these two species offered a rare opportunity to test the “Nearly Neutral” hypothesis of molecular evolution, which predicts that smaller population sizes of a given species will lead to an accumulation of detrimental variation (“genetic meltdown”) in the genome (1).

To identify mutations, the researchers identified single nucleotide polymorphisms (SNPs) between the two species by aligning their sequences against a L. africana (African bush elephant) genome. From this, they quantified stop codons, substitutions, and deletions. Functions of the deleted genes in both mammoths were inferred via analysis of orthologous genes (conserved sequences with similar protein functions) in mice. Overrepresented functions among the deleted genes for the Wrangel Island mammoth included major urinary and gastric-related proteins, lipocalins, pleckstrin, and pheromones. The mainland mammoth also contained gene deletions for important functions like aldo-keto metabolism, DNA repair, and transcription regulation. Overall, the study found that genetic meltdown had indeed occurred as mammoth populations declined in size. The Watkin Island genome had significantly more deletions, retrogrades, point mutations, and premature stop codons than that of the mainland mammoth. To determine whether this data matched with the Nearly Neutral hypothesis, Rogers and Slatkin (2017) performed a model simulation which assessed heterozygosity at non-synonymous sites (HN) relative to synonymous sites (HS) between the two mammoths (as heterozygosity depends directly on population sizes). The model values were less than what was empirically observed, and

they pose several hypotheses as to why (selection coefficients, an acceleration in generation time on Wrangel island, or founder effects during island invasion). According to Rogers and Slatkin (2017), the findings from these ancient specimens have relevant implications for conservation genetics work taking place today. If the genomes of the endangered species have experienced similar genetic meltdown to the mammoth, scientists should be weary of repercussions that might impede current population recovery efforts.

Also on March 2nd, Scientific American published a popular article entitled “See-Through Hair and Awkward Sexual Problems: The Woolly Mammoth’s Bitter End,” which describes and discusses the implications of Rogers and Slatkin (2017). The article opens with a brief overview of how the researchers compared the genomes of two mammoth populations and observed genetic meltdown. However, rather than reflecting the study’s focus on the Nearly Neutral Hypothesis, the article immediately turns its attention towards several of the phenotypes that Rogers and Slatkin (2017) inferred from the mutations in the Wrangel Island mammoth genome. The article describes how the mammoth’s coat acquired a “bizarre, satinlike translucence,” and how disruptions in urine protein production had the potential to “make LEFT: A reconstruction of the

Woolly Mammoth, Mammuthus primigenius, at the Aalborg Zoo Ice Age Exhibition in Denmark, May 2016. Photo by Honymand, Wikimedia Commons

UNIVERSITY OF PUGET SOUND | 21

are more cautious about jumping to conclusions or break a courtship” (2). The article taps into a than the Stetka article conveys. The researchers sense of humor here, engaging readers in imagery note that while the recently reduced population and situations the Wrangel Island mammoth would sizes of Indian elephants may also be at risk for have experienced. The situation, however, is more a similar accumulation of detrimental mutations, complex than the simple stories told by the popular this would need to be more fully investigated article. For example, Rogers and Slatkin (2017) do with multiple population genomic samples for mention an association between urinary proteins multiple individuals and timepoints (2). The and mate choice, but note that it is equally possible popular article suddenly turns to another topic: the affected urinary peptides “are not essential.”

The Woolly Mammoth Revival (WMR) Project. The The popular article’s evocative description also WMR Project is using CRISPR/Cas9 gene editing to leaves out key details about the mutations, such as produce a “mammothlike elephant” (Stetka 2017). why mutations may have been detrimental to the The article reaches out to co-author Rogers as well species. But for the coast mutation, for example, as Love Dalén (original sequencer Rogers and Slatkin (2017) draw from previous mammoth studies in their Love Dalén on the of the mammoth DNA), both of whom note the ethical concerns discussion section studies to explain Woolly Mammoth the study raises. Because elephants how with the loss of medullae that creates their protective stiff outer Revival Project: “They “have a capacity for suffering similar to our own,” introducing a coat, loss of FOXQ1 (the locus could be in for some detrimental mammoth mutation associated with this phenotype) may could seriously impact their quality have made them less able to adapt to surprises—possibly life (Stetka 2017). I thought the cold temperatures. I appreciated how satin-colored surprises of article succeeded at raising broader Rogers and Slatkin (2017) bridged their findings at the molecular with gastric irritation.” moral and philosophical questions about genetic engineering and level to how the mammoths would helped solidify the relevancy of have survived on an ecological level Rogers and Slatkin (2017). I was surprised to find throughout their research process. I failed to sense no mention of the WMR project in the research this same connection in the popular article, which article itself. Was such a topic too “controversial” focused on the phenotypic implications rather for the journal? Then again, Rogers and Slatkin than the methods of the study.

(2017) primarily concerned itself not with how sequenced mammoth DNA can or should be used I was more impressed by the second half in the WMR Project, but rather how it provides a of the popular article, which brought in an rare opportunity to see how genomes are changed unaffiliated biologist from the Swedish Museum by population bottlenecks – a different goal, with of Natural History to comment on the sobering different but equally valuable implications to implications the study has for current endangered consider. species (2). However, Rogers and Slatkin (2017)

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Tsimane’s Benefits from the Alzheimer’s Gene Mutation

BY MORGAN EDDOLLS

Popular Press Story

With memory decline, decrease in cognitive function, and expensive hospital bills, Alzheimer’s disease has been known to be a huge problem in the United States. Alzheimer’s disease can be developed from a genetic mutation known as the apolipoprotein E (E4) allele. This allele leads to a higher risk of many different problems later in life, like Alzheimer’s or cardiovascular disease.

While this allele is prevalent in the United States, it is actually seen more in tropical regions near the equator, and it does not seem to be as much of a problem in these communities (1).

Researchers studied a group of Amazonian forager-horticulturists known as the Tsimane. Researchers wanted to determine the impact of the E4 allele on this population. The Tsimane community has always lived isolated from the modern world, which also means they do not have any modern

medicine or amenities that other people around the world use every day. This makes the community more susceptible to different pathogens and parasites, like ones that attack cognitive tissue. It turns out that about 70% of the women in the Tsimane community are infected with roundworms. Since many of these parasites cause cognitive decline, it was assumed by the researchers that the E4 allele would increase this cognitive decline, but they were wrong. Researchers found that individuals who had the E4 allele, even those infected with parasites, had less cognitive decline compared to those without the E4 allele. From this, researchers think that this allele is extremely helpful in this population even though it is quite harmful in others (1).

Primary Literature Article

The apolipoprotein E (E4) allele is the most compelling risk factor of Alzheimer’s disease. It is seen all over the world, with more prevalence in tropical areas near the equator and in northern Europe. In general, carriers have a much higher chance of developing the disease compared to non-carriers, but both groups can get it. Women also have a much higher chance of developing the disease compared to men. There is still evidence of quicker cognitive decline and decrease in gray matter due to synapse loss if you have the E4 allele, even if you do not have Alzheimer’s. Besides cognitive problems the E4 allele also causes an increase in cholesterol and LDL, and a higher risk of cardiovascular disease (2).

While the E4 allele has many harmful effects, the allele might benefit non-industrialized populations that are exposed to many parasites, like the Tsimane population. The E4 allele seems to protect this population against parasites by inter-

LEFT: A dwelling of the Tsimane people. The Tsimane live in lowland Bolivia. Photo by Ben Trumble, CBC News

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fering with the clearance of infectious diseases, allele could potentially be advantageous to fitness in like viral hepatitis C, Giardia, and cryptosporidium. communities that are not industrialized and have a These infectious diseases increase cognitive decline, high rate of parasitic infection (2). which results in major decrease of productivity in all areas of life and health. This can have an especialComparison ly negative impact on foraging communities since lots of cognitive function is needed for foraging and

The popular article presented all of the hunting. The E4 allele ends up being more benefiinformation at a much more basic level compared to cial in this community for this reason. But scientists the scientific article, which made sense since it was have are not totally positive if this is the case for this geared towards a bigger audience, like the definition allele (2). of ‘allele’ that was provided for example. There were

To obtain evidence of this, researchers a few random facts that were used to persuade the studied the Tsimane population to determine the E4 audience that the research was completely relevant allele effect on the parasite burden in predicting the and correct. In the scientific article the researchers adults’ cognitive function and the provided specific percentages for who benefits that carrying E4 has in earactually showed less cognitive decline ly life, like with brain development “The E4 allele could with the E4 allele, whereas the popular and cognition. The researchers testpotentially be advan- article made it seem like everyone with ed 372 Tsimane patients aged 6-88 the E4 allele always benefitted. But the years old by taking a blood sample tageous to fitness in popular article summarized the reand having them perform cognitive communities that are search pretty thoroughly, even though tasks. The parasitic burden was they did not mention every detailed determined through different cell not industrialized and fact. counts, like leukocyte count (2). have a high rate of Opinion

Through the genotyping I found it very helpful to read the researchers determined that about parasitic infection.” popular article before I read the sciena quarter of the patients carried tific article. It gave me a quick summary at least one copy of the E4 allele. that was even more broad than the abBecause of this low number of frequency, it was stract of the original paper. After reading the scienassumed that they were E4 heterozygote carriers. tific article, I noticed that there were more hypothOut of these carriers, about 20 percent of adults eses that the researchers were considering in their older than 30 years old had a lower eosinophil research that were not mentioned in the popular count (used to imply parasitic infection) compared article. The popular article did not mention all the to non-carriers. With cognition, adults with the E4 conclusions that the researchers got, but I thought allele had worse cognitive performance, especialthey did a good job summarizing everything. I found ly fluid cognition. So overall there was a negative it a bit misleading that the popular article made it association between the E4 allele and cognition, but seem like all the results were 100 percent true, when a positive association between E4 and eosinophils. there was variation in the factors that made the reThis reveals that adults who have a high eosinophils sults true in the scientific article. But overall I found count and have the E4 allele will have better cognithat the authors of the popular article did a good job tive performance compared to the adults who also of summarizing the research and I would recomhave high parasitic burden and no E4 allele. The E4 mend it to someone who is interested in this topic!

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Just What the Heck is ∞?

The Theorems of Georg Cantor

BY JESSE JENKS

THEME 4: The Big and the Small “For after all what is man in nature? A nothing in relation to infinity, all in relation to nothing, a central point between nothing and all and infinitely far from understanding either.

The ends of things and their beginnings are impregnably concealed from him in an impenetrable secret . He is equally incapable of seeing the nothingness out of which he was drawn and the infinite in which he is engulfed.”

- Blaise Pascal, Pensées, 1669

What is ∞? The ‘lazy eight’ is often read as ‘infinity’. But what exactly does this mean? For thousands of years philosophers and mathematicians have tried to grapple with the concept of infinity, but it was Georg Cantor who, in the late 19th century gave us first tools to grasp this slippery concept. One of the most astonishing results in the history of mathematics is Cantor’s proof that there are infinitely many kinds of infinity! This result is known as Cantor’s theorem, but the way the theorem is often stated doesn’t quite capture the philosophical subtlety and issues of this result. This article will try to shed some light on this truly mind-boggling result.

One important way of thinking about infinity is to think of it as meaning ‘not finite’. In mathematics, this is really all we mean. Something is described as inifnite precisely when it cannot be described as finite. This concept will be the basis for many theorems. Cantor was able to do this with two relatively simple concepts: sets and functions.

Often called the ‘father of set theory’, Georg Cantor made enormous contributions to mathematics. In fact, set theory is now considered so fundamental, some people believe that almost all mathematics can described entirely in terms of set theory.

The reason many popular science sources do not go into detail about the proof of Cantor’s theorem is that it requires a bit of mathematical background to even state the formal result. However, considering how astonishing the result is, the proof is remarkably simple. Let’s start with a few definitions.

Sets: A set is simply any collection of “definite and separate objects … of our intuition or our thought”.

The objects in a set are called the elements of a set.

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For example the set S = {a,b,c} is a set containing three letters a, b, and c. We give it the name S so that we can refer to it later. In mathematics, we are often concerned with set of numbers. For example we could have a set M = {1, 2, 3} containing numbers. I like to think of sets as buckets, or bags.

Functions: A function is a way to relate two sets together. For example, if we have the set M and S (defined earlier), we could define a function f = {(1, a), (2, b), (3, c)}. This is captured with the more familiar notation f (1) = a. In this case, f is a mapping from M to S. In particular f (2) = b is read as f maps 2 to b. The defining characteristic of a function is that, the same element does not map to two different ones. For example if f(1)=b and f(1) = c, then f is not a function.

There are a few types of functions, but we are concerned with what are called bijective functions.

The function f above is an example of a bijective function. The important thing to take away here is that a function is bijective if every element in M can be uniquely associated with every element of S. This allows us to define our first important concept: the size of a set.

Cardinality: Two sets have the same size or cardinality if there is at least one bijective function between them.

For finite sets like M and S, it is very easy to show that they are the same size. But with infinite sets, it becomes much trickier.

Using these concepts, Cantor was able to show some really astonishing results. For example, we often think of a square and a line as being very different things. And generally, we think of two dimensional shapes as being fundamentally different from one dimensional shapes. But Cantor showed that a square and a line have the same size.

Here is a short (technically incorrect1) proof.

Think of the set of points in a 1 by 1 square. We could describe each point as a pair of numbers, for

ABOVE: Georg Cantor, 1845-1918, was a German mathematician who is known for inventing set theory.He also happened to be a skilled violinist. Photo: Wikimedia Commons

example (0.13, 0.24) would be a point in the square.

But now we can “interleaveâ€? the numbers to get the number 0.1234. In fact, we could do this with every single point in the square and we will always get a number between 0 and 1. In the same way, we could take a single number between 0 and 1, like 0.121212‌ and get a point in the square (0.111‌, 0.222‌ ). This way of associating every point in the square, with a number turns out to be a bijection!

So by our definition of size, a square and a line are the same size! In fact you can do this same trick with cubes and higher dimensions.

Power Sets: The power set of a set S is the set of all subsets of S. For example, with the set S = {a, b, c}, the power set đ?’Ť(S) = {{}, {a}, {b}, {c}, {a,b} {a,c}, {a,b,c}}. Notice that the set {} (called the empty set) is considered a subset of S.

[1] The problem comes from the fact that numbers don’t always have unique decimal expansions. For example 0.49999999‌‌ = 0.5. So the proof requires some finagling which makes it much more complicated. But the intuition is still good.

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What Cantor really showed is that, if you accept the existence of an infinite set, then you must also accept the existence of infinitely many sets which are larger than that infinite set.

Infinity has a long history in the philosophy of mathematics. One of the first introductions to infinity is when you first learn to count. To show that there are infinitely many numbers, we could assume there are only finitely many numbers. Since there are only finitely many, we can just pick the biggest number and add 1, giving us a bigger number. But if this new number is bigger than the biggest number, we get a contradiction, so there must not have been finitely many numbers. This is also interpreted as saying there is no largest number.

Although this way of establishing that there cannot be finitely many number is relatively simple, this basic idea is behind many theorems about infinity.

In fact, this technique is important enough to have its own name: proof by contradiction. For example, Euclid’s Elements includes a proof that there are infinitely many primes precisely because, if we assume there are only finitely many primes, we can come up with a new prime that is larger. Perhaps the most famous problems in the philosophy of infinity are Zeno’s paradoxes of motion. These paradoxes are thousands of years old, and yet philosophers are still debating these problems. This

ABOVE: A three-dimensional Cantor set.

Photo: Wikimedia Commons

just goes to show, our understanding of infinity is far from complete.

One complaint that is often made about mathematics, especially mathematical logic is that it is “too abstract”. I mean it doesn’t really matter if transfinite numbers exist or whether the law of noncontradiction really is a law, my toaster still works, my coffee machine still makes my coffee, the sun still rises. Why should anyone care? Granted, whatever implications the answers to these questions have, they will have little to no effect on our daily lives. The first response to this is that the “abstractness” of the questions is not a reason to dismiss them. In his essay Should Be Believe in Set Theory?, George Boolos points out that “we twentieth century city dwellers deal with abstract concepts all the time. We note with horror our bank balances. We listen to radio programs. All Things Considered is an abstract object. We write reviews of books ... we correct mistakes. And we draw triangles in the sand or on the board”. The difference between the abstract concepts we care about and the ones we don’t depends only on whether we use (employ these concepts) on a daily basis. And this is precisely why we should care about the foundations of set theory! Without some kind of set theory, none of calculus would make any sense. And in turn, none of physics, engineering, or really most of our understanding of the world. What if it turned out that the decades of work mathematicians had done on set theory had been a total waste of time?

What were the physicists doing? Why does calculus predict the behavior of physical phenomena so well? From a scientific point of view, the answer to Boolos would have to be yes. Clearly set theory of some sort is at work, and one that is at very close to ZFC. But why do the axioms of set theory tell us that sets of unimaginable infinite sizes exist? Is this just some quirk of set theory, meaningless byproducts?

Or is it really true?

Perhaps you believe that mathematics is just some system we use because it is useful. Nomadic herdsman used the concept of numbers 1, 2, 3, ... to count their sheep, or keep track of debts. The complexity of mathematics today is just the result of doing this for centuries. But consider the number of atoms in the universe, approximately 10^81.

This is an enormous, but finite value. It is finitists.

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No Skink No Crumble!

BY GABRIELLE GENHART-STIEHLER

ABOVE: A skink spotted by Gabby in Queensland, Austrailia.

Photo by Gabrielle Genhart-Stiehler

The Prickly Forest Skink: Species Profile

Scientific Name : Gnypetoscincus queenslandiae Range : Endemic to the Wet Tropics Bioregion on the northeastern coast of Queensland, Australia.

Habits : Nocturnal Insectivores, live under logs on the forest floor Size : Average 8.5cm long from tip of nose to base of tail Reproduction : Live-bearing 28 | ELEMENTS

Six hundred million years ago the supercontinent of Gondwana was formed. The land mass included present day Africa, Antarctica, Australia, and South America. Ancient rainforests dominated the landscape, but as the continents continued to drift the rainforest diverged into various climates. The northeastern coast of Australia is thought to have the sole continuously surviving patch of rainforest since Gondwana split. This area is the Wet Tropics Bioregion and is currently a world heritage site, renowned for its historical importance and biodiversity. Included in this bioregion are over 1,000 species of animals, each with their own habitats and eating habits. Many of these species are found on the forest floor, where logs and leaf litter make suitable habitats for smaller animals. One species that makes use of the forest floor are skinks. Skinks are the most diverse family of lizard with 1300 species worldwide, 202 living in the Wet Tropics bioregion. Many of the skinks within this bioregion are endemic, meaning they are found nowhere else in the world. Endemism is very high in the Wet Tropics bioregion due to its unique formation and origins from Gondwana. Endemism is an important measure of the biodiversity of an area because it represents the amount of unique organisms and roles that exist within the ecosystem. A specific endemic of the Wet Tropics forest floor is the Prickly Forest Skink.

The Prickly Forest skink is monotypic, meaning that it shares its genus with no other species of skink and is genetically isolated from all other genera. This skink has large eyes adapted to hunt its prey efficiently at night and coarse ridged scales lining its body. Unlike most other skinks, the Prickly Forest Skink is a nocturnal animal that seeks refuge under logs during the day. Because of their small range and often overlooked habitat, there is very little known about the Prickly Forest Skink.

Most research is limited to studying the genetics of skink populations within fragmented forests with little focus on specifics of the habitat (1). Our goal was to change that. We hoped that by searching for these skinks and studying their microenvironments, we could gain some insight into their preferred habitat. So we took to the rainforest.

We sampled fallen logs in the rainforest around Chambers Lodge in Queensland, Australia by dividing into two groups of four and two groups of five. Each group surveyed four separate 400m2 plots, sampling every log we came across. We also noted logs that were too large to roll and any logs that crumbled or broke apart easily when lifted.

“No skink, no crumble!” boomed through the forest as we recorded the absence of skinks under each log and the condition of that log. To better understand the area we were sampling we noted the canopy cover (how much light came through), the number of logs within the study area, softness and crumbliness of each log, and any significant plant life forms that indicate different rainforest types in the area. This allowed us to better understand what conditions are suitable for skinks.

Some research groups were more successful than others and were able to witness the Prickly Forest Skink’s extraordinarily large black eyes staring back at them from under a log, before expertly scampering away into the forest litter. After surveying 6400 m 2 total of regrowth rainforest, we only found a total of 11 Prickly Forest Skinks. These skinks were found in a range of log habitats, with no correlation to crumbliness or mushiness. The size of the skink also did not correspond to the size of the log.

However, with only 8 hours and 18 sets of eyes, our data collection was limited by these restrictions and a larger survey could reveal correlations that our data set doesn’t. It’s evident that we have a long way to go before understanding these rare reptiles and their habitat needs.

Habitat is an important aspect for any species living in the rainforest. The habitat an organism lives in provides shelter from predators and a food source. The Prickly Forest Skink uses the decaying

logs of fallen trees for both of these. Their habitat plays a huge role in their ability to thrive as a species, which is why forest fragmentation has detrimental effects on the Prickly Forest Skink.

Leaf litter is key to many endemic organisms within the rainforest. The Onowchilla, the Fern Wren, and the Brush Turkey extensively use the leaf litter by piling the leaf litter into one area. This exposes the forest floor, drying it out, and limits habitats for many skinks. One study revealed that forest fragments supported lower skink abundances,

ABOVE: A view of North Queensland. Photo by Gabrielle Genhart-Stiehler

ABOVE: The creek near the sampling location of Gabby and her classmates. Photo by Gabrielle Genhart-Stiehler

UNIVERSITY OF PUGET SOUND | 29

and smaller individuals, than comparable areas in nearby unfragmented forest (1). Forest fragmentation also has effects on the genetics of the Prickly Forest Skink populations within the forest fragments.

A study done in 2004 found that the rain forest was fragmented by logging and clearing for dairy farms in the early 1900s, most forest fragments have been isolated for 50–80 years (2). These large logging areas are then left to become regrowth forests with predominantly younger trees. Without a large disturbance such as a cyclone, these regrowth forests have few dead trees and logs for skinks to live in.

A regrowth forest is often too young to generate enough logs to support a healthy community of Prickly Forest Skinks, which leads to competition for limited resources.

These limited resources are affected by an increase in human impacts on rainforests with continued logging practices around the world, showing that regrowth forests are not specific to the Wet Tropics in Queensland, Australia. The future of rainforests is moving towards regrowth forests with fewer logs that small organisms need for survival.

Facts About the Prickly Forest Skink “Without a large disturbance such as a cyclone, these regrowth forests have few dead trees and logs for skinks to live in.”

“The Prickly Forest Skink is monotypic, meaning that it shares its genus with no other species of skink and is genetically isolated from all other genera.”

“Skinks are the most diverse family of lizard with 1300 species worldwide, 202 living in the Wet Tropics bioregion.”

ABOVE: Lizard Island, adjacent to the Great Barrier Reef, is home to a diversity of skink and lizard species. Photo by Gabrielle Genhart-Stiehler

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“The future of rainforests is moving towards regrowth forests with fewer logs that small organisms need for survival.”

All About Neutrinos: Tiny Leaders of the New Era of Astronomy

BY MEGAN REICH

the highest energy neutrinos come from cosmic You’ve probably heard of the protons, neutrons, rays originating far beyond our solar system. These and electrons that make up atoms, the basic cosmic rays, mostly made up of protons, violently building blocks that make up our matter-filled interact with the matter and radiation around them universe as we know it. But there’s another to produce neutrinos that propagate at energies fundamental particle zooming through the space over a million times greater than anything humanall around us at near the speed of light, billions of built accelerators have achieved. It is these highthem passing through our bodies every second – energy neutrinos that scientists have been trying the neutrino. Neutrinos were initially formed in to use as a trail of cosmic breadcrumbs that can the first second of the universe, before even atoms tell us about the locations and interiors of the were formed, and are one of the most abundant mysterious places where cosmic rays are born (3). particles in the universe (1). Neutrinos can be found pretty much everywhere, from the nuclear fusion reactions in stars like “Scientists have been But how did scientists figure out that the virtually imperceptible neutrinos our sun to the inside of our own bodies trying to capture existed in the first place? In 1930, from the radioactive decay of potassium (2). these fleeting ghosts the theoretical physicist Wolfgang observed that in his studies in an attempt to Pauli of radioactive beta decay, electrons Yet despite their ubiquity, neutrinos remain largely a mystery to scientists learn about extreme weren’t being emitted with the because they’re exceedingly difficult to environments in far- predicted full reaction energy. This apparent violation of conservation identify and detect. Neutrinos are like off reaches of the of energy and momentum could tiny fleeting ghosts. At only 1/500,000th be most easily explained by the the size of an electron, they can easily universe.” presence of another particle carrying fly through matter, unaffected by off the missing energy. Later, the magnetic fields. Neutrinos also hold Italian physicist Enrico Fermi named the particle a neutral charge, so they are unaffected by the a neutrino and developed a theory of beta decay electromagnetic forces that act on negativelybased on Pauli’s observations. charged electrons (1). This means they can travel in a straight line through the universe for millions or It wasn’t until 1956, however, that the neutrino was even billions of years, carrying information about first experimentally observed via a nuclear reactor where they came from along the way. Experiments

by Frederick Reines and Clyde Cowan Jr. at the suggest that neutrinos seem to remember their Savannah River Plant in South Carolina (1). Later origins, and scientists have been trying to capture in 1987, a rare opportunity to observe neutrinos in these fleeting ghosts in an attempt to learn about action came with Supernova 1987A. A supernova extreme environments in far-off reaches of the is where a star in its last stage of life undergoes a universe (5). final explosion, leading to the birth of a new bright stars that then gradually fades over several weeks Scientists can generate neutrinos in nuclear or months. Supernova 1987A occured on the edge reactors or particle accelerators here on Earth, but UNIVERSITY OF PUGET SOUND | 31

of the Large Magallanic Cloud, a dwarf galaxy close enough to earth that it was visible to the naked eye. At about two hours before visible light from the event reached Earth, neutrino observatories at IMB in Ohio, Kamiokande in Japan, and Baksan in Russia detected a burst of neutrinos (4). This was the first time that neutrinos emitted from a supernova were observed directly, marking the start of a new era of neutrino astronomy (6).

Although the field of neutrino astronomy is still in its infancy, the weak interactions neutrinos have with matter enable scientists to observe processes that are normally invisible from optical telescopes.

Neutrino astronomy observes astronomical events and objects with neutrino detectors in specially made observatories. Because neutrinos have such a weak signal, background noise must be reduced as much as possible. Thus, neutrino observatories are typically found deep underground or underwater (5).

One example of such an observatory is IceCube, completed in 2010. Located at the AmundsenScott South Pole Station in Antarctica, IceCube studies neutrinos inside a cubic kilometer block of extremely clear ice, purified by thousands of years of accumulated ice and snow. As neutrinos move through this huge volume of transparent material, they have the potential of colliding with the nucleus of a molecule of ice (5). This collision releases charged subatomic particles that travel faster than the speed of light. Similar to the sonic boom that a jet plane produces when it travels faster than the speed of sound, the particles leave behind a burst of of blue light, which are detected and amplified by photomultiplier tubes in the observatory (3). Neutrinos constantly race through the observatory – but it is only about ten times a year that a single neutrino will collide with a nucleus and be detected. Nevertheless, every neutrino counts: the light signals produced contain essential information about a neutrino’s path and energy, IceCube has observed the highest energy cosmic neutrinos ever seen to date. Detections of neutrinos at IceCube and other facilities are paving the way towards figuring out where the cosmic rays they originate in come from, and how neutrinos are able to reach such extreme energies (3).

32 | ELEMENTS

In recent years, scientists have gradually been discovering more about the nature of neutrinos.

In the 1990s, a team of Japanese scientists found that neutrinos are not massless, as was thought by particle physicists, but do have a tiny amount of mass (1). This may have something to do with why when the universe expanded and cooled, it came to favor matter over antimatter. is largely made up of matter, not antimatter (3). There are also three known varieties of neutrinos, or “flavors,” as physicists call them, each of which is associated with a different charged particle. The electron neutrino is associated with the electron, while the other two neutrinos are associated with heavier cousins of the electron known as the muon and tau (1). 2015, the nobel prize in physics is being awarded to Takaaki Kajita and Arthur B. Mcdonald for discovering that neutrino can actually oscillation between these flavors (3). From these discoveries and detections in observatories, neutrinos are becoming an important tool for probing beyond standard model physics and exploring fundamental questions at very high scales (6). Stay tuned for what these little ghost particles might reveal next!

ABOVE: With NASA’s Chandra X-ray Observatory, neutrinos have been observed in connection to outbursts generated by the black hole Sagittarius A. Photo: Wikimedia Commons

Is Publishing Possible as an Undergraduate?

BY HANNAH FLOREN

In the world of undergraduate natural sciences education, the glass ceiling that many students aim to break through is the opportunity to publish primary research in a scholarly journal. As undergraduate science majors we read so many primary sources for lab reports, research papers, and project proposals... the thought that our own work could be considered among these other familiar peer reviewed sources can seem a lofty goal. While it takes dedication to your work and persistence throughout the submission process, getting research published as an undergraduate student is an achievement within the reach of any committed scientist.

This semester I completed the process of publishing my first article in a peer reviewed journal, Marine Pollution Bulletin. The article was summarizing research I’ve done in the Slater Museum of Natural History regarding plastic ingestion in a small seabird, the Cassin’s Auklet, and I had the opportunity to collaborate and co-author the paper with my supervisor Gary Shugart. As a senior who has taken a myriad of science courses, it feels as though I’ve perfected the art of finding research articles for projects through Google Scholar and the Collins Library web portal. This is a skill many of us liberal arts students share regardless of our field of study.

Because of the high respect given to peer reviewed primary literature, I felt conditioned to believe that getting published was something only seasoned scientists with PhDs could achieve. However, after my experience submitting my work to Marine Pollution Bulletin this semester, I now strongly advocate that the process of publishing is a goal that students studying natural sciences at the University of Puget Sound are equipped to accomplish.

Prior to this experience I didn’t fully understand the process of peer review and how articles were accepted for publication in journals.

Aside from the actual article I wrote, I also had to

submit an abstract, keywords relevant to my research, and the names of suggested reviewers. This is where peer review enters the publishing process. The best suggestions for reviewers of a paper are individuals who do not have a personal connection with the author and therefore avoid any potential conflicts of interest, but who are knowledgeable in the field and have who have, ideally, published their own research about the topic. I decided to suggest a few of the authors whose work I cited in my article, and whose prior research conclusions had helped guide

THEME 5: Creativity “I am enough of an artist to draw freely upon my imagination.

Imagination is more important than knowledge. Knowledge is limited. Imagination encircles the world.”

Albert Einstein, 1929

UNIVERSITY OF PUGET SOUND | 33

me throughout my project. If the publisher approves unable to purchase the expensive color prints of the the suggested reviewers, and those individuals of my final paper and pay for open access, I was given agree to participating, their feedback is returned to a PDF of the official published edition, which I am the author anonymously. Any suggested edits the free to share for non-commercial purposes. Since I author chooses not to incorporate become an open completed the publication process, I’ve received many point of discussion, requiring a rebuttal to explain emails from professionals in the field requesting a why the edit is not necessary. At this point I realized copy of the article, and from other journals asking the importance of correctly citing me to submit my work. While I don’t have sources and presenting statistics, the time in my schedule as a student to “The publication which undergraduate professors keep writing articles for other journals, it so persistently drill into our heads. process taught me is reassuring to know that the opportunity Consistency is a valued pillar of exists and is within my grasp. published scientific research; without that pride in my own The publication process taught me the formalities and intricacies of work can help me that pride in my own work can help me the process, claims can lose their achieve success and can be beneficial to credibility and conclusions are more achieve success and others; I would gladly share my article difficult to agree upon. can be beneficial to with anyone interested because I want After the revision process is everyone to have the opportunity to others.” complete, the influx of emails from learn from what I completed. My advice the publishing company begins. to other undergraduate students and Authors can pay for open access to their articles, those wishing to publish primary research are to meaning that anyone can view and download them. collaborate openly and with your advisors and Otherwise, only subscribers of the journal in which mentors, ask for feedback regularly, and seize the the work was published have access. While I was opportunity to propel your work to the next level.

Nothing compares to the fulfillment of contributing quality work you are passionate about to a broadreaching community dedicated to solving problems and developing new ideas.

LEFT: Cassin’s Auklet specimens that Hannah used in her research, located in the Slater Museum.

Photo: Hannah Floren

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Entering the Allium: A “Lighter Side” of Science

Illustration By Megan Reich

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WHY ONIONS ARE COOLER THAN YOU Onions are one of the oldest crops cultivated by humans, dating back to 3500 B.C. in Asia and 2700 B.C. in Egypt.

Onions were worshipped by the ancient Egyptians, who believed that the sphereical shape and concentric circles of the vegetable were a symbol of eternity.

Onions were an acceptable form of currency in the Middle Ages and were commonly used to pay for rent, goods, and services.

The ancient Greeks believed that eating onions made you stronger, and athletes ate them before events in the Olympic games of the first century A.D. Since the 1940s, the onion has been used as a test system to detect for DNA damage by environmental mutagens.

Evidence has been found that derived compounds of onions have antimicrobial and antifungal properties, making them of possible beneift in heart disease and atherosclerosis, diabetes, cancer, and asthma.

Onions can also help tackle osteoporosis by destroying osteoclasts, bone cells which resorb bone tissue and weaken bones. “Ogres have layers� - Shrek.

By the Elements Staff Team 36 | ELEMENTS

COSMOPOLITAN d r e n

as m o h T it... t As u p ce n o n eds e Kuh c o r p e c n e i “Sc ral e n u f one e” m i t a at

What is why a truth and re we conce s rned o with the fi it in rst pl ace?

What’s Your 10 new Operating amendments Paradigm? to the National

STS: a Liberal Arts Degree for the 21st century

Environmental Policy Act that will make your head spin!

ts... s i t n e i c s , ut ...watch o put g n i e b e r you’ ope! c s o r c i m under the

ORGANIC CHEMISTRY MAD LIBS Separation of a Mixture by Extraction Work with a _________ (noun). Your mission is to separate a mixture of trans- cinnamic acid, 4-phenylphenol, and nicotinamide by extraction. Start by __________ (-ing verb) two grams of the mixture in approximately 50 mL of diethyl ether. Caution: Diethyl ether is extremely _________ (adjective)! Extract the ether twice with 5% _______ (noun) and then twice with 5% sodium bicarbonate. (Saturated sodium bicarbonate is _________ (adverb) 8%, so dilute it appropriately to get a 5% solution.) After ______ (-ing verb) the aqueous solutions (we will have 10% NaOH and 10% HCl available for neutralization), extract them with dichloromethane to obtain the ________ (adjective) compounds. (Do not use more than a total of 50 mL of dichloromethane when ______ (-ing verb) from the aqueous solution.) It is not necessary to extract the 4-phenylphenol with NaOH solution since it is the only _______ (noun) left after extracting the trans-cinnamic acid and nicotinamide.

Dry the organic solutions with sodium sulphate (or magnesium sulphate), filter (or decant), and _______ (verb) the solvent by evaporation. Weigh the products you obtain and save them for lab next week. You will do _______ (adjective) analyses on them next week. Obtain a melting point of the major product. How does your melting point ________ (verb) to the literature value?

38 | ELEMENTS Adapted From Luc Boisvert, “Chemistry 250 Lab - Fall 2014, Week 4: Separation of a Mixture by Extraction.�

SCIENCE ON YouTube is’t just for hilarious cat videos anymore. A growing mass channels feature educational science content that is just as entertaining as it is informative.

The creators of these channels provide an alternative to the textbook or classroom, teaching viewers both basic scientific concepts as well as translating

Sci Show

Hosted by Hank Green of Vlogbrothers fame, Sci Show covers everything astronomy to zoology with just the right touch of humor.

Sci Show rotates through a mix of talk shows, short science “doses,” and coverage of the latest in science, among other topics. Many of their videos ask strangely enticing questions, such as “What happens if you leave your splinters in?” and “What makes sourdough bread sour?” Sci Show also has separate Sci Show Space and Sci Show Kids channels.

Veritasium

Created by filmmaker Derek Muller, Veritasium makes science and engineering videos aim to deliver “an element of truth” via demos, experiments, and interviews. Like Sci Show, Veritasium’s videos cover a range of formats.

His “misconceptions” videos ask questions like “Where Do Trees Get Their Mass From?” and “Why are Astronauts Weightless?” Veritasium’s “Test Yourself” videos give viewers the opportunities to build their own experiments test their knowledge and reasoning skills (see “The Ice Cutting Experiment” and the “Slinky Drop”).

Reactions

Created by Adam Dylewski and produced by the American Chemical Society, Reactions uncovers the chemical reactions that happening all around and inside us in our everyday life.

According to the channel, they “answer the burning questions you’ve always wanted to ask” - Why does coffee make you poop? Why are avocados so awesome? How do you make your smartphone battery last longer?

the newest groundbreaking research and discoveries into language the layperson can grasp. Science education YouTubers are charismatically curious, chasing questions and trying things out for themselves D.I.Y. style. Here’s a list of several popular channels to explore:

minutephysics

On his channel minutephysics, physicist Henry Reich uses stick figure drawings and diagrams to explain physics concepts ranging from waveparticle duality to quantum tunneling within the span of just a few minutes. minutephysic’s simple and bite-sized explanations, visualized with just a whiteboard and some pens, are perfect for some on-the-go learning. The channel has even featured well-known guests such as astrophysicist Neil deGrasse Tyson and cosmologist Max Tegmark.

Conservation Strategy Fund

The field of conservation is interdisciplinary and complex. Conservation Strategy Fund is a non-profit organization with the goals to “make development smarter, quantify the benefits of nature, and create enduring incentives for conservation.” Their YouTube videos explain economic concepts through an ecosystem framework in order to educate conservationists on how to succeed through strategic thinking.

Numberphile

In Numberphile, Brady Haran makes you forget that you hate math - or maybe reminds you why you love it so much. Numberphile explores everyday things in life through numbers.

This channel has videos dedicated to prime numbers and pi, videos on how to master cards, the Rubik’s cube, and untangling knots, and even calculator unboxing videos.

UNIVERSITY OF PUGET SOUND | 39

Overheard Quotes from Science Professors: Spring 2017 Edition “How do you kill a log? Axeponents”

- Cynthia Gibson [Guest Professor Eric Jacobsen talking about the how his lab successfully synthesized a compound by including urea] “And then we had a urea... eureka moment”

- Eric Jacobsen

An

“...So who you would mate with on the first day of class would be different than who you want to mate with on the last day of class.”

- Siddharth Ramakrishnan

"It all depends on how height you dropped it, how g your planet is, how big your 2 is, and how speed your Vo is."

-- Rand Worland

exclu“We buy stuff and we eat stuff.”

“Check to make sure there’s no acetone. Or as they say in England, arsetone.”

- Steven Neshyba

“Everyday is better when you add an ICE table to it” - Megan Gessel 40 | ELEMENTS

- Eric Scharrer

“If you don’t want people to talk to you on a plane, just bring a math book and open it when they sit down”

- Cynthia Gibson

CITATIONS Evolution Misconceptions (Marchand) (1) Definition of EVOLUTION. (n.d.). http://www.merriamwebster.com/dictionary/evolution.

(2) Gould, S.J. 1989. The Iconography of an Expectation. Pages 23-52. Wonderful Life: The Burgess Shale and the Nature of History. W.W. Norton Company, Inc., New York, New York.

Evolvability: What Is It and How Do We Get It? (Moreno) (1) Cheney, N., Maccurdy, R., Clune, J., and Lipson, H. (2013).

Unshackling Evolution: Evolving Soft Robots with Multiple Materials and a Powerful Generative Encoding.

(2) Clune, J., Stanley, K. O., Pennock, R. T., and Ofria, C. (2011). On the performance of indirect encoding across the continuum of regularity. IEEE Transactions on Evolutionary Computation.

(3) Devesa, J., Almenglo ́, C., and Devesa, P. (2016). Multiple Effects of Growth Hormone in the Body: Is it Really the Hormone for Growth? Clinical medicine insights.

Endocrinology and diabetes, 9:47–71.

(4) Downing, K. L. (2012). Heterochronous Neural Baldwinism.

Artificial Life, 13. [Downing, 2015] Downing, K. L. (2015).

Intelligence emerging : adaptivity and search in evolving neural systems. MIT Press, Palatino.

(5) Grimes, J. A. and Hurst, J. W. (2012). THE DESIGN OF ATRIAS 1.0 A UNIQUE MONOPOD, HOPPING ROBOT *.

(6) Hornby, G. S., Globus, A., Linden, D. S., and Lohn, J. D. (2006). Automated Antenna Design with Evolutionary Algorithms. AIAA Space, pages 19–21.

(7) Kashtan, N., Noor, E., and Alon, U. (2007). Varying environments can speed up evolution. Proceedings of the National Academy of Sciences, 104(34):13711–13716.

(8) Kirschner, M. and Gerhart, J. (2005). The plausibility of life : resolving Darwin’s dilemma. Yale University Press.

(9) Mengistu, H., Lehman, J., and Clune, J. (2016). Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It. GECCO Proceedings.

(10) Mitchell, M. C. s. (1996). An introduction to genetic algorithms. MIT Press.

(11) Moczek, A. P., Sultan, S., Foster, S., Ledo ́ N-Rettig, C., Dworkin, I., Nijhout, H. F., Abouheif, E., and Pfennig, D. W. (2011). The role of developmental plasticity in evolutionary innovation. Proc. R. Soc. B. (12) Persson, B. N. J. (2007). Wet adhesion with application to tree frog adhesive toe pads and tires. Journal of Physics: Condensed Matter, 19(37):376110.

(13) Pigliucci, M. (2007). Do we need an extended evolutionary synthesis?

(14) Pigliucci, M. (2008). Is evolvability evolvable? Nature Reviews Genetics., 9(1):75–82.

(15) Poli, R., Langdon, W., McPhee, N., and Koza, J. (2008). A field guide to genetic programming.

(16) Rimbault, M., Beale, H. C., Schoenebeck, J. J., Hoopes, B. C., Allen, J. J., Kilroy-Glynn, P., Wayne, R. K., Sutter, N. B., and Ostrander, E. A. (2013). Derived variants at six genes explain nearly half of size reduction in dog breeds. Genome research, 23(12):1985–95.

(17) Stenzel, V., Wilke, Y., and Hage, W. (2011). Drag-reducing paints for the reduction of fuel consumption in aviation and shipping. Progress in Organic Coatings, 70(4):224–229.

(18) Tonelli, P. and Mouret, J.-B. (2011). On the Relationships between Synaptic Plasticity and Generative Systems. On the Relationships between Synaptic Plastic- ity and Generative Systems. 11:1531–1538.

(19) Wilder, B. and Stanley, K. (2015). Reconciling explanations for the evolution of evolvability. Adaptive Behavior, 23(3):171– 179.

State of the EPA: An Interview with Prof. Hodum (Saysana) (1) Juliet Eilperin, Chris Mooney and Steven Mufson. “New EPA documents reveal even deeper proposed cuts to staff and programs.” Washington Post, 31 March 2017. Web. https:// www.washingtonpost.com/news/energy-environment/ wp/2017/03/31/new-epa-documents-reveal-even-deeper-proposed-cuts-to-staff-and-programs/?utm_term=.727aaea1c73e Genetic Meltdown in the Woolly Mammoth (Reich) (1) Rogers, R. and M. Slatkin, 2017 Excess of genomic defects in a woolly mammoth on Wrangel island. PLoS Genetics 13: e1006601. doi:10.1371/journal.pgen.1006601. http:// journals.plos.org/plosgenetics/article?id=10.1371/journal. pgen.1006601 (2) Stetka, Bret. “See-Through Hair and Awkward Sexual Problems: The Woolly Mammoth’s Bitter End.” Scientific American, 2 March 2017. Web. Accessed 3 April 2017. https:// www.scientificamerican.com/article/see-through-hair-andawkward-sexual-problems-the-woolly-mammoth-rsquo-sbitter-end/ Tsimane’s Benefits from the Alzheimer’s Gene Mutation (Eddolls) (1) Lawrence J., 2016 Gene mutation associated with Alzheimer’s disease provides benefits to some populations.

Nat. Sci. News.

(2) Trumble B. C., Stieglitz J., Blackwell A. D., Allayee H., Beheim B., Finch C. E., Gurven M., Kaplan H., 2016 Apolipoprotein E4 is associated with improved cognitive function in Amazonian forager-horticulturalists with a high parasite burden. FASEB J.: fj.201601084R. (3) Trumble, Ben. Image in Zafar, Amina, “Amazon men in their 80s have the arteries of Americans in their 50s.” CBC News, 17 March 2017. Web. Accessed 16 April 2017. http:// www.cbc.ca/news/health/tsimane-artery-age-1.4029549 No Skink No Crumble! (Genhart-Stiehler) (1) Sumner, J., Moritz, C., and Shine, R. 1999. “Shrinking forest shrinks skink: morphological change in response to rainforest fragmentation in the prickly forest skink (Gnypetoscincus queenslandiae).” Biological Conservation 91 (2-3): 159-167.

(2) Sumner, J., Jessop, T., Paetkau, D., and Moritz, C. 2004.

“Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rainforest skink, Gnypetoscincus queenslandiae. Molecular Ecology 13(2): 259-269.

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All About Neutrinos: Tiny Leaders of the New Era of Astronomy (Reich) (1) Casper, Dave. “What’s a Neutrino?” University of California, Irvine, 1998. Web. Accessed 30 March 2017. http://www.ps.uci. edu/~superk/neutrino.html (2) Gallart, Sílvia Bravo. “Why Neutrinos Matter,” uploaded by TED-Ed, Youtube.com, 28 April 2015, https://www.youtube. com/watch?v=nkydJXigkRE (3) Marder, Jenny. “What is a Neutrino… And Why Do They Matter?” PBS NewsHour, 25 Jan 2011. Web. Accessed 30 March 2017. http://www.pbs.org/newshour/rundown/what-is-aneutrino-and-why-should-anyone-but-a-particle-physicistcare/ (4) Nave, R. “Electron Neutrinos and Antineutrinos.”

HyperPhysics, Georgia State University Department of Physics and Astronomy, n.d. Web. Accessed 30 March 2017. http:// hyperphysics.phy-astr.gsu.edu/hbase/Particles/neutrino.html (5) “Neutrinos: Nature’s Identity Thieves?,” uploaded by Fermilab, U.S. Department of Energy, 11 July 2013, https:// www.youtube.com/watch?v=RGv-pcKRf6Q. (6) Roberts, Glenn Jr. “The Burgeoning Field of Neutrino Astronomy.” Symmetry Magazine, 2 Oct 2015. Web. Accessed 31 March 2017. http://www.symmetrymagazine.org/article/ the-burgeoning-field-of-neutrino-astronomy Why Onions are Cooler Than You (1) Leme, Daniela Morais, and Maria Aparecida MarinMorales. “Allium cepa test in environmental monitoring: a review on its application.” Mutation Research/Reviews in Mutation Research 682.1 (2009): 71-81.

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Correction Statement: In the Fall 2016 issue, Elements attributed an incorrect name to the artist of the back cover illustration. The artist’s name is Kyrianna Bolles, not Kyrianna R Rayno.

Elements sincerely apologizes to Kyrianna for the miscredit.

...Interested in writing or contributing art to Elements Magazine for our Fall 2017 issue? We are happy to work with a range of formats, including:

Journalism covering local and global issues

Reviews of recent research work (on

campus or otherwise)

Conceptual or theoretical writing

Science culture Humor/satire Opinions

Visual art and poetry ...Get in touch with Elements (elements@ pugetsound.edu) to beging planning, writing, and editing with us!

Back cover photos by Megan Reich

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