BIOLOGY
MATH & STATISTICS
PHYSICS
SJS
Issue 05: Spring 2017
Swarthmore Journal of Science
International Silicon Valleys Where will the next Silicon Valley arise?
CHEMISTRY
ENGINEERING
COMP SCIENCE
Letter from the Editor BOARD
Spring 2017
Dear Reader,
Welcome to the Spring 2017 issue, the 5th issue of the Swarthmore Journal of Science. We are at the end of the school year, and this unfortunately means we must say goodbye to our dear seniors. While the discussion of goodbyes is often difficult, I would like to focus on another angle to the “end� of Swarthmore: the beginning of being citizens of the world.
EDITOR-IN-CHIEF
Outside college, we will all go out into many different fields. Some may become economists, others Philosophy professors and politicians. Regardless of our choice, we will certainly have interests outside of our majors and eventual jobs. This may be in the form of music, sports, current events, or movies. Being interested in multiple subjects is not something reserved for intellectually curious Swatties, however. This interest is a fundamental part of being a responsible global citizen, a person invested in the diverse events of the world. Somewhere within the list of topics critical to the world, science has a well-deserved place.
Helen Wang
Science is relevant not only to the world physically, but also culturally and ideologically. Knowledge about science can inform us in our everyday lives, from formulating our belief systems to choosing the right fad diet. The role of SJS, like the role of science communication, is to provide informative scientific articles to a general audience. We hope our articles are not only informative, relevant, and understandable, but also very engaging. Scientific topics ranging from new cancer treatments, planet discoveries, and self-driving cars are fascinating. The latter topic is even in this journal!
Aaron Holmes
MANAGING EDITORS Christina Labows
EDITORS Physics: Neeraj Shah & Katherine Dunbar Biology: Zelu Sibanda & David Tian Math & Statistics: Meghana Ranganathan Chemistry: Jennifer Guo Computer Science: Jimmy Shah Copy Editors: Lulu Allen-Waller & Vivek Ramanan Graphics: Emma Giordano, Letitia Ho, & John Sun
Before I conclude, I would like to thank the many great SJS board members for their continued diligence during the last year. Since the summer, they diligently collaborated with each other to create this journal and the issue last semester. I would first like to thank all the contributors who wrote well-researched articles and the editors who reviewed them. I would also like to Helen Wang and Christina Labows, our Managing Editors, for their great help with planning journal publications, board appointments, and campus-wide events. Last, but certainly not least, I would like to give a special thanks to Taylor Chiang, our layout editor, and the graphic design team of Emma Giordano, John Sun, and Letitia Ho. They diligently crafted the layout and graphics of this issue during the busy grind of the Fall and Spring semesters.
Layout: Taylor Chiang
I hope that you enjoy reading all the of wonderful articles in this issue. Ultimately, these articles are meant to foster dialogue with you, the reader, and the rest of the Swarthmore community. So, when you pick up this issue, share it with a friend and keep the conversation going.
swatjournalscience@gmail.com
CONTRIBUTERS Biology: Talia Borofsky, May Dong, Iris Chan, & Shivani Chinnappan Math & Statistics: Tushar Kundu Chemistry: Aly Rabin
JOIN THE CONVERSATION Connect with us on: https://issuu.com/swarthmorejournalofscience
Best,
https://www.facebook.com/SwatJournalScience
Aaron Holmes
http://pinterest.com/sciencejournal
Editor-in-Chief 2016-2017 2
CONTENTS 04
Should We Hit the Breaks on Driverless Cars?
06
Sans Gluten
08
Bleed: The Biology of Human Menstruation
10
International Silicon Valleys
13
Publication Process
16
Turkey Tresspassers
18
Finance, STEM, and the Liberal Arts
19
How Evolutionary Biology Improves the Understanding of Human Health and Disease
3
Should We Hit the Breaks on Driverless Cars? By Tushar Kundu
Joshua Brown had a love for technology. So much so that he named his Tesla Model S “Tessy”, and often filmed himself driving to show off Tessy’s various features. Tragically, the technology in which he placed so much faith ultimately proved prone to error. Last May, Brown had been driving with the car’s Autopilot feature activated when the autonomous driving system failed to recognize a white truck that had turned in front of him. Notably, this was the first fatal accident involving a car controlled by software and sensors, immediately alarming those who worry about autonomous vehicles’ ability to make split second decisions with lives at stake. While many people are rightfully focused on complex aggregate impacts on the economy, the environment, and transportation, Brown’s story raises a more fundamental question. Are autonomous cars safe? Following Brown’s death, Tesla looked to respond to the growing concerns. CEO Elon Musk was not swayed by the skeptics, as he penned a scathing email to a reporter in which he claimed “if anyone bothered to do the math (obviously you did not) they would realize that of the over 1M auto deaths per year worldwide, approximately half a million people would have been saved if the Tesla autopilot was universally available.” Musk continues provocatively: “Please, take 5 mins and do the bloody math.”
Let’s do just that. Although not apparent at first glance, the question “Are autonomous cars safer than human-driven cars?” is rather broad. To start, driver safety can be measured by a host of different metrics. Should we only look at fatalities, or should we include all accidents? Should we separate miles driven on the highway, for which speeds are greater but situational variation is minimal, from miles driven in the city? Clearly we must narrow our question. A possible solution is to compare basic fatality rates, or miles driven per fatality (mpf), for each mode of transportation. Americans drive 3 trillion miles each year and with 32,719 road accidents in 2013 (Bureau of Transportation Statistics, 2015) this corresponds to one death about every 92 million miles. At the time of the accident in May, Tesla claimed to have records of just over 130 million miles during which Teslas were driven with Autopilot activated. Simple comparison seems to favor Tesla; however as anyone who has taken a statistics course would point out, averages alone are not enough to determine if differences are statistically significant. Consider your favorite sports team. If they win three games in a row, would you predict that they will continue to win forever? Clearly not! You would probably want to see more games before making a prediction like that. (Note that we can’t eliminate the 4
possibility. If your team continues to win for years on end, perhaps it really is undefeatable and we should begin to look for divine explanations.) In the exact same way, we must also consider the total amount of miles driven using the Autopilot feature. After all it’s certainly possible that fatality rates are in fact higher for automated cars, but Tesla drivers were unusually lucky with only the single incident in the first 130 million miles of driving. Intuitively, the more miles automated cars drive while maintaining lower fatality rates, the more convinced we should be that they are truly safer. Statistics allows us to quantify how “convinced” we are using confidence levels. Confidence levels help us answer questions about the true values of parameters that we estimate using statistics (such as fatality rates). For example, based on our data, the difference we measured (130 mpf - 92 mpf = 38 mpf) is considered the most likely true difference in fatality rates. However, other differences also could be correct. By adding up the probabilities for all positive differences, we can measure how likely we think it is that the true difference in fatality rates is positive. When statisticians say the difference is statistically significant on a 5% level, this means that when we added up all the probabilities for positive differences, it summed to over 95%. Under certain assumptions, confidence intervals can be interpreted exactly how you would imagine. If we were to claim that the difference in fatality rates is statistically significant using a 95% confidence level, it would be equivalent to stating there is a 95% chance the fatality rates are different. We can now answer our two questions. Are the 130 million miles driven by the Tesla Autopilot system enough to make statistically significant conclusions, therefore justifying the assertion that autonomous fatality rates are lower? And if not, how many miles would be required? In a recent study by the RAND Corporation (2016), authors Nidhi Kalra and Susan Paddock find that the 130 million miles are not nearly enough. Even assuming zero deaths, autonomous vehicles would have to drive 275 million miles – over double Autopilot’s entire mileage to date - to establish with 95% confidence that autonomous driving fatality rates are at most the same as human drivers. Alone, this analysis is incomplete. In reality, it is very unlikely that autonomous vehicles will be able maintain a perfect record. Kalra and Paddock adjust their question by instead asking, if we assume the true fatality rate of autonomous vehicles is some percentage lower than for human drivers, how many miles would be required to detect the difference? Now we can address Musk’s statement directly. Claiming that autonomous vehicles would prevent half of all auto deaths implies they exhibit a fatality rate 50% lower than that of human drivers. Even if we were to assume this is true (which is not trivial), statistical analysis
shows that it would still require 496,518,349 or around 500 million miles to demonstrate a statically significant difference with 95% confidence. Although testing of autonomous cars has not reached the required thresholds, one could imagine that they will be there soon. After all, Autopilot was first offered in October, 2014. Another few years and the growing fleet of Teslas should easily log enough miles. However there is one more hurdle to clear. Not only should we care about the quantity of testing, but also the quality. All of our statistical analysis is built on the assumption that the miles driven by autonomous cars are a representative sample of all the miles driven in America. If this is not true, then there could be other factors that impact why we would observe lower fatality rates for autonomous cars. For example, it is probably safe to assume that Tesla owners are far richer than the average American. It follows that Teslas could be driven in disproportionality wealthy areas with well-maintained roads and signals. Then fatality rates could be driven down not because of the autonomous feature of the car, but because of the conditions in which they are driven. This is just one example of a sampling issue, but it is not difficult to imagine a host of other factors that could skew the data. Taken together, it seems that Elon Musk’s rush to judgment was premature. Not only are the 130 million miles driven by Tesla Autopilot not enough to compare fatality rates with human driving, it’s also unclear that the autonomous miles can be considered an accurate comparison. The inability to conduct the quality and quantity of testing required presents an issue, however it does not seem like the integration of driverless technology is slowing any time soon. The first self-driving commercial truck rolled out in Nevada in 2015, with many speculating that the trucking industry will be the first to feel the impacts of the new technology. No fewer than nineteen companies aim to have driverless car technology ready by the end of the decade. It appears that progress waits for no statistician. Literature Cited: https://www.nytimes.com/2016/07/02/business/joshua-brown-technology-enthusiast-tested-the-limits-of-his-tesla.html https://www.washingtonpost.com/news/monkey-cage/wp/2016/10/07/ are-you-safer-in-a-tesla-on-autopilot-as-elon-musk-says-lets-do-themath/?utm_term=.0f0214515c49 http://fortune.com/2016/07/05/elon-musk-tesla-autopilot-stock-sale/ file:///Users/tusharkundu/Downloads/RAND_RR1478.pdf https://www.theguardian.com/technology/2016/jun/02/self-drivingcar-elon-musk-tech-predictions-tesla-google https://electrek.co/2016/11/13/tesla-autopilot-billion-miles-data-self-driving-program/ 5
Sans Gluten By Aly Rabin
“Sans gluten”: Few phrases have as much shock value for an American studying in Paris. Translating directly to “gluten-free,” it is displayed with increasing frequency in French advertisements and outside Parisian restaurants. Bread is central to France’s culinary tradition and global reputation. The enormous “SANS GLUTEN” I saw advertised in the Paris metro, however, was prime evidence that the gluten-free trend had finally permeated one of the (arguably) most bread-obsessed nations in the world. According to the Consumer Reports National Research Center, one in three Americans believe they have at least some sensitivity to gluten, a group of proteins found in wheat (1). People with self-diagnosed “gluten sensitivity,” as it is frequently labeled, report classic symptoms like abdominal discomfort (and in some less-frequent cases, headache or numbness of the hands and feet) after a bread-filled meal (2). This sizeable percentage lies in stark contrast to the number of patients diagnosed with the autoimmune celiac disease, for whom ingesting gluten has painful consequences. The incidence of celiac disease in the United States is less than one percent (3). Both this gap between physician- and self-diagnosed cases of gluten sensitivity, and the increasing prevalence of gluten-sensitive individuals in Europe, bring up several key questions surrounding the gluten debate: how does the scientific community distinguish between real cases of gluten intolerance and self-diagnosed stomach problems (often augmented by the placebo effect)? Is there a scientific basis for this non-celiac sensitivity? The culprit underlying celiac’s serious symptoms is a miniscule 33-mer peptide, a subtype of protein called
gliadin found in gluten. Patients with celiac have overactive immune systems, and their T cells (a type of immune cell that attacks invaders) are hypersensitive to these gliadins, producing a painful inflammatory response in the gut and the breakdown of intestinal villi. The only known therapy for celiac disease is complete abstinence from any products containing gluten, including bread, pasta, and a large number of processed and canned foods (3). A number of studies have been conducted to address the growing number of patients with self-diagnosed “gluten sensitivity,” who report a number of uncomfortable symptoms after eating pasta or drinking beer. So far, no conclusive evidence has brought to light its sources or any reliable cures (2). As a result, the medical community has greatly contested the true nature of gluten sensitivity, with some even alleging that it is completely psychosomatic. The relationship between the psychological and the physical can certainly not be ignored here, as the placebo effect is particularly salient with regards to food; for a number of people who begin gluten-free diets or return to eating wheat, the knowledge that their diet either contains or lack gluten is enough to precipitate physiological changes (2). This does not discount, however, the real gastrointestinal symptoms a number of Americans are reporting. A number of scientists have attempted to expose other causes beyond gluten, some pointing to FODMAPS (fermentable oligo-, di-, and monosaccharides and polyols) including fructose, lactose, and other challenging-to-digest sugars (2). Other explanations seek to highlight the evolutionary basis for gluten intolerance, citing that the relatively short time in which humans have grown and eaten 6
finding cures for celiac; if our community seeks to best counter this issue, it must also attempt to disseminate correct information to the public and outweigh the strength of gluten-free marketing and otherwise-unsubstantiated claims. This is an issue of popular science. If gluten turns out not to be the underlying issue for a number of those with digestive issues, the public needs to find out from scientifically-backed sources. For France, where bread lies at the center of public life (only some exaggeration here), this is an existential issue. wheat has not allowed their digestive and immune systems to catch up (4). It is important to note that none of these findings or postulations have been adequately substantiated, leaving the mystery of gluten still at large. Meanwhile, the gluten-free industry is a multi-billion-dollar sector, and has taken hold at an international level. 63 percent of Americans believe that avoiding gluten is beneficial for anyone’s health, an again-unsubstantiated claim propagated by considerable advertising and media coverage (1). But for those without diagnosed gluten intolerance, most medical professionals recommend avoiding the gluten-free diet craze until this sensitivity can be confirmed; gluten-free foods often lack fiber and are considerably more expensive than unmodified products, and eschewing gluten in the first place makes diagnosis nearly impossible (1,2). The gluten-free fad has, however, proven helpful for the small population diagnosed with celiac disease; an abundance of products advertising their lack of gluten has made living without bread or canned foods slightly more manageable, by a number of reports (1). Beyond the uncertainties underlying gluten intolerance in the United States and on a global level, the gluten-free fad introduces a broader question: what happens when a disease becomes a trend? On the one hand, increased awareness for issues surrounding gluten helps patients living with celiac, and improves diagnoses for those suffering from digestive issues. Conversely, however, when the percentage of people undertaking this tailored diet vastly exceeds the proportion of the population with confirmed gluten intolerance, its validity is called into question. There is no denying that the trendiness of the gluten-free diet has led to an increase in incorrect self-diagnoses and a great deal of misinformation, propagated by advertisements and social media (2). The scientific community’s tasks surrounding gluten are not limited to further uncovering the biochemical basis for the disease, or to
Literature Cited: “6 Truths About a Gluten Free Diet- Consumer Reports.” 6 Truths About a Gluten Free Diet. Consumer Reports, Jan. 2015. Web. 09 Feb. 2017. Brody, Jane E. “When Gluten Sensitivity Isn’t Celiac Disease.” Well.blogs. newyorktimes.com. New York Times, 6 Oct. 2014. Web. Shan, L. “Structural Basis for Gluten Intolerance in Celiac Sprue.” Science 297.5590 (2002): 2275-279. Web. Velasquez-Manoff, Moises. “The Myth of Big, Bad Gluten.” NewYorkTimes.com. New York Times, 4 July 2015. Web.
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Bleed: The Biology of Human Menstruation By May Dong
In the past ten years, eight or more women have died in menstrual huts in rural areas of Nepal, garnering local and international attention (1). Menstruating women are considered unlucky and impure, and in more conservative areas, they are secluded from society for the duration of their menses. Menstrual huts are officially banned, yet fears of women contaminating the home persist. The belief that menstruating women are unfit for some aspects of societal or religious participation is not limited to rural Nepal; it is widespread across most major religions (2). It has been supplied as a rationale for preventing women from getting educated, going into politics, and, as recently as the 1960s, becoming astronauts (3). Nowadays technology, in the form of pads, tampons, cups, and menstrual suppression treatments, has contributed towards overcoming the stigma of monthly flow. Yet there is no denying that having a uterus which sheds its inner lining once every 28 days is an inconvenience. Having one’s period can be prohibitive to participation in work and school in countries where access to ‘sanitary’ equipment is limited or menstruation is considered dirty. Even in developed nations, periods are expensive to manage. According to the Absorbent Hygiene Products Manufacturing Association, the average British woman uses 22 sanitary products per cycle, summing to 11,000 in a lifetime (in terms of financial cost, Huffington Post claims women spend £18,000 on managing periods in a lifetime, which seems excessive to me). In addition, having one’s period can bring along a tangle of related discomforts
ranging from the normal― cramps, bloating, headache― to the clinical (painful menstruation, i.e. endometriosis, anemia(4)). From menarche, the onset of menses, to menopause, its finale, a woman might lose 15-25 liters of blood from shedding her endometrium (the uterine lining). For comparison, the adult human body contains about 5.7 liters of blood circulating at any given time (6). This blood loss, combined with the common symptoms and potential for abnormal menstruation, makes for a very uncomfortable and costly process. Why, then, do humans express what seems to be a maladaptive trait when our mammalian cousins do not? Anyone who owns a cat or dog might have noticed that other mammal species do not shed monthly blood (dogs can have bleeding but for different reasons (7)). Instead most female mammals have estrous cycles, in which the reproductive system can lie dormant for long periods of time. During dormant periods, the endometrium, the uterine lining in which a fertilized egg might attach itself to develop into a fetus, is not highly developed. The endometrium and ovarian follicles only develop during the first stage of estrous, immediately before the animal becomes fertile (8). In addition, decidualization, the stage where the uterine lining is in a state of high fertility and vascularization, is initiated only after the blastocyst (fertilized egg that has begun the first stage of development) has attached itself to the uterine wall. Therefore without pregnancy, when the cycle is over, there is no decidualized tissue to shed. In contrast, humans decidualize in response 8
to changing hormone levels rather than in response to the presence of an embryo (known as spontaneous decidualization). At the end of a person’s fertile cycle, the endometrial tissues are broken down and shed. This difference between humans and our mammalian cousins leads us to the rather obvious question: if there is an alternative to sloughing the endometriosis, why don’t we take that path? There is no consensus within the scientific community as to whether menstruation is adaptive or not. Two hypotheses in favor of an adaptive view of menstruation are that it aids in protecting the uterus from bacterial diseases transmitted by sperm (9) or that it is less energetically costly than maintaining the endometrium in a constant state of readiness (10). Emera et al. (2012) argue that neither of these ideas support an adaptive view of menstruation menstruation: sperm-transmitted pathogens are an issue in species that do not menstruate as well as in those that do. As for the energetic argument, most non-menstruating species do not maintain the endometrium in a highly fertile prepared state (the estrous has a stage of dormancy, or anestrous). Instead, they propose that menstruation itself is not necessarily adaptive but rather a direct consequence of decidualization. According to their hypothesis, spontaneous decidualization evolved as a response to conflicting ‘agendas’ between mother and fetus: it is in the mother’s genetic interest to invest in propagating her genome, whereas it is in the fetus’s interest to preserve its genome, which is different from its mother’s and from its siblings. This means that while the mother limits energy spent on any given pregnancy, saving energy for possible future children, the individual child’s evolutionary goal is to take as much energy for itself as it can. What this means for menstruation is that the differentiated endometrium exists as a sort of barrier to prevent the fetus from becoming too invasive and draining the mother of energy. Alternatively, it is possible that spontaneous decidualization evolved as a form of fetus selection. Since nurturing the development of an embryo is a huge energetic investment, it might make sense to terminate an embryo which would not be able to develop fully earlier rather than later in the pregnancy, even at the cost of menstruation. Just as the environment and selective pressures of the past have influenced the evolution of menstruation, so too will changing conditions affect its future. Age at menarche, for instance, is a factor of both genetics and environment. Higher body weight is inversely related to age at menarche; increasing weight in developed countries heralds earlier menarche (11). Coupled with increasing age at menopause, the uteri of developed nations are in for more work than ever. While there is no selective pressure on age of menarche and menopause, changing childbearing norms may alter sexual and genetic conflict. In 1911, the average number of children birthed per woman in the
US was 3.4 (12). In 2011, a century later, that number was 1.9. With fewer pregnancies per woman, energetic conflict between fetus and mother may decrease, removing selective pressure for menstruation. On the other hand, in developed countries where birth rates are low, there is little selective pressure against menstruation, since calories are easily accessible. It is also possible that an increased understanding of the hows and wherefores of periods will decrease the stigma and taboo that still surrounds periods. It’s a pity menstruation isn’t more openly discussed― the more you learn, the more you realize it is a bloody fascinating topic. Literature Cited: (1) Preiss, Danielle. “A Young Woman Died In A Menstrual Hut In Nepal.” NPR. 28 Nov 2016. http://www.npr.org/sections/goatsandsoda/2016/11/28/503155803/a-young-woman-died-in-a-menstrual-shedin-nepal (2) Raphael, M. 2005. Menstruation. Encyclopedia of Religion. Ed. Lindsay Jones. 9(2): 5866-5868. (3) Little, B. 2016. The Scientist Who Said Periods Weren’t a Big Deal. National Geographic Online. (4) (British) National Health Service. 2016. Periods. (5) Fraser, IS, Warner P, and PA Marantos. 2001. Estimating menstrual blood loss in women with normal and excessive menstrual fluid volume. Obstet Gynecol. 98(5 Pt 1):806-14 (6) American Red Cross. Blood Facts and Statistics. http://www.redcrossblood.org/learn-about-blood/blood-facts-and-statistics (7) Martin, RD. 2007. The Evolution of Human Reproduction: A Primatological Perspective. Yearbook of Physical Anthropology. 50:59-84. (8) Hill, M.A. 2017. Estrous Cycle, UNSW Embryology. Retrieved January 1, 2017, from https://embryology.med.unsw.edu.au/embryology/index. php/Estrous_Cycle (9) Profet, M. 1993. Menstruation as a Defense Against Pathogens Transported by Sperm. The Quarterly Review of Biology, 68(3):335386. (10) Strassmann, BI. 1996. The Quarterly Review of Biology, 71(2):181220 (11) Nichols, H.B., Trentham-Dietz, A., Hampton, J.M., Titus-Ernstoff, L., Egan, K.M., Willett, W.C., and P.A. Newcomb. 2006.From Menarche to Menopause: Trends among US Women Born from 1912 to 1969. Am J Epidemiol 164(10): 1003-1011. (12) Mather, M. 2012. The Decline in U.S. Fertility. Population Reference Bureau (13) Emera, D., Romero, R., and G. Wagner. 2012. The evolution of menstruation: A new model for genetic assimilation. Bioessays 34(1):26-35 (14) Chapman, T. 2006. Evolutionary Conflicts of Interest between Males and Females. Current Biology, 16(17):R744-R754. (15) Moss, R. 2015. Women Spend More Than £18,000 On Having Periods In Their Lifetime, Study Reveals. Huffington Post. 9
By Jimmy Shah
10
influx of interest from foreign investors, with Agnew and Murgia both citing Paris “emerging as a serious challenger to London and Berlin after long being considered one of the more parochial parts of the European tech scene.” Recently, local investors have even spawned Station F, a renovated train platform designed to hold 1,000 tech ventures in Paris. Many American tech giants such as Facebook have backed the projects, hoping to act as mentors to the elite batch of startups housed within the district. With housing developments planned near the station, Paris hopes to attract top-tier developers who may not have considered Paris a “tech city”. In India, an entirely different narrative exists. Names like Rahul Yadav and companies like Flipkart are much more familiar. India certainly has its own tech giants, but cities like Bangalore are now beginning to rise as tech capitals. In a similar fashion to Station F in Paris, India is funding its own incubator hub, referenced as the Startup Warehouse. As the PRI article notes, the goal is simple: “The idea is that over the next 10 years, we want to impact 10,000 startups,” says Ashok Madaravally, who oversees the Startup Warehouse, and is deputy director of the National Association of Software and Services Companies. “That means we help them get started, connect them with customers, get them significantly mentored and help them grow at a global scale.” Although competetion from China is steep and some argue that
A
As startups continue to emerge and expand their presence, one question that has venture capitalists and portfolio managers engaged is the rise of the of the next Silicon Valley. Surges in unicorns and housing prices suggest that Seattle, New York, and Chicago are all well-regarded as technology incubators. However, as McBride from Bloomberg notes, “Even the best of intentions and super-speedy internet isn’t enough to create a new Silicon Valley.” Although America has expanded to have booming hubs, other countries are still struggling to create their own technology revolution. From a lack of engineers and capital, to a complex cultural dynamic, the reasons certainly vary. However, the use of startup incubators has certainly driven growth in areas that seem promising to investors. Places like Paris, Bangalore, and Lagos are beginning to rise as the next centers of tech growth. For those who are unfamiliar, a startup incubator typically allows for small companies to live in close proximity to the hub for a short period of time, working with the incubator’s team to produce rapid growth. The incubator typically buys a small stake in the company for some small amount, hoping that the growth in the company will make monetary returns for the incubator. For example, Y Combinator, one of the more prominent incubators in America, will typically invest $120,000 for a 7% stake in the company. Some of those investments have yielded AirBnB and DropBox, companies that are now worth well over a billion dollars. With the aid of special government visas and a rise in funding, startups in Paris are beginning to challenge traditional notions. Recently, Paris has seen an
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the lack of physical infrastructure certainly raises doubts about the city, investments have poured in regarding the promising future of these startups. This sentiment is best captured by the secretary of e-governance for the state of Karnataka: “I think there’s absolutely no gain saying the fact that India is at least 20 years, in some cases perhaps 100 years, behind China in terms of physical infrastructure,” Srivatsa Krishna says. “But we are ahead of them in innovation, knowledge and the IT economy. And this hasn’t happened overnight. This has been going on for the last 25 to 30 years, to reach where we have reached today. And the good news for India is, it has only scratched a very, very small bit of the global pie. The way ahead is long. The rewards are many, and very, very
fruitful, and so are the risks. And we are very, very aware of that.” The third region I wanted to focus on was the development of tech in Africa. In a recent report, Mosher states, “Africa is in the midst of a tech boom that’s luring entrepreneurs away from tech centers in the United States and back to their home countries where opportunity beckons.” One of the biggest advantages to the developing startups is that they do not require physical infrastructure to operate, thus simply having the business exist in the digital domain. Bloomberg reports agree, citing that “almost half of foreign direct investment projects in Africa last year were in technology, telecommunications, financial services and consumer products.” This opportunity mostly comes from the younger demographic and the emerging middle class. A hub of code academies has helped develop talent locally as well. In Lagos, Nigeria, a new startup incubator called the Co-Creation Hub, trains future software engineers, and with the backing of both Zuckerberg and Chan, this startup incubator tactic certainly seems promising. Literature Cited: https://www.bloomberg.com/news/features/2017-02-28/why-it-s-sohard-to-build-the-next-silicon-valley https://www.ft.com/content/aac9d22e-dbd0-11e6-9d7c-be108f1c1dce https://www.ft.com/content/d0f0d09a-b6fc-11e6-ba85-95d1533d9a62 https://www.pri.org/stories/2016-05-06/indias-silicon-valley-bangalore-fast-becoming-serious-global-player http://www.usatoday.com/story/tech/2016/06/16/silicon-valley-watch-out-tech-thriving-africa/86009568/ https://www.bloomberg.com/news/articles/2016-09-20/as-commodity-slump-batters-africa-investors-turn-to-technology http://www.newsweek.com/2016/12/09/nigeria-startups-yaba-lagos-mark-zuckerberg-525824.html http://www.ycombinator.com
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My idea for this piece came to me when I fried my onions on too high of heat and looked away. With many of the pieces burnt, my decision to keep this batch was based not on how it would taste, but was far more serious: would I get cancer if I ate these onions? A month before that, my mom had mentioned that burnt food causes cancer. And indeed it was all over the magazines. Yet, so many different food items, life items, have been said to cause cancer. So I did not know whether to believe her, whether to eat these burnt onions. Information about health--what prevents diseases and what causes them--is all over the news. People often like to talk about this information with each other, with the statements always starting with, “they say….” But who are they? How is this information produced, and how does it make its way to the news? The process by which the results of medical studies find their way to popular society consists of a series of filters, starting with journal publications, press releases, presentation in the press, and ultimately people’s interpretations of what they hear.
Publication Process
Level 2: Publishing We, as students or admirers of science, often think of the peer review process as being flawless. However, this is simply not true. The publishing process is the main place where a lot of good information gets lost and a lot of bad information goes through. Scientists have called for reforms so that the peer review process encourages the publication of non significant results, and vetting for studies which are reproducible. Publication bias exists towards significant results for observational and laboratory experiments, and less so for randomized clinical trials. Significant results receive more attention through publication and presentations, than do null results. Furthermore, poor quality studies are more likely to produce significant results. Therefore, significant results have more impact on medical awareness and policy, even if they are of poor quality, which can be misleading and cause poor policy and medical decisions (Easterbrook 1991). Moreover, many of the results in journals are non-reproducible. Often, the methods are reported too briefly or inaccurately to allow other scientists to reproduce the experiment. For example, some articles published in Cancer Research in 2010 noted, “only 28% of papers reported that animals were randomly allocated to treatment groups, just 2% of papers reported that observers were blinded to treatment, and non stated methods used to determine the number of animals per group, a determination required to avoid false outcomes ” (Hess 2011 as cited by Landis et al. 2012). Such missing information makes it difficult to both judge the quality of a study and reproduce the study. It also means that
By Talia Borofsky
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the study’s writers can get away with drawing too many or over-dramaticized conclusions (Landis 2012). Peer reviewers must require that random allocation to treatment groups, blinded observations (where the observer does not know the treatment of the group they are observing), sample size, and data handling (Landis 2012) must be reported so that peer reviewers can vet-out poor and misleading research. Reforms to publishing are important to finding effective treatments for diseases. There is a huge problem with preclinical cancer studies not leading to viable treatments because the original study turned out to be non-reproducible. Level 3: Interactions with the Media How does science travel from scientists and journals to the news? There are multiple points of contact between the media and the scientific world. Journalists receive information through press releases by scientists and universities, at conferences for specific areas of science, and directly from published articles in scientific journals. For a scientist to publish in the most reputable journals, such as The Lancet and The New England Journal of Medicine, the Ingelfinger rule applies: research can only be published if it has not already been published in popular press (Pini 1995). The purpose of this rule is so that doctors know information before their patients do. In the past, release of information to the press before peer-review and publishing in journals has led to unnecessary panic among patients, which doctors were unequipped to deal with since they learned this information at the same time as their patients. However, journalists consider this rule to be frustrating. It results in news sources learning about information all at once, rather than when certain journalists take initiative, causing a mass competition to publish the best story first. As Altman, a former medical reporter for the New York Times, said in an interview, “it leads to overzealous competition among news organizations with a resulting surge of publicity”(Altman 1995 New York Times) which can cause certain research results to be blown out of
proportion. Reporting on science can be inaccurate and partial. Many journalists lack time and sometimes the scientific knowledge to check and interpret information from press releases and journals. It doesn’t help that press releases and journal articles are often obtuse and misleading. Furthermore, journalists only publish what they think will interest the public. That means that even if null results are published more often in journals, the bias towards significant results will remain in the press since they are just more interesting. Level 4: Public Choice and Interpretation of Information Sources Logically, patients should turn to their doctors first for information about their health, but as many of us know, it’s pretty hard to wait until you see your doctor to ask about those weird bumps on your arms. A study by Hess in 2005 showed that when asked who they most trust when they have a question about a medical issue, most people say they most trust their doctor, but in practice they are more likely to search the internet for cancer information than to ask a physician. This trend is increasingly accentuated for young people. Even after people have been educated in school or by a doctor about a medical issue, as Dorothy Nelkins explains in her book 14
vaccine-autism link spoke on entertainment shows, such as Oprah. By 2009, one fifth of American parents believed that vaccines cause optimism, and in a study in 2009, a tenth were not giving their children all the vaccines they need. (Freed 2010 as cited in Flaherty 2011) Do not get me wrong, mass media and the widespread availability of health information is not a bad thing. Studies have shown that availability of accurate information reduces child mortality (Head, Murray, et al. 2015). What I would like to emphasize in the previous statement is accurate. Ensuring that valid health information is widely available to the public is a multi-level process which is the responsibility of scientists, PEER REVIEWERS, research journals, and popular press journalists. The process by which research reaches the masses needs reform. On the publishing level, the peer review process must be more stringent, requiring transparent reporting of conflicts of interest, sampling methods, and data handling. The bias towards significant results needs to diminish. On the media level, journalists need the training and time to write studies which not only accurately summarize the results of studies, but must also express the limitations of these studies. They also need to diminish their bias towards significant results. Most importantly, the population should not feel they have to turn to unreliable sources for medical information. Most people prefer to get medical information from their doctor, but in practice turn to the internet. Doctors need to be made more accessible, so that patients feel it is convenient to ask them questions.
Selling Science, “They [the public] understand science less through direct experience or past education than through the filter of journalist language and imagery.” So what? Inaccurate, misleading, and over-dramaticized dissemination of medical information harms public health. As we have already discussed, non-reproducible studies can lead to failed and expensive attempts at designing new treatments for cancer. Furthermore, bad science news can cause panic or health fads in the public which ultimately are detrimental to public health. In the 2000’s, parents in the UK and the United States started refusing to give their children one of the greatest miracles of modern science--vaccines. Over the last one hundred years, vaccines have helped eradicate in some areas, and keep under control in others, diseases that used to kill or bring pain to millions of people: smallpox, polio, tetanus, diphtheria, and measles. But in 1998, a study by a Dr. Wakefield was released in The Lancet, an extremely prestigious journal, linking the measles vaccine to autism in children. A press conference was held, and vaccination rates dropped from 91% in 1998 to 80% in 2003 in England, and were only at 50% in London (Flaherty 2011). There’s a concept in public health called herd immunity, which says that for a disease to not enter and spread through a group of people, a certain percentage of people must be immune (Fine 1993). The immune portion of the population was not large enough to maintain herd immunity, and there was a fast increase in mease classes, and four children died (Flaherty 2011). By 2004, the paper was proven to be phony. Multiple studies, of different types, found no link between autism and the measles vaccine. The Lancet found out that the Wakefield had huge conflicts of interest which he did not reveal when submitting the article. He was acting as counsel to a case suing the measles vaccine company because the plaintiffs thought the vaccine had harmed their children. He was also applying to receive a patent for his own version of a measles vaccine. Investigators further found that he used non-ethical techniques in his experiments, biases subject selection to children with the MMR vaccine and autism, and altered data (Flaherty 2011). The mainstream media and the internet continued to circulate the false information that there was a link between vaccines and autism. Proponents of the
Literature Cited: Altman, Lawrence K. “Promises of miracles: news releases go where journals fear to tread.” (1995). Easterbrook, Phillipa J., et al. “Publication bias in clinical research.” The Lancet 337.8746 (1991): 867-872. Fine, Paul EM. “Herd immunity: history, theory, practice.” Epidemiologic reviews 15.2 (1993): 265-302. Flaherty, Dennis K. “The vaccine-autism connection: a public health crisis caused by unethical medical practices and fraudulent science.” Annals of Pharmacotherapy 45.10 (2011): 1302-1304. Grimes, David A., and Kenneth F. Schulz. “Descriptive studies: what they can and cannot do.” The Lancet 359.9301 (2002): 145-149. Head, Roy, et al. “Can mass media interventions reduce child mortality?.” The Lancet 386.9988 (2015): 97-100. Hesse, Bradford W., et al. “Trust and sources of health information: the impact of the Internet and its implications for health care providers: findings from the first Health Information National Trends Survey.” Archives of internal medicine 165.22 (2005): 2618-2624. Landis, Story C., et al. “A call for transparent reporting to optimize the predictive value of preclinical research.” Nature 490.7419 (2012): 187191. 15
Turkey Trespassers By Shivani Chinnappan
One of the novelties of visiting Australia is interacting with its unique and charismatic fauna such as the kangaroo, koala, and brush turkey. Although the latter may not be as globally recognized, they are a common feature in the backyards and parks of eastern Australia. Visitors will first recognize the large black brush turkey by its unique vertical tail feather arrangement, bright yellow wattle or neck, and flaming red head. Gender is identified by the presence of a yellow wattle in males, while females lack wattles completely. Brush turkeys belong to the mound-building megapode family, literally translating to “large footed” (Wildlife Queensland Snake Catcher Brisbane & Bird Management, 2016). Male brush turkeys encompass a significant paternal role: with their awkward feet the males gather litterfall into 1m tall mounds where females lay their eggs, then the mindful patriarchs regulate the incubation by adding or removing mound materials. Brush turkeys are native to rainforest environments present in the eastern side of Australia, with their distribution extending from the Cape York Peninsula to the Northern Suburbs of Sydney (Queensland Government, 2016). More recently brush turkeys have started to make their way into suburban environments that mimic their natural habitat. In these areas, they are able to develop their incubating mounds and forage in the leaf litter. Australian brush turkeys are omnivorous, meaning they virtually eat everything from their natural diet of forest fruits and small invertebrates to any and all human food scraps. As one article attests, “lots of people stagger outside before they’ve had their morning coffee and throw a tin of cat food down on the ground and go back inside and lots of brush turkeys chase away the pets and eat the food themselves.” (Coller-
ton, 2016) Although exotic to visitors, brush turkeys have proved to be quite the pest for Australian residents. They invade gardens, set up their mounds in backyards, and hunt for human food scraps. Australia has created a hugely successful tourism industry based upon the uniquely beautiful ecosystems present on the continent. As ecotourism increases, so does the impact of the human-wildlife interactions. The brush turkey’s exotic appearance and intrusive demeanor causes tourists to indulge the animals with scraps of food in exchange for a unique photo as a souvenir of their time spent in Australia. Either through intentional feeding or leaving scraps, humans are giving turkeys a large reason to stay near tourist populated areas. Human landscaping of parks, which alters pre-existing features to accommodate heavier human traffic, also impacts turkeys. Brush Turkeys prefer these wide lawns with dense plantings, which are suitable components for their mound structures. A study in the suburbs of Sydney found that brush turkeys are more commonly moving into urbanized areas to have better access to human resources (Birds in Backyards, 2016). Amplified visitation within parks and rural areas increases waste and disruption in these environments altering the habits of turkeys. Lake Eacham, a crater lake formed by ancient volcanic activity, lies within Crater Lakes National Park in the Wet Tropics of Northern Queensland. The lake is surrounded by rainforest vegetation, which supports a diverse and rare ecosystem (NSW Environment & Heritage, 2016). On a sunny afternoon Lake Eacham teems with life. Birds call out from the rainforest canopy, turtles bask on the logs dotting the lake’s shore, and crowds of both tourists and 16
area. However, in the transects further from the picnic area, an average of only 1 turkey was observed per transect. Conversely, mounds were far more numerous alongside paths outside the picnic area, on average 4 mounds were observed in these transects, in contrast 1 mound was seen within the picnic area. This demonstrated a desire for protection and separation of the young from the daily tourists at Lake Eacham. Our survey reached similar conclusions to as studies done in suburban Sydney. As population and traffic in rural areas increase, so does the turkeys’ likelihood to move towards these areas. The correlation could be a result of the landscape of the picnic site. There were broad local residents populate the picnic and swimming areas. lawns with areas of dense planted vegetation. These areas Intermixed with the sunbathers and picnickers, roam a allowed the turkeys to have mounds in close proximity sizable group of brush turkeys. to human interaction while being near enough to retreat In order to gain insight into the lives of these quickly. There was also the obvious attraction of food iconic birds, a group of nineteen School for International scraps that drew the turkeys to the picnic site. This inTraining students, ourselves included, spent a day tracking crease in the population of ‘wild’ species within suburban the movements and habits of brush turkeys around Lake environments gives rise to further issues. Eacham. We divided the park into five transects and spent Urban turkey invasion can have dire effects on an hour in each area. Transects included various walkan ecosystem as a whole. Brush turkeys are territorial ing paths both bordering the lake and within the nearby creatures, which could result in them outcompeting other rainforest habitat, as well as the aforementioned shoreorganisms for resources. They are also omnivorous, leading line and picnic area. During the survey period we looked to increased predation of small species. With emerging for turkey mounds, which serve as incubators for eggs issues surrounding turkey displacement, we must continue and noted the sex, approximate age, and behavior of the to observe brush turkey population dynamics as an indicaindividuals we encountered. As expected, we concluded tor of general ecosystem disruption. that brush turkeys were far more abundant in the picnic This survey is part of a larger study of the ecologiarea than any of the other survey sites. Brush turkeys at cal effect of ecotourism on natural habitats. Though it may this site were observed pacing around the picnic tables seem novel and exotic to feed brush turkeys, it severely foraging, especially when large tour groups would stop to changes their daily behavior and interactions with their eat meals or enjoy a cup of tea. The real show began when native environment. This trend is not unique to Australia the groups had departed. The dominant male of the area and Lake Eacham, it is a pressing issue worldwide. When would emerge first, carefully searching for leftovers, then travelling we tend to think of our experiences as unique the females would cautiously follow and peck through the and ephemeral, when in reality we are interacting with enscraps. Finally, young males would dart into the territory vironments and organisms that continue to contribute to in hopes of snagging a scrap only to be quickly chased their ecosystems after we leave. If we are to indulge in the away by the elder male. Although the turkeys tended to privilege of ecotourism and visit these natural wonders, we avoid the larger tour groups, there were multiple records need to put more emphasis on the “eco” part because it is of brush turkeys approaching small groups of visitors in the possible to “love them to death”. lakeside area, and were even observed to take food out of Literature Cited: people’s hands when offered. Turkeys clearly favored areas with high human visi- “Australian Brush-turkey.” Queensland Government. Department of Environment and Heritage tation, on average 8 turkeys were counted within the picnic Protection, n.d. Web. 08 Oct. 2016. “Australian Brush-turkey.” Welcome to Birds in Backyards. Birds in Backyards. Web 08 Oct. 2016. “Brush Turkeys.” Brush Turkey. Wildlife Queensland Snake Catcher Brisbane & Bird Management, n.d. Web. 08 Oct. 2016. Collerton, Sarah. “Man v Bird: The Brush Turkey Battle.” ABC News. N.p., 17 Aug. 2009. Web. 08 Oct. 2016. “Vegetation Formation Page.” NSW Environment & Heritage. Office of Environment Heritage, n.d. Web. 08 Oct. 2016.
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Finance, STEM, and the Liberal Arts By Neeraj Shah
People pursue liberal arts educations to develop broad skills that can increase their capacity to learn and adapt. This goes against the expectation that higher education should teach certain skills for certain careers. The “learnability” that liberal arts educations impart is increasingly becoming a requirement in many industries that normally require technical knowledge. From software development companies to trading firms, everyone wants adaptable candidates. Recruiters in finance particularly are vying for liberal arts college graduates more heavily than they have before. But, most seem to prefer STEM majors with liberal arts backgrounds. According to the United States Census Bureau, more than half of all STEM majors from all colleges across the country end up working in non-STEM fields. Only a quarter of physical science majors pursue careers in their fields. The majority of these STEM majors do not enter finance-related fields. It’s only for elite colleges with liberal arts programs that STEM graduates tend to pursue finance. This should not come as a surprise to many students at elite colleges. From universities like Princeton, almost 40% of students pursue finance upon graduation. Before the financial crisis, this figure was closer to 50%. A substantial subset of these students entering financial services come from STEM backgrounds. It’s likely that the large outflow of students from these colleges into finance is partially based on elite connections that schools already have. Nevertheless, recruiters from financial services try to highlight things like “how easily candidates can grasp new concepts” on job listings. Employers are more likely to select candidates who didn’t study finance in college if they come from liberal arts institutions. In addition to “learnability, recruiters are searching for quantitative and critical thinking skills, which are often found in STEM majors. David A. Thomas, Ph.D., dean of the McDonough School of Business at Georgetown University says “The use of quantitative modeling in trading and financial markets … calls for mathematical skills, computer programming skills and the kinds of things you learn in computer science and engineering programs.” He goes on to say, “I can teach you the finance, but I can’t teach you the computer skills.” STEM majors value financial careers and can start veering towards them even as underclassmen when they are undecided on which career path they may like to pursue. Not only are they promised high salaries, but they are 18
also often given a leg up during the recruiting process. Some see the number of STEM majors in finance as a wasteful and unnecessary brain-drain. At some elite colleges like Princeton and Swarthmore, there is an expectation that many graduate and do something to improve the world. Sendhil Mullainathan, a Harvard economics professor, argues that while people in finance certainly do serve an important purpose in any market, the social value that they create could be higher in other professions. Others point out that this the number of STEM majors going into finance isn’t as high as it seems. They argue that finance has become an umbrella term for a variety of fields that share little in common with one another. They also note that STEM graduates who enter these financial fields are primarily from elite universities. Its likely that recruiting practices and interest in finance won’t change in the coming years. The critical thinking skills of STEM majors will remain valued by financial institutions and they will continue to be incentivized to enter the industry. Recruiters know that as long as they have adaptable candidates, they can teach you finance.
Literature Cited: Kiersz, Andy. “Most STEM Majors Don’t End Up In STEM Jobs.” Business Insider. Business Insider, 10 July 2014. Web. 11 Feb. 2017. Mullainathan, Sendhil. “Why a Harvard Professor Has Mixed Feelings When Students Take Jobs in Finance.” The New York Times. The New York Times, 11 Apr. 2015. Web. 11 Feb. 2017. Peacock, Louisa. “Engineering Graduates Choosing to Work in Other Sectors.” The Telegraph. Telegraph Media Group, 29 Aug. 2011. Web. 11 Feb. 2017. Rampell, Catherine. “Out of Harvard, and Into Finance.” The New York Times. The New York Times, 21 Dec. 2011. Web. 11 Feb. 2017.
a population and change in frequency due to an environmental change (Fig. 1b, 1c). Early methods for studying human adaptations focused mainly on detecting hard sweeps to find mutations under strong positive selection that are swept rapidly through a population toward fixation. Common approaches to detect signatures of positive selection include applying statistical tests that identify either outlier variants that have been driven by natural selection to high frequency or unusual genetic patterns. Strong positive selection increases the frequency of beneficial alleles, leaving detectable patterns, called “signatures of selection�, in the genetic sequence. Comparing potential candidate gene regions with areas of the genome under neutral variation, in which alleles do not confer a selective advantage or disadvantage, has helped identify genes that are involved in skin pigmentation (1), tolerance to lactose (3), and susceptibility to type II diabetes (4). One study by Voight et al. in 2006 used the hard sweeps model to identify regions in the genome that were undergoing partial hard sweeps, which cause an increase in favored alleles but do not necessarily drive alleles to fixation (5). Specifically, candidate signals of selection were found in genes associated with skin pigmentation, transitions to new food sources, bone morphogenesis, as well as complex disease- related phenotypes. For example, CYP3A5 in Europeans (salt-sensitive hypertension), ADH in East Asians (alcoholism susceptibility), and the 17q21 inversion in Yoruba (fertility) were all identified as single nucleotide polymorphisms (SNPs) associated with complex disease-related phenotypes. These targets of selection have the potential of allowing researchers to track down the genes underlying complex diseases that are predicted by family history. Diseases such as diabetes and heart diseases are strongly associated with genetic factors and vary dramatically in severity and incidence in different populations across the world, thus making genome scans a viable way of parsing the genetics behind the variation in disease. With more extensive data, researchers began actively developing new methods for studying soft sweeps and searching for signals of selection from standing genetic variation. Over evolutionary time, selection can act on standing variation instead of new mutations that arise in the genome. This soft sweep model proposes that selection generates subtle changes in allele frequency on pre-existing variation at one locus or at many loci, which models polygenic adaptation. Human phenotypes are often polygenic, including common traits like height and skin pigmentation as well as risks to diseases like cancer and diabetes. Furthermore, polygenic traits are often widespread because populations can inhabit similar albeit geographically disparate environments, allowing populations with similar selective pressures to evolve the same set of adaptive alleles independently. While traditional approaches under a hard sweep model detect strongly selected alleles one locus at a time, the soft sweep approach
How Evolutionary Biology Improves the Understanding of Human Health and Disease By Iris Chan
While important medical advancements have emerged from research on disease treatment, identifying the genetic basis of human adaptations is crucial to understanding complex disease phenotypes. During the course of human history, modern humans have spread from Africa to occupy various habitats across a broad geographical range (1). As a result, humans have inhabited a myriad of new environments that have exposed populations to different diets, ecological niches, and pathogens, each of which has caused changes in the genetic architecture of different populations (2). To understand how different populations have adapted to varying environmental pressures, scientists began using genomic advancements to look across the genome for signatures of selection that would give clues to modern diseases. Despite the ever-accelerating pace of biomedical research, the causes of many common human diseases remain relatively unknown. Family history, which is one of the strongest risk factors for the majority of diseases, can offer an important clue to understanding how inherited genetic variation influences the risk of acquiring a disease. By studying the role of selection in shaping patterns of genetic diversity, we may not only improve our understanding of human evolutionary history, but also gain insight into the probability of developing diseases. With the advent of genomic screening, two different models have been used to identify signals of selection: hard and soft sweeps. While hard sweep models detect patterns of strong selection in which a single adaptive mutation rapidly reaches high frequency (Fig. 1a), soft sweep models detect multiple adaptive mutations that were previously present in 19
detects small shifts in sets of adaptive alleles that are broadly distributed. The new challenge, then, was to detect polygenic adaptation, which is not easily picked up by classic tests that had previously been developed to detect hard sweeps. In a 2010 study published by Hancock et al., researchers analyzed updated SNP data to detect subtle changes in allele frequencies of populations that share the same geography but are exposed to environments that vary by ecoregion, diet, or subsistence strategy (6). By detecting widespread signals that were shared among geographically distant populations, they found a different set of adaptive SNPs than had been elucidated in past studies that focused on hard sweeps. For example, they identified genes including KCNQ1 (type II diabetes) for populations with a main diet of cereals and MYC, BC042052 (urinary bladder cancer) for populations that specialize in pastoral subsistence strategies. Thus, the loci that were identified tended to have a global distribution and to show subtle, but consistent, differences in allele frequencies across populations. Based on this study and many others following the soft sweeps model, the results have expanded on previous scans that identified hard sweeps and filled an important gap in the study of the genetic basis of human adaptation. Integrating the study of human adaptations with the field of medicine may illuminate our understanding of complex disease phenotypes and allow medical professionals to better diagnose and treat patients. Further study may
increase our knowledge of important adaptive events in human evolution that are essential to understanding modern health and disease. Using functional tests, candidate genes that have been identified – and especially those underlying complex disease-related phenotypes – can be better characterized to assay their biological relevance in creating the vast array of phenotypic diversity that affects the health of modern humans. As new environmental conditions continue to shift, scientists will be presented with increasing opportunities to understand how alleles have undergone recent selection and may illuminate the complexities underlying modern diseases. Literature Cited: 1. Coop G, et al. (2009). The role of geography in human adaptation. PLoS Genet 5: e1000500. 2. Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, Nielsen R. (2011). Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet 7(11):e1002355 3. Bersaglieri T, Sabeti P, Patterson N, Vanderploeg T, Schaffner S, et al. (2004). Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74: 1111–1120. 4. Neel JV. (1962). Diabetes mellitus: A “thrifty” genotype rendered detrimental by “progress”? Am J Hum Genet 14: 353–362. 5. Voight BF, Kudaravalli S, Wen X, Pritchard JK. (2006). A map of recent positive selection in the human genome. PLoS Biol. 4(3):e72 6. Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, Di Rienzo A. (2010). Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proc Natl Acad Sci 107: 8924–8930.
Figure 1. Genetic signatures of positive selection according to the hard sweep, soft sweep, and polygenic adaptation models. Each row depicts changes in allele frequencies over time. Alleles are shown as circles on the chromosomes (shown as segments), and advantageous alleles are represented with a triangle. A: A hard sweep, in which a new allele (orange) arises in a population following a change in environment, is advantageous, and increases in frequency over time until it approaches fixation. B: A soft sweep from standing variation, in which an allele (green) that exists on different genetic backgrounds and is already present in the population becomes advantageous in a different environment. After selection, the genome-wide abundance of the favored allele has increased, but since the allele exists on different haplotype backgrounds, it does not become fixed at any locus. C: A soft sweep from standing variation on a complex trait involving multiple loci on different chromosomes (represented by segments in different colors). Following a change in environment, a set of alleles (yellow, orange, green) becomes advantageous and increases in frequency as a set. The graph shows a subtle signature of adaptation which includes subtle shifts in allele frequencies at multiple loci. 20
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Dear SJS: Now that I’ve read and critically analyzed SJS cover-to-cover, what do I do now? Whether you skimmed
Essie Mae’s or read it
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curled up in a Science Center chair, we hope that we have left you w ith a deeper appreciation for the fascinating real m of science. But above all, we hope that this journal inspires you, ou r readers, to continue to learn and engage w ith science and the wor ld around us!
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