Bioinformatics skills – How to get them and not get scared

by: Samridhi Chaturvedi
If you are working in the field of Ecology and Evolution, it is important to build a skills toolbox which can come in handy to visualize, analyze and work through your data. These skills are a set of standard practices that you could start developing which make your work easy and smooth. Here are some skills which can constitute your toolbox:

1) Learn a language

 

 

If you are dealing with big data (ecology or evolution), you will eventually have to develop programming skills to help you manipulate, visualize and analyze your data. This can be quite overwhelming if you do not have prior programming experience. To start developing these skills, you generally have to learn a programming language. I feel there are several languages which are being used in the field at present and each of them have their pros and cons. There is Perl, which is older and is great when working with regular expressions (read more about regular expressions here). There is Python which is newer and is more intuitive. Then there is C/C++ which are compiling languages and using them involves a steeper learning curve. C/C++ are used extensively for theoretical/mathematical modelling and also for developing packages. These are all important skills to build but it is important to recognize that you can spend a lot of time learning and implementing these languages.

I say choose one language between perl and python to start learning the ropes of programming. There are some really helpful interactive learning spaces for both these languages.

Here are the ones I have found helpful:

  • Jupyter (http://jupyter.org/). This is an IDE and interactive website which helps you practice Python interactively.
  • Learn perl (http://www.learn-perl.org/). This is my goto online IDE for learning and testing my perl code.
  • Regex (https://regexr.com/). If you are working on genomic data and use Regular Expressions in scripts to detect specific sample IDs, lines etc to modify your data or calculate number of mapped and unmapped reads in fasta files (just an example), this tool really helps you learn how to write regular expressions for your data. What more, you can actually paste a piece of your text and write a regex to detect specific matches.

The other language widely used for statistical analysis and data visualization is R (free) or MATLAB (paid). I use R extensively so here are my pointers for learning R:

The more you practice the more you learn. The earlier you can start learning R, the better!! This will save you a lot of time in dealing with your data. There are many different only resources for getting started in R, but here is one basic one: http://tryr.codeschool.com

Even after working with R for a long time now, I still find myself Googling for specific commands and options. Here are the three most trustworthy sites which always have an answer to my questions:

These websites also have defined sections which walk you through simple R commands. For example, the sections on plots tell you how to make different kinds of plots, how to modify them and customize them to your data.

Beyond all of these resources, a simple google search can always help you and StackOverflow always has some amazing solutions to problems. It was only in my second year that I realized a PhD in Evolutionary Genomics requires some kick-ass googling skills!

 

2) Choose your favorite script editor/text editor

 

While you learn programming, it is ideal to select a script/text editor and to fall in love with it! I say this because switching between various script editors can be confusing and time consuming.Script/text editors help you edit your code and keep everything organized. Here are some of my suggestions:

  • VIM/VI (http://www.openvim.com/). If you are a programming nerd and like to work on a Terminal, this might be a good choice. However, recognize that it requires some time to learn vim and it is not unusual to find yourself trapped in the editor and even wonder how to exit the editor! Having said that, once you get a hang of it, you really can do a lot with just one editor.
  • Gedit. This comes preinstalled with linux/ubuntu systems and is very very easy to learn. Probably the simplest text editor to start working with and to use everyday.
  • EMACS (http://emacs.sexy/). Similar to VIM and requires some learning but again really powerful.
  • ATOM/SUBLIME?NOTEPAD++ = Editors which are more user friendly and are almost like MS Word.

All these are great tools, but you can choose one which works best with your work environment. I personally use VIM because I work on a TERMINAL and usually work on a remote computer cluster.

 

3) Managing data – scripts, sequences

 

When it comes to managing your data and mostly your analyses, I find it useful to keep detailed notes for my workflow for every project I am working on. I use my lab’s google notes website to do this but you can use alternative notes taking tools to do this (Endnote, Google Drive). The main things which each project page consists of are : a) my folder and file details where I literally write out each folder and details of each of the file in the folder. It is also good to keep a “readme” file in the folder to help you remember what each file in the folder is about, b) I write out step by step notes of each analysis and describe the scripts I used for analysis. If there are some specific options used through command line tools, I describe each of these options, and c) A list of analyses I hope to do for the project in the future.

Believe me, you can forget your data locations within a week/month if you step away from the computer. I store all my scripts remotely on the institution computer clusters. Another way to archive important scripts which will be reused or modified in the future, is to submit them to GitHub (https://github.com/). This is also a good way to make your scripts public if you think this will help a broader audience in your field.

4) Latex

 

 

I learnt about LaTex after starting my PhD and I cannot emphasize the importance of the tool enough. It is very, very helpful in organizing your text (read manuscripts), saves time adjusting sizes of images and tables by clicking multiple times and definitely is cleaner. LaTex basically gives you the power to design and manipulate your text the way you like it and have the control on it. This can be amazing and definitely saves you a ton of time adjusting page limits. I highly recommend learning to use LaTex. I even reuse most of my manuscript outlines and then I have to make minimal adjustments for different texts.

You can basically use any of the editors above to write LaTex documents (this is also a language).  But there are several desktop versions for Linux, Mac, Windows which are user friendly and help you visualize your PDFs from the source Tex document. The best of them all is Overleaf (https://www.overleaf.com/). This is like Google Doc but for LaTex. It is online, autosaves and has many, many templates for various journals and for various documents (CV, Thesis etc.). In addition, it is easy to collaborate on overleaf as many people can work and edit the document at the same time. You can also see the PDF in real time which changes as you write you LaTex code (Super cool!!).

 

5) Important resources

 

Beyond these tips, here are some important resources and articles which helped me learn these skills better:

 

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“Zen Ecology” and the Origin of Scientific Ideas

by: Nick Waser and Mary Price [nickolas.waser@ucr.edu; mary.price@ucr.edu]

Professors of Biology Emeritus, University of California Riverside, Adjunct Professors, University of Arizona, Senior Investigators, Rocky Mountain Biological Laboratory

 

Recent evidence from cognitive science validates an older perception that creative thinking in humans involves two distinct processes—one that generates a sudden, intuitive insight, followed by a second process of deliberate rational analysis that error-checks and develops the insight. As Scheffer et al. (2015) point out (see also Scheffer 2014), modern science stresses the second approach at the expense of the first.  We are trained in a “scientific method” that is wonderfully efficient for evaluating alternative hypotheses against empirical evidence, but we receive virtually no training in how to generate novel ideas.  Scheffer and colleagues argue that taking time off from focused work to let the mind wander aimlessly is essential to the creative process both in science and in the arts (and when done in a natural setting seems to contribute as well to overall mental and physical health; see e.g., Fleischner 2017). But how many of us are encouraged to take time off for walks or daydreams, and how many conferences schedule unstructured free time?

In 2012 we had the good luck to help teach a field course for the Tropical Biology Association (TBA; http://www.tropical-biology.org) at the Amani Reserve in the Usambara Mountains of northern Tanzania.  Our co-teacher was the late Brian Moss, a retired lake ecologist from the University of Liverpool (see Jeppesen and Johnes 2016 for a lovely summary of his life’s work).  Our course brought together beginning graduate students from European and African countries.  The intent was to build connections and capacity and confidence for the students, beyond an introduction to local natural history, and this was done during a month of living together in Spartan facilities embedded in nature.

During the first week of the course Brian Moss led a “Zen Ecology” exercise.  “Zen” refers here to what Zen Buddhists call Zazen—a practice of seated meditation that is intended to lead to insight into the nature of existence.  After a brief discussion with each small group of students, Brian asked them to leave behind digital cameras and cell phones and to wander individually into the forest, armed only with notebook and pencil.  They were encouraged to engage directly with nature through their senses rather than through a device, and with no preconceptions about what they might encounter. When something caught their attention—a pattern of insect damage on a leaf, for instance—they were to observe quietly, then sketch what they saw, using words and arrows to clarify as they wished.  In essence, this is meditative, open-minded observation of the natural world. Brian talks more of this approach in an essay in the International Society of Limnology newsletter (see http://www.limnology.org/news/silnews62.pdf), without using the term “Zen Ecology” (but he did use the term with the TBA students.)

For many students the experience was transformative:  they had never before gone into nature without a goal or preconceived idea, and had never thought to use sketching as a way to see more completely.  And when they returned and shared what they had drawn and experienced with the other students, all sorts of ideas and questions emerged spontaneously and intuitively. These at first tended to be vague, but as students talked among themselves (gently guided by Brian) questions emerged more fully developed.  Some student research projects later in the course came from the Zen Ecology exercise.

Zen Ecology was a revelation for us as well.  We had struggled over decades to find a way to help students master the entire scientific process, from generating questions to devising and testing hypotheses, and had long thought that starting with unplanned observation and curiosity was key.  For years we tried the “fifty questions” exercise we had learned in Organization for Tropical Studies (OTS) field courses.  In this exercise, participants go into nature and return with questions to share with the group.  We had found, to our disappointment, that students often felt pressure to produce “clever” or “cutting edge” questions, and as a result to filter the thoughts that came into their heads rather than going into the experience with an open mind and heart.

We have found Zen Ecology less threatening than “fifty questions” for helping us attend to nature directly and completely, without barriers. For many people this exercise—contact with nature without the filter of devices or goals—truly seems to get at a wellspring of creativity.  What do we all want, if it is not access to such a wellspring, a source of ideas that can be winnowed and refined into novel and interesting research questions?

You may recoil at the idea of drawing insect damage on a leaf, or drawing anything at all.  You are no artist!  Grit your teeth and remember this:  the drawing is not intended as “art”.  It is a private record that helps you solidify and remember what you experience; think of it as a visual diary or journal. Consider that sketching was an essential tool for recording impressions in the days before photography, and that naturalists in those days surely had the same distribution of “artistic talent” (and lack thereof) that we all now have.  Most of all, recognize that sketching as a means of gaining “ownership” of an observation of nature has no substitute in electronic imaging, no matter how sophisticated that imaging is.

Since 2012 we have tried out versions of Zen Ecology with high school classes, undergraduate research interns, graduate classes, even groups of senior citizens (that moniker would include the two of us!).  We encourage you whenever possible to try your own version.  Try it for yourselves, and in your teaching and mentoring.  Please share with each other (and with us) what works and doesn’t!

 

References

Fleischner, T. L. (Ed.). (2017). Nature Love Medicine: Essays on Wildness and Wellness.  Torrey House Press, Salt Lake City.

Jeppesen, E. and P. J. Johnes (2016). Obituary: Brian Moss (1943–2016).  Hydrobiologia 778: 1–7. DOI 10.1007/s10750-016-2882-8.

Scheffer, M., J. Bascompte, T. K. Bjordam, S. R. Carpenter, L. B. Clarke, C. Folke, P. Marquet, N. Mazzeo, M. Meerhoff, O. Sala, and F. R. Westley. 2015. Dual thinking for scientists. Ecology and Society 20(2): 3. http://dx.doi.org/10.5751/ES-07434-200203.

Scheffer, M. (2014).The forgotten half of scientific thinking. Proceedings of the National Academy of Sciences 111, 6119.

Congressional Visits Day: Or how I learned to stop worrying and love policy

 

By Abigail Pastore

On April 26th, 2017 scientists from around the nation traveled to Washington, DC to meet with over 70 offices of US representatives to discuss the future of biological research in the United States.  This event was coordinated by American Institute of Biological Science and Biological Ecological Science Coalition.  I was honored to attend this event to represent the American Society of Naturalists.

During my two days in DC, I learned a lot about science policy and how capital hill works.  Below I describe what I learned during my experience.  On Day 1, I heard from many scientists who have worked in policy positions in DC, I learned how science funding works and I was trained on how to talk to politicians about science. On Day 2, we had congressional meetings!

DAY 1

As much as we sometimes ignore it, policy and science and inextricably linked.  To start with, most science is funded by government agencies like, NSF, NOAA, and NIH.   Subsequently we have a duty to disseminate our work to the population that is funding this research.  Ultimately, civilians who understand and value science will elect representatives who care about science as well.  Those politicians have the power to make the budgets that fund NSF and other organizations.  And ultimately management of our natural lands and wildlife comes from policy, not directly from scientists.  So scientists have a vested interested in being involved in all of these steps, not just the science part.

policy

Policy careers

Many of the participants at the congressional visit day spoke about their individual journeys that merged science and policy.  In fact there are many avenues and careers paths for scientists that include policy. For example, AAAS Science and Technology Policy Fellows facilitates scientists’ interactions with government organization as consultants, there are internships at the White House in the Office Science and Technology Policy, and NOAA’s Knauss Fellowship is for those interested in marine policy.  There are also several state level policy fellowships.  Furthermore, ESA has a policy section, where you can find the Ecologists Guidebook to Policy among other things.  Or check out ESEP, a science policy engagement coalition.  Most policy jobs involve a lot of communicating and translating science for a broader audience.

Public Engagement

Getting involved in science policy goes hand-in-hand with communicating to the public about science, and the benefits of science research for society.  For tips, check out Frontiers’ issue on public engagement.  Additionally, check out AAAS’s workshops for communicating science.  Ultimately, the most meaningful change happens at the local level, engaging with representatives in your home state puts a face and a story to these issues that is influential for politicians when they are making decisions about policy.

How the National Budget gets Made

Congress is the body of government that makes expenditures.  The president must make a budget request which must be approved by congress.  Every fiscal year, the president puts forth a budget which congress must approve.  Once congress gets the budget, it undergoes congressional hearings and budget resolutions.  Then an appropriations bill is drafted which would authorize the government to spend money.  This bill must be approved by the house and the senate before it is resolved in conferences, then signed by the president into law.  So ultimately representatives in the house and the senate are very influential in how the government spends money.

budget

Science funding makes up about 1% of the national budget.  And funding is expected to decrease due to sequestration and the new administration.

Preparing ‘the ask’

The goal of the congressional visit day was to advocate for science funding.  We went into each meeting asking for $8 billion for the National Science Foundation for fiscal year 2018.  We each prepared our own personal stories about how the NSF has affected us and the states we live in.  When preparing our stories we were charged to make three points that were, specific, memorable and demonstrative.  

DAY 2

Visiting Congress

I personally visited with 7 congressional offices from Florida, Maine and New Hampshire with a few other scientists.  In general, we met with congressional assistants that took notes in the meetings so they could report back to our representatives.  Everyone was very friendly, respectful and engaged.  I told my story about how NSF funding has allowed me to get training in cutting edge technologies to study bacterial communities which have broad applications for plants in an agricultural setting.  Others with me told stories of invasive species, wetland restoration and marine lab outreach programs.

I learned that congressional aids really love talking about invasive species.  I was impressed with all the positive feedback and support these offices expressed.  Even Marco Rubio’s office offered that Senator Rubio is in favor of research and development.  Ultimately we all have the power to make these kinds of connections in our home states.  Office visits are said to be the most influential visits for politicians.  It’s important to remember that these politicians are our representatives and it is their job to listen to us.  At the end of the day, we don’t know the balance of things to consider in the minds of politicians so our best chance is to lend support and tell compelling stories where we can.

money

 

ASN takes on the March for Science: The society that organizes together, stays together

Authors:  Emlyn Resetarits, Sheela Turbek, Shengpei Wang and Abigail Pastore

Note: The views in this article represent those of the ASN graduate council. 

How to get involved in DC?

You can get organized with other ASN, SSE and SSB members by filling out the survey here.

Looking for a ride?  Hotel sharing?  Want to organize a meet-up with other ecologists and evolutionary biologists?  Get organized in this Google Sheet!

 

Why Get Involved?

On April 22, 2017, thousands of advocates of scientific research will take to the streets in Washington D.C. and around the world through the March for Science to demand government support for the open exchange of scientific ideas. Many of the participants will be scientists themselves, who are concerned with the new administration’s steps to censor the scientific community and deny scientific findings on the basis of personal convictions.

The March for Science and its sister marches around the country have an inclusive mission – to bring together a diverse, non partisan group of people united by their respect for science as a tool for understanding the world around us and their desire to defend scientific integrity. The march seeks to humanize science by showcasing the diverse body of people dedicated to scientific research, encourage open communication between scientists and the public, and advocate for diversity and inclusion in scientific fields. However, above all, the march will be calling for evidence-based legislation that serves the public good.

Since assuming power, the new administration has threatened to roll back numerous environmental regulations originally put in place as a result of scientific findings regarding human and environmental health. The president’s persistent denial of climate change despite scientific consensus has raised fears that the United States will withdraw from the Paris Climate Agreement and overturn or weaken legislation enforced by the Environmental Protection Agency to regulate carbon emissions. Given the current administration’s ties to the oil and gas industries, many worry that public lands could be sold to private interests and the Endangered Species Act could go under fire, opening up protected habitat to energy development.

Also at stake is the ability of scientists’ to freely carry out research and publicly communicate their findings. In January, for example, a regulation was passed requiring that scientific studies from the EPA undergo political review prior to publication. The federal government froze all agency grants and contracts and imposed a gag rule against EPA employees, prohibiting them from posting on social media and communicating with reporters. The immigration restrictions reinstated by the president last month have additionally hindered scientific progress by jeopardizing international collaborations and leaving many scientists uncertain about whether to attend scientific conferences and conduct international fieldwork.

Historically, scientists have avoided getting involved in political advocacy in order to prevent science from being mischaracterized as a partisan issue. However, with the future of scientific research and evidenced-based policy so uncertain, the scientific community arguably cannot afford to remain silent. The March for Science this April will provide an opportunity for scientists to take a stand and demand continued support for publicly funded, openly communicated research.

 

How to get involved locally?

Getting involved in science policy can feel overwhelming.  How does one even begin to have an influence on such an old and established system?  The first step is to start at home!  Getting your friends and colleagues organized can be tremendously helpful to not only hold yourself accountable, but also by amplifying your voice and actions through your peer group.  Additionally, there are lots of groups that are already organized, finding them in your community means you don’t have to start from scratch.  Finally, contacting your representatives is the cornerstone of our democracy, your congresswomen and men, and senators were elected to represent the will of the people, so let them know what you want!  Find out who your local representatives are and email, call, or meet them in person. Getting on their email list will keep you updated, especially on when and where they can meet with the public. Most congresswomen and men, and senators have town hall style meetings locally that are open to the public, and these are one of the best places to express your concerns.

Creating a political action peer group.  – With so many important issues on the table, it’s challenging for any one individual to be informed and active on every issue.  Getting your friends together to meet, vent and divvy up the work is a great way to manage things.  Luckily technology is readily available to help you organize such an endeavor.  Google groups and google docs help facilitate organizing without the need for excessive emailing.  Use google sheets to outline the issues and have your friends sign up for the issues they want to follow closely and inform the group about.  Have a “weekly actions” to do list or find one online that you can share or divvy up with your friends.  Finally have a weekly/biweekly meeting with your friends in a comfortable space (perhaps with relaxing beverages) where you can vent, share and learn with each other.

Satellite Marches for Science: One easy way to get involved now is to attend the March for Science. Even if you can’t make it to DC, you can still make an impact and contribute to the cause by attending one of the satellite marches that’s close to you. Official information is available at https://www.marchforscience.com/satellite-marches/ . If there’s no local march planned for your city yet, hosting a satellite march is an even better way to get involved!

 

How to get involved digitally?

The power of the media is ever more prominent in our lives now, both personally and professionally, so is making your voices heard through digital platforms. Share your messages on your favorite social media, be it blogpost, twitter, facebook, or instagram. You can either create your own content or simply share contents from the community. In addition, contacting mainstream media allows you to reach an even greater audience, for example, the New York Times has a survey on the March for Science. Social media also allows us to infiltrate into circles with different opinions, by tagging them or commenting on their posts. This can alleviate information bias for us as well as people with different opinions. Regardless of the method, get involved is the best we can do.

In addition to getting involved with the March for Science specifically, sharing the spirit of science should be a persistent goal. We are in an age when facts don’t speak for themselves a lot of times. It’s increasingly a scientist’s job to communicate his/her scientific findings, and to advocate for the actions supported by current evidence. Even though connecting and persuading people with different opinions is hard, we need to persevere with the stakes so high. Using simple language and having a clear message is essential to communicate science to non-experts. And be open to different opinions. However, being open to alternative interpretations doesn’t mean that we should keep quiet about blatantly unsupported claims. Everyone has the freedom to express his/her opinions, regardless of accuracy, but we also have the right to, and should stand up when facts and evidence are being ignored or denied.

 

Call for Blog Contribution

Do you like our past blogs? Do you have something you want to share? Please contact us at asngrads@gmail.com.

This space is designed to provide a platform for students of biology to share their experience, advise, and resources. We aim to keep our blogs relevant to graduate students, but we are a pretty diverse bunch. So if you think your voices should be heard, please let us know.

 

Believing Science

by Shengpei Wang Feb 2017

The opinions expressed in this article are the author’s own and do not reflect the view of the American Society of Naturalists.

Section 1. Should we think before believing?

A simple sentence caught my attention today. “We believe […] that a unified ecology must start from individual-based ecology.” 1 It read naturally to me at first, but something seemed amiss: Is it legitimate for scientists to say we believe?

Since the earliest forms of civilization, we have pondered questions such as “How do we gain knowledge?” and “What do we believe?” Given the recent social and cultural climate, questions such as these should concern us now more than ever. In my opinion, science is the only reliable way of obtaining knowledge. Not everyone agrees, however.

Historically, knowledge had been derived from the views of leading political and religious authorities, but in time, theories and observations overtook the role as the primary source of scientific knowledge around the seventeenth century. This change was pioneered by early scientists such as Galileo, whose scientific discoveries not only laid the foundations to modern astronomy and physics, but more importantly, challenged the authoritarian view of knowledge. I don’t think any of us question the importance of observable facts, but many people in the US still question whether we can believe science. Can we truly believe patterns inferred from observations made by the scientific community? And can we truly understand what is not directly observed or even observable?

Scientific statements arise from logical deductions and inductions. Deductive reasoning generates definitive conclusions that are true as long all the premises are true. But scientific premises usually need to be tested or are derived from inductive reasoning. Induction, however, does not necessarily ‘test’ a premise but provides multiple lines of evidence of support. I regard the inductive approach as the source of open-mindedness that characterizes science, but to others it seems to be their source of doubts. If we truly believe in science and believe its findings, shouldn’t we know what makes scientific knowledge justified? And hopefully, we can persuade others to trust our logical conclusions if we are explicit about our reasons.

Section 2: What I have learned about epistemology.

Knowledge is generally accepted as justified beliefs, but there is no consensus of what makes knowledge justified. There is even skepticism about whether knowledge is possible at all.2 Although I will omit arguments of skepticism for practical reasons, I argue that we should judge scientific claims critically. Science seeks truth, but it does not possess it. Rather, science approximates truth.

Modern science is characterized by falsifiable claims, which can be demonstrated to be wrong if appropriate evidence is discovered. However, falsification is not the totality of scientific pursuit, because it does not generate new hypotheses by itself. This was also why I stumbled over the claim of we believe earlier. This claim is not an easily falsifiable claim, at least not with observations currently available. But is it not scientific? Other philosophical theories disagree that science should be solely characterized by falsification. For example, Imre Lakatos emphasized the development of theory through scientific programs, where existing principles guide new theories.3 By this token, claiming that we believe a novel prediction in light of existing theories and evidence is justified. Additionally, other approaches even allow for the quantification of levels of confidence based on existing knowledge, such as using conditional probabilities developed by Thomas Bayes. Despite the differences of these different philosophical theories, science is based upon the assumption of Uniformity of Nature, i.e. invariance of natural laws.4 This is necessary because we cannot possibly test a hypothesis in every possibly instance, and must generalize from limited observations.

Scientific methods discussed above ensure that scientific claims can be judged heuristically and beyond the specific context where observations are made; however, the claims are not objective in the sense that there is always subjective involvement. Even observations themselves are intrinsically influenced by our subjective experience, because all truth claims are states of minds.3 For example, an entomologist and a mycologist would notice very different types of organisms if they went on a nature hike together, and they would learn very different things regarding the local habitat. Furthermore, even if we were to start with the same observations, how we interpret our observations depends on both our existing knowledge and our expectations. This is also why some great findings, such as Mendel’s genetic theory, only gained prominence until rediscovered by scientist with very different mindsets. After all, science is not merely a collection of facts (observations), but a systematic synthesis of generalized claims. It results from our interaction with the natural world. We are part of both the process and the outcome.

I want to make a point here: I think the human aspect of science should be cherished rather than avoided. Even though scientific arguments are almost always influenced by subjective judgments, why shouldn’t I believe a premise if it is based upon all available evidence and the best judgment possible. The value of science for me is that it generates justified beliefs. I can believe a scientific claim if all existing evidence supports it, while maintaining an openness to change in light of new evidence. Additionally, just as there is no single view of the value of nature, the pursuit of knowledge can take on different meanings for different people. This is liberating rather than constraining, because it opens up opportunities for each person to define why and how nature or knowledge matters to them. Knowledge can be valuable to us in different but intimate ways. We can believe what we know.

Section 3: Resources

I hope I have incited some interest in you to learn about epistemology if you haven’t already. I have been inspired greatly by the book “What is this thing called Science?” by A. F. Charmers. It is a great read and very easy to follow. If you don’t want to read a whole book, the “Stanford Encyclopedia of Philosophy” is a reputable online resource open to the public. And there are always more journal articles waiting for discovery and many more exciting reads. Scientific findings are leading many philosophical developments, including evolutionary epistemology, neuroethics, and neuroesthetics.

Bibliography:

  1. Grimm, Volker, Daniel Ayllón, and Steven F. Railsback. “Next-Generation Individual-Based Models Integrate Biodiversity and Ecosystems: Yes We Can, and Yes We Must.” Ecosystems (2016): 1-8.
  1. Steup, Matthias, “Epistemology”, The Stanford Encyclopedia of Philosophy (Fall 2016 Edition), Edward N. Zalta (ed.), URL = <https://plato.stanford.edu/archives/fall2016/entries/epistemology/&gt;.
  1. Chalmers, Alan F. What is this thing called science?. Hackett Publishing, 2013.
  1. Gould, Stephen Jay. “Is uniformitarianism necessary?.” American Journal of Science 263, no. 3 (1965): 223-228.

Guide to the graduate interview season: Making the most out of your visits.

By Emlyn Resetarits Jan. 2017

It’s interview season for prospective graduate students! If you were lucky enough to be asked to come out for an interview, congratulations! Although acceptance is not a done deal, you have a good chance of getting accepted. Why else would they fly you out there? So, relax! The interview process is a two-way street: yes, your potential mentor and faculty are interviewing you, but you are also interviewing THEM. Finding the right mentor and department is very important for your later success as a graduate student.

Make the most out of your visit! This is your chance to assess how well a given department or advisor will fit you! All departments and mentors are looking for something slightly different in their graduate students, but here are a few tips on how to impress:

Before you arrive:

  • Read up on the faculty. Get a sense of what everyone does (in general terms), so that you are more prepared if/when you run into them. You don’t need to memorize their research, just get a sense of what they do. If you have a schedule beforehand of whom you will be meeting, focus on looking up these faculty members.
  • Make sure you can answer the following questions:
    • Why do you want to get a PhD/Masters?
    • What are your research interests?
    • Why are you interested in this university, specifically?
  • If there are specific faculty that you want to meet with besides your potential advisor, make sure to mention that when scheduling your trip. You want to make this visit as informative as possible.

During the interview/recruitment weekend:

  • Dress comfortably! You will be running around all day, continuously meeting faculty and students, and the last thing you want is to feel self-conscious or in pain because you decided to break in a new pair of shoes during this visit. A suit may be overkill, but also don’t wear sweatpants and a t-shirt. You’re not there to impress anyone with your sense of fashion, but looking sharp will help you give a good first impression.
  • Meet as many people as you can! This is your chance to get the details on the department, the university, and the people! Get to know what your potential faculty work on and what graduate school is like in this department!
  • For your meetings, treat them like a first date. What I mean is, give a quick summary of your interests and experiences, ask about what the other person does, actively listen and engage, and don’t be a creep. You should try and make all of your meetings (with graduate students, prospective advisors, and other faculty members) a conversation rather than an interview.

One way to impress people is to be prepared with questions. Even if you aren’t looking at any other places, asking probing questions makes you seem more desirable and more sought after. Also, it’s the best way for you to make your decision of where to go, if you do have multiple programs you are looking at.

Here are a few questions to ask when interviewing:

Ask your potential advisor(s):

  • What is their mentoring style? Are they hands off or hands on? Do they give deadlines to their graduate students or do they let their graduate students work at their own pace? Are they open to weekly meetings? Different students flourish under different mentoring styles. It’s important that you have a sense of what type of mentoring style you would like from an advisor, and see if you and your advisor are compatible.
  • What type of funding do they have and what funding are they applying for? What could that funding provide for you? Research money? RA positions? Conference fees? Some faculty may have a large grant, but if you aren’t interested in working on that specific project, then that funding might be unavailable for you. It is important that you figure out how much funding you may have to come up with yourself and how realistic that is.
  • Is your advisor thinking of moving from their current institution? This isn’t necessarily a deal breaker, but is important to know before you move to that institution for them. If your potential advisor is thinking of moving, make sure that there are other faculty members in the department that you could be advised by. I’ve know many students who have had to change labs because their advisors decided to move half way across the world for a new academic position. Most of these switches were successful, however, because there were other faculty members who had similar research.

Ask advisor’s graduate students:

  • What is your favorite and least favorite thing about your advisor? About the lab in general?
  • How collaborative is the lab? It’s nice to have the flexibility to do whatever project you want, but it can also get a bit lonely if you don’t have anyone working on a similar topic. Does your advisor collaborate with graduate students on projects? Do graduate students collaborate together?
  • How cohesive/social is the lab together? Does the lab do anything outside of work? Does everyone go home to their families at 5pm? Or does the lab go out for beers monthly and have a Christmas party? It’s surprising how much lab events can impact how you feel about graduate school and your lab in general.
  • Are you planning on pursuing a career outside of academia? How helpful has your advisor been in preparing you for this alternative career?
  • Does your advisor give quick and thorough comments on your papers? Does your advisor prioritize graduate students getting their papers out quickly? These questions are ones that are rarely asked during the interview process, but I think are some of the most important. I’ve known many fellow graduate students who have had a paper completed to the best of their ability, and are just waiting for comments from their advisor. For some students, getting feedback on their paper takes months and is like pulling teeth. There is very little more frustrating and demoralizing than waiting and waiting to submit a paper and feeling like you are getting farther and farther away from your goals. I have even known late-stage graduate students that have given up on academia entirely, because they are 6 years in and have not been able to submit any papers yet. Of course, if you just ask your advisor, it’s likely that they will tell you, “Yes, of course! I think it’s vitally important to help graduate students publish early and often.” Of course, faculty want this, but the question is, do they emphasize it in actuality? The best way to determine this is to ask late-stage graduate students in the lab if their advisor prioritizes this.

Ask any graduate student:

  • Do you think my potential advisor is a good advisor? If you ask enough graduate students this, you will be able to piece together an accurate representation of them, one that is perhaps more comprehensive than if you just ask graduate students from your potential lab. Graduate students from your potential lab may be more hesitant to give you the dirt on their advisor than others are.
  • Are you happy? This may seem like a stupid question, but it can tell you a lot about the graduate student climate.
  • Is the graduate student stipend sufficient for you to live comfortably? How will you get paid through the summer? Are you expected to teach your entire graduate career, or will you never be seen in a classroom? This is a big consideration. If you are applying for a PhD program in the biological sciences, you should NOT be taking out any loans, nor should you be eating only rice and beans and living in the windowless basement of some creepy man’s house to afford to go to school. While a program that offers teaching assistant positions only to students might provide you with the living wage you need to survive, you also have to consider how teaching time will impact your ability to finish your own research. During my interview at one school, I was scared away because many graduate students had to take out loans to afford to live there. While most graduate students are entering PhD programs without expectations of large wages in the future, that doesn’t mean finances should not be an important consideration when choosing your graduate school.
  • In a similar vein, ask what the housing market is like. You will be living in a place for 5-6 years and buying a house, if feasible, is a great alternative to paying rent for that whole time.
  • How cohesive is the graduate community as a whole? Do you feel like people are pretty social, outgoing, and have diverse hobbies? These will be your peers and your social circle for 5-6 years, so it’s important that you feel like you could have fun with them!

Ask faculty:

  • Ask them what they do! What projects are they most excited about currently? What projects are they planning for the future?
  • What do your graduate students do?
  • What graduate courses will you be teaching?
  • What resources are available for graduate students? Departmental grants? Sequencing facilities?
  • How collaborative is the department? This will give you a sense of the environment of the department. If the department isn’t very collaborative or a faculty member gives you a knowing look, then perhaps there is a lot of departmental drama or factions. A collaborative department is a good sign!

Of course, this is not a comprehensive list of questions to ask, but it should help you get the most out of your interview visit. Most of all, have fun and engage with people! Faculty, advisors, and current graduate students are looking for students that will be active members of the scientific community, that means they want you to be a dynamic human, not a work-obsessed robot!

Good luck!