From the computer screen to the lab bench: A physicist learns to do wet-lab biology

As Kenneth described in a recent post, the Center for Integrated Proteomics Research and the BioMaPS Institute for Quantitative Biology at Rutgers recently held a two-week “boot camp” program to cover a range of basic topics in molecular biology and biophysics.  The program was intended to serve the increasingly diverse community of scientists — with backgrounds ranging from physics and chemistry to computer science and mathematics — working in quantitative biology.

As a physics graduate student who works in the BioMaPS Institute, I was definitely in the target demographic.  In my undergraduate days I was mainly interested in particle physics and cosmology, so my coursework focused entirely on physics and mathematics.  I haven’t taken a biology or chemistry course since high school.  While I’ve certainly picked up a great deal of the necessary biology throughout my graduate research in biophysics, I could still use more breadth.

But I was primarily interested in gaining a very specific kind of breadth from the boot camp.  Besides having a background in physics, I am also a theorist by training, and I’d never had any experience doing “wet-lab” biology experiments.  (In physics, there is a very clear divide between theorists and experimentalists.)  But recently I’ve become interested in gaining some experience with wet-lab biology, both because it’s helpful for collaborating with experimentalists and understanding experimental papers, but also because there is a serious possibility I will pursue a combination of theoretical and experimental work next year as a postdoc.  Luckily, the boot camp included a week-long experimental lab for complete beginners like me, so it seemed like the perfect opportunity to try it out.

The best thing about having zero experience with something is that you can learn a whole lot really quickly.  So even the most basic, mundane aspects of doing the lab were new and exciting for me, things I had heard about in talks or read in papers but never really understood.  So this is how you pipette…and “streak a plate”…and purify proteins…and run a gel…and so on.  Here’s some photographic evidence (credit to Gail Ferstandig Arnold):

As someone who has worked only on the other side of research until now, it has been really eye-opening to have concrete experience doing experiments and generating data that previously existed only as abstractions in my theorist’s mind.  While I recognize that a week’s worth of exposure isn’t enough for me to jump right into doing all my own experiments as a postdoc — undoubtedly I’ll have to relearn all the stuff from last week again later — getting that first experience definitely gives me confidence for the future.

Biological Science Boot Camp: Bridging Theory and Experiment

Society is a complex network of people needing to effectively communicate. To advance the standard of living, it is imperative that communication exists between people who articulate different perspectives and work towards a common goal.  For example, teams of medical workers are needed to deliver healthcare, groups of politicians are required to debate public policy, and teams of scientists are vital in every branch of society.

In many instances, the complex nature of society requires scientists, politicians, and medical workers to work towards a shared goal. For this to occur, ideas need to be communicated effectively. Medical workers need to know the expected impact of a life saving drug developed by scientists, and politicians need to determine if the new drug meets regulatory policies.

Before a drug can be put in the hands of trained personnel, a team of scientists with diverse expertise in experimentation and theory need to design and thoroughly test the drug. However, theorists may not have the background to understand the limitations of experiments, and experimentalists may not have the theoretical background to simulate and model data. Effective communication and collaboration can bridge the gap between theorists and experimentalists.

This winter break, I am bridging the gaps in my science by attending the intensive two week interdisciplinary boot camp offered by the Rutgers Center for Integrative Proteomics Research. The boot camp offers an immersive experience for scientists interested in finding potential collaborators, and learning new methods, for exploring theoretical and experimental biology. The main tool being used to teach the many aspects of biology is the Green Fluorescent Protein, a Nobel Prize winning subject important for the advancement of biological science. This boot camp is offered Jan. 6-17, 2014, and is open to all.  For more information click here

Identity, Goals, and Diversity in Interdisciplinary Research

While I was an undergraduate physics major, my interests and research experiences were quite clearly of the pure physics variety: particle physics, cosmology, astrophysics.  There was never any question about my scientific identity or goals — I was unambiguously a “physicist,” and with that label implicitly came values about what I was supposed to study and how.

When I began graduate school, however, I found a new interest: biophysics, an interdisciplinary science if there ever was one.  While Rutgers has many physics Ph.D. students and faculty studying problems in biophysics and quantitative biology, I couldn’t help but suffer a bit of an identity crisis, albeit one more professional than adolescent in nature (not so much “Who am I?” but rather “What kind of job will I be able to get?”).  This seemed exacerbated by my specific research, which focuses on evolution; while physical analogies abound within the mathematical models, the phenomenon itself is plainly biological.  So when describing my work to others, I had to wonder: am I still a physicist?  Or am I a biologist?  Am I some type of hybrid, i.e., a biophysicist, and if so, what does that really mean?

Over time, though, I’ve come to believe what defines our identities as scientists is not so much what we study but how we study it.  More precisely, it is not the questions we ask but the kinds of answers we seek that are important in defining this identity.  Many different types of scientists (biologists, chemists, physicists, etc.) in a field like biophysics are basically studying the same problems — gene regulation, biochemical kinetics, protein folding, etc. — but their actual work may look completely different from each other’s on paper.  A good example is given by protein folding, the famous problem of understanding how a chain of amino acid molecules making up a protein folds relatively quickly into a unique 3D conformation (Ref. 1).  To a structural biologist or a bioinformatician, so-called homology-based methods provide an adequate solution.  These methods predict unknown structures of proteins using large databases of known structures and statistical algorithms.  To a physicist, however, this is not really a solution at all — it is a practical tool to make predictions, but it offers no insight into the fundamental physical principles underlying how the folding process occurs.

This issue has real consequences for a discipline, beyond just a little angst for students.  Despite all the good intentions of funding agencies, journals, and institutions toward cultivating interdisciplinary research, they run into problems when geneticists are evaluating physicists’ proposals by genetics standards or when mathematicians are evaluating biologists by mathematics standards.  As demonstrated by the example of protein folding, scientists can have genuine disagreements about whether a problem is even solved.  An interdisciplinary field must be aware of these different values and should openly discuss how to make different scientists’ goals and styles complementary for the sake of scientific progress.  Indeed, interdisciplinary research has tremendous power to meet the daunting challenges of the 21st century, but only when effective communication and collaboration exist to take advantage of it.

[1]  Dill KA, et al.  (2007)  “The protein folding problem: when will it be solved?”  Curr. Opin. Struct. Biol. 17:342-346.

Media Mouthfeel

Who am I? I thought I dispensed with such philosophical wormholes after the teenage angst years. My first year as a doctoral student at Rutgers has proved me wrong. Although the angst has mellowed now in my late 30s, I still dread the ubiquitous wine and cheese filled inquisitions about my research interests. I will confess to a degree of envy when my colleagues in other disciplines succinctly explain what they study. Math, in particular, tends to shut people up. The study of media on the other hand sparks loads of questions. Everyone has opinions about it. For those who embrace the postmodern world (I myself am suspicious of the adjective), everything is a text filled with gaps available to be read, even the cheese cube in your hand. I actually like this everyday quality of media, yet it encourages my “shiny object syndrome”—my habit of knowing a little about a lot, a kind of epistemology of distraction. This mindset seems antithetical to the scholar, the learned one able to pontificate on the political economy of toothpicks.

So I must focus at least in time for my qualifying exam circa the start of my third year. I have roughly 6 courses left of my traditional student life. Scarcity breeds abject terror. As a 16th grader, the paranoia of making them count looms large. I also have the awesome opportunity to take two courses outside of Rutgers through the research consortium. I need a plan, yesterday.

Of course, I have talked to my advisors. They are ever so patient with me. I tend to ask enormous questions such as “What makes media more or less democratic?” I get cranky thinking about techno-evangelists, those who have Internet technology saving the planet, as if cyberspace were free of race, class and gender. Would we even want such a place if it were possible? This is why I like science fiction novels. Maybe I should have chosen English. Disciplines are mere fabrications, artifacts of university politics. Do you see why my professors are so patient with me?

If you pass me the pinot noir, I will tell you that I want my research in media studies to convey hope—hope for our global liberty expressed locally. I told a colleague that this was a corny idea. She disagreed, suggesting that theory leads to anger (at the disconnects?), which eventually gives way to a longing for hope. This has a truthy ring to it, one that harmonizes with my conviction that culture is what we make it; culture is essential to freedom. Media are cultural channels, spaces carved out with rich striations and sediments for study–cultural terroirs. I tend to focus on who made the channel, when, where, why and how. Media production is my bailiwick, and I am developing a fondness for ethnography—minus the transcription part. My kind of work is open to interpretation. I wouldn’t have it any other way.