Field of Science

ChemCoach Carnival: What I do

I am late to the party, but SeeArrOh's ChemCoach Carnival has given me a chance to indulge in some narcissistic self-promotion. There many great entires on his blog so you should take a look. Here's my pitch.

Your current job.

I am an organic chemist turned molecular modeler at a small biotech startup in Cambridge, MA. I spend as much time looking at synthetic strategies, building block procurement, target selection and assays as I spend building models. I also spend a lot of time thinking about how my work fits within the broader boundaries of science.

What you do in a standard "work day."

As a lot of others scientists on this thread have emphasized, one of the great things about our job is that there is no “standard work day”. I am the lone modeler in a small startup so that requires me to wear several hats. I am as involved in discussing synthesis and assays as I am in docking small molecules to proteins or running molecular dynamics simulations. In addition I also need to occasionally look up building block availablity, talk to database and informatics specialists and arrange for presentations from outside vendors. The point is that in drug discovery and especially in a small outfit, you must be adaptable and be able to accomplish multiple, diverse tasks. This kind of capability makes you a valued member of the team, especially in a small company where your voice will be heard by everyone, from the intern to the CEO. It’s also a terrific learning experience in general.

What kind of schooling / training / experience helped you get there?

I have a doctorate in organic chemistry, although frankly that is just the means to an end. I switched from synthesis to modeling because I was clumsy in the lab and because I was interested in many different fields of science. I don’t regret my choice at all. Modeling allowed me to indulge interests in physics, chemistry, computer science and biology. I would say that if you have diverse scientific interests, modeling and simulation in a general sense would excellent career choices for you. If you are planning for a career in drug discovery or biotechnology, I would encourage you to soak up as much knowledge from diverse fields of chemistry and biology as possible. You won’t regret it.

This would also be the place for me to sneak in my favorite pitch regarding the history and philosophy of science. A simple piece of advice: study it. Science is done by fascinating human beings with all their flaws and triumphs. Your experiments are not being done in a vacuum. Reading up on the history of your discipline will give you the feeling of participating in a grand, unbroken thread of discovery going back to the Greeks. Even if you may not be a world-famous scientist or are not doing earth-shattering research, the simple fact that you are exploring the same laws of physics and chemistry that world-famous scientists once did will put you in their league and inspire a feeling of kinship. Studying the history of science will convince you that there are many who empathize and who have shared the same sense of despair and triumph that you do. Study the history of science, and you will know that you are not alone.

How does chemistry inform your work?

It is all-pervasive in my work. When I say I am a “molecular modeler”, I mean that in the broadest sense of the term. For me all of chemistry is largely about models, whether the models consist of structures scribbled on a hood or three-dimensional protein images built on a computer screen. A lot of people think computation in drug discovery is all about building regression models and writing fancy algorithms. But what it’s really about is data interpretation, and pretty much all this data is chemical. I cannot stress how important it is for a molecular modeler to understand chemistry, especially organic and physical chemistry. What has turned out to be an intractable problem has often proved amenable to a solution found in the principles of basic organic chemistry. In addition you have to have a real feel for structure-activity relationships and the basic physiochemical properties of functional groups. Useful numbers from thermodynamics and kinetics should ideally roll off your tongue like French verbs. A knowledge of statistics is also important. My background in organic chemistry is much more important than any facility with programming or knowledge of particular software that I may have picked up on the way. Those things you can learn, but the bedrock of your work will always be chemistry, even when it's operating behind the scenes.

Finally, a unique, interesting, or funny anecdote about your career*

Well, when I said I was clumsy in the lab I was thinking about the time I actually dropped a rotavap on the floor and broke it. My advisor, a generous man, said that maybe I was not quite cut out for working in the lab. It was the only time in my life that an embarrassing accident gently pointed out by a wise future advisor has fortuitously decided the trajectory of my career.


  1. "Well, when I said I was clumsy in the lab I was thinking about the time I actually dropped a rotavap on the floor and broke it."

    My first summer in my undergrad lab, I broke a fragile vacuum jacketed LN2 transfer line. I would have sworn it was installed securely, but I clearly was mistaken. Fortunately, we had another one, and my professor was very understanding. Although he did manage to convince me to eventually start working on a project which required liquid helium cooling, and its far-more-resilient metal transfer line.

    P.S. - I imagine you already saw this, but it only cropped up today in my Google Scholar Alerts - Yet another GPCR structure, but one I find more impressive, if only for superficial reasons. Heh.

  2. What would we do without professors who gracefully help us transit from mistake to stumbling mistake?

    Thanks for the GPCR structure, hadn't seen it. There's another one in Science last week, with the first bound peptide ligand. The floodgates seem to have opened.


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