Biocurious: Philip's Research

We need to stop pigeon-holing science

Posted 4 May 2008 by PhilipJ under Interdisciplinarity & Philip's Research

My brief anxiety over what kind of scientist I am was initially posted as a bit of a joke. As the resident wet lab junkie (scary!) in what is primarily an ultrafast optics group, having spent at least as twice as much time on sample prep over the past 8 months as I have on aligning lasers to do fancy nonlinear optics, it gets harder and harder to say things like “I’m a physicist“ with the same kind of certainty that I once would.

And you know what? That’s okay. The more I play in other sandboxes (or as the case has been, dark rooms*), the more I realise my own sandbox of physics is no “better” than anyone else’s. We’re just asking, and trying to answer, different questions.

This is all coming to mind because we just finished holding the annual Chemical Biophysics Symposium again, and on the first evening of every symposium there is a panel discussion on some interesting topic. Something that keeps coming up at these kinds of discussions is the “us” versus “them” comments, wherein “us” is invariably physicists (or physical chemists), who are the majority of the audience at the symposium, and “them” are those nebulous biologists who never seem to be around to offer a biologists viewpoint on science.

I have news for physicists who have woken up to find lots of fun problems in biology: most of us are solving physics problems in biological systems. We are nowhere near addressing most biological problems. It is flashier and more exciting to say we’re working on cancer, or drug deliver, or what have you, but in most cases we really aren’t working with biologists to help solve biological problems, despite claims that we are now starting to study biology the “right way”.

It is useful to recall Bob Austin’s take on the interesting problems in biology:

I want to do the big problems: I want to understand energy flow in biomolecules; I want to understand how genes are turned on and off; I want to understand the collective processes in cell growth; I want to understand how the brain works; I want to understand the origins of consciousness. […]

Nowhere above does he say “the physics of …”. It is great that physicists are turning to biology for new problems to solve, but I grow a little tired of the physics vs biology mentality. If we truly want to make great strides in understanding biological phenomena, we need to stop pigeon-holing disciplines. There is no “us” or “them”, “they” aren’t doing things incorrectly, we’re all simply using the tools we were trained to use to solve the problems we find interesting. What we really need to do is find better ways to share ideas, so that everyone understands exactly what they can contribute. We can’t be afraid to learn from each other, and in the case of biology, it is most certainly a two way street.

* More on this soon.

Comment [7]

Identity crisis

Posted 17 April 2008 by PhilipJ under Philip's Research

I just used ChemDraw for the first time! What does this mean???

Also, I’m studying for a biological chemistry final. It could hardly be more different than studying for a physics course. Blurring the line between the sciences in research is awesome, taking the other side of the line’s courses can be… tricky. Biology isn’t harder than physics, it’s just different.

Come on May 1st.

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SciBarCamp report: Digital lab notebooks

Posted 16 March 2008 by PhilipJ under Graduate School & Philip's Research

The first SciBarCamp is going on this weekend at Hart House at the University of Toronto. The basic idea of SciBarCamp is that of “a gathering of scientists, artists, and technologists for a weekend of talks and discussions.” The kinds of things that have been discussed this weekend are the forefront of science (quantum gravity, synthetic biology, open access, scientific software), and the interactions with science and technology and art. There’s an extremely interesting mix of people here today, from quantum information theorists from the Perimeter Institute to social scientists from OCAD, grad students, science writers, musicians, etc. Quite the eclectic group.

The “un“conference opened up with what was perhaps the most interesting discussion for me. It was by Corie Lok from Nature Networks and John Dupuis from York University on “Science 2.0”, or basically how technology is changing first the way we do science, and then how we publish and track science. Things like Connotea and del.icio.us were discussed as ways to keep track of relevant journal articles, but the discussion was dominated by discussion about keeping track of your experiments, and how this is changing in laboratory environments.

Many labs are moving to an all-digital lab notebook. Gone are pens and paper as the primary means of keeping track of your experiments, and they are instead being replaced by digital equivalents, such as wikis or some other, commercial software (which I unfortunately didn’t catch any names, but a google search brings up all kinds of examples). The advantages of such a “notebook” are clear: entirely searchable, easily referenced with hyperlinks, the ability to keep digital images and snippets of code, etc. There is also an advantage which hadn’t been discussed, but is something I’ve long thought about: legibility! If you’ve ever looked in another scientists notebook, you will quickly find that their writing may be atrocious (guilty as charged), and it quickly becomes an exercise in frustrating trying to interpret what was written.

Perhaps not surprisingly, this is being embraced in a big way by the big pharma companies, where it is crucial to have detailed records, and to keep them for a long time (something like the lifetime of a drug being sold + ten years). But there’s an advantage to graduate students in academic laboratories that hadn’t been addressed in the discussion, that came to me as I was talking about this to another grad student friend. It’s that of the copies. I graduated from SFU with my Master’s less than a year ago, but I could tell you basically no specific details on some of the more mundane, day to day experiments that I carried out. I’m sure the same thing happens to those who graduate with a PhD, and leave their lab notebooks behind. I’ve decided I want to keep this kind of information, and I’m still early enough in my PhD that it won’t be too hard to change.

To the other scientists reading this blog: have you changed to a digital lab notebook? Have you tried the switch and failed, or have things gone smoothly? What software did you decide on? I’m leaning towards a wiki, and I’ve decided it will be necessary to keep a paper notebook as well, but to make it degenerate information which will, at the end of every day, always end up in the digital notebook as well.

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Repoll: Windows in your office?

Posted 19 October 2007 by PhilipJ under Random Walks & Philip's Research

I have some exciting news.

Well, it isn’t exactly new, since I’ve been in Toronto for three months now. But it’s still exciting to me.

Last year I asked if there were windows in your office. Now I can happily change my answer to yes!

Yes, that is natural light saturating my digital camera! Now, I’m in a chemistry building, so the windows don’t open, but this is still significantly better than the concrete bunker I used to call an office.

How about you, has your situation changed?

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Carbon makes how many bonds?

Posted 9 September 2007 by PhilipJ under Philip's Research & Graduate School

Physicists have a knack for thinking we know everything, or at least that everything else is easy enough to learn, since, well, everything else isn’t physics. I’ve had the sense to not give in to this delusion too often, even though I decided that I could hack it as a PhD student in a chemistry department despite not knowing any chemistry. In my defense, my PhD program is called Chemical Physics, so this shouldn’t be entirely out of my realm.

Prior to accepting the offer here at the University of Toronto, it was agreed that my background would preclude me from TAing a number of courses, particularly those with the words “organic” and “inorganic” in them. Not that I couldn’t learn these subjects, the physicist in me likes to tell myself, simply that they are different enough from my formal training that I can’t pick them up without a reasonable amount of time and effort.

TAships were handed out a couple of weeks ago. As it happens, I was given the computational laboratory section of Intro Organic Chemistry I. An organic chemist friend of mine cheekily asked, “So, how many bonds does Carbon form?” Yes, I do know the answer. No, I am definitely not who you want teaching students about organic chemistry.

Luckily for everyone (though mostly the undergrads in Intro Organic Chemistry I!), I’ve since been switched to a physical chemistry course. The first disaster of PhD-life averted.

Comment [1]

Publication quality molecules

Posted 22 August 2007 by PhilipJ under Biocuriosities & Philip's Research

A couple of months ago AndrÃ© asked about making and sharing scientific figures, and there was some great reader feedback. I’ve got another, similar question, but this time specifically relating to molecular structures. What does everyone use to create high resolution, publication quality structural images of proteins?

Freelancing science partially answers the question. Pawel suggests