Biocurious

/ a biophysics blog

We need to stop pigeon-holing science

Posted 4 May 2008 by PhilipJ under &

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.

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Drew Endy on Engineering Biology

Posted 23 February 2008 by Andre under &

The third part of the Edge series “Life: What a concept!” is now online. This one is a talk with Drew Endy, a bioengineer at MIT. Despite existing for 30 years, we still haven’t realized much of the promise of biotechnology and Endy believes this is because we haven’t invested enough in making versions of biological systems that are easy to engineer.

America, 1860, machinists are building objects, steam engines, what have you. Nuts and bolts that hold together machines are specific to the particular machine shop that manufactures them. What that means is, if you buy some machine from a machine shop in Newark, New Jersey, and it breaks down in Chicago, you have to send it back probably to that specific machine shop, with the machines set to tool things on a particular set of designs in order to get the replacement part or to get the thing fixed.

In April of 1864, somebody says, enough; William Sellers of the Franklin Institute in Philadelphia gives a paper on a system for nuts and bolts. And he proposes the Sellers Screw Thread Standard […].

The consequence of this today is, when I go to the hardware store and get a nut and a bolt, so long as they don’t screw up the English/metric thing, I can take those two objects, and I can put them together. I don’t have to do an experiment. I don’t need to go talk to some Harvard professor to figure this out. I don’t need to do a controlled experiment to see if my first experiment worked. I just get the two objects and put them together.

So, Endy wants to do the same thing with biology. He draws an analogy with the development of computers that might convince you this is exciting. Computers went from large machines run by scientists to personal machines owned by large numbers of non-scientists (not necessarily non-experts!) that are programmable by anyone with time and motivation. Currently, synthetic biology is being done largely by big labs run by scientists, but engineers are also starting to take part, and according to Endy their different approach will yield many more benefits in the long term. I assume this passage is about Craig Venter, but please correct me if I’m wrong:

If you make biology easy to engineer, and you make it accessible, by definition people will learn about it, and write comic strips about it. You can talk to computer programming conferences about it, and it’s a different world. It’s a very different world from going around claiming that you’ve created life. It’s a very different world from going around filing patent applications that say you have invented the idea of a synthetic genome. It’s a very different world from going around and spending $40 billion on a classified biological defense facility, at the site of the past U.S. Offensive Biological Weapons program. And so there’s a cultural mismatch.

Again with the cultural mismatch. One group arguing that intellectual property needs to be controlled to be taken advantage of and the other arguing that new tools need to be open to everyone to be taken advantage of. It will be interesting to see how this plays out. I suspect it won’t be the case that one approach dominates but that we’ll end up with aspects of both coexisting for a long time, as is currently the case with open source and proprietary software.

Regardless of exactly how it develops, expect big changes in our ability to control biological systems and expect significant parts of biology to be reduced to information science, the same way significant parts of electrical engineering have been reduced to information science.

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Going to Biophysical Society Meeting?

Posted 31 January 2008 by Andre under &

I think it would be interesting to organize a pub outing for one of the nights during the conference. It can be hard to meet people at these big conferences (unless it’s through people you already know) so I thought I would cast a wider net by posting here. If you’re planning on attending and want to meet, let me know by e-mail or in comments. Feel free to suggest a good place to go if you’re familiar with the area.
true happiness
Drinking not required. DNA smiley from Paul Rothemund, as usual.

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It's like powering gym lights with treadmills...

Posted 14 November 2007 by Andre under &

You know those squiggly words you need to decipher to post comments on some blogs or to create new accounts at some sites? These can be annoying, but I hate spam as much as the next person so I don’t mind going through the slight extra effort. Now, that little extra effort can be harnessed to do good! Sean at Cosmic Variance describes a talk he attended by the inventor of the method. Basically, by flipping the problem on its head Luis von Ahn realized that all the work people are doing deciphering words could actually be applied to deciphering scanned texts that computers are having trouble with. Genius!

I love these kinds of ideas and it reminds me of one of these projects for taking advantage of large numbers of otherwise idle computers: using Playstation 3s to predict protein structures. A lot of console gaming systems are networked these days, so researchers can use them to simulate proteins when they’re not being used to simulate gun fights.

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Life: What, when, how?

Posted 10 September 2007 by Andre under &

Life is a great thing to think about. Not only can it be bewilderingly (and satisfyingly) complex, it’s quite relevant to us humans and for whatever reason we feel a certain harmony with it. We have an intuitive feeling for what is alive and what is not. Mice, cod, and pines—alive. Rocks, tables, and air—not. But when it comes down to giving a precise definition, it can be surprisingly difficult. All sorts of fringe cases refuse to simultaneously fit with our intuition and our definition. For an interesting review of some of the modern definitions that have been proposed, see John Wilkins’ recent post. Sean Carroll also comments and includes his candidate for a tricky case: the Milky Way itself.

Defining life can be a fun puzzle, but I don’t normally get too excited about it. In some ways it’s like defining scientific disciplines: some things are clearly physics or biology or chemistry, but lots of interesting things happen at the boundaries and it’s more interesting and productive to go after interesting problems than to worry too much about whether what you’re doing fits into a particular category. Similarly, it’s more interesting to study simple life, try to make it in the lab, or look for it on other worlds than it is to give a precise definition of what it is. On the other hand, the things that people decide to include in their definitions are a nice reflection of the state of our understanding and sense of fashion. There’s been a nice progression in sophistication and subtlety even if the result isn’t totally satisfactory.

When life started might seem to be a more concrete question but it suffers from the same kind of blurry boundaries as the question of what life is, and for the same reasons. If we limit ourselves to life on Earth (but why should we?), we can say that 5 billion years ago, there was no life, 3 billion years ago, there was. On this topic, I’d recommend that you watch this video of an informal talk by Craig Venter hosted by Edge. He has some interesting things to say about the diversity of life, but also discusses the possibility of panspermia and mentions that even if we discover evidence of life on Mars we won’t know if it had a unique origin there until we have a better understanding of the gene repertoire here on Earth (unless of course it turns out to be a completely different form of life). In any case, at some point, a transition was made between non-living and living and deciding exactly when that was relies on having a good definition of life, but again, deciding when it happened is not nearly as interesting as learning how it happened.

On this, there are also some interesting contributions at Edge. Freeman Dyson speculates about a possible “garbage bag model” for the first living (or almost living) things and Robert Shapiro gives perhaps the most important contribution to the “how” portion by discussing the implausibility of life starting with RNA (although his framework doesn’t really argue against the RNA world, it simply excludes it from being the first step in prebiotic chemistry). I tend to agree with Seth Lloyd that we probably won’t know for sure what conditions gave rise to life on Earth, but we might be able to demonstrate convincingly that complex chemical processes of the kind that would be required to create life are possible or even likely. I think that would already be very exciting, because it might not get directly to our distant roots, but instead might give us a glimpse of the roots of our distant cousins that might exist elsewhere. This approach also has the advantage that even if you don’t discover plausible life origins you might discover interesting complex chemistry and that’s almost sure to have its own rewards, practical or otherwise.

For some interesting further reading, check out Carl Zimmer’s latest article in Seed.

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How do you make and share scientific figures?

Posted 10 June 2007 by Andre under &

One of the most important parts of scientific communication is making figures that convey your results clearly and compellingly. These days, that means using software to arrange plots and images from other programs, add labels, and often draw simple cartoons or schematics to illustrate the central ideas. There are several features that I consider important for this kind of graphics software. It must support a variety of file formats and be able to export publication quality images. It should have convenient alignment tools so that your images can be easily centered with respect to each other or arranged into arrays. Importantly, the drawing tools should be flexible, give a clean professional looking end product, and not be to difficult to learn. These are not very stringent requirements as far as graphics applications go.

Since most science is collaborative (it’s rare to see single author papers in most journals), it’s also useful for each person involved in the project to have access to the same software for making corrections or suggestions for improvement. So the ideal scientific graphics software will also be compatible with several platforms (at least Windows and Mac) and cheap (preferably free).

Unfortunately, because of its ubiquity, Powerpoint is often the default choice for making figures despite its failure to meet most of the requirements outlined above. This is not acceptable to me, even though I’ve been using it recently because it’s what some of my collaborators use (before submitting anything to a journal I will most likely redo these figures in another program after the final versions have been agreed upon).

I’ve tried Omnigraffle and found that it was pretty good, but as far as I know, it’s only available for Macs. I haven’t used Illustrator but I’ve heard good things. Is it worth the money? Will I be able to convince collaborators to use it despite the cost?

What else is out there? What do you use for making figures?

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