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So far I’m very impressed by the level (and amount) of biological physics at the March meeting. There’s even more to be excited about this year than in previous years and I think it reflects physicists’ growing excitement about biology and a larger group of scientists realizing that they have things to talk about with physicists. It’s great to see.
One of the talks this morning was about how ants search when exposed to a new environment. When they find themselves in an empty, uniform, flat box, they seem to initially walk in a directed way away from the point of origin and then start a random walk to explore the new space. These experiments by William Baxter from Penn State have the appeal of simplicity, and they already yield interesting results. If one ant performs a random walk after a dash to a new area, what do two ants do? Do they avoid each other to make the search more efficient? So many great things to do. This also reminded me of a profile in em>Science (subscription required) last week that I wanted to write about anyway. If you have access, have a look. Awesome stuff.
There was also a nice talk by Elijah Bogart in Carl Franck’s group at Cornell. They’re using dicty as a model to study the lag phase of cell growth that precedes the exponential phase. Check out their paper in PRE and stay tuned for new results.
Finally, Greg Grason gave a beautiful talk on filament bundling and twisting. Bundles form when filaments are attracted to one another and this favours a hexagonal packing. In the absence of other factors, this should lead to infinite width bundles because the system could always reduce its free energy by adding another filament to the bundle. But, of course, there are other factors. One of those that Greg illustrated so nicely is that biological filaments are chiral, and that these chiral, twisted filaments would prefer a slight tilt when they pack together. This effect can lead to the formation of twisted bundles to accommodate this preference, but in this case, the filaments must bend and this has its own energy cost. Using mostly geometric arguments he was able to come to some neat conclusions about bundles. He and former postdoc advisor Robijn Bruinsma published some of this work in PRL and Greg has a new paper extending this work on the arXiv. This could be a link to the more recent paper, but I can’t check because I’ve been denied access to the arXiv using the convention center wireless:
Accesses from your site have triggered our automatic robot detection system.
Presumably the large concentration of physicists here has confused the server!
The 2009 Edge World Question is What game-changing scientific ideas and developments do you expect to live to see?. It seems like a lot of people ignored the question, but most were still an interesting read. As per previous years, here are a few of my favourites.
Alun Andersen thinks simple, engineered organisms that can soak up energy in a vat in any sunny spot and turn that sunlight straight into a precursor for fuel, preferably a precursor that can go straight into an existing oil refinery that can turn out gasoline are the solution to our energy problems.
Jesse Bering thinks we’ll come to realize that God needn’t actually exist to have evolved.
Mihaly Csikszentmihalyi argues that it is more important to understand events, objects, and processes in their relationship with each other than in their singular structure, which I would argue has been obvious for a long time already.
Keith Devlin thinks the mobile phone will reach nearly 100% of the human popluation.
Freeman Dyson, because he is already 85, changes the timescale of the question, and concludes radiotelepathy.
David Eagleman thinks we’ll give computers our consciousness.
Kenneth W. Ford thinks we’ll be able to read your mind.
Richard Foreman, quite sensibly, thinks everything won’t change.
James Geary agrees with Eagleman that we’ll see brain-machine interfacing.
Sam Harris thinks we’ll have a true lie detector, some kind of mind-reading device.
Roger Highfield thinks we’ll finally build fusion reactors.
Eric Kandel hopes we’ll achieve a biological understanding of mental illness.
Stuart Kauffman thinks that much of the universe stands partially free of physical law.
Andrian Kreye is also big into synthetic fuels.
Clifford A. Pickover things we’ll see a proof of the Reimann hypothesis.
Ed Regis brings up the (thanks to things like synthetic biology) now-passé idea of nanotechnology.
Carlo Rovelli, being open-minded, imagines no big changes coming.
Gino Segre thinks we’ll find additional space-time dimensions.
And while neither André nor I are part of the Edge crowd, I might imagine both our answers would be along the lines of The Most Exciting Future Biophysics Tool, as the implications of such an instrument go far beyond biophysics.
Happy New Year everyone!
If you could wish for any capabilities in an instrument to help you with your research, what would they be? It might not be hard to come up with a useful super power that’s way out of reach of current or near-future technology, but what about something you might actually have in the next 10 or 20 years?
One of my interests is high resolution imaging, either by scanning probe or fluorescence microscopy, and I’ve seen and taken advantage of some great electron microscopy as well (although I haven’t done any myself). Each of these methods in their current most common form has advantages and disadvantages: scanning probe microscopies tend to be slow but offer high resolution with little sample preparation, fluorescence microscopy suffers from lower resolution but has pretty good acquisition rate and molecular specificity, and electron microscopy involves more complicated sample preparation that can distort the sample and only provides a snapshot, but it can provide truly exquisite images at a range of spatial scales.
These methods are all providing new insights into every area of cell biology and biophysics—fluorescence microscopy especially is now a staple of almost every lab in these fields—but it’s the ways that these methods are being pushed beyond their current limits that are truly exciting. New tools have always provided new insights, but I think cell biology is poised to be completely revolutionized in the next few decades.
Take atomic force microscopy. High resolution in water, but painfully slow. Wouldn’t it be nice if it were faster? It is. The animated gif on the right is an AFM movie taken at 12 frames per second in Toshio Ando’s lab at Kanazawa University in Japan. You’re seeing a single myosin molecule undergo a conformational change in real time. Single molecule fluorescence methods have provided a lot of insight into the mechanism of molecular motor motion (they walk) but there are still finer scales to investigate and high-speed AFM may prove to be the tool of choice in the very near future.
That’s very nice for in vitro work, but ultimately cells are where the action is. I want an instrument that will reduce the vast majority of cell biology to computer science. That will “only” require the convergence of three existing technologies: cryo-electron tomography, environmental scanning electron microscopy, and femtosecond electron diffraction. The ultimate fantasy or course is an atomic scale femtosecond movie of a living cell over hours. That would give you a complete genetic, proteomic, biophysical, and biochemical picture of cell function. You would still need interesting perturbations to ask questions, but all the answers would be provided by a single instrument and clever data mining. Even relaxing the goal by orders of magnitude in every direction to 10 nm spatial resolution and millisecond time resolution in a one minute movie would be radical.
Sounds far-fetched, but don’t forget that we’ve already got Wolfgang Baumeister talking about the molecular sociology of the cell and visual proteomics and people like Philip’s advisor doing femtosecond electron diffraction. Environmental scanning electron microscopy works in water vapour. At a talk at the College of Physicians, Ahmed Zewail spoke about an instrument his group is developing for electron diffraction and imaging. He showed a picture of a cell they took with it and he says their goal is to do a single particle version of electron diffraction in a cell within a few years.
Maybe he wasn’t even exaggerating…
While on the topic of things that might be possible in the future, nanotech enthusiasts might be interested to know that Eric Drexler now has a blog called Metamodern.
Comment [3]
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.
Comment [10]
Biocurious is written by Andre Brown and Philip Johnson, since 2005. Content of the weblog is licensed under a Creative Commons Attribution-Share Alike 3.0 License.
