San Diego Hosts Second Biophysics Workshop

The APS held its second topical conference on "Opportunities in Biology for Physicists" in San Diego, CA, from January 30 to February 1, 2004. Robert Austin (Princeton University) and Herb Levine (University of California, San Diego) co-chaired the Steering Committee for the conference, which was aimed predominantly at graduate students and postdocs in physics considering applying the methods of physics to biological topics.

In 2001, the APS Executive Board decided that it would be advantageous to organize a different kind of meeting, a topical conference on an emerging field, that would prepare physicists for future opportunities. Thus, a conference was organized focusing on the interface between physics and biology and aimed at early career physicists who were interested in exploring the possibilities of entering this exciting field. That first conference was held in Boston September 27-29, 2002 (see APS News, November 2002), and was very well received. A follow-up survey revealed a great deal of interest in a second conference.

The San Diego meeting kicked off with a session on bio-informatics, which employs tools from data mining and pattern recognition to make sense of the massive amounts of data collected by biologists on a daily basis. "Scientists can list all the pieces of DNA, but we have no idea how they all fit together; it's a giant jigsaw puzzle," said Edward Marcotte (University of Texas, Austin) by way of example. While the completion of the Human Genome Project represents a major step forward, there are roughly 40,000 genes in the human genome, and one third to one half of those have completely unknown functions. "Thus far, we have successfully defined our ignorance," Marcotte joked.

Another area ripe for contributions from physicists is systems neuroscience, the subject of Saturday morning's session, which focused on two broad themes: (1) notions of learning, and (2) the emerging concept that the nervous system is not, as previously believed, about taking in information and processing it, but about transforming input information into a single binary decision. To that end, MIT's Sebastian Sueng described his work on the dynamics of neural networks and the concept of "reinforcement learning".

Computer scientists view learning as optimization, but Seung has proposed a new concept: learning by noise injection. He believes learning derives more from exploiting randomness.

His thesis is modeled on how birdsong is learned and generated, and draws on basic signal processing: birds seem to employ the equivalent of a nonlinear oscillator.

This is partially innate and partially acquired behavior. A male baby bird listens to his father's birdsong to form a template memory of the sound. Then the baby bird learns through trial, error, and iteration to reproduce the stored template sound; over time, his attempts improve thanks to repetition combined with auditory feedback.

To test his hypothesis, Seung constructed an experiment using a computerized "Frankenbird", which was "taught" by a recorded "tutor" of actual birdsong. While the final result was not an exact match, Frankenbird's song did show significant improvement over time.

Princeton University's Bonnie Bassler has been featured recently in both Nature and Scientific American for her potentially revolutionary work on cell-to-cell communication, which formed the basis for her Saturday afternoon lecture.

According to Bassler, bacteria have developed a chemical language, via the exchange of chemical signals, with the various chemicals representing "words," enabling individual bacteria to coordinate expression on a multi- organism scale. An example of this is the phenomenon of "quorum sensing" in various microbial life forms.

Bassler's research has focused on v. harveyi, a bacterium that seeks out other bacteria in order to clump together. When a critical threshold is reached, all the bacteria simultaneously activate an enzyme that causes them to glow.

Quorum sensing has also been observed in p. aeruginosis, which releases virulent pathogens when that critical threshold is reached. Although this field is only about 10 years old, there are some emerging applications in the pharmaceutical arena: designing drugs to block production of the critical enzyme, thus disabling the cell communication network of bacteria that emit dangerous pathogens.

Austin—Bassler's Princeton colleague—closed the session by describing his work studying chemotaxis and quorum sensing in e coli.

Other topics featured during the workshop were the specific neural mechanisms of perceptual learning; optical studies of direction selective cells in the retina; how microbial rhodopsins transduce light into biological energy and information; the packaging of DNA by single particles of bacteriophage; the use of DNA microarrays to infer genetic networks; engineered gene circuits; single molecule detection using nanoscale electronic devices; applications for biological polymers; and pattern formation and self organization.

Perhaps the highlight of the workshop, however, was Friday afternoon's panel discussion, featuring physicists who have successfully made the transition to the physics/biology interface, sharing their insights and experiences. The ensuing discussion focused in part on the need for better biological theory, although one audience member pointed out that almost all biological systems are highly complex, and physicists are still developing theories of complex systems.

Everyone agreed that ultimately, the distinction between physics and biology is arbitrary and largely meaningless. "Chemists never ask, 'Is this really chemistry?' But physicists are obsessed with this question," said Andrea Liu, a panelist from the University of California, Los Angeles. "The two fields should not be divided," agreed fellow panelist Valery Kalatsky (University of California, San Francisco). "Ultimately it's about interesting scientific questions." Moderator Jose Onuchic (UCSD) drove home this point: "At UCSD, we want the interface to thrive without all this quibbling about physics and biology labels."

An afternoon reception on the first day provided an opportunity for those researchers in biological physics and those who hire biological physicists to meet with the participants and to display posters or provide information in other forms.

There was also a "Lunch with the Experts" for student participants free of charge. Workshop attendance was once again limited to about 250 participants, in order to ensure better interaction between speakers and participants. External funding for the workshop (including travel grants for students in need of financial aid) was provided by NIST, NSF, DOE, the Office of Naval Research, and NIH, as well as Burroughs Wellcome and the Sloan Foundation.

Videotaped lectures and accompanying slides from the "Opportunities in Biology for Physicists" conference in San Diego can be found online at http://www.aps.org/meetings/multimedia/biology-2004.cfm.