Saturday, June 21, 2003

Great overview of Matt Ridley's work on Nature vs. Nurture in the edge. I wonder who will be the genius (like Einstein and Newton in physics) that puts together the theoretical model for how the Genome actually works. There is definitely an underlying theoretical structure to it that will enable predicted outcomes rather than the experimental trial and error approach we are working with now. [John Robb's Radio Weblog] Why would one expect a neat theoretical model in the style of physical theory? The genome is the controller for a complex machine in constant interaction with the environment. Take a large computer program in a similar role (modules are the analogues of genes). In many cases, the best way to find out what the program will do in some situation — remember, the program has a lot of local memory — is to run it and observe the results. That is, run an experiment. Approximate simulations may be useful, but they can also go wildly astray. What we need is not a grand unified theory — one is unlikely — but better biochemical and computational tools to measure, simulate, predict, and affect the genomic machine, allowing us to run much finer-grained experiments than currently. Ridley ends the interview with: There's no question that the discovery moves in silicon now. In other words, a huge amount of the significant stuff that we do next has to be both understood inside a computer and modeled inside computers. The modeling of gene interactions is something that is beyond the power of a man with a pencil. It's going to require people who are good at systems dynamics. [...] So I do think that bioinformatics is the way a lot of this is going. I agree with this as far as it goes, but it leaves out the importance of direct measurement and manipulation of cellular processes. 7:54:09 PM

NetNewsWire is a very nice news aggregator. A new version has been released along with a sale (through the end of June). This piece of software has changed the way I interact with the Web. [...] [The Crandall Surf Report 2.0] Nods. A while ago, I suggested that scientists should start publishing RSS feeds of their research reports, making it much easier for their colleagues to keep up with their latest ideas. I think we should do the same for talk announcements. I'll be pushing for something like that at Penn. The funny thing is that most people I mention this to who haven't used a good RSS reader have no idea of how powerful and convenient it is. 11:52:25 AM

Steve writes: A year ago Avi and I worked for the same organization. He has acquired a non traditional taste in computers. I used to work there too. I had been a long-time Mac user who finally gave up on Macs for anything but writing in 2000. I try to keep all of my work on a single portable machine. From early 2000 to mid-2001 I had to use Windows (briefly) and Linux (various distributions) on Sony and HP notebooks. I constantly fought problems with modem and wireless connections, sleep, screen resolutions. I got an OS X PowerBook G4 when I joined Penn summer 2001. Even with the early OS X sleep and modem glitches, things were much easier, and now I go for months without even thinking about support or configuration issues. I run a wide range of software from MATLAB to LaTeX. As Avi says, Keynote+LaTeX make for beautiful technical presentations. I add OmniGraffle for diagrams. There has been a good deal of rumor and speculation on the new professional line of Macs that might be announced on Monday [...] a 970 based laptop. The 15" size is the most appropriate for me, so I'll wish for that. cluster boxes [...] A 970-based PowerBook would be great. But I agree that good cluster gear would have a lot of impact in the science community. Right now, all of our backend computation is on Intel+Linux clusters. A good solution, except for two problems; The fastest x86 processors generate too much heat for 1U dual processor enclosures, so we have to lag behind in speed. We need more than 32 bits of address space, but current options for that are too expensive or nonstandard. For some of my current work, an 8 processor cluster with 64-bit addressing and a 64-bit JVM would be very useful. [Steve Crandall's Surf Report 2.0] 11:33:03 AM