Sunday, August 05, 2007

ISMB 2007 Vienna, Part I - Keynotes

I realize that I'm a bit late in covering a conference that occurred July 21-25, but I combined the conference with post-conference trips to Prague, Leipzig, and Berlin and have been busy at work since returning to Washington earlier this week.

There doesn't seem to have been much coverage of ISMB 2007 in the blogosphere (I've only found the coverage at Suicyte Notes,
and Fungal Genomes -- a few others had humorous posts about misadventures getting to Vienna, etc., but didn't cover any of the talks -- let me know if I missed any science-related postings).

In this first posting, I'll talk about my impressions of several of the keynote talks that made the most impression on me.

First of all, there was Michael Eisen's talk. Having worked with his brother, Jonathan, for some years, it was fun to finally see (and after the talk, briefly meet) the "other" Eisen. As would be expected from Mike's papers, his keynote largely dealt with the evolution of regulatory sequences in Drosophila. In the midst of this he made an offhand comment which generated both cheers and boos from the audience to the effect that bioinformaticians should stop working on microarray analysis methods "as nobody will be using microarrays in a couple of years". Well, we'll see.

Then, there was John Mattick's talk, which made me angry. Not because I disagree with his assertion that our traditional picture of gene regulation is incomplete, and that non-coding RNA-mediated gene regulation is going to be an important part of our revised picture, but I found his attitude towards non-eukaryotes (and even just non-mammals) annoying. According to John, the reason why "prokaryotes" are "simple" is that their gene regulation is just protein-based, while "higher organisms" require the use RNA as well. He even had graphs where "complexity" (how exactly is that defined objectively, now?) was the y-axis -- humans at the top, of course -- just like the medieval "Great Chain of Being" (minus the superhuman levels). The simple fact is that RNA based regulation isn't just limited to eukaryotes - non-coding RNA has been shown to be important in bacteria and archaea as well. Our picture of gene regulation in all domains of life is changing. Those on the quixotic quest to show that the evolutionary branch leading to humans is somehow "special" will have to look elsewhere.

And then there was Terry Speed's talk, which was one of those "historical" talks that some people see as a waste of time. Maybe it's because I once seriously considered becoming a historian of science, or perhaps it's just that I'm getting old, but I like such talks. And I learned a lot from it. For example, I always assumed that HMMs first entered biology from computer science in the context of sequence analysis/gene finding in the early 1990s, but Terry showed how people in pedigree analysis (including, if I recall from the talk, Eric Lander in his pre-genomics career) brought them into biology earlier.

I will write further on ISMB in subsequent posts.


neilfws said...

Looking forward to the rest of your ISMB posts. Just too late for Bio::Blogs #13, but perhaps we can include some in the next edition.

The Mattick lab are somewhat evangelical with their "RNA is everything" message. In Australia, people feel that they have to sell a message to get funding and they've gone for that message.

I think we should compile a list of so-called eukaryotic features and point to the prokaryotic examples. Internal membranes? Planktomycetes. Splicing? Inteins (protein splicing) and many tRNAs. Processes that use non-coding RNA? Numerous. Serine/threonine kinases? Check. Down with eukaryotic snobbery!

such.ire said...

Of course, there's also mitosis, which is starting to have analogues found in all sorts of prokaryotes.

elio said...

I found all you comments on the ISMB meeting enlightening and useful. I thoroughly agree with you regarding the Mattick simplistic-sounding world.

Thanks for sharing this.

(I had to look up what ISMB stands for)