money in, worries out

genehack on the road
Just thought I'd mention that I'm going to be tagging along with Laura as she travels out to Seattle for a meeting. We don't have any huge plans to do any tourist-y type stuff; we're just going to hang out and take it easy. I'm there from Friday to early Monday, so if anybody wants to meet up for a coffee or a beer (or a coffee beer), give a holler.

One of the better pieces I saw about Joey Ramone wasn't at a music site, and it wasn't over at Salon: it was the April 16th entry at Metascene. Just thought you might like to know that.

the map is not the territory
"A Map to Nowhere" takes on the recent announcements about the human genome and seems to come to the conclusion that the whole thing was a big waste of time, because it's looking more and more like the real complexity in the genome is combinatorial, arising from different arrangements of exons to create different proteins, which are processed and regulated in different ways.

It's difficult for me to critique any of the author's points, because he's coming at the question from such a completely odd angle -- yes, it turns out that the genome might not be as important as we had believed, and some of the hype about medical advances might turn out to be hype, but we had no way of knowing this ahead of time! In order to find out that the genome isn't the whole story, we had to sequence that genome, and having done that, it will still be a useful tool in figuring out what's going on inside our bodies, especially in figuring out when something goes wrong inside our bodies. What else would the author have had us do, other than sequence the genome? He doesn't say, preferring instead to make snarky asides about who said what about whom at the press conference. Phef.

Finally, let me note something that I haven't seen mentioned anywhere else. There have been several stories recently about the discrepancy in gene numbers -- 30,000 from the genome sequence, up to 120,000 if you believe some companies (bearing in mind that the companies think that having more genes increases shareholder value, of course). One of the reasons for this confusion is that the word gene is over-loaded. It means different things in different contexts, or when said by different speakers. In fact, if you ever have a chance to watch two molecular biologists interact, you might see something akin to the handshaking that modems do when they link up. Highly trained people, who work with these concepts day in and day out still have to query each other to establish what somebody means when they say "gene" -- are we talking about DNA or cDNA? If cDNA, from normalized libraries? What tissue type? How many isolates before you believe it's not just a sequencing artifact? PolyA-primed or random primed? Cap-selected or not? The answers to each of these questions, and more, all factor into a complicated internal equation that puts a probability on whether or not you've really got two different "genes" or just two isolates of the same "gene". Moreover, everybody's internal equation is just a little bit different -- some people call things different based on very little evidence; others want strong proof before they'll concede that more than one "gene" has to be involved.

This semantic confusion and contextual ambiguity is at least partially responsible for the controversy over how many genes there are. Add in a need on the part of the media to simplify these concepts, a need that results in a "gene" being different things to different people, and you've got a real mess. Just something to keep in mind the next time you see a number appearing before the phrase "genes in the human genome".