genomeboy.com

• A friend emailed me yesterday, referenced this article on how Knome will offer complete personal genome sequencing for $350,000 and asked, “And you get yours for free??” (Alas no!)
• And last week, The Economist (still unencumbered by bylines) wrote, “Two firms have unveiled products that allow the ordinary punter to get his genome decoded [emphasis mine] for about $1000.” (The article also says, “All people are 99.9% identical, genetically speaking.” Come on, mates–you’re better than that!)

What we have here, I think, is a failure to communicate. According to the New York Times, for a thousand bucks deCODEme will test about a million DNA variants or SNPs, while 23andMe will test about 650,000 SNPs. That’s 0.033% and 0.022% of the haploid human genome, respectively. These “variome” analyses may prove to be incredibly useful and perhaps even a terrific bargain for punters of all stripes, but is it accurate to call them “getting one’s genome decoded?”

What PGPers will get — we think:) — are our complete exomes, that is, the entire protein-coding portion of our 20,000+ genes*. This, I’m told (anybody have a reference?) works out to about 60 million base pairs or roughly 1% of the diploid human genome. George (who, it should be noted, co-founded Knome) has told us our exomes will cost…drum roll please…about $1000. Do I sometimes tell people I’m getting my genome sequenced? As a shorthand, yes, but I shouldn’t. It’s an exome, not a genome.

For their $350k, Knome customers, I presume, will get something like 6 billion base pairs, that is, essentially complete diploid genome sequences just like Venter and presumably, Watson, received. (Read Hsien’s interview with the Knome CEO.)

Are any or all of these services worth it? I have no idea and I’m not sure anyone else does, either. This issue — a genome: what is it good for? — is at the heart of what the PGP is all about. It’s partly a matter of personal taste, of course: is an incomplete and often inscrutable translation of the Rosetta Stone at whatever resolution still worth some amount of money and the space it takes on your bookshelf? I’m inclined to say yes, but I can’t say until I’ve seen mine and lived with it for a while. I have no sense about how the rest of the world feels; however, I will say that in contrast to the enthusiasm I see in the blogosphere, a fair number of my colleagues at Duke, to say nothing of people I’ve talked to at the NIH, tend to roll their eyes when I start yammering on about personal genomics.

Can these companies make meaning out of this stuff? What are customers’ expectations and what should they be? Will new information bring clarity or confusion?

I hope to find out. Next week I will be in the Bay Area visiting some of these folks, asking questions, learning more about what they do, and eating obscene quantities of Asian food.

*Behold, the incredible shrinking genome!

UPDATE: I should add that we will also get our variomes typed via Affymetrix Genome-Wide Human SNP Arrays (don’t quote me on the version).

Over at Discovering Biology in a Digital World, Sandra Porter has a great post about the disconnect between scientists and science educators as exemplified by the frequent lack of access scientists have to pedagogy journals. Frankly, I think most scientists don’t take the education literature seriously, even when they do have access to it. There is a presumption that education research is squishy, anecdotal and not to be trusted. Is it true? Sometimes. Is it a fair generalization? Not in my (admittedly limited) experience. Social science is hard to do well, but that doesn’t mean folks in the hard sciences are justified in dismissing it wholesale.

Beyond methodological questions, I think the inferiority complex science educators feel lives on for another reason: I think the digital divide Sandra describes is emblematic of a more longstanding cultural one, namely, the divide between teaching and research. Teaching is simply not rewarded in most basic science departments the way it is in the humanities, where it is the raison d’etre as much as scholarship is (or at least it is comparable). I mean, anyone can teach, right? (insert irony emoticon here). Has anyone gotten rich doing so? How about your graduate TA and her multiple sections of Bio 101? And will your $20,000 collaborative education project with the local museum ever attract the same attention or please as many administrators as your colleague’s $5 million cancer study? Please don’t get me wrong, I’m not speaking with any bitterness whatsoever–that’s just how life is. Yes, there are funding agencies that have endeavored to reward innovative science teaching at the K-16 levels. Are they are exceptional? I don’t know.

In any case, that teaching scientists don’t have access to science education journals strikes me as shameful but hardly surprising. However much hand wringing we do over the US lag in training the next generation of scientists, if history is any guide I suspect science education will always labor in the shadow of the science itself.