Helicos Biosciences is reporting the re-sequencing of the M13 viral genome.
What’s really cool about this is that it’s sequencing-by-synthesis, requiring no amplification before sequence reading, so there’s no biasing of the populations of DNA fragments. Here’s a short overview of how their sequencing by synthesis works:

So it’s still a shotgun-style technique, and the problem has been getting long enough read lengths to assemble the pieces into a whole sequence. Think of it like a jigsaw puzzle. The smaller the pieces are, the more you have that look identical, and the harder it is to figure out where to put them. Given 3 x 10⁹ bases in the human genome, you’d need a read length of about 17 base pairs to be certain of ending up with all different pieces. They report average read lengths of 23 bp, with each individual sequence chunk represented about 150 times, and every part of the genome represented. This allows them to keep the error rate low enough that they could sequence different strains of the virus, and reliably pick up the genomic differences between the two. The paper doesn’t say how long this takes, but their marketing material says the process takes only one day.

The technique as practiced by Helicos has one major drawback, however, that will limit how low it can take the cost/base. It requires very expensive optics, since you’re essentially doing FRET on an array of targets. The list price for their instrument is $1.3 Million, with a consumables price of $18,000/sample, placing it out of reach of many institutions.

Illumina, another company with a sequencing-by-synthesis application, gets around the expensive optics issue by doing a clever solid-phase amplification of their target strands, essentially growing little colonies of identical strands in situ. A sales rep told me they’re selling around $500K, but didn’t have details on the consumables cost.

Long-term, I’d expect the Polonator to be the most widely adopted platform, due to their aggressive pursuit of royalty-free technology and low instrument cost. There’s a good thread to follow here, if you’re interested.

23andme and Navigenics take note: They’re not offering a direct to consumer service, yet, but there’s no way a SNP scan can compete with a full sequence, once the cost comes down.

via HotCites, more on this story at in-sequence.

I’ve been a big supporter of the idea of having all the candidates get together for a roundtable on science-related issues. I’m subscribed to the mailing list for Science Debate 2008, which has been trying to organize such a debate. The organizer recently pointed out that the candidates are attending the Compassion Forum, which is a debate on “moral issues”. I don’t know if there’s more going on behind the scenes regarding why the candidates would chose to attend one conference and not the other, but it just seems to me like the Democratic candidates, at least, would want to seize the advantage provided by the recent weakening of the religious right, and it also seems like attending a forum on moral issues might not be the best way to do that. Maybe they’re trying to catch some swing votes, but they certainly shouldn’t give out the impression that moral issues remain the most important issues for this election, because that’s exactly what led to their loss last two times. You know Obama and Clinton would both kill McCain in a science debate.

Here’s the email:

I am sorry to send two emails in such short succession, but I thought you should know that after declining our invitation to debate science in Pennsylvania, Barack Obama and Hillary Clinton yesterday agreed to attend “The Compassion Forum,” a forum of “wide-ranging and probing discussions of policies related to moral issues.” CNN will serve as the exclusive broadcaster of the “presidential-candidate forum on faith, values and other current issues” at Messiah College near Harrisburg, Pa., April 13 at 8 p.m. You can read more here.

Perhaps among the moral issues discussed should be whether they have a moral obligation to more fully engage on science issues, since the future viability of the planet may hang in the balance, for starters. Is there a larger moral imperative? How about the future economic health of the United States and the prosperity of its families? Science & engineering have driven half our economic growth since WWII, yet but 2010 if trends hold 90% of all scientists and engineers will live in Asia. Then there are the moral questions surrounding the health of our families with stem cell research, genomics, health insurance policy, and medical research. There’s biodiversity loss and the health of the oceans and the morality of balancing destruction of species against human needs and expenses, there’s population and development and clean energy research, there’s food supply and GMO crops and educating children to compete in the new global economy and securing competitive jobs. Science issues are moral issues.

I would encourage you to write letters to the editor, emails to the campaigns, and blog postings pointing this out. And if you can, support our ongoing effort to turn this country around.

Shawn Lawrence Otto

ScienceDebate2008.com

Two smart people I read, who probably don’t know each other, and work in disparate fields, both have a post today about using a distributed collection of data and analysts to answer problems that we’re just now being able to address.

Here’s Jon Udell talking about distributed communities of climate scientists studying CO₂ fluctuations.

Here’s Steve Hsu talking about the quantitative finance firm Horton Point, and how they’re assembling teams of academics from diverse fields such as psychology and data mining, to come up with dynamic models of how markets work.

iPS cells, though quite different and yet uncharacterized, are easier to generate.

This is going to be considered a victory by those who fear progress, but whatever. The science is moving forward based on rational decisions. That’s the important thing.