So the plan is to get a DNA sample from anyone arrested for a federal charge, and anyone picked up on immigration charges. This will add more than a million records to the database every year.

One of the strongest arguments against consumer genetic profiling is to prevent this information from becoming available to law enforcement. With the horrible record they have of keeping our private information secure, I don’t think they can be trusted with this kind of information, but can it be stopped? Is there any way to prevent the dystopian future of not only medical, but marketing and economic and employment decisions made about you based on your genetic profile?

I know many people take the position that they’ve got nothing to hide, so they’re not worried, and anyways, they’d willingly give it up if it could help apprehend rapists. In fact, enough people who are related to you probably think this way that it doesn’t really matter if they don’t get everybody, but I am starting to feel like this is Pandora’s box.

The average citizen and the average lawmaker doesn’t deal with huge databases, doesn’t understand statistical inference, and just isn’t equipped to consider the effects something like this will have on society. I don’t think I’ll feel comfortable with this information even being collected until there’s a framework controlling who gets access to what, monitoring who got access to what and what they did with it, and providing for remedies to the affected people when someone’s information gets accessed without authorization. We can’t have such legislation until lawmakers properly understand the issues. How many of them don’t even understand the difference between correlation and causation? Many tenured faculty don’t even fully appreciate the difference, so how can a layman?

We don’t even have appropriate remedies when credit information gets breached. Companies voluntarily decide to offer credit monitoring to affected people. That’s the remedy provided consumers, and it’s based on voluntary disclosure of the breach. How would someone even know that they were affected by inappropriate disclosure of their genetic information?

I know everyone is worrying about the economy, the elections, the war, the olympics, the pope, and everything else that’s grabbing the headlines, but it’s a critical failure to let this slip by without appropriate public comment. The Register, a UK IT publication, is covering the story, but there’s little mention in the domestic media. Here’s a article from the Washington Post, which isn’t on the front page, but can be found by searching for “NDIS federal”. There’s actually nothing on Google News about this either unless you search, which only turns up the article above.

You’ll see a banner between in between the title and post(or another location – this is just an experiment) for some items on the page and in the feed. I won’t see them, because Firefox is blocking them, but they looked relatively unobtrusive and highly targeted in IE. If you have any comments, please leave them here.

After a few months, I’ll re-consider whether it has been worth it.

It’s short, and it’s pretty great. Honestly.

Raj, Bohemian

via

One issue is that cognitive enhancement as a research area suffers from the same problems as life extension, unfortunately, in that it kinda attracts a different sort of person. Most researchers feel it’s more noble to fix something that’s broken instead of trying to improve something that’s currently working, however inefficiently. I generally agree with that sentiment, but certainly there is some worth to improving things, too. I’m not suggesting that more brainpower should be spent on inventing “smart drugs” than on curing cancer, but, as many have noted, this isn’t a zero sum game. There’s just so little that’s been done in the past decade on “nootropics” that there must be just bushels of relatively low-hanging fruit, ripe for the picking, and if gains could be made relatively quickly, they’d have a large payoff because they’d be applicable to everyone, instead of just the people with disorder or disease X. There would also be an additive effect of increasing the rate at which progress could be made in all the other fields.

This kind of work will face the same class issues as other types of medical research like genomic profiling, with people worrying that the discoveries will only be available to those who can afford it, thus widening the have-have not gap still further, but that’s not really a good argument for not doing the research, because it has to be available before it can become affordable, doesn’t it?

It’s a difficult thing to argue for, trying to fix something that ain’t broke, but I’m convinced given the utter lack of progress in this area over the past decade, that just one competent researcher in this area could make significant advances relatively quickly. Am I wrong? Has there been significant advancement in the last decade? Am I being too hard on sports performance researchers?

Checking Usenet, they’re still talking about the same stuff they were 10 years ago:
ginkgo
choline
huperzine
DMAE/centrophenoxine
vinpocetine
piracetam
hydergine

Little of this is available OTC in the US. The only thing I’m aware of with US OTC availability that’s not essentially repackaged caffeine is this stuff.¹ Has anyone tried these? Let me know in the comments.

1. I personally like it; I’m not connected to the company in any way.

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.