genomeboy.com

I don’t know who picks out his clothes, but this Jeff Beck guy is pretty good.

Dan Vorhaus has written his usual cogent and insightful review of the issues raised by Amy Harmon’s piece on the Havasupai tribe and its settlement with Arizona State University. In my view, the core of the matter is fairly simple:

“I’m not against scientific research,” said Carletta Tilousi, 39, a member of the Havasupai tribal council. “I just want it to be done right. They used our blood for all these studies, people got degrees and grants, and they never asked our permission.” [emphasis added]

If, as researchers, we can’t be bothered to 1) tell research participants what they’re getting into insofar as we know; 2) respect their cultural beliefs; 3) go back to them if our plans change and ask for their consent again; and 4) share with them what we find and what we think it means in a timely and ongoing fashion, then we will find human subjects increasingly hard to come by…and increasingly litigious.

Billy Bragg in NatureNews:

Belonging goes beyond science. It’s very tenuous. Is identity genetics, or is it a fundamental personal construct? I believe it’s a construct: DNA can tell you things, but it can’t define you. We have choices. I’m not interested in identity itself — this thing you construct for the public like a mantelpiece — but in what it does for you. It gives you a sense of belonging.

Veteran science reporter Constance Holden has died.

The New York Times:

Twenty-one college football players have collapsed and died as a result of training over the past decade. At least eight were carriers of the sickle-cell trait, a genetic disorder that can unpredictably turn deadly during rigorous exercise.

***

Dr. M. A. Bender, the director of the Odessa Brown Comprehensive Sickle Cell Clinic in Seattle, said scant research had been done on the connection between exercise and the sickle-cell trait.

“There isn’t the data in terms of how often it occurs, what the real risk is, and what underlying factors may be involved,” he said.

***

Many researchers say the best solution is to use training practices that protect everyone from the risks associated with overexertion. One model is the Army, which no longer screens for the trait but takes across-the-board precautions. Since the change in practices, studies have shown, soldiers with the trait have no higher risk of dying in basic training than those without.

• Carrier status matters, even beyond making reproductive decisions. Whether screening has been demonstrated to save lives or not, wouldn’t you want to know if vigorous exercise made you more apt to keel over and die than most other people?
• Three decades after keeping SCT carriers out of the Air Force Academy, there still “isn’t the data?” How is that possible?
• Gene-environment interactions matter. What we eat, how we train, how we sleep, how we respond to stress, etc. Each of these interacts with our own particular genomes. We will only understand these interactions if we systematically pay attention to them.
• How many other supposedly “recessive” traits can be detected in the heterozygous state with careful observation? I’d bet you dollars to donuts there are hundreds if not thousands of them.

Times Online:

RICHARD DAWKINS, the atheist campaigner, is planning a legal ambush to have the Pope arrested during his state visit to Britain “for crimes against humanity”.

***

Dawkins, author of The God Delusion, said: “This is a man whose first instinct when his priests are caught with their pants down is to cover up the scandal and damn the young victims to silence.”

I am always astonished by how much one can learn for free on the interwebs and how quickly. The Genomics Law Report has not one, but two terrific analyses of the ruling striking down gene patents. Here, arguably, is the nut graf from the second:

With the decision only hours old, the headlines are already starting to roll in. “The End of Gene Patenting?” “Judge Rejects Patents on Genes.” “Judge Nullifies Gene Patents.” While it is clear that this decision is headline news, it is equally important not to overstate either its legal significance or its likely practical effect. The limited legal reach of the opinion—unless and until it is upheld by a higher court—has been discussed above. Less certain is its practical effect, including how businesses, clinicians and patients may change their behavior in response to the ruling.

My own thoughts:

1)  The ACLU and its allies, to clumsily mix sports metaphors, threw a Hail Mary and put on a full-court press.  They assaulted gene patents not on technicalities, but essentially on what is patentable and on First Amendment grounds (although the latter did not really figure in the decision). They won big and they got a summary judgment.  I am not a lawyer nor do I play one on TV, but I was surprised this did not go to trial. Both sides appealed to emotion and hyperbole during oral arguments, but I thought the plaintiffs were over-reaching unnecessarily and history was certainly not on their side. And I thought they were probably ten years too late. Good thing for them they didn’t ask my opinion…

2) Near-term business may not change much for anyone involved, but I imagine this will be appealed all the way to the SCOTUS, because both sides perceive there to be too much at stake to accept losing.

3) But even without appeals, this is hardly an “all clear” from a practical standpoint. If you had $50 million bucks lying around, would you enter the breast cancer genetic testing market in the US? I wouldn’t. Myriad’s been at this for well over a decade and it’s had the market all to itself. The legal hurdles may have been dealt with and barriers to entry may be pretty low at this point, but so what? Even if you could undercut its price by more than half, would you want to compete with the iPod?

4) The initial patents on BRCA1 and BRCA2 were awarded in 1997 and 1998 (pdf). I suspect that by the time this gets definitively sorted out, many if not most of those patents will have expired. Both sides will have spent a lot of money on something whose ultimate outcome was inevitable from the beginning. And with whole-genome screening around the corner and 23andMe already returning a small subset of BRCA mutation results, I’d argue that to continue fighting the last war is both myopic and a disservice to one’s shareholders. Myriad Genetics has made a boatload of money on BRCA testing and continues to do so–fine, bully for it. It was and is simply playing by the rules that were in place. And the company does a fine job screening these two genes and has for many years (I’ve been tested myself via DNA Direct). But was an exclusive license necessary to grow the BRCA testing market? Case studies prepared by my colleagues and me strongly suggest that it was not. And so to start singing apocalyptic refrains seems to me to be way, way off base. Monopolies are not necessary incentives for innovation in DNA diagnostics. Check out CF testing in the SACGHS report.

5) Judge Sweet chose to release his ruling on the eve of Passover. So what’s the message? “Dayeinu?” “Why is this product of nature different from all other products of nature?” “Next year in Salt Lake City?” “Let My Patents Go?”

On April 24th and 25th in Cambridge, MA, the Boston Open Source Science Lab will be amplifying and sequencing genes for anyone with 40 bucks.

Together, we’ll use the polymerase chain reaction (PCR) to amplify a fragment of one of your genes and have the DNA sequenced. The event will be part of the Cambridge Science Festival and will run from 12 - 4 pm on April 24th and 25th.

We’re doing it at the bosslab, located at 339R Summer St, Somerville, MA 02144, at Sprout. The cost of materials is $40 / person.

I will provide primers that will enable us to amplify sections of several popular genes. If you have a particular gene of interest, please get in touch…

That sound you hear is hundreds of clinical geneticists’ panties getting in a wad. And maybe a few IP lawyers, too…

See you there, you DIY rascals you!

Cystic fibrosis screening in the real world:

Dr. Highsmith agrees that one “extremely good aspect” of CF newborn screening programs is that when an affected baby is identified and brought to a CF center, “you certainly get clinical improvement.” However, he asks, “What happens when you find carriers?…what is the cost of that strategy from both a medical and a parental stress viewpoint?”

Am I to understand that one of the complaints against newborn screening for CF is the “unintended consequence” of finding carriers? Hoo boy.

Alex Chilton, 1950-2010