Sean Carroll in “Cooperstown of Evolution” on NPR’s Morning Edition

For those of you still with a chance to listen to NPR’s Morning Edition, there’s a really nice piece withJoe Palca following Sean Carroll as he gets a chance to look at the notebooks of Darwin and Wallace during a recent visit to London. 

Of course you can also listen to it online.

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Bash my brother’s paper – for the good of mankind

My brother’s lab has a new paper in PLoS One, and he wants to use it to jumpstart our efforts to get postpublication commenting rolling:

I am offering up my paper as a case study. If you comment and ask questions or make critiques, I will try to respond. And if you think something in our paper is wrong or weird, please say so. If you think something in our paper is supported by other work we do not cite, please say this too. If you have anything useful to say, please make comments.

How do you do this? 

  • Go to the paper at the PLoS One Web Site.
  • In the upper right click on “Login” if you have an account or “Create account” if you do not.
  • Return to the paper once you are logged in
  • Find some part of the text you want to comment on
  • Highlight that text and click over on the right “Add a note” or “Make a comment”
  • Fire away.
Posted in open access, PLoS | Comments closed

Obama and Copyright

I haven’t been so worried about the Conyers bill to end the NIH Public Access policy because I figured even in the unlikely event it got through Congress, Obama wouldn’t sign it. But then I read this post by Seth Johnson about “stacking” of the Justice Department with veteran copyright defenders. I’m still not all that worried, but I’m a bit more so now and think we should really ramp up the pressure to make sure this doesn’t get to Obama in the first place.

Posted in open access, PLoS, science and politics | Comments closed

Conyers reintroduces bill to kill NIH Public Access Policy

John Conyers (D-MI) has reintroduced his publisher-backed “Fair Copyright Act”  which would effectively end the NIH Public Access Policy by eliminating the government’s right to impose conditions on grants that would give the government the right to distribute works arising from federally funded research.

As many have pointed out, the whole premise of the bill is absurd. Publishers are arguing that the NIH has taken their copyright. But, of course, if that were true, they would already have protection under federal copyright law, and they would be suing the government. Instead, they are pushing legislation that would actually remove the governments right to distribute work it funds, thereby clearly demonstrating that they believe the government’s action is perfectly legal under copyright law.

What is particularly galling is that Conyers held hearings on this bill last year, in which a LOT of important issues were raised about the bill, and there were many on the committee who were skeptical about it. So, what does Conyers do with all that useful feedback? He ignores it, and introduces exactly the same bill in the new Congress. One hopes such an ill-conceived piece of public policy would have no hope when Congress has many more important things on its hands, but one never knows. Let’s hope it dies in committee. But just to be safe, let the members know how you feel.

It’s hard to know why Conyers is doing this. He receives some modest contributions from Elsevier and some others in the publishing industry – but it’s hard to imagine $4,000 buys a piece of legislation.  Conyers has recently reorganized the House Judiciary Committee in order to take control of intellectual property cases, so maybe this is part of a more broadly orchestrated “defense” of copyright.

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PLoS NTD features in Nicholas Kristof’s Op-Ed about Guantanamo

Last year, Peter Hotez published an editorial in PLoS Neglected Tropical Diseases in which he proposed that rather than just close the prison at Guantonamo Bay, we instead establish a “center of excellence on the diseases of poor that … would directly address poverty and health disparities in the worst-off nations in Central and South America and the Caribbean”. The meat of his proposal is:

America has an enormously impressive track record of developing and testing life-saving vaccines and drugs. It is therefore surprising that American leadership in biomedical sciences and its remarkable legacy for saving lives abroad has never been embraced as a meaningful component of American foreign policy. The US spends approximately $100 billion annually on health research and development, including $28 billion by the NIH and $57 billion by industry.

The neglected tropical diseases represent some of the most important poverty-promoting disease conditions. By establishing a center of excellence on the diseases of poor, at Guantanamo, the United States Government would directly address poverty and health disparities in the worst-off nations in Central and South America and the Caribbean. Such a center could conduct translational research to develop new drugs and vaccines for neglected diseases, possibly in collaboration with research institutes and public sector pharmaceutical manufacturers in some of Latin America’s so-called innovative developing countries, such as Argentina, Brazil, Cuba, and Mexico. It could also promote clinical research and take on the control of some of the more pressing public health threats in the Caribbean region, including vector-borne diseases such as dengue. It would serve as a vital resource for training physicians, scientists, and public health experts, and meet an important demand for training in applying appropriate technology to global public health practice.

Through a focused initiative on lymphatic filariasis and schistosomiasis, a well-resourced biomedical institution located at Guantanamo could lead a path to eliminate these scourges from the Caribbean region [16] and forever wipe out an important element of slavery’s legacy [10]. The facility could even take on some neglected tropical diseases that remain important yet often hidden public health problems among the economically disadvantaged and under-represented minorities living in the US, such as cysticercosis, dengue, leptospirosis, toxocariasis, and congenital cytomegalovirus infection and toxoplasmosis [17].

Now Nicholas Kristof is picking up the charge. He concludes his recent Op-Ed on how to appropriately deal with the legacy of Gitmo, “Putting Torture Behind Us“, with a plug for Hoetz’s proposal:

Imagine if people around the world came to think of Guantánamo as a place where America led a battle against hookworms and leprosy. That would help us fight terrorism far more effectively than the prison at Guantánamo ever did.

Hear, hear.

Posted in open access, PLoS, politics | Comments closed

My favorite paragraph of snarky music commentary ever…

From a 1995 New Republic diarist by Roger Rosenblatt which frequently pops into my head (and which I dredged up in Lexis):

As soon as I find out where Andrew Lloyd Webber lives I’m going to stalk him, watch his every move, get as close to him as his clothing. If he goes to a gambling casino, I will bet on his numbers. Should he visit a race track, I’ll bet my kingdom on his horse. Webber is, I have concluded, the luckiest man who ever lived–a creator of sensationally successful musical plays so sensationally bad that at the moment you think “this can’t get any worse”– referring to his music or someone else’s lyrics (it hardly matters)–it does get worse, it gets twice as bad; and then you think, “Well, the fellow has hit rock bottom this time,” and thwack–the floor drops out from under you and down you go again. Whooo!

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Weekly Address from Obama’s Science Gurus

The scientific community is quite rightly celebrating the replacement of the ascientific Bush with the assertively pro-science Obama, and the elevation of a cadre of outstanding scientists (Varmus, Lubchenko, Chu et al.) to cabinet or advisory positions. But given how much has been written lately about an increasing divide between science and the public, and growing public rejection of things universally accepted amongst scientists, I’ve been surprised at how little of the discussion concerning the presidential transition has been focused on reinvigorating public support for the government’s role in funding and promoting science.

I would like to see Obama’s science team take a creative new approach to this challenge, and parallel the President’s weekly address with a “Weekly Science Address” – a video posted on YouTube as well as a radio version – in which they describe something cool that government scientists or government-funded scientists have done that week.

The focus would not be on the high-profile results – the stuff that already gets written up in the popular press – but on the scientists, the way they work, the questions they are addressing and the tools they’re using to go after them. They would be short and fun – a kind of elevator pitch for government science. Maybe I’m overestimating public interest, but if done right, I think these could be very popular. People care about medical research, about space missions, about fighting global warming, protecting the oceans – and they could care about lots of other things, including even “fruit fly research in Paris, France“. 

And next time there’s a Congressional attack on the NSF budget, or a politician takes a unwarranted crack at an important project, people will be there to say “Hey, I heard the president’s science guru talk about that, and it’s actually pretty cool.”

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Will Saletan’s incorrect conclusions on ACTN3 and race

While I was poking around for stories about ACTN3, I came upon this Slate piece from the usually reliable Will Saletan about the ACTN3 test and race.

The story has a generally accurate discussion about ACTN3 allele frequencies and race, and I agree with most of what he has to say. But Saletan makes a factually incorrect statement about the relative value of race and genetics in predicting athletic performance:

Race is a less, not more, reliable gauge of physical characteristics than genes are. In fact, that’s one of the chief consolations of nontherapeutic genetic testing: No matter how inaccurate genes are as a predictor of this or that ability, they’re more accurate than predictions based on race. And the sooner we get past judging by race, the better.

Really? Saletan needs to be careful here. Let’s take the cast of ACTN3. Research shows that elite power athletes very rarely have the homozygous null X-X genotype at ACTN3, which is found in approximately 20% of the global population (it varies geographically, but this is not relevant to my point). Now consider (as Saletan does) the Olympic sprint finals, which consisted entirely of men of West African descent. And let’s assume (although they haven’t been tested) that none of these men had the X-X genotype. If you were trying to predict the probability that an individual was going to be in the Olympic sprint finals in 2012, what would you rather know – their genotype or their race? Genotype will narrow it down to around 4.5 billion people. I don’t know how many people there are of West African descent there are on the planet, but it’s probably a few hundred million. Now, of course, both of these methods will do an awful job of picking Olympic athletes out of the general population, but you’ll do 10x better making the prediction based on race alone than you would on ACTN3 genotype alone.

Now Saletan may be right (he very likely is) that there are other undiscovered genetic variants that collectively explain variation in sprintng ability. And once we know all of these factors we’ll probably be able to do a better job of identifying great sprinters than we would by just picking random West Africans. But as things stand race is a better predicter, Saletan is simply wrong when he says, “No matter how inaccurate genes are as a predictor of this or that ability, they’re more accurate than predictions based on race.”

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The awful NYT story on ACTN3

A lot has been written about the genetic test for ACTN3 being marketed by ATLAS Research as a way to direct ones children towards the appropriate athletic endeavors since a story on the test appeared in the NY Times last week. Daniel MacArthur, in particular, has done a great job explaining the science behind the test and what it can and can not tell us here and here.

Various people are also issuing the usual lament about how journalists don’t understand science, and some have wondered why the NYT chose to write about this test now given that a similar test have been available overseas for months. I haven’t, however, seen anyone comment on how awful the actual NYT article was.

Why on Earth was this story on the front page of the NYT? Some random company trying to hock a bogus DNA test clearly hooked an ambitious NYT sports reporter with a story about how DNA could predict whether a kid was going to be a good athlete. But what would make this press release into a news story? Maybe if people were actually using the test…

The Times clearly wants us to think they are – they put a picture of a cute kid having his cheek swabbed right at the top. But notice that nowhere in the article does it say that ANYONE has taken the test. Two parents are quoted offering commentary on the test, but neither says that their kid has or will be tested. And the photo caption is telling – no name and nothing about the kid being tested, just the oddly generic  “DNA collected by swabbing the inside of a cheek can be used to determine whether a child is likely to excel at a particular sport.”

As far as I can tell, the reporter, Juliet Macur, thought the story sounded kind of interesting and flew to Boulder to meet with the people from the company. Then they went down the hall to Boulder Indoor Soccer (which is mentioned in the article and conveniently shares a building with the company behind the test – one assumes they are somehow linked) and asked a few parents what they thought of the test. One of them asked the obvious questions – who’s behind it and what will it set me back, which get’s transformed into:

When Donna Campiglia learned recently that a genetic test might be able to determine which sports suit the talents of her 2 ½-year-old son, Noah, she instantly said, Where can I get it and how much does it cost?

The implication is clearly that she’s really excited about the test, but I think it’s a misleading presentation of an innocent question. Of course sports reporters make their bread and butter sensationalizing banal sideline banter, but I expect higher standards from the front page although I guess that’s what you have to do when the meat of your story is a marketing pitch, quick reaction from two parents, and a staged photo.

The deceptive presentation continues with the obligate quotes form experts:

Dr. Stephen M. Roth, director of the functional genomics laboratory at the University of Maryland’s School of Public Health who has studied ACTN3, said he thought the test would become popular. But he had reservations.

“The idea that it will be one or two genes that are contributing to the Michael Phelpses or the Usain Bolts of the world I think is shortsighted because it’s much more complex than that,” he said, adding that athletic performance has been found to be affected by at least 200 genes.

Don’t you think he meant it as a BAD thing that the test would become popular? The way the paragraphs are structured implies the opposite.

But what really galls me about the piece is the way in which giving it this much play undermines human genetics in the guise of promoting it. Let me just say that I think the science behind ACTN3 is, while by no means perfect, actually pretty good. The ACTN3 X allele really does seem to affect muscle performance, and seems to be generally incompatible with being an Olympic calibur power athlete. However the way the test is being marketed is clearly bogus – little Johnny or Jenny had like a 1 in 1,000,000 chance (and that’s being pretty generous) of being an Olympian in a power sport before the test and either 1 in 800,000 or 1 in 2,000,000 afterwards. Not so useful.

The story actually does an OK job of discounting the value of the test – but that’s why I think it’s a bad thing for human genetics. Given that no one is actually taking the test yet, the only real excuse for publishing the story on the front page is as a sort of expose of genetic charlatans. The reporter doesn’t directly say it,  but one gets a clear sense at the end of the day that the test is not useful. And front page stories in major newspapers about bogus genetic tests make genetic testing as a whole seem useless. This didn’t need to happen – the NYT should have realized they had a non-story about a non-test and buried it.

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Don’t vote for my opponent. He believes in Genetic Medicine!

A reader sent me the following letter sent out by Fresno County Superior Court judicial court candidate Jim Kelley in his campaign against Douglas Treisman:

October 28, 2008

Dear Voter:

My name is Jim Kelley and I am a candidate for Fresno County Superior Court Judge.  Judges play an important role in our community, yet the local race is receiving very little attention.  The law states that judicial candidates cannot take a position on any issue that may come before the court, so voters have little information on the candidates.

Jim Kelley is endorsed by judges, prosecutors, local police chiefs and former Sheriff Richard Pierce.  Douglas Treisman is endorsed by law enforcement unions and activist groups.  Below is some information that you will not learn from the media.

Jim Kelley

Jim is a career prosecutor and lifelong Fresno native who has served as a reserve deputy sheriff for ten years.  Jim will hold people accountable for their actions. As a judge Jim will follow the law, not create the law.  Jim Kelley is widely considered to be the more conservative candidate.

Jim is recommended on the statewide Christian voter website www.electionforum.org which is an organization opposed to judicial activism.

Douglas O. Treisman

Mr. Treisman moved here from back east, and he and his wife are proponents of genetic medicine.  He is a founding board member of Genetic Medicine of Central California, and she is a genetic counselor.  Douglas Treisman is endorsed by local unions and the Central Valley Progressive Political Action Committee www.cvppac.org  The CVPPAC is outspoken against Prop 4 (parental notification on abortions for minors) and against Prop 8–they support same-sex marriage.

In addition, a few years ago, Mr. Treisman led the charge to abolish the annual Christmas Party sponsored by the Prosecutors’ Association (because it was not politically correct.)  The Association now holds a “Holiday Party.”  (Jim Kelley and his wife, however, still host a Christmas Party in their home every year and invite all the prosecutors.)  Mr. Treisman will define the term “judicial activist.”

Jim won the June primary, now let’s finish the job.  On November 4, elect Jim Kelley.

-Jim Kelley

I realize the election is over, but I thought this was worth posting just to make sure that, in the glow of Obama’s victory, we don’t forget the ominous rise of anti-science rhetoric from the right in this year’s campaigns.

Maybe “genetic medicine” is some kind of pro-life code word – the organization that Treisman supports does prenatal genetic counseling. But clearly he felt it was more powerful to go after Treisman’s belief in science, rather than the particular practices he supports. And it wasn’t like Kelley buried this flaw of Treisman’s along with his litany of other complaints – it was in the first sentence of Kelley’s critique (right after being from “back east” – you know, the place where they worship that demon – DNA). Kelley is clearly saying “Treisman believes in science – he’s not one of US”.

And – scarily – it worked! Kelley won.

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