random picks

In order to unclutter my twitter (and maybe reduce the number of shared items in google reader), I'll try to aggregate interesting articles into blog posts. Here is my first attempt!

Surprising AIDS Vaccine Success Praised and Pondered (Jon Cohen @ Science 326 (5949): 26; 2 Oct) [behind a paywall]:

Even skeptics are careful not to rain on the parade. "Looking at the numbers, it's underwhelming to me," says Ronald Desrosiers, head of the New England Primate Research Center in Southborough, Massachusetts. "But I want to sit tight and get a bunch of people to do analyses and see whether the protective effect holds up."

Data Call Into Question HIV Study Results (Gautam Naik and Mark Schoofs @ WSJ.com; 12 Oct):

Researchers from the U.S. Army and Thailand announced last month they had found the first vaccine that provided some protection against HIV. But a second analysis of the $105 million study, not disclosed publicly, suggests the results may have been a fluke, according to AIDS scientists who have seen it.

The second analysis, which is considered a vital component of any vaccine study, shows the results weren't statistically significant, these scientists said. In other words, it indicates that the results could have been due to chance and that the vaccine may not be effective.

Cern physicist admits links with al-Qaida (AP in Paris @ The Guardian; 11 Oct):

A French physicist arrested last week while working at the world's largest atom smasher has told investigators he corresponded over the internet with a contact in north Africa's al-Qaida branch, a judicial official said today. The exchange vaguely discussed plans for terror attacks, but nothing concrete was planned.
...
At work, the physicist had no contact with anything that could be used for terrorism, the European Organisation for Nuclear Research has said.

U.N. Envoy Calls Afghan Fraud Widespread (Anand Gopal @ WSJ.com; 12 Oct):

The head of the United Nations mission in Afghanistan, who has faced sharp criticism from his former deputy for not moving aggressively to expose vote-rigging in the August presidential elections, said Sunday that there was "widespread fraud" during the poll.

Mr. Galbraith subsequently charged that Mr. Eide had avoided releasing what the U.N. knew about the fraud because he feared further destabilizing Afghanistan's weak government, a charge Mr. Eide denies. The American diplomat also accused Mr. Eide of being biased in favor of President Hamid Karzai, whom observers and diplomats have said benefited the most from the vote rigging. Mr. Eide declined to address this allegation.

When Moore means less (The Economist; 6 Oct) About Michael Moore's newest movie, Capitalism: A Love Story:

It is hard to believe that Mr [Michael] Moore wants to be taken seriously, given that the only economics he offers in support of his analysis is supplied by his friend, Wallace Shawn, a character actor who appeared in “The Princess Bride” and who took a few classes in the dismal science. The capitalism he describes as “evil” and in need of being eliminated is clearly a straw man. To top it all off, he ends the movie with a rousing version of the socialist anthem, “The Internationale”.

The leading capitalists of the past 30 years, and especially in the run-up to the recent crisis, should probably be grateful for Mr Moore’s lack of seriousness, because the movie contains plenty of moments that could have been used to make a genuinely insightful documentary.

The Weekend Interview with John Mackey: The Conscience of a Capitalist (Stephen Moore @ WSJ.com; 3 Oct):

For the 12th straight year, Mr. Mackey's company has been praised as one of the "100 Best Companies to Work For" by Fortune Magazine. Whole Foods sells healthy food, practices "socially responsible trade," and prides itself on promoting foods that are grown to support "biodiversity and healthy soils." Mr. Mackey donates 5% of company profits to charity and has been one of America's loudest critics of runaway compensation on Wall Street.
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Yet his now famous op-ed incited a boycott of Whole Foods by some of his left-wing customers. (...) Free-market groups retaliated with a "buy-cott," encouraging people to purchase more groceries at Whole Foods.
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"President Obama called for constructive suggestions for health-care reform," he explains. "I took him at his word." (...) What Mr. Mackey is proposing is more or less what he has already implemented at his company—a plan that would allow more health savings accounts (HSAs), more low-premium, high-deductible plans, more incentives for wellness, and medical malpractice reform.

Democratic Donor Gets 24-Year Term (Chris Herring @ WSJ.com; 30 Sept):

A federal judge Tuesday sentenced Democratic fund-raiser Norman Hsu to more than 24 years in prison for illegally funneling money to U.S. political candidates and for defrauding investors in a multimillion-dollar Ponzi scheme.
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Mr. Hsu rose from being a relatively unknown businessman in California to a prominent fund-raiser who pulled in hundreds of thousands of dollars for Hillary Clinton and some other Democratic politicians.

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Phylogenetics, by Joe Felsenstein

Luke J. Harmon and Dan Rabosky recently e-enterviewed Joe Felsenstein. Here are some interesting points:

Luke: What are the most exciting recent developments in systematics / comparative methods?

Joe: The availability of genome-scale information is certainly one. The arrival of a generation of young researchers who are comfortable with statistical and computational approaches is another. But the most important development is reflected in recent work on coalescent trees of gene copies within trees of species. What this does is tie together between-species molecular evolution and within-species population genetics. Those two lines of work have been developing almost independently since the 1960s. But now, with population samples of sequences at multiple loci in multiple related species, they are coming back together. This is not another Modern Synthesis, but it is a major event that needs a name. How about the "Family Reunion"? Long-estranged relatives who have not been in touch are getting together.

(...)

Luke: What do you think about the current trend in phylogenetics (and, lately, comparative biology) towards Bayesian approaches?

Joe: I am a curmudgeon on this, in that Bayesian approaches do not feel right to me. So I have been resisting them. Bayesians were unhappy with the treatment of Bayesian Inference in my book, in that I did not give them four chapters, the last of which ended by declaring victory. I think we're all Bayesians when we come to cross the street, balancing evidence of approaching cars against our priors. But that's where one of the criticisms of Bayesianism comes in -- do we all have the same priors? Is there necessarily a single prior that you can use that will be broadly acceptable to your readership? If not, then maybe the reader of the paper should instead be given the likelihood curve so they can apply their own prior to it. For phylogenies, priors giving equal probability to all topologies (or to all labeled histories) would be noncontroversial. But the part of the prior that puts distributions on branch lengths could be wildly controversial. There is also the issue of whether some things, such as whether the sun will rise tomorrow morning, really should have a prior.

People should be Bayesians if that fits with their philosophy of doing science. But not just because a Bayesian program happens to run faster than a non-Bayesian one. They should also realize that we will continue to have both Bayesians and non-Bayesians. Biologists sometimes think that this controversy emerged in their field and will be settled there -- that one more really good argument and everyone will become a Bayesian. They might not be aware that Bayesian arguments have been around since 1764. There is no new decisive argument that's going to arise in our field.

The issue to contemplate is the priors, not the details of MCMC techniques. We have not yet seen a case where an important conclusion depends strongly on what prior you assume. Perhaps we never will, but if a case like that arises, and causes trouble for Bayesian approaches, people should not be too surprised.

The commentaries are also very enlightening.

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