A tale of two pigs

I don't usually mix my own research into this blog, but I make exceptions for influenza. As everyone knows (if you're awake and sentient), there's been a huge outbreak of swine flu recently, starting a few weeks ago in Mexico, which has now spread all over the U.S., Europe, New Zealand, and elsewhere. You can read all about it in the major news media, so I'll just focus on a couple of things you might not find elsewhere.

First, the swine flu has been reported to be a mixture of human, avian, and swine influenza viruses. Although the source of these reports is the CDC, that's not an accurate picture. I read today in The Washington Post that this epidemic started when a single pig was infected simultaneously by bird, pig, and human viruses. That's a reasonable inference from the reports in the media, but it's not true.

In fact, as a number of researchers have now discovered, the new swine flu is a mixture of two different swine flu viruses. It's definitely a novel strain, but it's pretty clearly a mixture of two already-circulating pig strains. That sounds less exotic than the "human-bird-pig" theory, and it is. The reason for the "triple reassortant" story is a bit complex, but (to simplify a bit): the history of one of the two parental swine flu strains indicates that part of that strain originated in birds - well over a decade ago. That strain is sometimes called "avian-like" as a result, but it's not an avian flu strain now. Second, the history of the other strain includes a small piece (one gene) that appears to have originated in humans - over 15 years ago. Again, it's a swine flu virus now, but there's a piece of it that might have come from humans. The event that created today's swine flu - the one we're worried about - is a combination (called a reassortment) between two pig strains, pure and simple.

The other point I wanted to make is about data sharing. The sequences from the U.S. isolates have been deposited in GenBank - the public DNA database - immediately, and this allows people like me to start our analysis without delay. Many of us have been arguing for years how important it is to get the data out to the community fast, in order to accelerate the pace of scientific discovery. However, the isolates from Mexico have NOT been put into GenBank, even though these sequences first went through the CDC. Instead, they went into a database called GISAID, which was originally set up to facilitate sharing of avian influenza. Unfortunately, GISAID changed their data release policy about six months ago, and there's no guarantee that sequences deposited there will ever become public.

The CDC has been depositing influenza sequences in GISAID as if this were equivalent to making them public. It's not, and they shouldn't pretend otherwise. The CDC has not always been supportive of publicly releasing flu data - in fact, for years they deposited some of their sequences in a private database. They've recently made public statements about their commitment to public data release of influenza sequences, but it doesn't seem that they are following through with this commitment for all of the sequences from the swine flu outbreak. (Don't get me wrong: the CDC is doing a fantastic job in trying to track and understand this outbreak, and their work is incredibly important to public health, especial concerning the flu. I'd just like them to be a big more open with their data.)

One last note, a technical one. I've looked at the Mexican sequences (I have a GISAID account) and the California sequences, and they are virtually identical. So it would appear that any differences in virulence are due to differences in the people being infected, not to the virus itself. At least that's what it looks like so far - the situation is changing rapidly.

Former NIH director Bernadine Healy joins ranks of pseudoscientists

It’s very sad to learn that someone in a position of scientific prominence has thrown her support to irrationality, unreason, and pseudoscience. This has happened before – as when noted physicist Peter Duesberg became a prominent AIDS denialist - but I still hate to see it. Perhaps I just have high expectations of people with scientific training.

Today’s topic is Bernadine Healy, former Director of the National Institutes of Health, who has very publicly joined pseudoscientist Andrew Wakefield and his compatriots who support the claim that vaccines cause autism, despite overwhelming evidence to the contrary. (Actually, Wakefield is worse, since he’s the person who nearly single-handedly invented the claim and made it public with his poorly done, and probably fraudulent, 1998 study in The Lancet.)

Bernadine Healy now writes a blog for U.S. News & World Report, and in her most recent posting she comes out very publicly in favor of “more research” on the link between autism and vaccines. Actually she’s been singing this tune for quite a while – she wrote a similar article a year ago. Healy’s argument is that she is in “the crossfire” in this debate, and she wants to pretend that she’s just being reasonable, trying to mediate between two passionate advocacy groups. “These are all reasonable issues, and considering them with some flexibility would go a long way to resolving many of the frictions aired by Larry King.”

What?? [Excuse me while I take a few deep, calming breaths.] Dr. Healy, do you seriously believe that we should let Larry King determine the direction of public health research? How the heck did you ever get the job of NIH Director? (Actually, this is easy to find out – she got it because she was a prominent Republican – unlike other NIH directors, she was never a highly-regarded biomedical scientist. She went on to run, unsuccessfully, for the U.S. Senate. She only lasted 2 years as NIH director. She later became head of the U.S. Red Cross, but only lasted 2 years there as well. End of digression.)

After setting herself up as a supposed "reasonable" voice, Healy goes on to make a series of poorly reasoned arguments, repeating some wildly misleading claims and outright falsehoods, making it clear where her sympathies lie. Healy has swallowed the pseudoscientific nonsense of the anti-vaccinationists hook, line, and sinker. Her article reads like a manifesto of the prominent anti-vax group Generation Rescue, whom she cites as if they are a source for scientific data. (I guess the former NIH director doesn't know how to use NIH's PubMed literature database.)

Of course, other anti-vaccinationists love this stuff – and they love her. David Kirby, the journalist who makes his living by scaring people about vaccines, has applauded her on his Huffington Post blog. (The Huffington Post has provided a platform for many anti-vaccinationists, unfortunately.) Age of Autism, another prominent anti-vaccination group, made her their “Person of the Year” in 2008 – which any decent scientist should be ashamed of.

Let’s look at just two of Healy's many false arguments. She writes that “shockingly, a study comparing groups of vaccinated and unvaccinated children… is long overdue.” Here, she is parroting a call by Jenny McCarthy for such a study – nice job, Dr. Healy, taking your scientific advice from a former Playboy playmate. The fact is that this study has already been done – multiple times, in fact. Studies in the 1990’s and 2000’s involving over one million children have compared groups of vaccinated and unvaccinated children and found no link between vaccines and autism, and no link between thimerosal and autism. That’s right, Dr. Healy – you could look it up if you cared, but apparently you don’t.

Second, she asks “are we overvaccinating our children?” This is right out of the Generation Rescue talking points list. There is no scientific evidence that "overvaccinating" is a problem – the word itself is an invention of the anti-vaccination groups. In fact, we have dramatically reduced the rates of many childhood illnesses, some of them fatal, through the wide use of vaccines. There are millions of people alive today who would be dead if not for vaccines. Ever heard of polio and smallpox, Dr. Healy? But that’s not enough for Healy – she just wants to perpetuate the myth that this is a serious scientific question. Without any scientific evidence to support her, she questions the need for vaccines against chicken pox, hepatitis A, hepatitis B, diphtheria, tetanus, and pertussis – ignoring the enormous public health benefits that we have derived from vaccines against these illnesses.

She even throws in outright falsehoods such as “Influenza vaccine [is] mandated here starting at age 6 months.” Sorry, but no, Dr. Healy, the flu vaccine is not mandatory. The CDC recommends the vaccine, but that is a far cry from “mandating” it. In fact, the CDC recommendation is necessary in order to get health insurance companies in the U.S. to cover the vaccine. This is ridiculously easy to look up, so I have to conclude that Healy just doesn’t care.

Bernadine Healy is using her status as a former NIH Director to give her credibility on the vaccine-autism question. Sadly, it seems to be working - she's certainly attracted a great deal of attention, and all because of her implied claim to expertise on any biomedical issue. But it appears that she's more interested in the media attention (Larry King Live!) than the facts.

For more on this issue, I highly recommend Orac’s recent post on this topic. He eloquently expresses the excruciating pain that many of us feel at the inexcusable stupidity expressed by ex-NIH Director Healy. And kudos to blogger Josh Witten for adding Bernadine Healy to his “Festival of Idiots.” I couldn’t agree more.

Should we have prayer at graduation ceremonies?

I usually stay away from the topic of religion on this blog, but events this week at my home institution, the University of Maryland (UMD), prompt me to comment.

It's rare for the University Senate at UMD to make bold moves, but to my surprise, they did exactly that last week. After studying the issue for years, they voted overwhelmingly (75% in favor) to eliminate the prayer at graduation. Critics of the prayer had pointed out that it was divisive - usually it has been a Christian prayer, and many students, faculty, and parents attending the ceremony are non-Christians. UMD is a public institution, and of course the Constitution of the U.S. prohibits states from endorsing any religion. A Jewish history professor, Marsha Rozenblit, said that "the real concern .. is the separation of church and state."

Nonetheless, I was surprised when I read, on the front page of the Washington Post, that UMD was eliminating the prayer ceremony at graduation. Another step forward towards rational behavior, and away from primitive superstitions - hurrah! (I'd like to report that UMD was being a leader here, but in reality we are just following other large state universities. The University Senate committee studying the issue looked at UC Berkeley, U. Illinois, U. Michigan, UNC, and UCLA, and found that none have prayer at their campus graduation ceremonies. But still, better late than never.)

The religious right immediately went on the attack, not surprisingly. The ultra-conservative Washington Times wrote that UMD is "on a mission to demonstrate its hostility to the core values of the community" and accused the university senate of "religious intolerance." They also claimed that "only a small group of anti-social cranks in the 'large and diverse' student community would feel alienated by a nondenominational prayer." Sorry, Wash Times, but calling us names doesn't advance your argument - and they have no evidence that only a "small group" want to eliminate prayer at graduation. In fact, every student representative in the University Senate voted to eliminate the prayer. One of them, David Zuckerman, said "Unfortunately, President Mote does not respect that we are the students who represent the student population in the shared government system."

Now for the bad news: in a surprising rebuff to the University Senate, UMD's president, Dan Mote, rejected their proposal and decided that prayer would continue exactly as before. (The Senate is only "advisory" to the President, so he has the power to reject their advice.) The student newspaper, the Diamondback, had reported that President Mote "rarely ignores the university's most powerful legislative body, which directly advises him on policy." Well, not this time. I can only guess at Mote's reasoning, but he issued a written statement that said:
"For many people, a prayer of gratitude and a moment of reflection are an important part of our commencement tradition. A great many people who participate in our ceremonies either embrace this tradition or are willing to allow others who value it to have it as part of the ceremony. After careful reflection, I have decided to continue our current tradition with respect to the invocation at commencement."
This is startlingly bad logic. It reflects the tyranny of the majority - exactly the sort of behavior that the Constitution prohibits in the First Amendment. Just because "many people" want a prayer doesn't mean they can impose their religious beliefs on others. I'm afraid that President Mote surrendered to political pressures (perhaps from the state legislature) rather than standing up for the students, the faculty, and the Constitution. This is really disappointing.

Missed in all the hubbub over this topic is this: graduation is a celebration of learning and academic achievement. Religion has no place in the graduation ceremony of a secular university: students don't come here to study religion. Why not have a lecture from a physicist, or a biologist, or a historian? At least that would be appropriate. Religion calls for strict, unquestioning adherence to dogma, while a university education teaches students (I hope) to question, to explore, and to reason about the world.

I hope the university senate at UMD makes the same recommendation again, and again, until President Mote follows their advice.