Breakthrough study of 2011 and the tools for curbing HIV

The journal Science has named the HPTN 052 clinical trial, a study looking at the ability of antiretroviral medication to prevent HIV transmission, as the 2011 Breakthrough of the Year:

Led by study chair Myron Cohen, M.D., director of the Institute for Global Health and Infectious Diseases at the University of North Carolina at Chapel Hill, HPTN 052 began in 2005 and enrolled 1,763 heterosexual couples in Botswana, Brazil, India, Kenya, Malawi, South Africa, Thailand, the United States and Zimbabwe. Each couple included one partner with HIV infection. The investigators randomly assigned each couple to either one of two study groups. In the first group, the HIV-infected partner immediately began taking a combination of three antiretroviral drugs. The participants infected with HIV were extensively counseled on the need to consistently take the medications as directed. Outstanding compliance resulted in the nearly complete suppression of HIV in the blood (viral load) of the treated study participants in group one.

In the second group (the deferred group), the HIV-infected partners began antiretroviral therapy when their CD4+ T-cell levels—a key measure of immune system health—fell below 250 cells per cubic millimeter or an AIDS-related event occurred. The HIV-infected participants also were counseled on the need to strictly adhere to the treatment regimen.

It was found that those taking the medication while their immune system was still highly healthy were 96% less likely to transmit HIV to their partners. This result was so stupendous that, even though the trial is still ongoing, an early public release of the findings was ordered. It is important that people know how to best combat transmission. That spread of information is what is needed to prevent the spread of infection:

“On its own, treatment as prevention is not going to solve the global HIV/AIDS problem,” said Dr. Fauci. “Yet when used in combination with other HIV prevention methods—such as knowing one’s HIV status through routine testing, proper and consistent condom use, behavioral modification, needle and syringe exchange programs for injection drug users, voluntary, medically supervised adult male circumcision, preventing mother-to-child transmission, and, under some circumstances, antiretroviral use among HIV-negative individuals—we now have a remarkable collection of public health tools that can make a significant impact on the HIV/AIDS pandemic.”

“Scale-up of these proven prevention methods combined with continued research toward a preventive HIV vaccine and female-controlled HIV prevention tools places us on a path to achieving something previously unimaginable: an AIDS-free generation,” Dr. Fauci added.

I added the emphasis to the above excerpt because I am reminded of the utter irresponsibility displayed by PZ Myers on this issue in the past. While I still very much like what the guy has to say on many subjects, he was dead wrong to dismiss any one of the listed tools. In this case, he specifically dismissed the notion that there is any evidence whatsoever that circumcision has any impact on HIV infection rates. As I’ve documented elsewhere, he is absolutely wrong on the facts. That evidence does exist and it is important that it is known. That is why Dr. Fauci noted it amongst all the other ways we must use to combat this disease. HIV/AIDS is one of the most serious epidemics facing the developing world today; no one should be proud to exacerbate the problem, especially when the motivation is ideological in nature – we’re talking about god damned human lives here.

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Nope, wrong

PZ has a post about circumcision where he goes through the arguments in favor of the procedure based upon a video. (I haven’t watched the video nor will I because from what I gather it’s just a hack piece which does not focus on circumcision as performed by medical professionals in a medical setting.) Two of the arguments he quotes are apparently from a single guy and should just be boiled down to one: ’cause religion says to do it. Another one appeals to tradition, which is also a bogus argument, but then PZ has this last one:

The health benefits. Total bullshit. As one of the speakers in the movie explains, there have been progressive excuses: from it prevents masturbation to it prevents cancer to it prevents AIDS. The benefits all vanish with further studies and are all promoted by pro-circumcision organizations. It doesn’t even make sense: let’s not pretend people have been hacking at penises for millennia because there was a clinical study. Hey, let’s chop off our pinkie toes and then go looking for medical correlations!

PZ is wrong. The evidence has not suddenly vanished that circumcision prevents the transmission of HIV in high risk groups. Furthermore, it is blatantly invalid to dismiss this evidence because it may be used by pro-circumcision organizations, whatever those are.

If PZ wants to argue that circumcision holds little to no health benefits in places like the United States and other low risk nations for certain diseases, he can do that and be perfectly accurate. But if he wants to argue that circumcision has zero benefits in all circumstances, then he is in denial of the preliminary evidence.

Law versus theory

PZ has a couple of posts going right now where he takes down some common creationist canards. One post absolutely wrecks Ann Coulter (who, incidentally, has some real kiddie rhetoric going on – it’s just awful), and the other takes on Bryan Fischer. Each post is excellent, but PZ skims over something I would like to address in the latter link. Here are some excerpts from Fischer’s writing:

First Law of Thermodynamics. This law (note: not a theory but a scientific law) teaches us that matter and energy can neither be created nor destroyed…

Second Law of Thermodynamics. This law (note: not a theory but a law) teaches us that in every chemical or heat reaction, there is a loss of energy that never again is available for another heat reaction…

There are two kinds of people who have confusion over what a scientific law is versus what a scientific theory is. The first kind includes much of the general public. These people will have a basic misunderstanding, but they don’t tend to go about basing arguments upon it. The second kind, however, is an ugly little bunch. They include the likes of Fischer who also share the general lay public’s misunderstanding, but they then go about premising a bunch of bullshit on it.

A scientific theory and a scientific law are effectively the same thing. The latter term tends to be used more in physics than anywhere else, but that is a matter of history and convention more than anything. There is no magic property that makes the theory of gravity any different from the law of gravity. Both terms describe the same thing. We’re merely talking about banners and titles here, nothing of scientific value. Any person interested in science ought to learn this pretty quickly.

I recall sitting in an introductory biology course many a year ago when one student asked the professor the difference between a theory and a law. It is rare (though not absent) for “law” to be used in biology, so I’m not sure what spurred the question, but the professor answered it exactly right: There is no significant difference. I had a good deal of respect for the student at that moment. He was ignorant of something, so he got an answer. Creationists like Fischer, however, don’t do that. They understand the way we conventionally use terms and assume they can aptly apply that understanding to science. They cannot. They are wrong and scientifically irresponsible to do so.

But who’s willing to bet Fischer keeps pretending there is a difference even after being told there isn’t one? I am.

Shared errors

Over at Pharyngula, PZ Myers has a post which first destroys some creationist misconception, but then, far more interestingly, goes on to interpret a recent peer-reviewed paper on copy number variants, or CNVs. The whole piece is worth reading, but what I think is worth of a little extra attention is the brief point our shared errors.

An architecture does not imply intent or purpose, but they often imply a history. The pattern described — that chimps and humans share some common structural elements in their genomes — is better described as evidence of common ancestry than of well-designed function. An intron, for instance, is a piece of random, usually useless DNA inserted into the middle of the sequence of a gene that must be excised from RNA before it can be used to make a functional protein. It’s a little piece of garbage that must be cleaned up before the gene product can do its job. That a human and chimpanzee gene has identical introns is an example of an architecture, true enough, but it is of a shared error. Some all-knowing god—he seems to be consistently making the same mistake.

Okay, let’s take the recent hoo-hah with Coldplay and Joe Satriani. Basically, Satriani is claiming Coldplay ripped off one of his songs. There is some fairly compelling evidence to this claim, but it is far from airtight. What we have are four of the same chords repeating through parts of the songs, but only three consecutive notes are truly in common. We can potentially call this one a coincidence (especially since this song has been around forever and Satriani is only suing now that after Coldplay has won a slew of awards. Essentially, we see two instances of people creating similar things.

Now let’s consider someone learning the Satriani song. I don’t feel like finding the actual chord progressions, so let’s just say it goes A, B, C, D. The person begins to learn things, but is apparently a horrible musician and substitutes an F# for the C. Okay, fine. So we have a version of the song out there which is now A, B, F#, D. Now let’s say this person has a friend who wants to rip the song off. But instead of listening to the original Satriani version, he listens to the mutated version with the F#. Now we have some evidence of a copycat. It isn’t very strong evidence because there is just one error. In both instances, we have just four chords. But let’s say another error is made further along in the song. A chord in the bridge is misinterpreted by the original person learning the song. And, naturally, the copycat makes the same error. As we go deeper and deeper into errors, we begin to get better and better evidence of a common origin – the friend was learning from the interpreted version of the song, not the Satriani version, because it is unlikely he would make, say, 5 of the same errors as his friend. The chance for coincidence shrinks while the odds of identifying the correct source rise.

The way this is like CNVs is that we are seeing common errors being made again and again – and these errors are present in both human and chimp genomes. Of course, it should be noted that it isn’t entirely clear if these errors were directly inherited from a common ancestor or if it was the hotspot for ‘making’ errors is what was inherited, but at any rate, it is evidence for our common ancestory with the other apes. There are far too many common errors being made to simply file this under ‘God did it’. The evidence says that is – still and again – superfluous.