The value of repetition

One of the most important things I heard while in college came from one of my favorite biology professors. It happened in an early intro class half-filled with bio majors, half-filled with people looking for a course with a lab. He was covering the basics of science itself, speaking to the value of repetition:

Science is all about reproducibility. If you can’t reproduce your data, it’s all a load of horseshit.

That isn’t to say a person can automatically discredit some new piece of research simply because it’s new and has therefore not yet been reproduced. What it means is that when scientists do attempt to reproduce previously found results, they need to be successful in order for the results to be accepted. An unfortunate side effect of human nature means that we don’t see negative results published as often as we should – unless, of course, they disprove what someone else has already published – but these results do still happen every single day. That’s just science.

This all brings me to a recent piece of news:

Scientists have managed to repeat one of the biggest medical breakthroughs of the last few years.

Almost exactly one year ago, Johns Hopkins researchers made national headlines when they announced that they’ve vanquished the AIDS-causing virus from a child born to an HIV-positive mother in Mississippi. They began antiretroival treatment before the baby was 30 hours old. She’s now 3.5 years old and still virus-free, even without treatment in the last two years. Researchers have puzzled over how it happened, and many remain skeptical. The child was only the second person ever to be “cured” of HIV; the first was an adult through a stem-cell transplant. Since it’s difficult to prove that the body has been completely cleared of HIV, Nature explains, being “functionally cured” means the virus is effectively controlled and the immune system stays healthy without treatment.

Just yesterday, doctors announced that they have cleared the virus from a second baby infected with HIV. This girl was born in Los Angeles last April to a mother with advanced AIDS who had not been taking her medication. With aggressive treatment beginning just four hours after her birth, the virus was undetectable within 11 days, the New York Times reports.

A sample size of 2 does not scientific fact make (though there are upwards of 8 other unconfirmed cases around the world), but it cannot be understated how much this bolsters the legitimacy of attacking HIV in infants this way. It could turn out that the virus is still living somewhere in the bodies of these children – adults who have been functionally cured have had the virus return shortly after certain surgeries such as bone marrow transplants – so this remains a game of wait-and-see. However, if this proves to be an effect method for curing HIV, then not only will there be immediate benefits to HIV-positive newborns, but some insight may be spread into how we can better detect the hidden HIV in adults patients who are functionally cured.

Thanks for being wrong

I am finishing up the final portion of a paper concerning HIV and circumcision. Normally this would be a pretty big endeavor since it involves reading a lot of papers, but I have an advantage. Commenters like Ichthyic and Roxeanne have forced me to correct so many stupid things they’ve said on the issue that I’m already fairly familiar with the material. So I would like to thank those two: I really appreciate the utter wrongness with which you have each approached science. Your ideological commitments have really made this project of mine a breeze. Thanks.

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.

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.

The danger of false beliefs

A few months ago Wendy Pollack went to cause harm to people in Tanzania by providing them with false hope. She led sick people – specifically those with HIV – to believe that unproven and even blatantly discredited ‘medicine’ could help them become healthier. It was an awful tragedy and we can all be thankful that she has finally left Africa all together. She still practices her form of harm in America, but she at least faces some regulations here. (A complete outlawing of her shenanigans would be preferable.) It is easier to combat the misinformation of chiropractors and other sham-practitioners in a developed nation, even if they still manage to cause damage. Unfortunately, places like Tanzania do not have the institutions or medical infrastructure to implement procedures to protect its people, so even with people like Pollack safely thousands of miles away, alternative medicine practices still run rampant:

Hundreds of albinos are thought to have been killed for black magic purposes in Tanzania and albino girls are being raped because of a belief they offer a cure for AIDS, a Canadian rights group said on Thursday.

At least 63 albinos, including children, are known to have been killed, mostly in the remote northwest of the country.

“We believe there are hundreds and hundreds of killings in Tanzania, but only a small number are being reported to the police,” Peter Ash, founder and director of Under The Same Sun (UTSS), told Reuters.

This is a tragedy exactly along the same lines as what the entire alt-med crowd does. These random and inane – and often dangerous – faith-based ideas take off within a certain population and real human lives are put at risk. There is no evidence to back up any of these stupid and harmful beliefs, but evidence matters less and less as people get sicker and sicker. That’s one reason homeopaths are so successful in ripping people off.

What is happening in Tanzania right now rises to a level slightly above what most alt-med people do, but it really isn’t that far and away different. Remember Lawrence Stowe? He bankrupted sick people, drawing them away from real treatment. Many of those people died as a result of his actions – and he knew they would. Even where the people were terminal and could not be cured, he hastened death and increased pain. It’s standard practice for the alt-med crowd and I see no difference between that and what’s going on in Tanzania right now.

2010: FTSOS in review, July to September

This is the third installment of the 2010 review of FTSOS. See the first two here and here.

July:
Some of the smaller posts I’ve made that I think deserve a little more attention are the ones where I emphasize that biology is all about shape. The article I wrote about the fight against HIV is one of those posts. Research earlier this year found at least one location on HIV molecules that remains a consistent shape between individual viruses. This is important because HIV’s ability to be differently shaped in different parts of a single body makes it difficult to combat.

I also wrote about the difference between atheists, new atheists, and anti-theists. One of the public relation problems for atheism is that it is viewed as a dirty word. People assume it means absolute certainty, and that is seen as arrogant. It’s ironic because belief in God usually comes with certainty and that isn’t seen as being so arrogant, but I digress. Atheism is not certainty. Furthermore, where it is involved in new atheism and anti-theism, atheism acts as a descriptive base; new atheism and anti-theism are normative positions.

One of my all-time favorite posts is the one about photolyase and cancer. Photolyase is a protein that captures light and uses two of its constituents (a single proton and single electron) to force contorted nucleotides back into place. It is not present in humans, but is common in plants and other animals, helping to keep their genes functioning properly. This may be one reason we’re more susceptible to cancer than many of our fellow organisms.

August:
This was a skimpy month for FTSOS. I was away on a couple vacations for the bulk of the month, so the majority of the posts were either from my “Thought of the day” series or they were pictures/YouTube videos. But for what was there, I couldn’t resist pointing out and expanding on a fantastic quote from the judge who said Prop 8 in California is unconstitutional. In his quote he said a ban on gays getting married fails to advance any rational cause. I compared that sentiment to the idea that the majority cannot be allowed to discriminate simply because it is the majority.

I also made a post about a website devoted to philosophical thought experiments. The thought experiment I chose to highlight was Judith Jarvis Thompson’s Trolley Problem. My big motivator was a recent discussion with another blogger who laughably claimed that the trolley experiment was merely a logistical exercise, not an exercise about morality. To date he is still the only person in the world to believe that.

I also went through a few theistic arguments that are obviously failures. The most notable in my mind is the argument that says everything has a cause, therefore the Universe had a cause. There are two major problems with this. First, then why not just say a sort of ‘exo-nature’ caused the Universe? There is no need for consciousness – in fact, that only makes the theistic argument less probable. Second, the whole basis for this argument rests in the idea that forces result in reactions. For instance, if I push a chair, that chair moves; I applied a force. This is basic physics. But the whole shebang of forces and equal and opposite reactions? We’re talking about the science of what we know that happens within the Universe. And all we know necessarily breaks down prior to the Big Bang. The First Cause argument cannot be used because it rests about an unwarranted extension of science. Religion abusing science? Crazy, I know.

September:
The beginning of September was just as skimpy as the end of August because I was still on vacation. But while I never gave a huge post on the subject, the defining moment of the month (and year and decade and…) for me was my hike of Kilimanjaro. I have started writing about it at this point – just not for FTSOS. But in lieu of that you can read the account of the journey from my fellow group member and current Facebook buddy Jim Hodgson.

I also gave a very lengthy post on why prostitution ought to be legal. No one seemed to care, but I put a lot of effort into, so I thought I would mention it here. Basically, we make the practice illegal because of our own discomfort with sex as a society. We also draw false correlations between it and other illegal activities: of course one illegal thing will bring with it other illegal things if it’s something people want. Finally, for the safety and health of all involved, it would be better to legalize and regulate prostitution than keep the old system we have now.

One of the most popular posts on FTSOS that people found via search engines was the one where I lamented low science and math scores in the United States. A lack of funding relative to other areas, hostility towards science, and a general anti-intellectual trend in the U.S. all contribute to the decline of America on the world stage in education.

Another lament was my post about the anti-vax crowd causing deaths. The fact is, people who advocate against vaccines or for made-up alternatives to vaccines are making the world a more dangerous place, making people sick and even causing deaths. Get vaccinated – and, if you have them, especially get your children vaccinated.

Once again I really want to highlight a fourth post here. In this case, it is the one I made about the Problem of Evil. This has forever been an issue that no Christian (or other relevant believer) has been able to resolve. If God is good and evil exists, then we need to answer why. Appealing to free will fails because while God is necessarily good, free will does not need to necessarily exist. In other words, God is required to be good; he is not required to create free will.

Expect October to December tomorrow.

Follow-up: HIV, controllers, and progressors

I’ve just got a quick link to add to my post earlier this month on HIV. There is also a post on the NOVA website from Kate Becker, a science writer I’ve come to enjoy quite a bit. She covers science as well as anyone.

HIV: It’s still all about shape

The last time I wrote about HIV, I made the point that biology is all about shape; keep that idea in mind and a lot of things will suddenly start making a lot of sense. In that instance, I was writing about antibodies that were able to nearly universally attack HIV based upon one particular location on the virus which did not change shape. In this post I want to talk about a new study concerning protein differences.

To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and analyzed the effects of individual amino acids within the classical HLA proteins

HIV controllers are just what you probably think they are: they are people whose bodies are able to control the impact of HIV. They maintain healthy levels of helper T Cells. Progressors, on the other hand, are people who follow the expected course after they contract HIV. In this study, a large group of controllers were taken and had their genomes compared to progressor genomes. Researchers found more than 300 (313, to be exact) SNPs on the chromosome 6 that separated these two groups.

This is a pretty specific area with a small amount of difference. In fact, on the HLA-B protein, a difference of just 5 amino acids makes all the difference in a single groove. It appears as though this is one of the most important differences between controllers and progressors, constituting a significant region which enables the immune system to control and limit the proliferation of HIV. The amino acid sequence changes the shape of the groove in controllers as compared to progressors. This change protects the controller against HIV and its deadly consequences.

Precisely how this change in shape keeps HIV from turning into AIDS has not yet been made clear, but it is very promising. Given the current state of research, I’m willing to predict we’ll see a cure for HIV before we see a cure for cancer.

The fight against HIV

In biology, it’s all about shape. Enzymes, proteins, antibodies, blood vessels, cells, everything. They work best when they fit best or match in shape best. That’s why two new HIV antibodies have such potential.

Scientists report they’ve discovered possible new weapons in the war against HIV: antibody “soldiers” in the immune system that might prevent the AIDS virus from invading human cells.

According to the researchers, these newly found antibodies connect with and neutralize more than 90 percent of a group of HIV-1 strains, involving all major genetic subtypes of the virus.

That breadth of activity could potentially move research closer toward development of an HIV vaccine, although that goal still remains years away, at best, experts say.

HIV molecules evolve at a rapid pace. This makes it nearly impossible to produce antibodies at rates and in quantities sufficient to combat the disease on a long-term basis. However, there is one part of an HIV virus which remains virtually unchanged. This is important because it means there is a site with a consistent shape on the virus. That’s where these antibodies are being directed, thus offering a potentially powerful new tool in the fight against HIV.

Explaining denialism

It’s ever so common to come across an evolution denier only to discover the person is also a global warming denier. This may be chalked up to ideology – American conservatism practically demands a god and it’s too pro-business to accept the science of global warming (or at least the predicted consequences). But another reason must often be sought; the denialism can extend beyond a conservative agenda. This includes HIV denial, vaccine denial, second-hand smoke denial, and a host of other forms. In fact, the anti-vax movement will often find sympathies on the left.

Some of the common underlying themes of denialism are alleging conspiracies, moving the goalposts in the face of evidence, and manufacturing evidence. In other words, it’s all very anti-scientific. But it isn’t necessarily an outright hostility towards science that causes this – though many conservatives suffer from such an affliction. Instead, it’s the way many people tend to think.

All denialisms appear to be attempts like this to regain a sense of agency over uncaring nature: blaming autism on vaccines rather than an unknown natural cause, insisting that humans were made by divine plan, rejecting the idea that actions we thought were okay, such as smoking and burning coal, have turned out to be dangerous.

This is not necessarily malicious, or even explicitly anti-science. Indeed, the alternative explanations are usually portrayed as scientific. Nor is it willfully dishonest. It only requires people to think the way most people do: in terms of anecdote, emotion and cognitive short cuts. Denialist explanations may be couched in sciency language, but they rest on anecdotal evidence and the emotional appeal of regaining control.

Emotional appeals are not always bad. When they are mixed with substance, they make for powerful rhetoric. But often, entire arguments are premised in emotion. Take creationism/intelligent design. It isn’t that there’s any evidence for it; many people recognize that natural selection is a blind process which builds piece by piece, bit by bit, thereby not being random and not being improbable, thus making all life the product of purely natural processes. God has no place to go but out. Since no science supports creationism/intelligent design, an emotional response is the result – to the detriment of science.

[Seth Kalichman of the University of Connecticut at Storrs] believes the instigators of denialist movements have more serious psychological problems than most of their followers. “They display all the features of paranoid personality disorder”, he says, including anger, intolerance of criticism, and what psychiatrists call a grandiose sense of their own importance. “Ultimately, their denialism is a mental health problem. That is why these movements all have the same features, especially the underlying conspiracy theory.”

Neither the ringleaders nor rank-and-file denialists are lying in the conventional sense, Kalichman says: they are trapped in what classic studies of neurosis call “suspicious thinking”. “The cognitive style of the denialist represents a warped sense of reality, which is why arguing with them gets you nowhere,” he says. “All people fit the world into their own sense of reality, but the suspicious person distorts reality with uncommon rigidity.”

The likes of Maloney and Moritz certainly fit this profile. Both have had some of the most radical reactions to criticism I’ve seen since grade school, they both are clearly angry (especially Maloney), and both actually have taken measures to expand their web presence upon its destruction by Pharyngula and FTSOS (Moritz on Facebook, Maloney everywhere else), apparently believing what they have to say is too important to be drowned out by facts, evidence, and other pesky things.

But this extends beyond those two. Many creationists fit this profile. Just wait for one to write an editorial to a paper. The emotion, the anger. Then respond. Watch for the screeching about tone, respect, not being nice enough. And I don’t mean to watch for those reactions from my style of writing (though I get those, too). The most tempered response is met with hostility.

But as damaging as denialism has been to science education, it has had more immediate, more serious consequences.

Denialism has already killed. AIDS denial has killed an estimated 330,000 South Africans. Tobacco denial delayed action to prevent smoking-related deaths. Vaccine denial has given a new lease of life to killer diseases like measles and polio. Meanwhile, climate change denial delays action to prevent warming. The backlash against efforts to fight the flu pandemic could discourage preparations for the next, potentially a more deadly one.

If science is the best way to understand the world and its dangers, and acting on that understanding requires popular support, then denial movements threaten us all.

Science is, in fact, the best way of knowing.

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