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.

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New warning labels for junk alt-med vaccines

The alt-med crowd is notoriously anti-vaccine despite the high level of safety of vaccines – even despite how many lives vaccines save every year. Real medicine being so effective against what were once devastating, wide-spread diseases just doesn’t fit the alt-med narrative. Yet does that stop them from peddling their own ‘vaccines’? Of course not. And would you believe it? Their vaccines aren’t even effective:

Health Canada is cracking down on the sale of so-called homeopathic vaccines that are falsely promoted by some naturopaths and homeopaths as safer and more effective than traditional vaccines.

The department has altered the document that outlines how homeopathic vaccines should be used, saying they must now contain the following warning: “This product is not intended to be an alternative to vaccination.” The document, called a product monograph, was updated June 24, one month after The Globe and Mail published a story outlining the concerns with homeopathic vaccines.

“We’re very glad … they’ve taken this step,” said Jamie Williams, executive director of Bad Science Watch, a Canadian advocacy organization that led a campaign against homeopathic vaccines. “We feel that it will be a help to consumers who might not have been getting the full information to make a more informed health choice before this.”

But what’s in these so-called vaccines, you ask? Well, ultimately nothing. But they made sure to take a gross path to that nothing:

Homeopathic vaccines, also known as nosodes, are made from infected saliva, feces or other material. The substance is mixed with alcohol and diluted until it is harmless, according to the homeopathic and naturopathic practitioners who sell the products. They say nosodes produce an immune response and that research shows it protects as well, if not better, than traditional vaccines.

In other words, they disinfect some feces or spit before essentially filtering it back to water. Anyone looking to imbibe this malarkey would be better off spitting into their Brita water filter and drinking the purified water that comes out. At least then they would have a water filter in addition to having wasted their time. And as for what research shows? It’s a lie. People who promote this sort of quackery cite poorly done studies with a tiny number of participants; the studies are never replicated and they never appear in any journal with any dignity. It’s all agenda-driven drivel that, in the end, makes the homeopath a butt-load of undue money. Take this advice from Jamie Williams, executive director of Bad Science Watch:

“Do not listen to somebody in a health store who’s trying to sell you $30 worth of sugar pills,” he said.

Those poor devils

Tasmanian devils are notoriously nasty, even to each other. They have teeth and aren’t afraid to use them. As a result, they tend to bite and nip at the faces of their brethren. And unfortunately, this has resulted in the spread of a contagious form of cancer that has wiped out 70% of the population.

But there is good news. Researchers have discovered that the reason the tumors are able to spread so efficiently (escaping immune system detection) is that its cells lack major histocompatibility complex molecules, or MHC molecules. The Tasmanian devil’s immune system can’t ‘see’ what’s coming. This, of course, isn’t unique amongst cancer cells, but what is a little different is that these MHC molecules aren’t simply broken via mutation. They are actually turned off due to regulation. This means they are intact and can be turned back on. (It also means that, in conjunction with the contagious factor, it wouldn’t be inappropriate to consider this cancer a separate organism, however parasitic.)

There is hope for the Tasmanian devil, albeit far down the road. Until then, quarantine and luck are the only viable solutions for saving this animal from extinction.

HPV vaccines do not lead to greater sexual activity

For quite some time now we have been hearing counter-common sense arguments that claim the administration of HPV vaccines will make young girls more likely to engage in sexual activity. One recent study shows those arguments to be bogus:

Adolescent girls who get the human papillomavirus (HPV) vaccine are no more likely to show signs they may be engaging in sexual activity than girls who do not get the vaccine, according to a new study that challenges a widely held belief…

Researchers from Emory University in Atlanta followed electronic data of nearly 1,400 girls aged 11 and 12 between July 2006 and December 2010 to see whether they received at least one dose of the vaccine within the first year and whether they were later counseled about contraception, acquired a sexually transmitted disease or became pregnant.

More than a quarter of girls ages 15 to 17 report being sexually active, according to the CDC.

The study followed the girls to the age range where sexual activity would have been initiated, according to the researchers.

The nearly 500 girls who received at least one dose of the vaccine were no more likely to be diagnosed with a sexually transmitted disease, discuss contraception or become pregnant than the nearly 900 girls who did not get the vaccine, the study found.

“We couldn’t directly look at sexual activity, so we looked at external outcomes that would suggest sexual activity,” said Dr. Robert Bednarczyk, clinical investigator with the Kaiser Permanente Center for Health Research Southeast, and lead author of the study.

The sort of arguments that inspired the above study are of the same sort that inspire studies which show that abstinence-only education is an abysmal failure. Again and again, social conservatives and overly worried parents will claim or wonder if the exposure to greater information will cause their children to become sexually active at a young age. Only the wonder is justified; over and over we are seeing that access to proper information and sound medical protections are the correct path to take.

Marijuana, new evidence, and changing views

I haven’t written about the legalization of marijuana very much on NBS, but I have long been in favor of it. No study has ever established a causative link between marijuana and cancer (or any other major disease), and I don’t think it is particularly detrimental to society to allow people to smoke it. Moreover, criminalizing the plant only creates an atmosphere of violence and real crime, not to mention the creation of criminals from the non-criminals who get locked up for using or selling it. That said, however, some new evidence has forced me to reel my views back at least a little:

Researchers found persistent users of the drug, who started smoking it at school, had lower IQ scores as adults.

They were also significantly more likely to have attention and memory problems in later life, than their peers who abstained.

Furthermore, those who started as teenagers and used it heavily, but quit as adults, did not regain their full mental powers, found academics at King’s College London and Duke University in the US.

Those who started later in life – usually during their college years – also experienced a drop in IQ, but were able to recover relatively soon after quitting.

I don’t particularly have a horse in this race – believe it or not, I do not smoke anything and I have no desire to ever start – but I’ve seen plenty of promising people lose track of their lives because of weed. Some have gotten things back on track and the others certainly could do the same, but that’s lost time and productivity. I think the world would simply be a better place with legalization and regulation of marijuana, especially where minors are concerned – and there’s good evidence behind that view.

The nature of science

I’ve said time and time again that solid science does not come from individual studies sitting all by their lonesome. Rather, it comes about as a result of a body of evidence. That isn’t to discredit any individual study that may be released, but instead to point out that the very nature of science is to discover and expose and correct for flaws. That cannot possibly be accomplished if one person or group comes up with a finding and everyone says, ‘Oh, good. Let’s just go with that.’ And that brings me to this recent study on children who live with dogs in their first year of life:

The study of nearly 400 children found that dogs were especially protective, and the babies who lived with dogs during their first year were about one-third more likely to be healthy during their first year, compared to babies who didn’t have a pet in the home. Babies with dogs in the home were 44 percent less likely to develop an ear infection, and 29 percent less likely to need antibiotics than their petless peers.

“Children who had dog contacts at home were healthier and had less frequent ear infections and needed fewer courses of antibiotics than children who had no dog contacts,” said the study’s lead author, Dr. Eija Bergroth, a pediatrician who worked at Kuopio University Hospital, in Finland, at the time of the study.

There is no reason to doubt the methodology of this study, as far as I know. There is no reason to doubt its integrity. This isn’t a highly complicated paper about kin selection or something of that nature where the logic can get quite counter-intuitive. This is a relatively straight-forward study, by all accounts. However, that does not mean it actually is better to have dogs around infants:

Previous research on pets in the home has suggested that animals, and dogs in particular, may provide some protection against the development of asthma and allergies. But, other studies have found that household pets may increase the number of respiratory infections in children, according to background information in the study.

Yet, on the flip side once again, this doesn’t mean it’s bad to have dogs (unless the child has allergies, of course). What this means is that there are some interesting results, both of which fit well into independent theories. For the previous studies, we know that animals carry plenty of germs and disease, so it wouldn’t be surprising to learn that they tend to transmit that sort of stuff to babies – basic germ theory. However, for this recent study, we also know that the immune system tends to do better when exposed to diverse environments early in life. That gives it a chance to build a working ‘knowledge’ of what it must resist. So which is the correct model?

We don’t yet know.

I personally lean towards it being better to have pets in the home, in part because dogs and cats are linked to greater happiness, which in turn is linked to a healthier body, but I’m not staking a claim to anything one way or another. The scientifically responsible thing to do here is to wait for a more robust body of evidence.

That’s how this whole thing works.

James Cameron and the Mariana Trench

I’m a movie fan and I certainly have enjoyed the work of James Cameron, but I’ve never thought of him as awesome. Of course Titanic was great. And, despite the storyline not being anything new, Avatar was visually spectacular (especially since I saw it in an IMAX). And I guess he’s done other stuff? I don’t know, but that’s what IMDB claims. Anyway, as far as I know, he’s a pretty good director. For that, I view him favorably. But for what he’s about to do I’ve already decided I view him as just fantastic:

In the coming weeks, the director of “Titanic” and “Avatar” will climb inside the Deepsea Challenger, a single-pilot submersible vehicle he helped design, and dive to the Challenger Deep, the lowest point in the Mariana Trench in the Pacific Ocean 200 miles southwest of Guam. Once he’s there he plans to spend six hours on the ocean floor collecting scientific samples and filming for a 3-D theatrical feature documentary that will also be broadcast on the National Geographic Channel.

This will be just the fourth time any man-made craft has gone that deep and just the second time any person will find themselves submerged so far. The first time people sunk to the bottom of the Mariana Trench was in 1960 when U.S. Navy Lieutenant Don Walsh and Jacques Piccard took on the challenge. Once they hit the bottom, they found they had disturbed some bottom-dwelling fish. This was incredible. Just a handful of decades earlier it was still thought that no life could exist below about 2,000 feet. The thinking was that no light could ever penetrate that deeply, so there would be no viable ecosystem that far down. The first trans-Atlantic communications cables to be pulled up for repairs, however, were found to be encrusted with barnacles. They had been laying about 2 miles beneath the surface.

Fast forward the better part of a century and we’ve discovered, with the movement of that bottom-dwelling fish and a few shrimp, that life can exist anywhere underwater. Just anywhere. But here’s the crazy thing: We have been able to send people to the bottom of the ocean for longer than we’ve been able to send them to the moon, yet we’ve visited the latter far more times than we’ve even seen the former, much less visited it. And isn’t that bizarre? Imagine we knew nothing of the flora and fauna of a place like California and in order to learn about it all we send a couple of non-scientists to take a quick glance at the first few forms of life they see. That’s a fair approximation of how much we know about the Mariana Trench. Don’t we want to know more about all the life that exists in this amazingly exotic locale?

I’m glad that not only is a human going to once again visit such an incredible place, but that this human happens to be a big-name celebrity. Who knows what this will do for deep-sea exploration, but at the very least it will get the attention of people who normally would never know anything about any of this. Education is fun. I can’t wait to read about the experience and see the video.

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.

Final total lunar eclipse until 2014

The final total lunar eclipse for the next three years is set to take place this Saturday morning. It apparently will be pretty awesome for those on the west coast of the U.S., showing off some purdy deep reds, but I’m sure it won’t be disappointing on the east coast either.

It is scheduled to start at 1:45am EST and continue for a couple of hours. By 3:05am, the moon should be completely engulfed by Earth’s shadow.

Exciting expectations: NASA finds planet in habitable zone

The Universe is enormous. Just enormous. It isn’t possible to truly grasp the scope of space out in…space. There are literally more stars – far more stars, in fact – in the Universe than there are grains of sands on all the beaches and in all the oceans of Earth. It’s really mind-boggling. But that mind-bogglitude (yeah, “bogglitude”) does lead to a few things that are comprehensible and expected. Enter NASA’s recent discovery:

NASA’s planet-hunting Kepler spacecraft has confirmed the discovery of its first alien world in its host star’s habitable zone — that just-right range of distances that could allow liquid water to exist — and found more than 1,000 new explanet candidates, researchers announced today (Dec. 5)…

The potentially habitable alien world, a first for Kepler, orbits a star very much like our own sun. The discovery brings scientists one step closer to finding a planet like our own — one which could conceivably harbor life, scientists said.

“We’re getting closer and closer to discovering the so-called ‘Goldilocks planet,'” Pete Worden, director of NASA’s Ames Research Center in Moffett Field, Calif., said during a press conference today.

This is certainly exciting, but it is also practically expected. With the billions and billions of galaxies out there, along with the trillions and trillions of stars and planets, there is bound to be more than a few balls of rock that are very, very similar to Earth. Moreover, not only is our galaxy quite common, but so is our solar system. We have an average star with an average array of planets. There isn’t anything special or privileged about our location. To believe otherwise is to be deluded or desperate or tremendously small-minded. We’re going to see many more Earth-like planets in the coming years.

I expect the future findings of NASA to be very exciting indeed.