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.

The Second Law of Thermodynamics

To the right is one picture out of a series that was taken after the Bill Nye-Ken Ham debate the other night. Creationist question Creationists were asked to write questions that they would like to ask of Nye. (I’d link the whole series, but it came from BuzzFeed. I already feel dirty enough having clicked the link myself.)

To answer the man’s question, the second law of thermodynamics does not disprove evolution. The second law states that the entropy of an isolated system never decreases. That is, things because less orderly and more chaotic over time without an input of energy from an outside source. Since the Universe is an isolated system as near as we can tell, all the organization we see will eventually dissipate – no more stars or planets or black holes or anything else that uses energy. Eventually even all atoms will cease to move.

Creationists believe this fact of the Universe applies to evolution because they view evolution as greater and greater organization over time, and that requires an input of energy. They’re right so far. Where they fail is in their belief that greater and greater organization is not possible over time. As best as any rational person can tell, creationists appear to believe Earth is a closed system and that with enough time it should all fall away. Except it isn’t closed. That big yellow ball in the sky has a tendency to provide us with more energy than we know what to do with. (Not that we’ve been the best at harnessing it.)

Of course, we don’t need to even go as far as the Sun – at least so long as we aren’t talking about plants or photosynthesizing bacteria. We take in energy all the time. It ultimately comes from the Sun and, to an extent, Earth’s core and magnetic field, but on a day-to-day level, we don’t exist in a closed system at all. A dinosaur that killed another dinosaur had a source of energy to take in: the dead dino. An early hunter-gatherer would find energy by hunting and gathering. And right now I’m about to go find some energy in a hot chai tea.

Avoid these sources for your science

This is a very brief and very far from exhaustive list of sources one ought to avoid when looking for any sort of scientific information. After each person and/or organization is a list of the area in which they most commonly spread lies:

Deepak Chopra – Quantum physics, alternative medicine Adams – Alternative medicine, vaccines – Evolution, intelligent design

Dr. Oz – Alternative medicine, apple juice

Andreas Moritz (though he is now deceased) – Cancer, HIV/AIDS, Diabetes, all around quack

WattsUpWithThat/Anthony Watts – Global warming

Dr. Keith Ablow – Psychiatry, youth psychology, gender issues

Stanislaw Burzynski/Burzynski Clinic – Cancer, quack treatments

Marc Stephens – Mostly law, but he lied about being a lawyer in order to try and protect the Burzynski Clinic

Get vaccinated

It never ceases to amaze me just how many anti-vax people there are out there. Every time I bring up the topic it isn’t the pro-vaccine people who come out in support. No, instead it’s almost exclusively the anti-vax quacks. I suppose the same thing happens with circumcision, 9/11, and a history of Obama’s life: the anti-circumcision crowd, truthers, and birthers are going to immediately overwhelm the discussion. But even with this massive selection bias, the sheer number of nuts out there is incredible. I suspect to see as much regarding this post, should it garner a response at all. However, as a decent human being with a little bit of knowledge, I feel duty-bound to present a few vaccine facts.

Vaccines are incredibly safe. This is true of all vaccines, but especially of the flu vaccine. The most likely side effects anyone is going to suffer are mild soreness or a low grade fever. A study from about 10 years ago did find that one version of the swine flu vaccine from the mid-70’s was associated with a tiny increase in Guillain-Barré syndrome, but correlation is not causation. No one knows why there was such an association, but for this reason those with a history of the syndrome are cautioned and should speak with their doctor to assess their exact situation. Also, those with severe egg allergies are cautioned, plus those who are currently sick with one thing or another should wait.

Vaccines change each year because of evolution. From time to time I’ll hear an objection to the fact that the flu vaccine is different each year. Why, the argument seems to go, scientists are just guessing. That’s not true. While they are making an educated guess, it’s more than just throwing up a prayer and hoping they get it right. Each year’s vaccine is based upon the most recent research and information available. This is necessary because of the speed of a virus’ evolution.

Everyone over 6 months old should get vaccinated. This, of course, takes into account the caveats I’ve already presented, but for the vast majority of people, vaccination is recommended. Vaccines save lives, and if that’s not important enough to you for some crazy reason, they also save money by cutting down on sick days.

The flu vaccine is effective. Exactly how effective the flu vaccine is will vary from year to year, as well as from age group to age group. A person’s overall health is also a factor. In general, though, the vaccine’s effectiveness ranges from 50-80%. The most common (and most annoying) ‘counter’ to this is to look at absolute risk reduction. A person who does this is usually either a quack or has gathered information from a quack. It isn’t that absolute risk reduction is invalid. It’s a perfectly good way to understand how wide-spread a disease or sickness is and how our health policies are dealing with it. For the flu vaccine, the actual reduction in risk is about 1.5%. That sounds miniscule, but we can make a lot of things sound miniscule. What’s happening here is we’re looking at the total population and calculating the number who would get the flu without any vaccine. That’s a very small percentage. Then we’re looking at how likely it is that of the percentage that actually gets vaccinated is going to not get the flu as a result. Again, this is useful. However, when presented in the context of this discussion, it isn’t useful. It would be as if someone argued that since the absolute risk of contracting HIV in Tanzania is very low over, say, intercourse with 5 different partners, the 97-99% effectiveness of condoms is moot. Why, who needs condoms? You probably won’t contract it anyway! Pshaw.

Vaccines, not sanitation, have eradicated or nearly eradicated disease. While it’s obviously true that increased bathing, hand washing, and better filtered water have made us healthier and less likely to contract various diseases, these alone cannot get rid of disease. Smallpox has been eradicated for over 30 years now because of vaccines, not because more people than ever are buying bars of Irish Spring soap. Polio is nearly eradicated because of vaccines; India was recently declared polio free – that isn’t a country exactly known for its impeccable sanitation practices. Yellow fever persists because so many people go unvaccinated (even though the vaccine is 99% effective), and no amount of sanitation is going to change how many people die from it each year since its primary vector is the mosquito.

There are far more thorough sources out there that have vaccine facts covered in much better detail than I have here, so this is far enough for me. I simply wanted to address some of the issues that bother me the most about the vaccine misinformation floating about. For nearly every single person, vaccination is the smart option. The caveats are small and specific, the side effects minor and manageable. Get vaccinated.

Fun fact of the day

Have you ever wondered why the average human body temperature we always hear about is 98.6 F? How did they get so specific? Did they conduct a bunch of studies and actually come to that exact average?


It’s simple, actually: The rest of the world uses the metric system, so we tend to list the average human body temperature at 37 degrees Celsius. That isn’t to say that’s the exact number. It isn’t; human body temperature naturally fluctuates slightly throughout the day, so there really is no exact number. It just so happens that the average temperature is around 37 degrees Celsius, which, you guessed it, is equivalent to 98.6 degrees Fahrenheit.

Circumcision as a public health policy

At this point it has been established that circumcision reduces female-to-male HIV transmission rates by around 60%. Like it or not, the science is in. Now the question has shifted to being about why it reduces transmission, as well as how we can best introduce circumcision has a public health policy. On the first point, the general answer is that the foreskin is a relatively large surface area subject to tearing and softer (non-keratinized) skin. On the second point, though, I wasn’t aware of any actual policies in place to save the lives of men and women in regions particularly vulnerable to the spread of HIV. As it turns out, multiple sub-Saharan countries have undertaken measures to dramatically increase circumcision rates – though much work is still required:

Zambia is still 75 per cent short of its target of two million circumcisions by 2015. So is Uganda, having completed 1.5 million towards its 4.1 million target. Kenya has achieved its target in numbers – but not among the “right” men.

The donors who are pouring cash into male circumcision following the landmark 2006 study which showed that it reduced the risk of HIV infection by 60 per cent, have neglected a crucial factor – the attitude of women.

A man who gets circumcised is often viewed as a man who is looking to sleep around as much as possible. And, indeed, this has become something of a problem, as HIV rates in some areas have remained steady. This may also be due to men not waiting the necessary 6 week healing period – 40% of newly circumcised men had sex while still healing, actually resulting in an increase in their likelihood of contracting HIV. Furthermore, we may be seeing the problem of moral hazards at play. This is where risk is reduced for one thing or another, so people are less cautious in return. Some examples are playground materials and car safety. In playgrounds, children are often getting hurt as much if not more than in previous years because they’re playing on soft wood chips or rubber, leading them to believe they can fall harder and get hurt less. With cars, safety has greatly increased and deaths have fallen, but accidents remain steady or on the rise. People with seat belts are willing to speed more than those without them.

But the real problem in these sub-Saharan nations is a lack of education and peer support:

Carol Musimami, one of 30 “technical advisers” who counsel the men, said: “You will see the older ones come after dark. They don’t want to be with the youth. We are targeting the 25 to 35-year-olds –they are the ones with the money, they buy the women, they are exposing themselves [to infection]. But they are hard to get. They don’t want others to know,” she says.

Leadership is key. In Kenya, the circumcision programme in Nyanza province in the west – one of the three centres in the landmark 2006 trial that proved its effectiveness – was faltering when Raila Odinga, the Prime Minister and a member of the non-circumcising Luo tribe, responded to protests from tribal elders fearing the loss of their identity by declaring: “We don’t lead with our foreskins, we lead with other faculties. This is a medical issue.”

The speech, in 2008, proved a pivotal moment and more than 500,000 Luos have since been circumcised.

This is a major issue in global health. Science can find all sorts of answers to major problems, but that doesn’t mean it’s all just a matter of policy implementation after that. For instance, Jimmy Carter and WHO launched a campaign to eradicate Guinea worm disease in 20 African nations in the 1980’s. The primary approach to this was to make sure people had clean drinking water. With funding, wells were built and larvacide was added. However, one of the biggest pushes was to get people to drink clean water was to give them simple cloth filters. Unfortunately, this came with two problems. One was simply logistical: the filters clogged. The other was that the cloth material was too aesthetically pleasing, so people would often use them as decorative items. When the Carter Center, Precision Fabrics, and DuPont worked together to distribute plain nylon cloth filters (and education), the problem quickly shrank. There were 3.5 million cases of Guinea worm disease in 1986. As of 2005, the number had dropped to 11,000. This underlines the need for cultural understanding in addition to the simple cold science of the matter. Greater peer interaction and promotion of circumcision may be the key in getting places like Zambia to that 2 million goal.

At any rate, I’m very pleased to hear about these ongoing efforts to spread circumcision in developing nations in order to curb the spread of HIV. This is a triumph of common sense, global health initiatives, science, and basic humanity.

Cell type, HIV transmission, and circumcision

This is taken from a paper I did in a capstone course for my undergrad studies. I happened to come across it recently and I thought it would be interesting to post here.

Cell type matters in HIV infection. Transmission is higher amongst homosexual men who engage in rectal intercourse where the cells there are different as compared to cells on the genitals. Thin columnar epithelium that lines the rectum is assumed to facilitate the transmission of HIV; thick stratified squamous epithelium lines the vaginal and oral mucosa and appears to transfer protective properties against HIV acquisition. Video image analysis has shown that the latter is nine to twelve times thicker than the former [2]. In addition, intercourse causes more severe trauma to the former, thus allowing viruses better access not only beyond the mucosa, but, for the rectum, a richer bed of blood vessels.

Keratinized cells are a known protector against HIV. Like the body surface of a scorpion, they prevent attachment and entry of foreign agents. In both circumcised and uncircumcised men a keratinized, stratified squamous epithelium covers the penile shaft and outer surface of the foreskin. This acts as a protective barrier against HIV. However, the inner mucosal surface of the foreskin is not keratinized [1]. Furthermore, this surface is rich with Langerhans’ cells, cells which have been associated with higher rates of HIV infection due to their expression of CD4 glycoprotein which bind directly to gpl20 on the surface of HIV [2]. Since the foreskin is pulled back during intercourse, the surface area containing Langerhans’ cells is increased, thus giving HIV more opportunities to infect a host.

Observational studies back up the hypothesis that circumcised men are less susceptible to HIV infection. A 1989 study found uncircumcised men to be over 8 times more likely to be infected versus circumcised men [3]. A 1996 Ugandan study compared HIV infection between religious groups. Once abstinence, alcohol consumption, and number of sexual partners were accounted for, it was found that the likely reason Muslim men had lower rates of HIV infection versus other religious groups was due to higher rates of circumcision [4]. A 1999 study found that circumcision amongst rural Ugandans provided significant protection against HIV infection, but only if it occurred prior to the age of 20 [5].

Another 1999 study looked interviewed close to 200 uncircumcised men and close to 200 circumcised men. Amongst non-Muslims, circumcised men were found to have a greater risk profile than uncircumcised men. That is, those who were circumcised engaged in riskier behavior and had more partners on average. However, particular sex practices and hygienic behaviors were not notably different, and so they did not account for the higher risk of HIV infection amongst uncircumcised men [6].


The paper continues with a discussion germane to the requirements for the particular assignment, so I won’t reproduce any more here. However, it should be noted that the science on the matter does continue into more recent years, resulting in most major health organizations (WHO, UNAIDS, etc) supporting male circumcision in developing nations as one valuable method in the fight against HIV/AIDS.




4. Kiwanuka, Noah; Gray R., Sewankambo N.K., Serwadda D., Wawer M., Li C. (7–12 July 1996). “International Conference AIDS.”. Religion, behaviours, and circumcision as determinants of HIV dynamics in rural Uganda. Vancouver, British Columbia. Retrieved 2008-09-25

5. Kelly R, Kiwanuka N, Wawer MJ, et al (February 1999). “Age of male circumcision and risk of prevalent HIV infection in rural Uganda”. AIDS 13 (3): 399–405.

6. Bailey RC, Neema S, Othieno R (November 1999). “Sexual behaviors and other HIV risk factors in circumcised and uncircumcised men in Uganda”. J Acquir Immune Defic Syndr. 22 (3): 294–301.

Marketing that tricks you

A show on the National Geographic Channel called Brain Games has a good track record of exploring and explaining how our brains work, especially in every day circumstances. It’s probable that a good deal of why they work how they do has an evolutionary basis, but it’s also likely that some of their operation is simply incidental, an accident of our emergence from the jungles to the savannah to civilization.

One of my favorite episodes is called “Power of Persuasion”. It’s all about how marketers and advertisers get you to think what they want you to think. The show conducted an experiment (for which there was already ample, controlled evidence) where they sold popcorn to unsuspecting movie-goers. The first set of movie-goers was given a choice between a $3 small bucket and a $7 large bucket. Even when prodded to go for the more expensive choice, most people chose the $3 bucket. When interviewed later, people said they felt like $7 was way too much, and besides, the smaller bucket was more than enough anyway. The second set of movie-goers, however, was given a different set of choices. In addition to the $3 and $7 buckets, they had the option of a $6.50 medium bucket. Many of the patrons chose the medium bucket. When they did, the person behind the counter asked if they wanted to upgrade to the $7 bucket. After all, it was only another 50 cents. A significant percentage of people took the bait, purchasing the large bucket. In their interviews, they said it seemed like they were getting a better deal. Even while making the purchase, some could be heard saying, “Well, it’s only another 50 cents.” People believed they were getting a better deal.

What underlies this exercise is that an extra data point was introduced. In the first scenario the information was limited. Regardless of the price per ounce (which wasn’t given), the $7 bucket was well over twice the price of the small, but it certainly didn’t appear to be twice as big. The perception of the large bucket’s value was low. However, people in the second scenario had a third data point. The small bucket may have still been the best deal, but the $6.50 bucket normalized the prices on the higher end. The $7 bucket’s price was still over twice the price of the small bucket, but it was relatively close in price to the medium bucket; two of the choices had similar prices, so the highest price no longer seemed so extreme. Then when given the choice to spend a relatively small amount more (50 cents), the most expensive bucket seemed like a downright deal.

Now think to all the times you’ve done this. When you look into buying an item, are you only looking at the quality? Or are you looking at the value you’re getting? How often have we all opted to buy the medium-priced item because we don’t want something cheap, but the highest priced items are too much? And how often have we allowed ourselves to spend just a little more because the next product level was so close to what we were willing to spend on a slightly inferior item? I don’t know about you, but I think about this every time an employee at my local cafe asks if I want to upgrade from a medium to a large for just another 30 cents. It seems like a good deal, and maybe it is, but do I actually want more chai tea or do I just want more value?