As I’ve noted before, our bodies are riddled with microbes – there are more of them than there are of us (if you go by shear number). But where do they come from? Each individual has a complex ecosystem of commensal (harmless) microbes that live on our skin, in our nose, mouth, ears and gut, and we lay the foundations for this ecosystem at birth. According to a new study in the Proceedings of the National Accademy of Sciences (PNAS), different methods of birth (traditional vs cesarean section) have very different outcomes in terms of what bacteria end up colonizing you:

The goal of the present study was to obtain a community-wide perspective on the influence of delivery mode and body habitat on the neonate’s first microbiota[…] We found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode. Our results also show that vaginally delivered infants acquired bacterial communities resembling their own mother’s vaginal microbiota, dominated by Lactobacillus, Prevotella,or Sneathia, and C-section infants harbored bacterial communities similar to those found on the skin surface, dominated by Staphylococcus, Corynebacterium, and Propionibacterium.

It’s been known for a long time that c-section babies were more prone to allergies and asthma, and there’s a strong link between commensals and the immune system, but exactly what the difference was remained obscure. Basically, what this paper shows is that the types of bacteria that get us started are established very early.

Babies born through the traditional route are very quickly exposes to the bacterial communities of their mothers – both vaginal and gut bacteria (women often defecate when giving birth). Once these bacteria get established, they fill up all the niches, and prevent other bacteria from getting a foothold. By contrast, c-section babies don’t have this initial exposure – the womb is fairly sterile, and the conditions of this surgery prevent contact with the mother’s other mucosal surfaces. Because of this, the infant is ripe for colonization from the myriad of bacteria found everywhere else, from the nurses and doctors that handle them to the bacteria on the skin on the mother’s breast when feeding.

It’s important to note that we can’t yet draw a distinct causative link between early establishment of bacterial communities and future disease (allergies, asthma etc), right now it’s just correlation. And though infants are colonized by very few types of microbes, as they develop, the microbial ecosystem diversifies into thousands or millions of different species. Researchers are hard at work using new technologies to try to figure out all the different things living in an adult gut (given the spiffy name, “the microbiome”), and we’ve barely scratched the surface.

The one thing that is clear is that the little things living in us and on us can have a profound effect on our health, and with new research, hopefully we can use that knowledge to our advantage.


As I wrote earlier, scientists have a bit of a PR problem in communicating their science to the public. In the most recent issue of Nature, Naomi Oreskes and Erick Conway highlight the problem with respect to climate change (sorry, it’s behind a paywall, but I will quote them at length):

[…] opinion polls have repeatedly shown that large numbers of US citizens — and many in Canada, Australia and some parts of Europe — disbelieve the scientific conclusions. A December 2009 Angus Reid poll found that only 44% of Americans agreed that “global warming is a fact and is mostly caused by emissions from vehicles and industrial facilities”. There has been essentially no change in public acceptance of the scientific conclusions since the 1980s, with the public continually muddling the facts — believing, for example, that the ozone hole is the main cause of climate change.

In a recent book, these same authors showed how much of this public doubt was sewn in the later part of the 20th century by a few right-wing scientists who also worked to obscure the connection between tobacco and cancer and between CFC’s and ozone depletion.

What is particularly important to understand is how the industry used the trappings of science to make its case. It created the Council for Tobacco Research (originally the Tobacco Industry Research Council, but it dropped ‘industry’ on advice from a public-relations firm), along with various newsletters, journals and institutes, to publish claims. And it recruited scientists to speak up for this work, because it was obvious that tobacco-industry executives would lack credibility — although often the scientists had little or no expertise in medicine, oncology or epidemiology.

This strategy of creating a ‘scientific Potemkin village’ was applied to global warming too. During the period that we scrutinize in our book, the Marshall Institute didn’t create its own journal, but it did produce reports with the trappings of scientific argument — such as graphs, charts and references — that were not published in the independent peer-reviewed literature. At least one of these reports — read and taken seriously by the administration of former US president George H. W. Bush — misrepresented the science by presenting only part of the story. NASA climate modeller James Hansen and his team had demonstrated in the peer-reviewed literature that historic temperature records could be best explained by a combination of solar irradiance, volcanic dust, and anthropogenic greenhouse gases. The Marshall Institute report included only a single piece of Hansen’s graph, using the fragment to make it seem as if there was a poor link between carbon dioxide and climate warming, and to argue — against Hansen’s analysis — that the real culprit was the Sun.

Of greatest interest to me, however, was the identification of several of the problems scientists have in combating this type of approach.

One reason that the public is confused is that people have been trying to confuse them, in large part by intentionally waging campaigns of doubt against climate science. Doubt-mongering is an old strategy. It works because if people think the science is contentious, they are unlikely to support public policies that rely on that science[…]

[Those scientists] who engage in discussion discover a frustrating situation. Whatever facts one supplies, the sceptics continue to challenge them or offer alternative explanations. One cannot call one’s opponent a liar because it just seems desperate and ad hominem. Nor does it work to debate their points, because that feeds into the ‘controversy’ framework: the sceptics say there is a debate, you say there isn’t — voilà, they have proved their point.

The authors also point out some suggestions, some of which I agree with whole-heartedly, and others that are a bit more complicated:

For too long, the scientific community has subscribed to the idea that the ‘real work’ of science takes place in the lab or in the field, and that taking the time to communicate broadly doesn’t count. This assumption needs to be rethought, and the academic reward systems changed to encourage outreach. Contrarians do take the time and, given their tiny numbers, have had an enormous effect. In the nineteenth and early twentieth centuries it was much more common for scientists to write books aimed at the educated public; this tradition could be revived.

No argument here. Right now, tenure, promotion and pay grade at large research universities are largely based on grants and peer-reviewed publications. Having a few positions that are dedicated to public outreach, and are based on popular science publications and community education would be invaluble.

Scientists have much to learn about making their messages clearer. Honesty and objectivity are cardinal values in science, which leads scientists to be admirably frank about the ambiguities and uncertainties in their enterprise. But these values also frequently lead scientists to begin with caveats — outlining what they don’t know before proceeding to what they do — a classic example of what journalists call ‘burying the lead’.

A few weeks ago, 255 members of the US National Academy of Sciences wrote a letter in response to recent attacks on climate scientists. The Academicians began by noting that “science never absolutely proves anything”, and went on to explain that “when some conclusions have been thoroughly and deeply tested, questioned, and examined, they gain the status of ‘well-established theories’ and are often spoken of as ‘facts’”. Although this care and nuance is intellectually scrupulous and admirable, being so philosophical about the ‘factual’ nature of climate change doesn’t serve public communication.

This reminds me of the “just a theory” argument of evolution-deniers. The way that scientists use the word “theory” and the way that scientists use the word “theory” are drastically different, and this was deliberately used by the opposition to obscure the solid state of the fact of evolution. As a scientist, I do have qualms about over-stating certainty, but at the same time, I recognize that we need to speak differently to a general audience than we do with our scientific peers. I don’t mean talking down to the public, but rather changing our vocabulary so that we’re actually communicating what we intend to communicate.

The authors also make several other good points about scientists knowing their history and journalists stating their sources (often the “experts” on the anti-science side are scientists but in completely unrelated fields), but unfortunately, these are suggestions for when we’re called to debate, which is something we want to avoid anyway.

The article ends on a simultaneously optimistic and ominous note, and I’ll leave you with that

Of the many cases of doubt-mongering that we have studied, most ended for the better. At a certain point, the companies manufacturing chlorofluorocarbons (CFCs), admitted their link to ozone depletion and did the right thing by committing to phasing them out. The public is now firmly convinced of the link between cigarettes and cancer. Inductive reasoning implies that the same should happen with climate change: the consensus scientific view will eventually win public opinion. But in the meantime irreversible damage is being done — to the planet, and to the credibility of science.

From global warming to evolution to vaccine safety, the public consistently (and sometimes increasingly) doesn’t know or doesn’t believe the scientific consensus. A new piece in Wired magazine claims this is because scientists are bad at PR:

On the final day of last winter’s meeting of the American Association for the Advancement of Science, a panel convened to discuss the growing problem of climate change denial. It went poorly[…] What the scientists should have been asking was how they could reverse the problem. And the answer isn’t more science; it’s better PR[…]

“They need to make people answer the questions, What’s in it for me? How does it affect my daily life? What can I do that will make a difference? Answering these questions is what’s going to start a conversation,” Bush [CEO of a PR firm] says. “The messaging up to this point has been ‘Here are our findings. Read it and believe.’ The deniers are convincing people that the science is propaganda.”

It’s hard to argue that good PR might improve science outreach, but there are several problems with this approach. One, as the author notes, is that scientists hate the idea of “spin.” You shouldn’t have to spin good science, the evidence should speak for itself. Unfortunately, the vast majority of Americans don’t have the ability to interface directly with the evidence; most scientific journals are locked behind pay-walls, and even with access, the general public would be hard pressed to penetrate the dense, jargon-filled articles. After four years of college and several years working in biology labs, I finally started getting proficient at reading primary biology papers a year into graduate school.

Another problem: who pays for the PR? It’s all well and good for Tiger Woods to pay a professional PR firm, but scientists spend enough time writing grants for money to do experiments. And scientists are mostly decentralized, there’s no organized structure for coordinating this sort of effort even if it was desired. Maybe the government could step in, but politicians are generally scientifically illiterate, and some are in the anti-science camp themselves.

I have mixed feelings, but I think the best place to start is with education in schools. That’s more of a long term strategy though. In the short term, I’m not sure what to do, but professional PR people are probably not the answer.

If Donne were alive, he might revise his meditation to “No child is an island”. Or, more precisely, no twin is an island in the Florida public school system. Researchers published in Science last week that 1st and 2nd graders’ abilities to reach their genetic potential for learning (in this case, their achievement on the Oral Reading Fluency test) is positively moderated by their teachers’ abilities. That is to say, gene (student ability) by environment (teacher skill) interactions are important for early learning. When twins are taught by a highly skilled teacher, measured by reading gain achieved by non-twin classmates, much of their reading fluency is explained by genetics, and these children can be said to “develop at their optimal trajectory“. However, poor teaching impedes a twin’s natural ability to read well, hence there is a low genetic variance component, meaning “genetic differences are left unrealized“. This study is also a good introduction to how scientists address the age-old Nature vs. Nurture debate. When scientists talk about parsing the relative contributions of genes and environment to a trait, in this case, reading skill, monozygotic (identical) and dizygotic (fraternal) twins are the perfect test subjects because they share 100% and 50% of their genes, respectively. This allows researchers to estimate the environmental contribution to reading skill success variation for monozygotic twins, and then, deduce the additional contribution of genetic variation to reading skill variation for dizygotic twins (and this works out nicely in most cases because, for almost every trait, a dizygotic twin is more different from his twin than a monozygotic twin is to his).

An editorial from the Chicago Tribune on Monday gives me an opportunity to discuss something I’ve been meaning to talk about for a while: the retraction (pdf) of the scientific paper in The Lancet that originally proposed a link between MMR vaccinations and autism.

The story got plenty of press, touched off a raging debate about the safety of vaccines, and scared many parents away from inoculating their kids.

There was just one problem. Researchers hadn’t actually proved a link between the vaccine and autism. They were pushing a theory, one that lead researcher Andrew Wakefield was paid nearly half a million pounds to pursue. He was paid by lawyers who were trying to prove that the MMR vaccine caused autism.

As this article notes, the original paper got tons of press, and a movement started that has convinced millions of parents not to vaccinate their kids. In the 12 years since the original paper was published, many other, more thorough investigations have found no link.

A dozen epidemiological studies have not found a link between the MMR vaccine and autism. But the fear of a link remains. And some parents complain that kids receive too many vaccines. In 1960, young children were routinely vaccinated against five diseases: diphtheria, pertussis, tetanus, polio and smallpox. The CDC now recommends vaccination by age 2 against 13 diseases.

But negative results don’t generate the same kinds of screaming headlines, and the “controversy” continued. Dr. Richard Horton, the current editor of The Lancet, put it well in a recent interview on NPR’s On the Media:

This was a system failure. We failed, I think the media failed, I think government failed, I think the scientific community failed. And we all have to very critically examine what part we played in this. I think the media certainly did sustain the story over a decade. It became a political story, with did Tony Blair have his son vaccinated with MMR or not, suddenly a huge media furor around that.

Andrew Wakefield would make many statements during the course of those ten years, each of which was dutifully reported as if it was the gospel truth. Profiles of him were written as this charismatic doctor saving the lives of children. I mean, I think we all have to look very carefully at ourselves and say, we really messed up here[…]

We used to think that we could publish speculative research which advanced interesting new ideas which may be wrong, but which were important to provoke debate and discussion. We don’t think that now.

This is a basic problem with scientific outreach – journalists often report sensationalist stories based on major advances, but major advances are rare. Furthermore, the implications for the major breakthroughs often aren’t understood for years, after a great deal of follow-up – certainly long after the “newsworthieness” has gone away. As any grad student will tell you, science is long, plodding work. Victories are small and far between, but there’s an inexorable march towards understanding. Unfortunately, you’ll never see that on the front page.

From xkcd:

Correlation does not imply causation, but it does waggle its eyebrows suggestively and gesture furtively while mouthing 'look over there'

In April, I took a micro course called “Scientist as Citizen,” which is basically a workshop for scientists who want to know about interacting with the public, specifically through journalism. It was taught by Cornelia Dean, Science Editor at the New York Times, so she has a lot of experience dealing with scientists and trying to communicate science to the public.

Unfortunately, many scientists are wary of science journalists. It’s tough to explain your research in a way that other people will understand, a process made more difficult because of the different ways that scientists think as compared to the general populace (and that includes science journalists who are by and large NOT scientists themselves). In this class, Ms. Dean brought up several examples of these differences, but there is one that I thought was especially insightful.

A lot of people tend to assume correlation = causation; cum hoc ergo propter hoc. My favorite illustration of this fallacy is in an open letter written to the Kansas City School Board regarding their fight to get Intelligent Design taught in schools

You may be interested to know that global warming, earthquakes, hurricanes, and other natural disasters are a direct effect of the shrinking numbers of Pirates since the 1800s. For your interest, I have included a graph of the approximate number of pirates versus the average global temperature over the last 200 years. As you can see, there is a statistically significant inverse relationship between pirates and global temperature.

Ms. Dean said something that I think bears repeating, “A correlation is not an answer, it’s an opportunity to ask a question.” Scientists generally know this when it applies to their research, but even scientists can be mislead by this fallacy in their day-to-day lives. It seems natural to assume that when two things follow a similar trend, they must be related in some way, especially when you have other reasons to believe it.

When two trends seem correlated, there are 3 possibilities:
1) One thing may cause the other: “Global warming is caused by the decline in pirates.” However, even in this case, it can be tough to determine the direction of causation – how can we be sure that the increasing global temperatures are not to blame for dwindling pirate activity?

2)  Both trends are caused by some third factor yet to be determined: “The use of fossil fuel powered ships causes global warming and makes it more difficult for pirates to catch them in their sail-powered frigates.”

3) The trends are caused by unrelated factors giving the illusion of correlation.

Ultimately, it can often require rigorous, controlled experimentation to accurately determine causal relationships, and that’s one of the places where science really shines.