Re-report


There’s a great article at Gizmodo about attempts to find new antibiotics by tapping into the local knowledge of healers in the rain forests of Belize:

It grows wild along the shores of the New River, among the Mayan ruins of Lamanai, next to the lilies that are home to little yellow birds that skip across the pads. Inside Belizean plants used for generations by native healers, a suite of chemicals produce a natural “anti-quorum sensing” effect that interrupts bacteria’s ability to communicate. And bacteria that can’t communicate don’t go pathogenically virulent.

At least that’s the hope. If they’re right, they’ve discovered the herbal equivalent of Neosporin.

Quorum sensing by bacteria is a hot new field of research, as disrupting bacteria’s ability to communicate may be an incredibly efficient way to prevent their adverse effects. The article also describes the sometimes eccentric head of the company (McAfee of computer anti-virus fame), and some of the political and scientific barriers to research of this type. The article is quite long, and it’s a bit sparse on the actual science, but it’s well worth the read.

A recent paper published online in the Proceedings of the Royal Society B (I have no idea what the B means, but maybe one of you can clarify with a comment) draws an enticing connection between whale excrement and climate change.  Because this study involved whale poop, it even made the mainstream news.  The folks at MSN were even nice enough to provide an areal photo of what it looks like when a whale goes to the bathroom.  I have been lucky enough to experience this first hand on a whale watch when a whale shared the contents of its bowels with those of us aboard the ship, so this study had a little bit of a personal connection for me!  Hat tip to Chrissy at Working Through the Blue for pointing me towards this article.

The paper (entitled “Iron defecation by sperm whales stimulates carbon export in the Southern Ocean”) can be found here, and seems to be available for download without subscription.  You might be wondering whether this study draws a connection to the microbial world, or if I am just excited to write about whale poop… I assure you there is a connection.  In most environments certain nutrients are limiting, and therefore control the rate of primary production.  This means that no matter how much energy (food, sunlight, or chemical energy) is available, the microbes that form the base of the food pyramid can only convert that energy into biomass (storing carbon in the process) when that limiting nutrient is present.  In the case of the Southern Ocean, iron is the limiting nutrient.  The microscopic phytoplankton floating at the surface take CO2 out of the atmosphere and convert it to biomass that eventually falls through the water column and acts as food for other organisms.  However, they are restricted in how fast they do this because there is not much iron dissolved in these surface waters.

This is where the Sperm Whales come in.  These giants descend into the cold dark depths to feed (mostly on squid), and come up to the surface to breathe and relieve themselves.  It turns out that their waste is iron-rich.  By depositing this lovely substance in the photic zone, they apparently stimulate primary productivity.  This means that the photosynthetic plankton absorb CO2, grow, reproduce, are eaten, and so on, and eventually organic material sinks down and provides energy to life in the darker regions.  But wait you say (being the savvy reader that you are), don’t the whales exhale a lot of CO2 back into the atmosphere?  Yes, they do, but according to the modeling of these researchers, the plankton take up much more CO2 as a result of the iron released by the whale than the whale releases.  “By enhancing new primary production, the populations of 12,000 sperm whales in the Southern Ocean act as a carbon sunk, remivong 2 x 105 tonnes more carbon from the atmosphere than they add during respiration”.  They go on to suggest that the reduction of whale populations due to whaling is likely to have diminished this carbon sink.

How did the scientists calculate all of this?  They first assume that these whales eat only cephalopods (mostly squid).  I do not study whales, so I don’t really know how accurate of an assumption this is, but it seems to be true for this region (in other areas sperm whales eat more fish).  Then, they used published reports of the amount of iron in cephalopods, and then calculated the amount of prey consumed by the whales by averaging previous studies that had estimated how much these animals eat.  From what is known about iron retention in marine mammals (maybe as low as 10%, they used 15% as their estimate), they were then able to estimate how much iron must be released by the whales during defecation.  They then had to figure out how much of that iron stays in the photic zone long enough to initiate primary production.  They did this by assuming (based on observations) that undigested squid beaks sink almost immediately, but that the liquid material stays around for a long time (this is admittedly non-quantitative).  Finally, they know the form that iron is generally found in the gut (ferrous salts), and they know that that form  can be expected to dissolve quickly and therefore would hang around in the photic zone.  Their estimate was that 75% of the defecated iron would stay around in the photic zone.

I explain this because while headlines like “whale poop may help offset CO2 emissions” are certainly catchy, to gauge the accuracy of this claim it is important to know how the numbers were crunched.  Flashy findings like this can trickle into the mainstream news, but people generally don’t get an explanation of why they should believe this.  [SoapBoxAlert] I think this is part of why it can be so hard for non-scientists to determine which bits of “science” to “believe” and which to be critical of, especially when it comes to climate change [now back to the regularly scheduled science].

In this case the researchers have made some very interesting calculations (they also provide estimates of the losses in carbon sequestration that historical whaling may have caused).  I think it is important to know that their numbers are based on a model rather than actual measurements of the iron concentration of whale feces or what happens to that iron over time.  Models are only as good as the data that go into making them, and in this case it seems (to me, admittedly knowing very little about whales) that they have done a pretty good job.  Whales are very difficult animals to study, and something as simple as sampling their feces would take much more time, energy, and money than you might thing, so I am certainly not faulting the authors for this.  Similar calculations were done to estimate the rate of carbon withdrawn from the atmosphere, and then sunk, but since this is already getting long, I will spare you those details.

In summary, this study provided me the opportunity to write about whales, poo, microbes, the carbon cycle, and scientific methods at once… what better way to spend a Sunday morning!

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.

Carl Zimmer does a great job discussing the role the role that microbes play in global carbon cycling here.  He focuses on how microbial carbon cycling relates to climate change.  Through their metabolism, these organisms are responsible for moving a huge amount of carbon around the planet (cool semi-related fact: marine microbes produce more oxygen than all land plants put together), but we barely understand who they are and what, exactly, they do.  This is one reason that predicting climate change is so difficult!

A new study in the journal Pediatrics looks at potential health and developmental risks associated with giving babies lots of vaccines very early versus spreading them out over the first few years of life. Short story shorter – there are none:

The analysis found little difference in results for children in both on-time and delayed vaccination groups. The on-time group did slightly better on an intelligence test and a little faster on a test asking children to name things. “There’s not a single variable where the delayed kids did better,” Dr. Smith said.

Of course, as the WSJ article points out, delaying vaccination does put kids at greater risk for the infections that vaccines help prevent. But is this research going to convince the anti-vaccine parents out there? I doubt it.

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.

Jonah Lehrer has a great article in the NYT magazine about depression and some recent research that suggests it may have some benefits.

If depression was a disorder, then evolution had made a tragic mistake, allowing an illness that impedes reproduction — it leads people to stop having sex and consider suicide — to spread throughout the population[…]

The alternative, of course, is that depression has a secret purpose and our medical interventions are making a bad situation even worse. Like a fever that helps the immune system fight off infection — increased body temperature sends white blood cells into overdrive — depression might be an unpleasant yet adaptive response to affliction. Maybe Darwin was right. We suffer — we suffer terribly — but we don’t suffer in vain.

It’s an interesting take on a pressing problem in psychiatry and society, but what really sets Lehrer apart is his willingness to accept and respond to criticism. Evidently, he received many responses from interested parties, and he took the time to publicly acknowledge and respond to these critiques.

In an ideal world, I would have spent another thousand words or so outlining the neuroscience of depression; there is always more to say about a subject as rich and complex as mental illness.

I know next to nothing about neuroscience, so I would have taken everything he wrote in that article at face value. However, there is clearly plenty of nuance that he necessarily had to leave out due to the medium – the fact that he knows this and made the effort to clarify sets him apart from science journalists that just transcribe the latest university press-release. And it should be a reminder that science is complex, and not easily distilled in a news article, even for the best of them.

Update: There’s another post from Jonah with answers to questions regarding this article – it’s a great discussion, I wish there were more like it. And these sentences apply to almost all new science research, especially when it comes to studying human behavior:

One of the most challenging aspects of studying depression is the vast amount of contradiction in the literature. Virtually every claim comes with a contradictory claim, which is also supported by evidence. I tend to believe this confusion will persist until our definition of depression become more precise, so that intense sadness and paralyzing, chronic, suicidal despair are no longer lumped together in the same psychiatric category.

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