So that’s what chemistry is good for…

Stinky stuff! This fits perfectly with my biased preconceptions. So here are two examples of chemistry used to analyze things you’d normally run away from.

The oldest traces of human poop have been dug out of a cave in Spain — and it’s Neandertal poop. It’s about 50,000 years old, and it’s been reduced to a compressed, thin smear of organic compounds, so I guess it isn’t actually so stinky anymore, but there was enough of it to analyze chromatographically. In case you’ve wondered your whole life about what Neandertal poop would look like, here you go.

Microphotographs of a slightly burned coprolite of putative human origin identified in El Salt Stratigraphic Unit X (sample SALT-08-13). The images under plane polarized light show the pale brown color and massive structure of the coprolite, as well as the common presence of inclusions, which are possibly parasitic nematode eggs or spores.

Microphotographs of a slightly burned coprolite of putative human origin identified in El Salt Stratigraphic Unit X (sample SALT-08-13). The images under plane polarized light show the pale brown color and massive structure of the coprolite, as well as the common presence of inclusions, which are possibly parasitic nematode eggs or spores.

Dead for 50 millennia, and what we know about this dead person is that they took a massive dump that was full of parasites. TMI.

I thought the paper was preliminary and rather general — they don’t or can’t make very specific conclusions, but then, I imagine they were excited to be the first to get any discussion of Neandertal feces into the scientific literature. We do know a couple of things: Neandertals ate both their meat and their vegetables, and they had gut bacteria with similar physiological properties to our own.

Taken together, these data suggest that the Neanderthals from El Salt consumed both meat and vegetables, in agreement with recent hypotheses based on indirect evidence. Future studies in Middle Palaeolithic sites using the faecal biomarker approach will help clarify the nature, role and proportion of the plant component in the Neanderthal diet, and allow us to assess whether our results reflect occasional consumption or can be representative of their staple diet. Also, this data represents the oldest positive identification of human faecal matter, in a molecular level, using organic geochemical methods.

Besides having corroborated our method and obtained the first evidence of an omnivorous Neanderthal diet from faeces, our results also have implications regarding digestive systems and gut microbiota evolution. Approaching the evolution of the human digestive system is difficult because there is no fossil record indicating soft tissue preservation. Our results show that Neanderthals, like anatomically modern humans, have a high rate of conversion of cholesterol to coprostanol due to the presence of bacteria capable of doing so in their guts. Further research will allow us explore this issue in the context of human evolution.

I said I had two unpleasant examples of useful chemistry, and here’s the second: using the characteristic odors of different stages of decay to quantify the time of death.

An international research team used two-dimensional gas chromatography time-of-flight mass spectrometry to characterise the odours that create this smell of death:  volatile organic compounds (VOCs).  By measuring the VOCs released from pig carcasses the team identified a cocktail of several different families of molecules, including carboxylic acids, aromatics, sulfurs, alcohols, nitro compounds, as well as aldehydes and ketones. The combination and quantities of these VOCs change as a function of time as a cadaver goes through different stages of decomposition.

I think I’m getting a sense of the difference between chemistry and biology. I prefer the bodily fluids in my subjects to be fresh, preferably spurting; chemists seem to favor observing the degradation and volatilization of fluids from dead things. Chemists may offer their repudiations of my sentiments in the comments.

Time to kill all the kittens

I think that’s the only reasonable response. We’ve been conditioned to think that animals are all furry and big-eyed and most importantly, cute, and every animal that isn’t must be reclassified as vermin. We’re going to need a radical readjustment of the public; every time you send someone a LOLcat, a thousand annelids and a million arthropods die in despair.

At least, that’s how I feel on the news that the Smithsonian is closing their Invertebrate Zoo. There are some fucked-up priorities here.

The Smithsonian says the Invertebrate Exhibit costs $1 million a year to operate, and that necessary upgrades to the facility will cost another $5 million. "We have several other fundraising priorities which preclude us from launching a… campaign for the invertebrates to stay in their existing space," reads a statement on the Zoo’s Facebook page.

The National Zoo’s annual budget runs about $20 million, with its friends group kicking in another $4 to $8 million a year. Which basically means the Zoo has decided it can’t afford to allocate five percent of its annual budget to educate the public about 97 percent of the animal species in the world.

“Priorities”. What defines their priorities? An accurate presentation of the science, or pandering to brains high on fluff? I suggest we start feeding the Red Pandas to the octopuses until those priorities get readjusted.

Not All Physicists

Sean Carroll criticizes those physicists who say silly things about philosophy, answering three common, and erroneous, complaints from the ‘philosophy is dead!’ mob. It’s pretty good, and I was thinking that maybe this would finally sink in, but then I read the comments. Oh, boy.

My favorite was the guy who said philosophy is pointless and that there’s nothing that a philosopher can do that a good physicist cannot. If you ever wonder why physicists have a reputation for arrogance, there it is: do they really believe that the 4+ years of graduate work required to get a Ph.D. in philosophy involves doing nothing? That has to be the case. I took a look at the degree requirements for several doctoral programs in physics: Houston, Tulsa, Stanford, and NYU (just the ones that came up first in a google search). Despite the word “philosophy” in the title “Doctor of Philosophy”, none of them require any coursework in philosophy. Not one bit.

Physics isn’t the only discipline with this flaw, though; it isn’t a requirement in any biology program that I know of, and though I’ve tried to squeeze a little bit into our undergrad biology program, there’s considerable resistance to it. In general, science programs aren’t very good at giving any introduction to philosophy — so it’s always amusing to see graduates of these programs lecturing, from their enlightened perspective, on the uselessness of this discipline they know next to nothing about.

I feel the same annoyance at this know-nothing attitude that I feel towards all those people who claim to know everything important about evolution — it’s so easy, they’ve mastered it with a little casual reading on the side. And then I mention a big something like drift or founder effect, or some fascinating little thing like meiotic drive, and they’re completely stumped. Didn’t know that before. But they know all about evolution, yes sir!

Some of them are physicists, too.

Come for the Oz-kicking, stay for the information

This is an excellent piece on that quack, Dr Oz, by John Oliver. The first 5 minutes is spent mocking the fraud, but then, the last ten minutes are all about the real problem: the evisceration of the FDA’s regulatory power over supplements, thanks to Senators Hatch and Harkin.

OK, there is a silly bit at the end where they show that you can pander to your audience without lying to them about the health benefits of magic beans, but still — let’s beef up the FDA, all right?

Boeing employees of Seattle, I hope you choose wisely

When I was growing up in Seattle, my family rode the Boeing roller coaster. Long time residents know what that is: the constant cycle of hirings and layoffs by the company. My father was always trying to get employed there, but it was always temporary as Boeing constantly expanded and contracted its workforce. So one year, we’d move into some nice new tract house in the suburbs, live well, and take advantage of all the benefits: vaccinations, regular check-ups, and lots and lots of dental appointments. The next year, Dad would get laid off, have to take jobs pumping gas, or reading water meters, or doing custodial work (or multiple combinations of the above to make ends meet), we’d move again into some shabby rathole, and no more visits to the dentist or doctor. We really were at the mercy of Dad’s employer for basic health care.

So good news for Boeing employees now! They still try to provide good worker benefits, and you’ve got your choice of two health care providers. You can choose UW Medicine, cutting edge stuff from one of the best universities in the country (said as an alumnus, of course), with access to all of the latest treatments. Or you can choose the Providence/Swedish plan, if you like good care for all of your bits except the nasty ones, which you think deserve only medieval punishment.

Because Providence/Swedish is a Catholic health care ministry, employees who choose the Providence/Swedish option will be subject to care that is limited by Catholic doctrine as laid out in the Ethical and Religious Directives for Catholic Health Care.   Providence very clearly says that “As a Catholic health care organization, we require adherence to all Ethical and Religious Directives as a condition of medical privileges and employment.”  These ERDs forbid contraception,  “direct” abortion in all circumstances, research that relies on embryonic stem cells, and participation with WA’s Death with Dignity Law.

Wow, what a tricky choice.

Creationists, climate change denialists, and racists and the credentialism strategy

Credentialism always makes for convenient excuses. We love to construct simple shortcuts in our cognitive models: someone has a Ph.D., they must be smart (I can tell you that one is wrong). Someone is a scientist, they must have all the right facts. And of course, the converse: we can use the absence of a Ph.D. or professional standing, to dismiss someone.

Creationists are very concerned about this, and you see it over and over again: the desperate need to acquire a degree or title, even if it is from some unaccredited diploma mill or a correspondence school, in order to justify their wacky beliefs. Or they invent reasons to discredit the other side’s credentials: Ken Ham loves to trot out that nonsense about historical and observational science, a badly drawn distinction, to imply that the scientists who study evolution aren’t real scientists. Whereas he, of course, is the honest arbiter of good science.

Climate change denialists love to do it, too: Bill Nye isn’t a real scientist, you know. You can ignore everything he says because he’s an engineer and children’s TV host, so you should listen to what the TV weatherman says instead.

None of that matters. Ideally, you judge the validity of a scientific thesis by the quality of the data and the experiments behind it, not the academic pedigree of the author. If a children’s TV host accurately explains the evidence behind a conclusion, that’s what matters. You don’t get to ignore the evidence because the presenter is a mere educator (or even, a mere weatherman).

But you know who else indulges in this fallacy, other than creationists and climate change denialists? Nicholas Wade. He has taken to rebutting critics of his racist book by declaring them non-scientists. For instance, in response to a review by Pete Shanks, Wade declares that all of the people who dislike his book are not competent to do so.

Shanks failed to notice, or failed to share with readers, the fact that scientists critical of my book have attacked it largely on political grounds.

Although a science writer, Shanks is at sea in assessing scientific expertise. He places excessive weight on the views of Agustín Fuentes, the author of two of the five critical reviews that have appeared on The Huffington Post. To ascertain a scientist’s field of expertise, all one need do is consult their list of publications. Fuentes’ primary research interest, as shown by publications on his website, is the interaction between people and monkeys at tourist sites. I don’t know what the scientific merit of this project may be, but it establishes Fuentes’ field of expertise as people-monkey interaction. If you seek an authoritative opinion on human statistical genetics, the principal scientific subject of my book, he would not be your go-to expert.

Stunning, ain’t it?

Like all scientists, you have to focus: that Fuentes has published on a specific research problem does not in any way imply that he lacks a broader knowledge of a field. And if you’re going to play the credentialism game, Fuentes has degrees earned in the last 25 years in zoology and anthropology, with advanced degrees in anthropology, and a professorship at Notre Dame. Wade has a bachelor’s degree from 1964 in some general discipline called “Natural Sciences”. No disrespect, but I teach undergrads, and there is a world of difference between an undergraduate degree and a graduate degree — so for Wade to dismiss Fuentes for an inappropriate educational background is grossly hypocritical.

Furthermore, apparently some of his other critics are so non-sciencey he doesn’t even have to mention them. Jennifer Raff is a post-doc studying the genomes of modern and ancient peoples in order to uncover details of human prehistory — that couldn’t possibly be relevant. Must be political. Jeremy Yoder is a postdoc studying evolutionary genetics at the University of Minnesota. Couldn’t possibly have greater expertise than Wade. Must be political. Greg Laden has a Ph.D. in Archaeology and Biological Anthropology from Harvard. Must not have learned a thing. Must be political. Eric Michael Johnson has a mere Master’s degree (well, he still outranks Wade) in evolutionary anthropology, and is only now working on a Ph.D., so he can be ignored. Must be political.

Now don’t go the other way and assume a fancy degree makes them right — you have to look at the arguments and evidence to determine that. But one thing you can know for sure: when someone stoops to rejecting a criticism by inappropriately and falsely nitpicking over the legitimacy of their training, you know they’re desperate. You also know they’re damned lousy scientists.

That also goes for the HBD racists who think calling evolutionary biologists “creationists” is an effective strategy.

Greg Laden must be another of those creationists

By the criteria of those HBD kooks, anyway. He’s published a take-down of Nicholas Wade’s book in American Scientist, pointing out the familiar scientific consensus that inflames them so.

As soon as it appeared, Wade’s book touched off a firestorm of controversy—as he surely knew it would. It’s the latest in a series of dispatches concerning human variation, whose authors in recent decades have starkly divided into two camps, one centered in anthropology and the other in psychology, political science, and economics. Wade is in the latter camp. The Bell Curve: Intelligence and Class Structure in American Life, a widely read text by psychologist Richard Herrnstein and political scientist Charles Murray in 1994, proclaimed intractable human differences in ability between races; the authors based their views on disputed work published by Canadian psychologist J. Philippe Rushton in the 1980s and early 1990s. Meanwhile, anthropologists had developed a divergent concept of human variation, reaching the collective conclusion that the human species is not compartmentalized in races or subspecies (interchangeable terms in zoology). In 1998 the American Anthropological Association adopted its Statement on Race asserting that the best available research shows race to be a social construct that is biologically invalid.

The HBDists were threatening to vote for me as creationist of the year — I thought I’d be a shoo-in, especially if I recognized it as a pointless poll and asked all of you to vote for me. But maybe now there’ll be enough competition that I shouldn’t get cocky. I think the HBD poll would have to include most of the anthropologists on the planet.