It’s an anniversary!

Ten years ago today, the Lancet issued a formal retraction of Andrew Wakefield’s notorious bogus paper claiming a link between MMR vaccinations and autism. The paper was wrong, it was shoddily done, and the work hasn’t been replicated.

Ever since, Wakefield has been living in shame, no one treats him as an authority anymore, and of course no one would claim that vaccines cause autism anymore.

Why do scientists cheat?

I am dismayed at this emerging story about fraud in science. It stars Jonathan Pruitt, a professor at McMaster University who studies variation in individual behavior and how it affects group behavior. I’d heard of him since he’s doing a lot of work in social spiders.

He built up several productive collaborations, in particular with Kate Laskowski at UC Davis, sharing data with her that she used in several publications. That’s where the story turns dark, because Laskowski later examined the data in more detail and found multiple examples of blocks of data having been duplicated, padding the data set with more replicates than were actually done. He’d actually passed her a poison pill that tainted all the work they’ve done together; her papers are no longer trustworthy, and she has retracted them.

Laskowski is being heroically restrained in her reaction to this betrayal — I’d probably be throwing things and saying lots of not-nice words. Pruitt also seems to be peculiarly blasé and detached from the problem, conceding that there are serious problems in the data set, but not offering any explanations about how this has happened (again, if some of my data were found to be bogus, I’d either be furious and trying to track down the source of the bad data, or, if I were guilty of doing the duplications, I guess I’d be trying hard to deflect.)

There’s a lot of discussion and dissection of this issue going on, and most of it seems to be rightly concerned with making sure Pruitt’s coauthors aren’t hit with serious splash damage. At some point, though, there has to be a reckoning, and the source of the contamination tainting so much work will have to be dealt with. So far, everyone seems to be strangely cautious and circumspect.

I will not say Jonathan Pruitt is a victim, but he is part of the tragedy. Will we ever really know what motivated him? I decline to guess. He burst on the animal behavior scene with his first paper in 2008 and immediately began publishing at such a prolific rate that in another year or two he would have overtaken my own 41 year career in numbers of publications. This output got him a lot of academic success leading to his current position (current as I write anyway) of Canada 150 chair at McMaster University.

What Jonathan Pruitt produced was so far beyond average, it is hard to believe anyone would feel pushed to that level. But others feel pressure to produce in academia.

Fine. I’m not involved in any of this concern, so it’s not my place to say how the victims ought to respond. But I would say that the slower the build-up, the bigger the explosion, and so far this is looking to be a truly ugly meltdown at some point in the near future. Keep an eye on Jonathan Pruitt, there will be a supernova at some point soon, and not the good, pretty kind.

I’m mainly dismayed at the failure of scientific ethics. You don’t make up data! Ever! Every year I’m in student labs, explaining to students that “your data is your data” (I literally say that a lot, I’m afraid), and if your experiment didn’t come out the way you expected, or the data are ambiguous about what the one true Answer is, your job isn’t to make the data fit, it’s to rethink your work, track down sources of confusion, repeat the work, analyze the results appropriately, and if it doesn’t support your expected answer, revise your expectations.

That’s easy for me, though. The students don’t have a publication in Nature or a tenure decision in their favor, so they’re lacking all that unscientific pressure to get the neat, tidy, snazzy answer with beautiful p values.

It’s going to be a long semester

Tuesdays I have a morning class and an afternoon lab; sandwiched in between was a discipline meeting. I think I’m plum wore out today.

Just to make it more awful, the first genetics assignment is due tomorrow, and I made an awful hash of it, trying to juggle multiple textbook editions, so the students are all confused. So I made an announcement that the assignment is basically cancelled, ignore everything I said, and I’ll come in tomorrow with a whole new problem set that we’ll work on together. What a mess. I’m exhausted just thinking of sorting it all out.

A whole lot of chompin’ and sexin’ going on

This is a beautiful video about the arachnids of Uruguay — great videography and information, and some spectacular closeups of spiders in action. They do seem to spend a lot of time murdering insects and sucking them down, and the sex scenes, especially in the sexually dimorphic species, can be graphic and moderately distressing — tiny males scurrying up to the abdomens of huge females, it’s like trying have sex with a wall topped with fangs that can descend when you’re done and kill you.

It’s all still pretty, and now I want to visit South America. I’ve been to Ecuador, but that was before I discovered the wonders of spiders. I should go again, except…damn this legal weight on my shoulders.

Everyone needs more training to deal with racists

Adam Rutherford is coming out with a new and timely book, How to Argue with a Racist, expected here in the US in early February. I’ve already pre-ordered a copy, and if you’re interested, you can get a taste of the story in The Guardian.

In the 19th century, Darwin’s half-cousin Francis Galton and others tightened their scientific arguments for race though, as Darwin noted, no one could agree on how many races there actually were, the range being between one and 63. Galton was an amazing scientist, and a stunning racist. The most delicious irony about him is that the field he effectively established – human genetics – is the branch of science that has demonstrated unequivocally that race is not biologically meaningful. Modern genetics clearly shows that the way we colloquially define race does not align with the biology that underpins human variation. Instead, race is a cultural taxonomy – a social construct. This doesn’t mean it is invalid or unimportant, nor does it mean that race does not exist. Humans are social animals, and the way we perceive each other is of paramount importance. Race exists because we perceive it.

That’s one message I wish I could get across to all the so-called “scientific” racists. The consensus of real, honest science is that the artificial categories people assign to races don’t exist as biological phenomena. You only find it in the pages of racist ideologues like Charles Murray or hothouse niches on the internet for dishonest cranks like Steve Sailer. Or right-wing think-tanks. Or misinformed YouTubers who got millions of views by parroting bigotry.

I think this book ought to be required reading for journalists and other media spokespeople who seem to be responding to the rise of racism among people with power with nothing but rank credulity and reporting that just echoes the biases without criticism. Maybe the Democratic presidential nominee, whoever it might be, ought to read it to be prepared for debates with our racist president.

The one that got away…in the Mesozoic

It was a bad day for both the squid, Plesioteuthis, and the Rhamphorhynchus that was skimming over the water, trying to snag dinner. The squid got stabbed by a sharp fang, and the reptile lost a tooth and a meal. We know this because of the beautiful fossil found with a broken off tooth preserved in its mantle.

Plesioteuthis subovata from the Late Jurassic Solnhofen Archipelago. An adult specimen, 28 cm long, preserved with ink sac and duct, arm-head complex, well-preserved mantle musculatures (transverse striation) and a pterosaur tooth. (B) Close-up of the 19 mm long, slightly curved Rhamphorhynchus muensteri tooth crown under normal light. (C) Ultraviolet (UV) light reveals that the tooth apex is partially covered with now phosphatized mantle tissue.

Ouch.

Direct evidence of successful or failed predation is rare in the fossil record but essential for reconstructing extinct food webs. Here, we report the first evidence of a failed predation attempt by a pterosaur on a soft-bodied coleoid cephalopod. A perfectly preserved, fully grown soft-tissue specimen of the octobrachian coleoid Plesioteuthis subovata is associated with a tooth of the pterosaur Rhamphorhynchus muensteri from the Late Jurassic Solnhofen Archipelago. Examination under ultraviolet light reveals the pterosaur tooth is embedded in the now phosphatised cephalopod soft tissue, which makes a chance association highly improbable. According to its morphology, the tooth likely originates from the anterior to middle region of the upper or lower jaw of a large, osteologically mature individual. We propose the tooth became associated with the coleoid when the pterosaur attacked Plesioteuthis at or near the water surface. Thus, Rhamphorhynchus apparently fed on aquatic animals by grabbing prey whilst flying directly above, or floating upon (less likely), the water surface. It remains unclear whether the Plesioteuthis died from the pterosaur attack or survived for some time with the broken tooth lodged in its mantle. Sinking into oxygen depleted waters explains the exceptional soft tissue preservation.

So now we know that Pterosaurs ate soft-bodied cephalopods.

I wouldn’t have recognized this spider from last week!

Before I left for the Twin Cities this weekend, I’d fed the spider colony fat juicy waxworms, and they fell upon them furiously. Today I checked on them, and boy were there a lot of bloated, indolent spiders lounging about in their webs, reluctant to even move. One surprise…I took a peek at Yara, who I’ve photographed before, and the change was striking, not just in her size, but in her pigment patterns.

Look how dark she is! This isn’t just the lighting, either — I tinkered a fair bit to get good illumination. Compare it to the previous photo, where she’s much lighter in color, and I would have said she was one of the more lightly pigmented members of the colony. Now I’m wondering how rapidly they can change color and what prompts it, especially since I’ve been following pigment development in the babies.

I was also looking at cobwebs today. There might be some potential for student projects here.