There is so much garbage in the peer-reviewed literature

You should read the whole comic — it’s painfully accurate.

I’ve seen academics form publication rings — not just agreeing to cite each other’s work, but make each other co-authors on all of their papers. I’ve witnessed colleagues put each other down by snarling impact factors at each other. Academia does get ugly.

That said, I don’t know that the remedies suggested in the comic are practical. Maybe the first one would work: having standards and requirements for data sharing, the better to confirm the work. ‘No scientist could possibly object to that,’ I simper naively. Unless there are patents involved.

The second is for universities to change their hiring policies to encourage greater breadth, which would be great, except that the grand poobahs who administer universities tend to be completely disconnected from both the research and teaching going on.

The third is for the funding agencies to wake up and stop throwing all the money to the big flashy projects. There are things like that going on right now, but you know who has the most power in peer review? The scientists who do big flashy projects.

I like this one.

Heh. Where have I heard of that one? The catch there is that that was published by another kind of ring of crackpots, publishing in an obscure specialty journal edited by more crackpots. They can do that. There’s nothing illegal to stop them, and it’s all encouraged by Elsevier, which only cares about money.

You might notice that more than a few people jumped on that as one of the dumbest papers ever written, but there are no academic incentives at all to do that — you can’t get tenure by being good at cleaning up the droppings of bad science, and if anything, it counts against you. Maybe that’s something that could be fixed, but I’m not counting on it.

So, yes, read it, great comic, very accurate, but maybe too optimistic. We need good goals to work towards, though.

We need bigger spiders in Minnesota

Poking around in the weeds as we do every summer, looking for spiders, one thing we turn up a lot are frogs. Big frogs. They like to nestle in some nice shady leaves during the day, and we occasionally part some leafy foliage to find a frog looking back at us, as if wondering how dare we intrude on his home. I’ve often thought they need a good predator to teach them a lesson.

Like a clever huntsman spider.

Retreat and predation event near retreat of Damastes sp. (a) Spider specimen of Damastes sp. (THC140, adult female), the prosoma and opisthosoma are approximately 1.5 cm in length (smallest square = 0.1 cm)—Observation 1; (b) Damastes sp. feeding on Heterixalus andrakata (frog) inside of the retreat, built of leaves of Tambourissa sp.—Observation 1, (c) Predation event where Damastes sp. captured Heterixalus andrakata near the retreat—Observation 1; (d) Damastes sp. hiding in the retreat, built of leaves of Cedrela odorata—Observation 4

These cunning ambushers from Madagascar use silk to stitch together a few leaves, making a nice shady refuge that might appeal to a frog looking for respite from the daytime heat. The frog snuggles in, not noticing the large-fanged venomous arthropod lurking in the back, and then snicker-snack, he’s a juicy piece of meat being sucked dry by Damastes.

I don’t know about you, but if I poked my face into a local bush and saw a big glorious spider instead of a fat frog, I’d be delighted. It’s not likely, though, since our harsh winters tend to kill off most of the spiders, giving them only a short growing and breeding season.

Maybe this would be a bright prospect from global warming? Do you think Republicans would be even more resistant to the idea of good legislation if they thought climate change would create a better environment for big hairy blood-suckers? They do have some things in common.

Seattle will allow you to rot!

Yay for the Pacific Northwest! The first official human composting service in the US has opened. They stuff your corpse in a cylinder with wood chips and rails that automatically rotate your rotting body to maximize the rate that you decompose.

I am impressed with how quick the process is — two months, and then you get to be put into the garden.

The Recompose process takes 30 days in a vessel full of wood chips and straw, then another few weeks in “curing bins,” large boxes (one per person) where soil is allowed to rest and continue exhaling carbon dioxide. Once that process is complete, friends and chosen family can either retrieve the soil themselves, or donate it to an ecological restoration project at Bells Mountain near Vancouver, Washington. So far, most have elected to donate.

What I also find appealing is that the service is based in Kent, Washington, which is where I grew up. There’s nothing special about the location except that I like the symmetry of being recycled back into the place I began when I end.

I’m not the only person with reservations about Eric Lander

500 women scientists feel the same way.

…we can’t help but notice that the recently announced nomination of presidential science adviser Eric Lander fails to meet the moment. His nomination does not fill us with hope that he will shepherd the kind of transformation in science we need if we are to ensure science delivers equity and justice for all. We had high hopes that the Biden administration would continue its pattern of bold nominations when envisioning a newly elevated cabinet position of science adviser. There was certainly no shortage of options, with a deep bench of qualified women and Black, Indigenous and people of color (BIPOC) whose expertise and experience can transform the place of science as a tool for justice.

Lander, an MIT geneticist and former co-chair of the President’s Council of Advisors on Science and Technology (PCAST)—exemplifies the status quo. With this nomination, the opportunity to finally break the long lineage of white male science advisers has been missed. This was a chance to substantively address historical inequalities and transform harmful stereotypes by appointing someone with new perspectives into the top science adviser role. Despite a long list of supremely qualified people that could have held this position and inspired a whole new generation of scientists, the glass ceiling in American science remains intact.

While we can celebrate the Biden-Harris administration’s commitment to science, we must recognize that Lander has a reputation among some scientists for being controversial, and colleagues have criticized him for his “ego without end.” We cannot forget that in 2016, Lander wrote a widely criticized history of the revolutionary technology CRISPR, dubbed the “Heroes of CRISPR,” that erased the contributions of two women colleagues. This conspicuous exclusion is emblematic of the forces in science that hold back women and scientists of color from attaining the level of prominence he enjoys.

They also reminded me of that time Lander toasted James Watson.

Whoops.

The article also has suggestions for how Lander could improve his role as a science advisor.

Spider skeleton

It must be convenient to be a spider at Halloween. To decorate, you just rummage through your closet and pull out an old molt — instant skeleton!

The good news, too, is that my latest generation of spiders are growing up, and starting to molt. Here’s a shed spider cuticle I found today.

They shed by popping open the top of their head, which you can see at the top left, and then back out, pulling their legs up out of the old limbs. I keep hoping to catch them in the act, but I think they do it in the middle of the night, to minimize the danger while defenseless.

I put a picture of her post-molt down below.

[Read more…]

Today at 3 central time, EVO-DEVO

I’m going to put off the celebratory imbibery a bit longer today so that I can talk about development of the nervous system.

I’ll be stone cold sober, but I might still be a little giddy. I’ll be discussing “Evolving specialization of the arthropod nervous system”, published in PNAS in 2012, sort of — there’s lots of good stuff in there, but I might dwell on neurectoderm formation a bit longer than Jarvis, Bruce, and Patel. Because it’s cool.

Last call: if you want join me over Zoom, send me an email, maybe I’ll send you a zoom link. Otherwise, feel free to join the YouTube chat!

It is appropriate that today I would be reading about a fossilized dinosaur butthole

Nice. Paleontologists found a fossil Psittacosaurus with beautifully preserved scales — they can even see signs of the pigments coloring it — and best of all, they found a perfectly preserved cloaca.

The Frankfurt specimen of Psittacosaurus sp. (SMF R 4970) from the Early Cretaceous Jehol deposits of Liaoning exhibits the best preservation of scale-clad integument in any non-avian dinosaur yet described. Preservation of colour patterns and countershading allowed a detailed reconstruction of this individual’s physical appearance suggesting it was camouflaged for life in a shaded lighting environment. It was previously noted that the cloacal region was preserved2, but its detailed anatomy was incorrectly reconstructed. We show here that the fine anatomy of the vent is remarkably well preserved and can be retrodeformed to illustrate its three-dimensional nature. The vent’s scale anatomy and pigmentation are distinct from adjacent body regions, and although its anatomy does not reveal much information about the ecology, or sex, of this dinosaur, it suggests possible roles for visual and olfactory signalling.

The caption to this figure is messed up. The top half, labeled A, is “Cloacal vents across the tetrapod phylogeny”. The text below refers to the bottom half only, and should be specifying B, C, and D rather than A, B, and C. Looks like a job for an editor.

(A) Cloacal vent region preserved in Psittacosaurus sp. SMF R 4970, photographed with crossed polarised lighting. The specimen is exposed in oblique (right) latero-ventral view. The ischial callosity is defined by its bulging appearance on top of the ischium, having large, rounded scales that are heavily pigmented centrally but become lighter marginally. Posterior to the ischial callosity is the cloacal vent, partly obscured by a preserved coprolite and rock breakage. The lateral lips are defined by their distinct outline, indicated by relief and break of slope due to overlap, and are covered by highly pigmented and overlapping scales with lighter margins (Figure S1C,D). (B) Interpretative drawing of the same region as in (A). (C) 3D reconstruction of the cloacal vent in lateral view. (D) Phylogeny of tetrapods illustrating the diversity of cloacal vent morphologies. Two alternative reconstructions are presented for Psittacosaurus sp. depending on whether the cloacal opening forms a slit onto the dorsal lobe, as in crocodylians (ii), or a rounded hole between the lateral lips, as in birds (i).

I’m doing it again!

Another conversation about evo-devo! On Wednesday at 3pm Central (note change in time: I’m teaching again, so had to work my schedule around genetics lectures and labs).

This week, we’re talking again about a paper from the Patel lab, Evolving specialization of the arthropod nervous system, published in PNAS in 2012. If you’ve read the paper and want to help me explain it, drop me a line and maybe I’ll send you a link.