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.

$cience gets a seat at the table

We got some wonderful news from Joe Biden last week.

President-elect Joe Biden announced Friday that he has chosen a pioneer in mapping the human genome — the so-called “book of life” — to be his chief science adviser and is elevating the top science job to a Cabinet position.

It’s about time! It’s astonishing that we’ve gotten by without a science advisor to the president or congress, or when we do have one, they’re ignored, but that’s Republicans for you.

Then, this being Joe Biden, he just has to screw it up. He has nominated Eric Lander for the position. If I had to name anyone who is the personification of Big Science, of Corporate Science, of $cience, I’d immediately say Eric Lander, the director of the Broad Institute in Boston. I can see why he was chosen: he’s a successful player, a brilliant man, a knowledgeable molecular biologist, a fantastic organizer — he knows how to run a big lab and a big institute, and is going to fit comfortably into an even bigger position. The man is a machine, and is good at running other machines. One thing Lander has in buckets is ambition.

But…

(You knew that was coming, right?)

First, let’s get a minor issue out of the way. Lander had a brief, tangential association with Jeffrey Epstein. He was photographed attending a meeting at Martin Nowak’s office (Nowak was a significant recipient of Epstein’s largesse and should be looked at more critically), but I’m saying, “So what?” I’m sure Lander gets dragged into all kinds of meetings he’d rather not participate in, as the head of the Broad Institute. There’s no evidence of any other association with Epstein other than that a well-known Harvard professor invited him to meet, and Lander seems to have been uninterested in Epstein.

“Martin invited me to an informal sandwich lunch at his institute to talk science with various people,” Lander told BuzzFeed News by email. “I was glad to do it. Martin didn’t mention who’d be attending. I had not met Epstein before, didn’t know much about him, and learned that he was a major donor to Martin’s institute.

“I later learned about his more sordid history,” Lander added. “I’ve had no relationship with Epstein.”

I think it’s fair to say that Epstein went out of his way to brush shoulders with every big name scientist he could find, Lander is one of the biggest, so he tainted him along with a lot of others.

Far more concerning to me is his attitude towards other scientists who were not under his thumb. Jennifer Doudna and Emmanuelle Charpentier won the Nobel Prize in Chemistry for 2020 for their work on CRISPR/Cas gene editing, and only Doudna and Charpentier. Eric Lander was behind a massive campaign, using all his clout with science publishers and corporations, to promote Feng Zhang, who had also done work on CRISPR, but most importantly, was an employee of the Broad Institute. Lander really wanted the Broad to get the credit for such an important discovery.

So Lander wrote a paper titled “The Heroes of CRISPR” (I was already cringing at just the title) which downplayed the role of Doudna and Charpentier — barely mentioned them at all — and played up the role of others. Like Zhang. Like the Broad Institute. It was bad science and bad history, but it would have been great propaganda if it wasn’t so blatant that everyone caught on to what he was doing.

This controversy does not mean that the work on CRISPR-Cas9 was not initially motivated by a desire to advance scientific knowledge, as Lander asserts in his review. Prizes and patents pollute the story and increase what is at stake, but do not, it is to be hoped, prevent curiosity from being one of the wellsprings of scientific discovery and innovation.

What is new and remarkable is the form that Eric Lander gave to his participation in the debate: the writing of a comprehensive history. Many readers have already pinpointed some problems with this historical record, in particular factual errors. The emphasis Lander places on those involved varies: Zhang’s work from his institute receives a full-page description, whereas the contributions of Doudna and Charpentier are much more briefly described. Rhetorical strategies, such as positioning in paragraphs, were also used to emphasize the value of some contributions over others. For example, Doudna is first mentioned in the middle of a paragraph, as the direct object rather than the subject of the sentence. Charpentier’s name appears at the bottom of a paragraph.

Oh, and he was neck-deep in a patent dispute over CRISPR, a significant fact that he did not mention.

What that all means is that Lander’s reputation among scientists isn’t exactly glowing.

Current and former colleagues contacted by STAT described Lander as brilliant, prickly, and brash, as having “an ego without end,” as “a visionary” who “doesn’t suffer fools gladly,” and as “an authentic genius” who “sees things the rest of us don’t.” Lander won a MacArthur Foundation “genius” award in 1987 at age 30. Since 2009, he has co-chaired President Obama’s scientific advisory council.

In case you’re wondering why Biden picked him, there’s a hint in the above sentence.

Lander was not present at the creation of the $3 billion project in 1990 [the human genome project], but the sequencing center he oversaw at the Whitehead Institute became a powerhouse in the race to complete it. Much of that work was done by robots and involved little creativity (once scientists figured out how to do the sequencing). Some individual investigators felt they couldn’t compete against peers at the sequencing centers in the race for grants.

“He became a symbol of plowing lots of resources into industrialized, mindless science that could be run by machines and technicians and so wasn’t real biology,” said one scholar of that period. “Eric came to embody Big Science in that way.”

More than that, Lander played an outsized role in the project relative to his background and experience. A mathematician by training, after he graduated from Princeton in 1978 and earned a PhD in math in 1981 at Oxford University as a Rhodes Scholar, he taught managerial economics at Harvard Business School from 1981 to 1990. He slowly became bored by the MBA world and enchanted with biology, however, and in 1990 founded the genome center at the Whitehead. It was hardly the pay-your-dues, do your molecular biology PhD and postdoctoral fellowship route to a leading position in the white-hot field of genomics.

Maybe Lander is the future of Big Science, where the Little Scientists get replaced by armies of technicians marching through protocols with the goal of getting a patent and corporate sponsorship, but I don’t have to like it.

Have you ever seen a spider’s heart beat?

Now you can! I saw that I can easily visualize the hearts beating in my baby spiders.

It made me think of those Pro-Life Across America billboards that show a picture of a cute baby and declare “My heart began to beat at 18 days!”, as if that was a significant event. So I take it anti-choicers who see this video will forever after be kind to spiders?