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.
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.
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?
Science magazine says The legendary dire wolf may not have been a wolf at all, while the actual article published in Nature says only Dire wolves were the last of an ancient New World canid lineage, and says that grey wolves and dire wolves are not as closely related as previously thought.
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
OK, then, what is a wolf? If we saw a large canine that hunted in packs nowadays, wouldn’t we call it a wolf, while recognizing that it could be distinguished scientifically as a different species? What does “closely related” even mean?
I looked at the results.
Just to put it into context. if dire wolves and grey wolves diverged less than 6 million years ago, that means their relationship is comparable to that of modern humans and chimpanzees, which diverged about 6 million years ago, too. Meanwhile, the various local house spiders I study diverged 50-100 million years ago. Would we have an article declaring that chimpanzees aren’t apes? I don’t think so.
Dire wolves were wolves. They’re a distinct lineage with an interesting history, but I’m not particularly interested in arguing about whether certain colloquial terms or folk taxonomy are appropriate.
Reminder: we’re going to talk about color patterns today at noon Central time.
I encourage you to feel free to interrupt with questions/comments in the chat, and also if you’ve read the paper you can request a Zoom link by email.
I had a productive discussion with Phrenotopian, Jackson Wheat, and Nesslig 20 yesterday, in which I got lots of suggestions for how to make the science content of my YouTube channel more interesting. Now I just have to implement them! Starting on Wednesday!
I’m going to talk about evo-devo again, but with a revised format that allows for more actual discussion. So, on Wednesday at noon Central time, I’m going to fire up Zoom and Keynote and YouTube, all at the same time, and talk about Evolution of Coloration Patterns, a 2008 paper by Meredith Protas and Nipam Patel. You can give me feedback as we go in the chat, but also, if anyone wants to participate directly and put their face/avatar on screen, we can do that, too. Just send me an email, and I might send you a link back if 1) you promise to have read the paper, and 2) you think you have something to say.
I have other changes in mind for the future; maybe I’ll allow voice chat from the FtB Discord at some time. Not yet, though, but I’ll be experimenting.
Today was a big spider maintenance day. I’ve got three lines of spiders I’m raising — R (from a spider collected at Runestone park), H (from the local Horticulture garden), and M (from the Myers garage) which I’m trying to bring to maturity, so they’re getting lots of food and care, which I want to start inbreeding and generate 3 lines of related spiders so I can start assessing their variation…and then start cross-breeding. It’s going to take a while.
Anyway, down below the fold is one that’s definitely male and might be ready for mating after the next molt. His palps look painfully swole.
Not for me, of course — people don’t eat food in the lab — but for the adorable baby spiders, who got some delicious live flies and immediately wrapped them up and sucked their brains out. I’ve got two photos of two different spiders that adopted remarkably similar feeding behaviors, biting their prey in the head and slurping up their juices.
Did you know classes start in 2½ weeks? It’s astounding; Time is fleeting; Madness takes its toll…but rather than doing the time warp, unfortunately, I spent several hours doing basic custodial work in the lab. First, a colleague and I scrubbed up the cell biology lab, shuffling computers into storage and putting away glassware, because that space will be used for a different course Spring semester. It’s tidy! And shiny!
Then I went into my lab, which is cluttered and grimy, and I need to make a few trips to a dumpster and polish up a whole lot of stuff — the sink is piled high with empty spider vials that need washing, for one thing. Today I set aside all the menial labor, though, and instead dismantled my microscope and cleaned up all the optics. That was fun! I may do it again tomorrow!
The filth wasn’t as bad as I feared, fortunately. One glass surface had accumulated a bit of dust and grime, and was fairly easy to wipe clean. I did have to take apart a few subassemblies, but thankfully, good German engineering made it easy.
I had to test it out with a few photos, but whereas the engineering was cooperative, the spiders were not. The entire interior of their condo cube was an intricate network of spider webs everywhere, so opening up the cube always tore their webs, making the kids frantic and excited, so they were mostly unwilling to sit still for their portrait.
I put a sample spider photo below the fold, and you’ll see what I mean — it’s all criss-crossed with silk, and I played a few lighting games to make it visible. Also note that the image is much, much better than the last spider photo I posted here.
This morning I resolved to figure out what was going on with my muddy images from microscope. The first step was a general cleaning, and I discovered a real horror. Here’s the trinoc head for my Wild M3C:
See that tube on the right, for the camera? I looked down it. GAAAAAA. Dust and dirt and I swear, cobwebs all over. It’s a 30 year old microscope, and we’ve had microscope technicians come through every couple of years to do general maintenance on all the teaching scopes, but that tube may not have been cleaned ever in all that time. There’s a very important mirror down at the bottom of that L-shaped widget, and I think the only way I can get at it properly is to dismantle the whole device — there are a couple of tiny metric hex bolts holding it all together, and I guess I’m going to have to take it apart and try not to break everything.
Anyway, I did push the dirt around a little with a microfiber cloth, and it’s slightly better, but I think it’s filmed over with something that is fouling the image. I took a test photo of this little guy, and it’s an improvement, but still far from perfect. The image through the eyepieces is beautifully crisp, so I’m definitely blaming the problem on that little mirror and decades of neglect.
‘Ware spider below the fold!
