Another bad memory

Oh, no. You must understand, in the late 80s and 90s, growth cone navigation was my jam. It’s what I was doing research on, and my head was full of papers from that era. Netrin, robo, slit, various molecules that attracted or repelled growing axons to establish the pattern of connections in the early developing brain…that was what I did. Now I learn that some of those papers, those written by Marc Tessier-Lavigne, were a lie.

Marc Tessier-Lavigne, the former president of Stanford University who resigned following scrutiny of his published papers and an institutional research misconduct investigation, has retracted a third paper, this one from Cell.

Last week, Tessier-Lavigne retracted two articles from Science that had been published in 2001.

The Cell paper, A Ligand-Gated Association between Cytoplasmic Domains of UNC5 and DCC Family Receptors Converts Netrin-Induced Growth Cone Attraction to Repulsion, was published in 1999. It has been cited 577 times, according to Clarivate’s Web of Science.

In my circles, Tessier-Lavigne had a colossal reputation — he was turning out all this work from a prestigious, well-funded lab with an army of students and post-docs. I was teaching developmental biology, talking about netrins, with a textbook that already cited the Tessier-Lavigne work. Such cool stuff, and it can’t be trusted anymore.

Worse, can we trust Cell magazine? They’ve posted the retraction, and it admits that the editors didn’t care about faked data.

In 2015, we, the authors, consulted with Cell editors about issues that had been brought to our attention about this paper, specifically image splicing in Figures 3C, 5A, 5B, and 7B–7D and duplication of blank blots in Figure 7C. Cell declined to publish a Correction at that time because in 1999, when the paper was published, the journal did not have policies prohibiting unmarked image splicing and because, for the duplication, there was insufficient information to determine intent, and the impact of the duplication on the paper’s conclusions was limited. In 2022, when new concerns were raised, Cell posted an Editorial Expression of Concern (Cell 186, 230 [2023], https://doi.org/10.1016/j.cell.2022.12.019) while an institutional investigation was conducted. The investigation is complete and has revealed further issues including manipulation of data-containing portions of Western blot images in Figures 3A–3C, 7A, 7B, and 7D, undermining confidence in the paper’s conclusions (https://boardoftrustees.stanford.edu/wp-content/uploads/sites/5/2023/07/Scientific-Panel-Final-Report.pdf). As a result, we are retracting the paper. We regret the impact of these issues on the scientific community.

Yikes. All it should take is one fudged image to cast doubt on the entire paper. If you’re faking data, we have sufficient information to determine intent — I was brought up with strict instruction that you never never never never ever do that.

What a disgrace. Shame on Tessier-Lavigne, and shame on Cell.

MORE SPIDERS

I saw the mommy spider spin the egg sac on 21 August, and this morning, the 6th of September, they finally emerged. These are Parasteatoda tepidariorum — note the leopard pattern on the abdomen. That’ll turn into a more complex mottling as they get older. Also see how the legs are mostly pale, but with distinct bands.

Steatoda triangulosa has a longer incubation time of 30 days, and the spiderlings emerge with pale abdomens and black, hairy legs.

The important thing about this is that we can nail down how long the incubation period for both species is under our specific culturing conditions. Now we wait for the Steatoda borealis egg sac to hatch out so we know its incubation period. Then…comparative embryology!

By the way, the lab was hectic this morning, with 150 tiny baby spiders, each about 3/4 of a millimeter long, emerging all at once and immediately trying to disperse. There was a cloud of barely visible dots all radiating out instantly from the locus of their home vial, while I was frantically trying to gather up individuals and put them in separate containers. Some, I’m sure, escaped.

Hmmm, is it ever a good thing when a scientist says that?

Since I avoid posting spiders here, you’ll have to go to Patreon or Instagram to see the baby picture.

I refuse to mansplain vaginas to you

Instead, I’ll let the Vagina Museum talk about spider vaginas (actually, they’re called epigynes…oh crap, I did it anyway.)

Very few people are interested in spider epigynes, so here, here’s a whole article about vaginas. They’re rather nifty organs, you know, with many different names.

Hah! You probably thought I was going to list a bunch of slang terms, didn’t you?

How about if I show you pictures of vaginas instead?

[Read more…]

The crunch begins

I have resolved that this year, I will get all student assignments graded within 24 hours of their scheduled due date. Guess what? First formal assignment was turned in yesterday for cell bio. I also had to compose a practice exam for Fundamentals of Genetics, Evolution, and Development, which was posted this morning and will be due on Monday.

I can tell already that my discipline is going to be murderous, requiring intense bouts of activity, since I won’t allow myself to drag things out over several days. Periodically intense pain vs. chronic pain? Which is worse? I’ll find out.

Yikes, low enrollments are a problem

I still have to do something about the lack of garish chemicals. They’re mostly clear or gray or cloudy.

Every fall I teach 3 lectures a week in cell biology, and it used to be 3 lab sections. We pared it back to two labs this year, and then…one of them was drastically under-enrolled, so we’re shifting everyone in it to our Wednesday afternoon lab. I’m only teaching one lab this year??!? Feels like cheating.

I’ve still got at least one class every weekday, but suddenly a big block of time opened up for the spiders, which is good. My first year classes are filling up, which probably means I’ll be back to the usual number of lab sections next year. If you want lots of one-on-one attention in biology, though, this is the year to be here.

Open the floodgates

That Washington Post series on arch-racist Ales Hrdlicka has really stung the Smithsonian. The Secretary of the Smithsonian has written an op-ed apologizing for its history.

Anthropologist Ales Hrdlicka served as the head of the Smithsonian’s physical anthropology division from 1903 to 1941, when the majority of the human remains in our collections were obtained. During Hrdlicka’s four decades at the institution, he oversaw the acquisition of hundreds of human brains and thousands of other remains. The overwhelming majority of these remains were taken without the consent of the deceased or their family members, and Hrdlicka took particular interest in the remains of Indigenous people and people of color to undergird his search for scientific evidence of white superiority.

It was abhorrent and dehumanizing work, and it was carried out under the Smithsonian’s name. As secretary of the Smithsonian, I condemn these past actions and apologize for the pain caused by Hrdlicka and others at the institution who acted unethically in the name of science, regardless of the era in which their actions occurred.

I recognize, too, that the Smithsonian is responsible both for the original work of Hrdlicka and others who subscribed to his beliefs, and for the failure to return the remains he collected to descendant communities in the decades since.

OK, that’s a good start, but so far it’s just words. Tell me what you are doing, because that’s where the excuses get weak. The material changes so far are that they have repatriated a few thousand remains, they have formed a task force, and they promise future policy changes.

Our forthcoming policy will finally recognize these remains not as objects to be studied but as human beings to be honored. It is a long-overdue shift, and I regret that human bodies were ever treated with such disrespect at our institution.

If I may suggest an alternative response: reverse the obligations. Assume every single piece of flesh or bone must be traced to their origins as quickly as possible and returned to their peoples; the priority is to get rid of all of it. If anything is to be retained, someone must be named as responsible for the objects, and must have a specific scientific plan for extracting information from them in the near future, and then returned. Right now, everything is backwards, where we just assume if someone has a bunch of bones in a barrel, well, it belongs to them, even if all they can say is a vague assurance that it’s in a “teaching collection.” I always wonder what they plan to teach with them.

If you want to claim something is scientifically valuable, the onus is on you to justify that claim.

Charles Murray is still an ignoramus

I’ve been telling you, Charles Murray is an ignorant hack. I can’t stand listening to this know-nothing pontificating on genetics when he’s so full of shit on the topic, which doesn’t stop him from being arrogantly confident about it.

Anyway, here’s a good critique of The Bell Curve — it’s hard to believe we still have to argue about it.

Understandably, these arguments provoked the ire of progressively minded scientists and commentators. However, the sweeping and reflexive manner in which opponents of the hereditarian arguments advanced their objections to The Bell Curve often led these critics to adopt counterproductive conclusions. Unhelpfully, they conflated two distinct issues. The first is the question of what it means to claim that something is genetic, and the second is the inevitability of certain life outcomes based on the biology of a particular organism.

Properly speaking, genetics concerns some characteristic of an organism varying across individuals in a group in a given context. It is, by definition, not an explanation of the behavior or development of a given individual in a given instance. Conflating the issue of the causes of differences with that of the inevitability of the development of a particular organism is an important part of the hereditarian rhetorical strategy deployed by the likes of Herrnstein and Murray. To the extent that their arguments have managed to gain some traction in the world, it has been because they have managed to convince their critics to commit the error for them.

Whoa there — the heart of my criticisms of Murray has always been that genetics is not as determinative as the naive people who learned about Punnett squares in fourth grade think. But do go on, this is an important definitional issue and bears repeating.

But the confusion in Murray and Herrnstein’s thinking doesn’t just stop at their pessimism about the kind of practical responses to differences purportedly caused by genetics — it goes all the way down to their understanding of what genetics is. Let’s start by clarifying what we mean by “genetic” and outline why that which is genetic is not necessarily inevitable. For one, genetics deals with groups of organisms rather than the life outcomes of individual organisms. All organisms have genes, but it takes groups of organisms to have genetics because genetics is ultimately about how variation is structured within a group.

Take a single tomato plant in isolation. It has a genome that is between one-fourth and one-third the size of that of a human’s in terms of the raw amount of DNA. Inside its genome are a few tens of thousands of genes, which, in this case, are stretches of the genome that form a chemical template for the cellular production of the proteins and other biochemicals that are vital for the structure and function of organisms. However, since we are dealing with a single plant at a single point in time, there is no comparative context that would allow us to identify the differences among organisms that characterize the rich diversity of life.

Exactly! This is also why it’s important that students actually do real crosses with real organisms. The abstractions of theory might tell you that oh, one quarter of the progeny will have a particular phenotype, but when you sit down and have to closely examine a thousand flies, you get to see all the variation you did not predict and you learn that it’s never as simple as the models tell you it is. The variation is also interesting.

But yes, genetics is fundamentally probabilistic. You can’t use it to predict individual destiny. It’s also the case that genetics has significant interplay with the environment.

But even having many organisms to compare is not sufficient for a biological system to display genetics in the proper sense of the term. Genetics in the sense that matters is ultimately about variation that arises from genetic differences. To see this, think again about tomatoes. They can be cloned with ease by taking cuttings from a single plant and growing them in their own allotments of soil. Genetically, the different newly individualized plants will be identical to one another, with the exception of a very few mutations — spontaneous changes to DNA that can occur during cellular replication.

If we were to compare a large number of these cloned tomato plants, we would find many differences among them. The shape and sizes of leaves would differ, as would the coloration of the fruits and the pattern of branching along the stalks. Since, on account of being clones, the plants are all genetically identical, these differences could not be attributable to genetics. While each of the plants has genes and we have a group of plants to form the basis for comparison needed to establish that there is variation, there are no genetic differences among the plants that could account for any of that variation. That is, while our tomato plants have genes, they display no genetic differences among one another despite having physiological differences.

Yes, that’s always been obvious if you actually look at populations. I had tanks of zebrafish that were about as genetically uniform as you can get, highly inbred for over a century — yet I could recognize individuals in a tank and see differences in behavior. I’ve only been inbreeding spiders for a half dozen generations, but I don’t see variation diminishing, at least not yet.

How do people take Murray seriously when his fundamental understanding of biology is so wrong?

The horrible ghouls of 20th century anthropology

This is a photo of Mary Sara, an 18 year old Sami woman who traveled to Seattle in 1933, accompanying her mother, who was getting cataract surgery. While there, Mary died of tuberculosis, which is tragedy enough…but then the ghouls arrived.

The Smithsonian wanted her brain.

The young woman — whose family was Sami, or indigenous to areas that include northern Scandinavia — had traveled with her mother by ship from her Alaska hometown at the invitation of physician Charles Firestone, who had offered to treat the older woman for cataracts. Now, Firestone sought to take advantage of Sara’s death for a “racial brain collection” at the Smithsonian Institution. He contacted a museum official in May 1933 by telegram.

Ales Hrdlicka, the 64-year-old curator of the division of physical anthropology at the Smithsonian’s U.S. National Museum, was interested in Sara’s brain for his collection. But only if she was “full-blood,” he noted, using a racist term to question whether her parents were both Sami.

The Smithsonian houses over 30,000 body parts, including hundreds of brains.

Nearly 100 years later, Sara’s brain is still housed by the institution, wrapped in muslin and immersed in preservatives in a large metal container. It is stored in a museum facility in Maryland with 254 other brains, amassed mostly in the first half of the 20th century. Almost all of them were gathered at the behest of Hrdlicka, a prominent anthropologist who believed that White people were superior and collected body parts to further now-debunked theories about anatomical differences between races.

There they sit to this day, gathered by Ales Hrdlicka, who somehow became a curator at the Smithsonian and a prominent defender of racist pseudoscience.

Hrdlicka, who was born in what is now the Czech Republic, received medical training from the Eclectic Medical College of New York City and the New York Homeopathic Medical College in Manhattan before moving into the field of anthropology. He was seen as one of the country’s foremost authorities on race, sought by the government and members of the public to prove that people’s race determined physical characteristics and intelligence.

He was also a longtime member of the American Eugenics Society, an organization dedicated to racist practices designed to control human populations and “improve” the genetic pool, baseless theories that would be widely condemned after the Nazis used them to justify genocide and forced sterilization during the Holocaust. In speeches and personal correspondence, he spoke openly about his belief in the superiority of White people, once lamenting that Black people were “the real problem before the American people.”

“There are differences of importance between the brains of the negro and European, to the general disadvantage of the former,” he wrote in a 1926 letter to a University of Vermont professor. “Brains of individual negroes may come up to or near the standard of some individual whites; but such primitive brains as found in some negroes … would be hard to duplicate in normal whites.”

That is truly remarkable. The article focuses on the abuse of autonomy of so many people who had their brains scooped out and sent off to Washington DC, and that is definitely an important issue. But I was reading it and asking myself, “What science was done? What did we learn? What did he discover to justify calling the brains of black people ‘primitive’?” It turns out to have been nothing.

The extent of Hrdlicka’s own research on the brains is unclear. When a professor wrote to him and asked about the differences he found between the brains of people of different races, he replied that research studies showed the superiority of White brains, without citing any studies of his own. He published a 1906 study on brain preservatives, recording the weight of human and animal brains and comparing how they fared in a chemical solution. But The Post found no other research on the brains by Hrdlicka.

I know a bit about neuroscience, and I find the whole approach unproductive and baffling. Sure, you could do crude measurements, weighing brains and slicing them open to measure the gross morphology of regions and nuclei…but we know that all of that is so variable and often so irrelevant to the functioning of those brains that you can’t learn anything from it. We simply don’t know enough about the details of how brains work that, aside from major abnormalities, you can’t conclude anything about the minds housed in those lumps of meat by hacking them up, and you especially couldn’t do anything with the information in the early 20th century.

Basically, Hrdlicka was nothing but an obsessive and rather morbid collector. His ‘credibility’, what there was of it, rested entirely on accumulating the largest collection of brains, like bloody tragic Pokemon. He didn’t have to think. He didn’t have to study. He was just gathering gory fragments of human beings and parading them before other bad scientists who thought this was an accomplishment. The Smithsonian should be ashamed, we should all be ashamed that this charade of race ‘science’ was perpetrated for so long, and that people continue to think this was a useful approach to justify their bigotry to this day.

Hrdlicka really was a ghoul. When an exhibit of Filipino culture, represented by a large number of people from that country, was held at the World’s Fair, he had one thing on his mind: “That summer, Hrdlicka headed to St. Louis, hoping to take brains from Filipinos who died.” He collected four brains from the unfortunate people who died incidentally there (tuberculosis and pneumonia were Hrdlicka’s friends).

Ugh. The Smithsonian, and other museums around the country, need to address this ugly stain on their history, and make amends to the people they exploited for such stupid ends.

Science relies on honest observation

Elisabeth Bik is getting mad. She has spent the better part of a decade finding examples of scientific fraud, and it seems to be easy pickings.

Although this was eight years ago, I distinctly recall how angry it made me. This was cheating, pure and simple. By editing an image to produce a desired result, a scientist can manufacture proof for a favored hypothesis, or create a signal out of noise. Scientists must rely on and build on one another’s work. Cheating is a transgression against everything that science should be. If scientific papers contain errors or — much worse — fraudulent data and fabricated imagery, other researchers are likely to waste time and grant money chasing theories based on made-up results…..

But were those duplicated images just an isolated case? With little clue about how big this would get, I began searching for suspicious figures in biomedical journals…. By day I went to my job in a lab at Stanford University, but I was soon spending every evening and most weekends looking for suspicious images. In 2016, I published an analysis of 20,621 peer-reviewed papers, discovering problematic images in no fewer than one in 25. Half of these appeared to have been manipulated deliberately — rotated, flipped, stretched or otherwise photoshopped. With a sense of unease about how much bad science might be in journals, I quit my full-time job in 2019 so that I could devote myself to finding and reporting more cases of scientific fraud.

Using my pattern-matching eyes and lots of caffeine, I have analyzed more than 100,000 papers since 2014 and found apparent image duplication in 4,800 and similar evidence of error, cheating or other ethical problems in an additional 1,700. I’ve reported 2,500 of these to their journals’ editors and — after learning the hard way that journals often do not respond to these cases — posted many of those papers along with 3,500 more to PubPeer, a website where scientific literature is discussed in public….

Unfortunately, many scientific journals and academic institutions are slow to respond to evidence of image manipulation — if they take action at all. So far, my work has resulted in 956 corrections and 923 retractions, but a majority of the papers I have reported to the journals remain unaddressed.

I’ve seen some of the fraud reports, and it amazes me how stupid the scientists committing these fakes must be. It’s as if they think jpeg artifacts don’t exist, and can be an obvious fingerprint when chunks of an image are duplicated; they don’t realize that you can reveal cheating by just tweaking a LUT and seeing all the duplicated edges light up. The only reason it’s done is to adjust your data to make it look like you expected it to look, which is an obvious act against the most basic scientific principles: you’re supposed to use science to avoid fooling yourself, not to make it easy to fool others.

This behavior ought to be harshly punished. If image fakery became in issue when one of my peers came up for tenure or promotion, I’d reject them without hesitation. It’s not even a question: this behavior is a deep violation of scientific and ethical principles, and would make all of their work untrustworthy.

Also, this is a problem with the for-profit journal publication system. Those scientists paid money for those pages, how can we possibly enforce honesty? The bad actors wouldn’t pay us for journal articles anymore!

But guess what happens when Elisabeth Bik takes a principled stand?

Most of my fellow detectives remain anonymous, operating under pseudonyms such as Smut Clyde or Cheshire. Criticizing other scientists’ work is often not well received, and concerns about negative career consequences can prevent scientists from speaking out. Image problems I have reported under my full name have resulted in hateful messages, angry videos on social media sites and two lawsuit threats….

Things could be about to get even worse. Artificial intelligence might help detect duplicated data in research, but it can also be used to generate fake data. It is easy nowadays to produce fabricated photos or videos of events that never happened, and A.I.-generated images might have already started to poison the scientific literature. As A.I. technology develops, it will become significantly harder to distinguish fake from real.

Science needs to get serious about research fraud.

How about instantly firing people who do this? Our tenure contracts generally have a moral turpitude clause, you know. This counts.