I am vindicated!

I have long been disgruntled by that popular video from Harvard and XVIVO — you know the one I’m talking about, the computer animation of a kinesin walking along a microtubule, carrying a massive vesicle. I wouldn’t use it in my classes because it’s too slick and well-done, and presents a too persuasive view of how the cell works. Where is the constant jostling by water molecules? Where is the stutter in a motion driven stochastically by molecular interactions? Where are all the other proteins competing for binding? It’s rigged to make the motion look so purposeful, which is why that video is so popular among creationists.

I’ve been huffy about it for over a decade, but no one cares, no one listens. But maybe you’ll listen now: Eric Betzig, winner of the chemistry Nobel in 2014, is saying exactly the same thing.

There is a place for simplified illustrations of biological processes. I use them all the time, to get across the specific interactions I’m trying to explain. But there is no place for hyper-detailed animations that portray the interior of a cell as a vast cavernous space with a scattering of robots carrying out missions along precisely engineered pathways.

The end of a distinguished legacy

Some of the best years of my youth were in high school…but not in high school. During those years, we lived in a nice old house in the center of town, my parents and six kids, which was going to change after I graduated, when I moved to another state, my brother joined the army, and my parents moved to another town, after the rental home we lived in was torn down by the Catholic church. There was a sharp division ahead of us.

Before all that changed, though, we lived in this nice older house that was only a few blocks away from the public library. Every day after school I would go to the library and hang out until my mother would send one of my younger siblings over to tell me to come home for dinner. I had a favorite spot in the library, a large table facing the periodicals section, and the first thing I’d do was scan the racks to see what new journals had come in. I liked Natural History, Smithsonian, and especially Scientific American. SciAm would engage me for several days as I would read it cover to cover. Every month throughout my high school years. That’s what made those years happy and memorable because I was a nerd, who missed out on all that socialization that normal kids experienced.

It’s the end of an era now, though. Scientific American is dying. Guess why.

Last year, a Breitbart article had criticized Springer Nature, Scientific American’s German owner, for attacking those “skeptical of the coronavirus vaccine” and spreading “gender insanity.” “No more taxpayer money for woke publishers!” declared Donald Trump Jr., retweeting the article. In June 2025, Axios reported that all federal subscriptions to Springer Nature publications had been canceled. Although Trump officials later walked back the bulk of the cuts, they had shocked the scientific community: Without access to Springer Nature’s thousands of journals, including the prestigious Nature publications, researchers at federal agencies—from the NIH to NASA—would struggle to stay abreast of scientific developments. The company itself, meanwhile, risked losing as much as $25 million in federal contracts.

So if Ewalt had asked people to keep Trump out of the headlines last summer, it was because corporate higher-ups were visiting the site all the time. “And if they saw the word ‘Trump,’” he said, according to the recording, “they were wetting their fucking lederhosen.” People had no idea how “lily-livered and weak-kneed and cowardly” Springer Nature was, he said. “They are so fucking afraid of the Trump administration.”

Springer Nature no longer owns it. SciAm has been bought by a company called LabX. This is not good news.

In the immediate aftermath of the sale, staffers were left scrambling to learn more about Scientific American’s new owner. Previously, LabX’s best-known publication had been Discover, a onetime dentist’s office stalwart that was hollowed out by private equity buyers in the aughts; according to multiple staffers, the ownership transition seemed rushed, chaotic, and disorganized. When one worker reached out to a former employee of one of LabX’s other publications, the stories they heard—including ones related to editorial independence—were part of why they turned down their job offer, they said. (LabX did not respond to multiple requests for comment.)

I remember Discover. It was not one I ever looked forward to reading — too shallow, never providing much to engage with.

At least one freelancer has already written publicly about their negative experience with the new Scientific American, and two more editorial staffers were laid off at the end of September, including Megha Satyanarayana, Vergano’s former colleague in the opinion department—who declined to comment for this piece—and a data reporter. Vergano remains worried that LabX seems more interested in “gee-whiz stuff” than critical, substantive reporting. From what he’s seen of their publications, he said, “they produce things that are schlockfests. And we were doing good work at Scientific American.”

The end is near. The schlockification has begun. I don’t think the new SciAm will be inspiring many high school students to pursue careers in science.

It looks like it’s Nobel season

The winners of the Nobel in Physiology or Medicine have been announced: it’s Karl Deisseroth, Georg Nagel and Peter Hegemann, for their work in optogenetics.

Back in my day, we’d have to pull a fine glass electrode and jab it into a cell to put an electrical current in it, and see what twitched or secreted or changed gene expression in response. It was admittedly a bit clumsy and had side effects: most of the cells I stabbed would die in response. Optogenetics lets a researcher modify the genetics of precursor cells so that they would produce a novel channel, a light sensitive rhodopsin derived from algae, that lurked in the membrane, and would only open when a light was shone on it. Instead of a needle, you could aim a laser at the cell, and trigger a current across the membrane non-invasively.

It’s a neat trick. You can have a whole nervous system laid out on your microscope, loaded with inherited copies of this rhodopsin, and cruise around zapping cells with a beam of light, and see what happens when those cells are stimulated. Or put a fiber optic in a brain and switch on neurons with a pulse of light. There are so many fun things to do!

Mmmm…hot soup

We all know that the dinosaurs were wiped out by a massive meteor strike, 65 million years ago. We know where it struck: off the Yucatan peninsula, forming the Chixculub crater. What I didn’t know was that the impact was so fierce that the site was burning hot for millions of years afterward.

The collision was intense enough to cause deformation far beneath the surface. Subterranean effects reached 35 km (almost 22 miles) down, and included the melting an immense amount of rock. Exposure to seawater made that rock porous. As hot water seeped into the pores, a hydrothermal system formed. The hot water gushing into an isolated region of the freezing depths could have attracted microorganisms and possibly other life forms that were otherwise struggling to survive.
…
Traces of argon found inside a rock are indicative of potassium decay. Since the gas will also escape from molten rock, this provides a measure of when the rock solidified. How much time has passed since that rock melted can be determined from potassium-argon dating, which involves measuring the amount potassium-40 isotope present relative to the argon-40 it decays into. Levels of argon meant the hydrothermal system stayed heated from 66 million years ago, when the asteroid first hit, to 58 million years ago.

With 8 million years of heat and nutrients, life had more than enough time to colonize the hydrothermal system in the Chixculub crater. Pickersgill also ran computer simulations of hydrothermal activity in that location. Results suggested that cooling to 90° C (194° F) took between 1.5 and 2.3 million years after the impact at depths of one kilometer. Cooling to below 50° C (122° F) took up to 5 million years, still enough heat for colonies of microbes to thrive. After 6 million years, significantly less hot water was flowing, and by 8 million years, the flow had ceased. These results matched the rock age found by isotope analysis.

The impact had consequences for millions of years — it killed the world and set a pot to simmer for long ages afterwards.

Revisiting Whalefall

I didn’t believe the hype nonsense about Whalefall, but I’m not a marine biologist. Maybe a marine biologist would see a way that a whale could swallow a man who would survive for an hour? I’m willing to be persuaded.

This sane, sober, well-informed video doesn’t do it for me.

I am interested in the tactics the defenders of the movie take. One event is improbable, unlikely but well, maybe possible; another event could only happen under rare circumstances; yet another event could happen if a confluence of different conditions occurs; add them all up, and presto, declare it could happen. That’s not how things work.

I learned something I hadn’t really thought through. Whales have a complex ruminant stomach that is muscular and crushes and tears food before passing it on to an acid-filled forestomach. I don’t care how many faint “maybes” you stack up, once you hit a single “impossible,” you’re done.

Another sign of America’s anti-science turn

We lived in Philadelphia in the 1990s, and we made fairly frequent day trips to the downtown. Because I was a science nerd, there were three destinations we prioritized over all the history and art museums: the Mütter Museum (because it was kind of gross), the Franklin Institute (great hands-on interactive exhibits for the kids), and my favorite, the Academy of Natural Sciences of Philadelphia. It’s a great working science museum with about 200 years of active research housed behind its doors. They also regularly hosted science meetings, so I’d go there for the regional meeting of the Society for Neuroscience, and Philadelphia science fairs were held there. It’s a real jewel in the center of the city.

It’s a great place. I miss the opportunity to visit it.

But now I learn that it was bought up by Drexel University. This was part of an ugly consolidation of academic institutions that distorted higher learning in the the region — they also bought up the Medical College of Pennsylvania, Hahnemann University, and Salus University, as part of a pattern of expansion. They slapped their name on the Academy of Natural Sciences of Drexel University (I will never call it that.) And now, on September 1, they abruptly announced that they were closing the Academy as of September 30. That’s rather short notice for a collection that has been growing since 1812.

At the time I lived there, Drexel had a great reputation as an engineering and computer science school, but apparently they’ve now become a massive do-everything school with a focus on making lots of money, and screw science and history. Drexel has become the bad guy in this story.

Keep up with the news at the Save the Museum page, and sign the petition. What the hell happened to Drexel?

We really are deficient in development education

This figure, used by ScienceDaily, is totally irrelevant to the topic and has a caption that doubles-down on the nonsensical part of the article: “The human brain may actually be two ancient nervous systems fused into one, a discovery that could transform how scientists study brain development and devastating neurological diseases.”

I guess I should address this, since so many people are emailing me about it. There is an article titled “Stanford scientists discover the human brain may actually be two separate organs”, which takes a basic reality of developmental biology and blows it up with a ridiculous conclusion. No, your brain is not two separate organs, any more than your liver is multiple organs because it contains multiple tissue types — that, for instance, there are different lineages of hepatic progenitor cells in liver differentiation that produce hepatocytes and cholangiocytes. We take this for granted; development is a hierarchical, branching process, and so yeah, we see sequential separation of developmental lineages. It’s to be expected! We don’t promote the work by claiming various organs are in fact multiple organs.

The sensationalist spin is being placed on competent work that traces markers that distinguish regions of a single organ, markers that have a deep history in both development and evolution. Calm down. This is a routine observation that does have some practical uses.

The weird twist was put on it by the Stanford press office and ScienceDaily. The actual paper (which is fine) it is based on is titled “Two parallel neural ectoderm progenitors contribute to the developing brain”, a much more sensible and accurate title, although it also claims that the brain is a “composite organ”, which is a little bit silly. Every organ is a composite organ in some sense. We are a multicellular gemisch with some regional organization.

Development is hierarchical and sequential. It’s disappointing that this isn’t taught in grade school.

WHY?

A recent article in Science has been deleted and a curious editorial comment added to it. The article title is Your heartbeat quietly shapes how your brain processes information, and the editor’s note is:

Editor’s note, 16 September, 3:05 p.m.: Although no specific errors in this story have so far been identified, we have removed it after determining the author was impersonating the identity of an established science journalist, both with the News editors at Science and with sources in the story. Furthermore, two of the quotes provided by the author have since been found in previously published stories by other writers.

The attributed author was Caroline Williams. The real Caroline Williams has written elsewhere:

Fake Caroline update:

The person who was impersonating me managed to get an article published in Science, under my by-line. And they got paid for it!

I’ve seen the pitches (bad), and the email chain between editors who weren’t all that impressed, but googled me and decide to take a punt. When the article came in it was dry, clunky and badly written, but after several rounds of editing they managed to get it into a publishable state. It went online in June and was up until yesterday when it became clear they (and I) had been scammed.

Link to the retraction / editor’s comment here: https://lnkd.in/eSQ2XEAJ

The whole thing makes me feel sick. I know from my work as an editor that the reputational damage is real. Had I pitched a story to them afterwards they would very understandably have said “Hell no!”. Who has the time to do someone else’s job? They tried “me”, “I” didn’t deliver, so no thank you.

I have no idea how many more editors out there have me on their ‘do not commission’ list because of this person’s actions. There may also be several scientists who will not want to talk to me because they’ve had a bad experience with the fake one.

More broadly, if this is a wider scam (and based on what others have told me, I think it is), it is potentially a serious issue for science journalism and journalism in general. And I’m not sure what we can do about that.

On the plus side, I now have some very nice contacts at Science and Nature and plan to write something better for them as soon as possible. And the fact that payment was made opens up the possibility of tracking down who is behind this. Watch this space…

It’s weird. Fake Caroline got nothing out of this but a paycheck, which does make me wonder how much one gets paid for a news article in Science. It can’t be much, given that scientists who publish there get nothing, and are in fact expected to pay the journal for the privilege.

There is a great deal of gain to one’s reputation, but not if you publish under someone else’s name, obviously. You can’t list it on your CV.

It can hurt the real writer’s reputation — now editors might be on the alert that submissions by “Caroline Williams” could be fraudulent. But this is a lot of effort to go to for a weak effect on someone. I can’t believe this elaborate fraud was a devious hit piece.

So now I’m left wondering why anyone would do this. Is there some subtle scam at play?