Here we go again

Are you ready for another pandemic?

No, you are not. And this one has the potential to be worse than COVID.

Cases of H5N1, the bird flu, are on the rise. Bird flu is bad — the cases are limited right now, because most of the transmission is from birds/cows to humans, and not human to human, and most of us don’t cuddle chickens that often. Please don’t start.

We’re definitely not at the point where we should panic and shut everything down, but we are at the point where we should be preparing, building up stockpiles of vaccines, and developing new vaccines (there is no commercially available RNA vaccine for bird flu yet). If the virus mutates, as viruses are wont to do, a variant could spread with stunning speed.

But don’t count on those vaccines saving us if this virus does what flu viruses sometimes do, and turns into a pandemic form. It won’t oblige humanity by slowly mutating, giving people a chance to ramp up vaccines quickly.

“It is going to happen fast,” says Ali Khan, dean of the University of Nebraska Medical Center College of Public Health and a veteran of numerous disease outbreaks, from influenza to Ebola.

The world just saw this happen. COVID appeared suddenly and spread globally before alarm bells rang. Even with the new, quick-turn technology of mRNA vaccines, it took just about a year after SARS-CoV-2 started its global spread to get the first doses into arms. By that point, 300,000 people had died in the U.S. and hundreds of thousands more—possibly millions—died around the world before vaccines were fully deployed.

Viruses reproduce at a phenomenal rate, faster than we slow clumsy vertebrates can adapt. You just know, though, that the guy Trump wants to appoint to run the NIH is going to argue for “herd immunity” the instant a pandemic takes off. In fact, this country has been working to undermine even a minimally responsible pandemic response for the last few years.

When COVID broke out, people were largely open to vaccines. Then-president Donald Trump touted his government’s rollout of the vaccine, but he has since helped feed vaccine skepticism. Neither Trump nor his Democratic opponent for president, Vice President Kamala Harris, mentions pandemic preparedness in their respective campaign platforms.

Even uptake of routine childhood vaccines is falling. “The lack of trust around vaccines does put us in a very bad place. We do know that people are dying because they are not getting vaccinated against COVID,” Khan says. The U.S. Centers for Disease Control and Prevention reports that only 11 percent of adults and just 7 percent of pregnant women have received the latest COVID vaccine.

Some states have loosened vaccine requirements and recommendations, something that worries Khan and other public health experts. Vaccines cannot help anyone if people don’t get them. Politicians who don’t promote the need for pandemic preparations are gambling that the next one won’t hit during their terms in office. “This is all going to potentially come home to roost with the next pandemic,” Khan says.

I got my COVID vaccine. It won’t help against bird flu, though. Meanwhile, the idiots are pushing the public to take greater risks. Remember all the fools touting raw milk for some absurd reason? That had consequences in California.

The source for all those bird flu cases in California was a few cow herds, herds specifically raised to produce raw milk, from a company called Raw Farm, run by a guy named Mark McAfee. Remember that name; it could go down in history, just like that of Mrs O’Leary. McAfee has some political opportunities in the current climate.

As bird flu has spread among poultry and cattle in the US this year, raw milk has seen a new wave of interest and some high-profile supporters, including Robert F. Kennedy Jr., President-elect Donald Trump’s choice to lead the US Department of Health and Human Services.

Raw milk was on a laundry list of items that faced “aggressive suppression” by the US Food and Drug Administration, Kennedy said in a post on X in October. In a fact sheet shared with CNN on Monday, Raw Farm said its CEO, Mark McAfee, “has been asked by the RFK transition team to apply for the position of ‘FDA advisor on Raw Milk Policy and Standards Development.’ ” CNN has reached out to the Trump transition team for comment.

Imagine a pandemic with RFK jr and Jay Bhattacharya in charge. Or don’t, if you don’t like nightmares. We are so screwed.

Oh, and for those people who look at a table listing a mere 57 cases, who think that’s minor and nothing to worry about, that’s just human cases. The virus is thriving in herds of cattle and flocks of birds, you know, those animals most of us eat.

In updates since November 27, the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) confirmed 14 more H5N1 outbreaks in dairy cattle, all involving California herds. The latest additions push the state’s total to 475 and the national total to 689 across 15 states.

Also, APHIS confirmed more H5N1 outbreaks in poultry in six states. All involve commercial farms. In California, the virus struck poultry farms in three counties—a duck breeder and a broiler facility housing more than 266,000 birds in Fresno County, a turkey farm in Merced County, and a commercial hatchery in Tulare County.

In Minnesota, the virus hit two more turkey farms in Meeker County, one of which has nearly 242,000 birds.

Similar outbreaks were confirmed at turkey farms in North Dakota (Ransom County), South Dakota (Beadle and Faulk counties), and Utah (Sanpete County).

In the south, the virus was confirmed at a broiler farm in Tennessee’s Gibson County that houses 37,200 birds. The outbreak is Tennessee’s first since October 2023.

Think of those as vast culture dishes where H5N1 is proliferating and mutating at a furious rate. Give ’em time, we’ll get a deadly variant popping out eventually.

An hour of mathematical genetics homework

We Americans have all had a pleasant Thanksgiving and possibly an indulgent Black Friday, but it’s time to get back to work. Yesterday, Zach Hancock gave a presentation on why the hereditarian fallacy is a fallacy — the math doesn’t work. The video demonstrates an important truth: biology requires math. In this case, it’s a fairly simple level of math, so if you know a little algebra and maybe a little statistics, you should be able to cope.

It’s an important message, too. Racism and hereditarianism are built on a false premise, and anyone who tries to use population genetics to argue against evolution or for racism doesn’t understand some rather basic stuff.

It gets in some good digs against Steven Pinker, too, who clearly doesn’t understand genetics or basic math.

Now get to work. Your break is over.

Science has always been political…but especially now

Augustin Fuentes has a letter in Science. It’s pretty good.

Science, both teaching and doing, is under attack. The recent US presidential election of a person and platform with anti-science bias exemplifies this. The study of climate processes and patterns and the role of human activities in these phenomena are at the heart of multiple global crises, and yet the scientific results, and the scientists presenting them, are attacked constantly. The dissemination of knowledge on health involving reproduction and human sexuality is increasingly marked for attack (in Russia, Uganda, and the USA), and researchers in these areas are often the target of extensive political pressure. The massive attack on the science and the scientists behind vaccines, pathogen transmission, and public health during the COVID-19 pandemic and beyond is well documented, as are attacks on basic science education and the practice of science (for example, in Hungary and the USA). Even in the arena of biodiversity conservation, there is growing politicization of the data and political targeting of the scientists producing it. According to the US-based National Association of Biology Teachers (NABT), climate change, reproduction, vaccines, and other evidence-based scientific topics are being deemed “controversial” by school boards and state officials and are being removed from state-approved teaching resources across the country. Core research on health, climate, human biology, and biodiversity is being undermined by private foundations, governments, and anti-science ideologues.

Whether science is political, and if it should be, is an age-old debate. Some assert that scientific institutions and scientists themselves should seek to remain apolitical, or at least present a face of political neutrality. Others argue that such isolation is both impossible and unnecessary, that scientists are and should be in the political fray.

But…is there really a serious debate about whether scientists should be politically neutral? In my experience, the question is settled: scientists should be activists. I emerged from the University of Oregon in the 1980s; Aaron Novick was the chair of the department. He was a veteran of the Manhattan Project, who protested against the Vietnam War, and was on the board of the Bulletin of the Atomic Scientists. I worked with George Streisinger for a year, and he was even more radical. His family fled Hungary as the Nazis came to power, also opposed the Vietnam War, and when I knew him, was campaigning against mutagenic pesticides and testifying for the Downwinders, and writing editorials on the dangers of radiation.

What debate?

Excellent images of a few things

Would you like some free biological illustrations that aren’t the products of an AI’s unrestrained imagination? NIH BioArt is such a source.

These are bold, simple illustrations with limitations. There is a section on arthropods, but it doesn’t contain any spiders, or much of anything outside ticks and mosquitos. If you want a graphic of a tick, it’s got you covered. Here’s a tick for you:

KITTY!

External appearance of three-week-old heads of large felid cubs, right lateral view: (A) Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, frozen mummy, Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene

I understand that the internet likes cats, so here’s one, a 30,000 year old mummified sabre-toothed kitten.

It has a distinctively large mouth and massive neck muscles, but the canine teeth haven’t elongated yet — they say the age is equivalent to a 3 week old lion cub. I would guess that sabre-tooth canines might interfere with nursing.

The frozen mummy of Homotherium latidens (Owen, 1846), specimen DMF AS RS, no. Met-20-1, Russia, Republic of Sakha (Yakutia), Indigirka River basin, Badyarikha River; Upper Pleistocene: (A) external appearance; (B) skeleton, CT-scan, dorsal view.

It has toe-beans!

Coincidentally…

In that treasure trove of old documents from my mother, I found this little surprise: she’d also saved one of my extra figures from my research at the University of Oregon, the stuff that led to me working with Judith Eisen.

Photograph of horseradish peroxidase labeled spinal motoneurons

That’s another oldie — Mom must have asked what the heck I was doing in the lab, and I gave her an old print and tried to explain it to her. And she salted it away for 40 years!

One of my role models, recognized

My experiences in grad school were mostly happy ones, and I credit that to the fact that I was lucky to work with good people. I entered the lab of Charles Kimmel, working on zebrafish neuroscience, and stumbled my way through several projects before Chuck suggested a new one: he recommended that I use a fluorescent lineage tracer dye, rhodamine dextran, injected into midblastula cells, which we’d allow to develop into a larva in the hopes that some of that dye would end up in the neurons I was interested in.

This was a cunning strategem. First of all, this was a labor-intensive project; we’d have to do a hell of a lot of injections to get the dye into the few cells we cared about by happenstance. We’d eventually do the experiment and get a yield somewhere under 5%. The other angle is that he already had someone lined up to work on the idea, and I was being drafted to assist in the experiment.

I didn’t mind. That someone was a new post-doc, Judith Eisen, and I think we worked well together. Judith was intimidatingly intense, but nice. We got into the rhythm of this experiment smoothly. In the evening (this was a timing-dependent experiment, you had to start with embryos of a certain age) we’d get together over a beaker with hundreds of embryos, and then we had to work fast, because there was a narrow window of time to get the injections done. I’d line up ten or so embryos on a slide, and pass them to Judith, who was poised over the microscope with a microinjector, and bang bang bang, she’d shoot up single cells with the dye. I was the loader, she was the gunner. We’d set up maybe a hundred embryos before stopping and letting them then develop.

The fun work started the next day. We’d go through the previous night’s collection, put each embryo under a fluorescence microscope with a silicon intensified target camera and take pictures. Most of them we’d throw out — they had labeled skin cells, or labeled kidney, or labeled notochord, or whatever, which might be useful to someone, but not us. We wanted labeled spinal neurons. We’d get a few.

The next step might sound crude, but it was the 1980s, it was what we could do. We’d see a glowing cell on the video monitor, and we’d tape a piece of transparent plastic on the screen and outline all the cells with a sharpie. Then we’d come back to that special cell over the course of the day, and draw on that same piece of plastic with a different color. Our data was these sheets with the changing shape of labeled cells.

I vividly remember our eureka moment. We were going through our daily labeled embryos, and we had this one fish that looked familiar, a cell that looked like one we’d seen before. We sat there and made a prediction, I bet we knew exactly how that cell would develop in the next few hours. Judith grabbed all our data and spent an afternoon manually aligning all these drawings — our simple technique had some virtues, in that we could so easily align analog pictures — and came back and could say that we had precisely three cell types that had a stereotyped pattern of outgrowth.

Those were great times, and it was most excellent working with Judith. Some of my happiest memories of working in science were from those years in Chuck’s lab, partnering with Judith, so the latest news from Oregon makes me even happier: Judith Eisen has been elevated to the National Academy of Sciences! That is a well-deserved honor, and I’m happy for her.

What I learned from that experience was that a key ingredient of good research was collegiality, mutual support, and cooperativity. I think that’s what I took away from my training, that I should model my own mentorship in the years since on that of Judith Eisen and Chuck Kimmel.

Science needs specific, informed, productive criticism

Professor Dave demolishes Sabine Hossenfelder.

I feel that. The topic of my history class last week and this week is about bias in late 19th/early 20th century evolutionary biology, and how we have to be critical and responsible in our assessment of scientific claims. It’s tough, because I’m strongly pro-science (obviously, I hope?) but I keep talking about dead ends and errors in the growth of a scientific field, and I have to take some time to reassure the students that our only hope to correct these kinds of problems is…science. I also have to explain that the way the errors are discovered is…science, again.

I’m not specifically interested in Sabine Hossenfelder — I don’t watch her videos, not even the ones that might contain good information — but I am concerned with the general problem of how anti-science propaganda manages to advance the causes of dogma. If science gets something wrong, as it does sometimes, it does not mean that superstition or bigotry are right. Raging against the whole of the scientific establishment and the scientific method is how you get RFK Jr put in charge of the NIH. I don’t think that even Hossenfelder believes that will be an improvement.

Another step in the evolution of multicellularity

I’m not a fan of phys.org — they summarize interesting articles, but it’s too often clear that their writers don’t have a particularly deep understanding of biology. I wonder sometimes if they’re just as bad with physics articles, and I just don’t notice because I’m not a physicist.

Anyway, here’s a summary that raised my hackles.

Chromosphaera perkinsii is a single-celled species discovered in 2017 in marine sediments around Hawaii. The first signs of its presence on Earth have been dated at over a billion years, well before the appearance of the first animals.

A team from the University of Geneva (UNIGE) has observed that this species forms multicellular structures that bear striking similarities to animal embryos. These observations suggest that the genetic programs responsible for embryonic development were already present before the emergence of animal life, or that C. perkinsii evolved independently to develop similar processes. In other words, nature would therefore have possessed the genetic tools to “create eggs” long before it “invented chickens.”

First two words annoyed me: Chromosphaera perkinsii ought to be italicized. Are they incapable of basic typographical formatting? But that’s a minor issue. More annoying is the naive claim that a specific species discovered in 2017 has been around for a billion years. Nope. They later mention that it might have “evolved independently to develop similar processes”, which seems more likely to me, given that they don’t provide any evidence that the pattern of cell division is primitive. It’s still an interesting study, though, you’re just far better off reading the original source than the dumbed down version on phys.org.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii—a close relative that diverged from animals about 1 billion years ago—undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

Much better. The key points are:

  • C. perkinsii is a member of a lineage that diverged from the line that led to animals about a billion years ago. It’s ancient, but it exhibits certain patterns of cell division that resemble those of modern animals.
  • Symmetry breaking is a simple but essential precursor to the formation of different cell types. The alternative is equipotential cell division, one that produces two identical cells with equivalent cellular destinies. Making the two daughter cells different from each other other opens the door to greater specialization.
  • Palintomic division is another element of that specialization. Many single-celled organisms split in two, and each individual begins independent growth. Palintomic division involves the parent cell undergoing a series of divisions without increasing the total cell volume. They divide to produce a pool of much smaller cells. This is the pattern we see in animal (and plant!) blastulas: big cell dividing multiple times to make a pile of small cells that can differentiate into different tissues.
  • Autonomy is also a big deal. They looked at transcriptional activity to see that daughter cells had different patterns of gene activity — some cells adopt an immobile, proliferative state, while others develop flagella and are mobile. This is a step beyond forming a simply colonial organism, is a step on the path to true multicellularity.

Cool. The idea is that this organism suggests that single-celled organisms could have acquired a toolkit to enable the evolution of multicellularity long before their descendants became multicellular.

I have a few reservations. C. perkinsii hasn’t been sitting still — it’s had a billion years to evolve these characteristics. We don’t know if they’re ancestral or not. We don’t get any detailed breakdown of molecular homologies in this paper, so we also don’t know if the mechanisms driving the patterns are shared.

I was also struck by this illustration of the palintomic divisions the organism goes through.

a, Plasma membrane-stained (PM) live colonies at distinct cell stages, highlighting the patterned cleavage divisions, tetrahedral four-cell stage and formation of spatially organized multicellular colonies (Supplementary Video 5). b, Actin- (magenta) and DNA-stained (blue) colonies at distinct cell stages showcasing nuclear cortical positioning, asymmetrical cell division (in volume and in time) and the formation of a multicellular colony. This result has been reproduced at least three independent times.

Hang on there : that’s familiar. D’Arcy Wentworth Thompson wrote about the passive formation of cell-like cleavage patterns in simple substrates, like oil drops and soap bubbles, in his book On Growth and Form, over a century ago. You might notice that these non-biological things create patterns just like C. perkinsii.

Aggregations of oil-drops. (After Roux.) Figs. 4–6 represent successive changes in a single system.

Aggregations of four soap-bubbles, to shew various arrangements of the intermediate partition and polar furrows.

An “artificial tissue,” formed by coloured drops of sodium chloride solution diffusing in a less dense solution of the same salt.

That does not undermine the paper’s point, though. Multicellularity evolved from natural processes that long preceded the appearance of animals. No miracles required!

If it’s not one thing, it’s another

It was hard to get motivated this morning — Fridays are typically low attendance days in the classroom, and I had worked hard to get today’s topic condensed down into a lot of digestible information (we’re talking about the rediscovery of Mendel, the biometrician and Mendelians arguing with each other). I had a presentation that was pretty tight and I thought would help make the conflict comprehensible to a group of liberal arts majors, none of whom are biology majors.

So I get to class today, and was pleasantly surprised to see that I had 80% attendance, which is kind of a miracle. I tell you, standing at the front of a classroom with only 3 students who don’t really appreciate the work you put in to the class is mighty depressing. So I was temporarily heartened that maybe this lecture wouldn’t go to waste, I fired up my laptop and the projector and got ready to tell this exciting story…and the projector is glitched out. It’s not connecting to anything, and is showing me a message that the projector and microphones were not receiving any data since 5:21pm yesterday. Isn’t technology nice that it has become so sophisticated that it can tell you precisely when it broke down?

I fumbled with it for about 15 minutes — that was the show today, watching the old geezer prof toggling switches and poking at a keyboard in front of the class, and seeing everything fail. I ended up giving up, giving them a brief oral summary of the history of biology from 1900-1915, telling them I’ll give them all the details on Monday, and sending them home early. So many smiles from the students! I didn’t tell them that I don’t find that encouraging at all.

Now I’m sitting in an empty classroom waiting for the IT people to show up. At least I can cheer myself up by thinking, hey, this isn’t the worst thing to happen this week.