A science rally!

I was in St. Paul, or transiting to and from St. Paul, all day yesterday for the grand #StandUpForScience rally. As you might expect for an event organized by science nerds, it was flawlessly executed: it started exactly at 3pm, had about 10 speakers, and finished precisely at 5pm. The speakers were all brief and to the point. We had several state legislators talk about the importance of science education and the contributions of science to our state’s economy, and several people with direct experience of the impact of Trump’s chaos — one young woman had just finished a post-doc and got a job with a state agency (the forest service, I think) the week after the election, and walked into a demoralized office where no one knew what was going to happen to them. She found out: she was fired 3 weeks after starting, with 2 hours notice.

Some people talked about social and economic justice, in particular, the Hennepin Energy Recovery Center (HERC), which I knew nothing about until yesterday. It’s a big incinerator which converts trash to energy, which is nice, but somehow it got located to the center of a district filled with low-income and minority residents. Funny how that happens.

Science and DEI are intertwined — so many first generation scientists were reliant on DEI initiatives to get their careers started. One speaker suggested a good question to ask critics of DEI: What, specifically, are they opposed to? Is it diversity, do they dislike people of color working in science and engineering? Is it equity, the idea of equal pay for equal work, do they think brown people should get less support? Or is it inclusion, the idea that minorities should be able to work shoulder to shoulder with existing, dominant groups? There’s no good answer to those kinds of questions, and they’re all just hiding behind an acronym, afraid to spell out what they actually want.

Another theme of speakers and participants was the raging inequality in this country. Mention the word “corporations” and you heard a chorus of “boos”. A lot of the signs people were waving targeted the wealthy and unfair tax laws, that the Trump regime was robbing science to make the rich richer. Everyone in this crowd hated billionaires in general and Elon Musk in particular. That guy is so desperate for attention and respect and popularity, and he has made himself the #1 enemy and object of contempt by scientists & engineers & teachers & health experts. Chalk that up to yet another tremendous failure by Musk the Incompetent.

It seems the greed of the wealthy in this country has inspired a lot of people to look favorably on communism and wealth redistribution and the social safety net and mutual aid. That’s going to backfire spectacularly on the upper class. This event sounded like a communist rally at times, good for them.

Also, I got to meet many fellow angry supporters of science, including commenter foolishleader who does have a spectacular octopus hat.

I’m looking forward to more Stand Up for Science events!

Furious overconfidence does not counter the evidence

Here’s another wild creationist claim that just popped up from the YouTube algorithm. It’s a shouting match between a Muslim creationist (Subboor Ahmad) and an individual from the crowd, who is challenged to define evolution. He says “natural selection plus mutation,” which prompts this furious response from Ahmad.

If it’s natural selection plus random mutations, it becomes epigenetics.

What? No it’s not. That’s absurd. It just tells me that Subboor Ahmad knows nothing about evolution.

It also includes a clip of an encounter between Ahmad and Aron Ra, in which Aron correctly points out that drift is the major driver of evolutionary change, and Ahmad blows up in fury and accuses him of being drunk.

A creationist denies molecular evolution

Last night, Aron Ra got into a discussion about a claim that protein evolution is impossible, specifically, that different protein families could not have evolved. Here is the provocative and baseless claim.

There is no research that says protein evolution is possible, unless you appeal to evolution. That’s circular.
There is no research published that explains how a new protein family, with stable novel folds, can evolve in the rugged evolutionary landscape. Only conjecture and always with an appeal to the theory. That’s called theory laden evidence.

I have issues with the premise that evolution is fact (bad science). That demands a better definition of evolution so I’ll clarify, I have problem with the premise that random mutation, gene duplication, gene transfer, gene shift, and anything I may have missed, under the influence of natural selection is sufficient to produce biodiversity.

Perhaps a new mechanism will be discovered, but at present there is no evidence that evolution is possible beyond an appeal to evolution.

There is a barrier to protein evolution. Gradual change doesn’t provide a path from one protein family to another because the landscape is rugged. Point mutations will lead proteins off the functional cliff. Duplication doesn’t fit the bill either, not enough variety. Fact is, without some sort of bridge protein evolution is inconceivable. No bridge has been found.

I’m not claiming that there isn’t one or that it will never be found, I’m saying there is no evidence for one. It’s a leap of faith to say it happened.

I know you’re not a fan of that word, faith, but there is no alternative. The only justification for that faith is ontology. It’s your belief in naturalism which cannot be proven one way or the other. in fact, the very problem I’m discussing here is a thorn in the side of naturalism.

You’ve waged a lifelong war against theism and always appeal to intellectual honesty. Well, I’m being intellectually honest. There in no evidence that evolution is possible because protein evolution has no known solution.

Proteins exist on peaks separated by valleys where function drops off completely. The “rugged landscape”. The peaks play home to a variety of related proteins with limited variety of amino acid sequences called families. A peak is more like a plateau. Small changes can produce variety of function and fitness. Large changes cause function to collapse into a valley where the protein gets deselected.

The amount of change required to find a new stable fold with novel function, a.k.a. a new family on its own plateau, far exceeds what proteins can tolerate by incremental change without losing all function. This is not controversial.

Proteins need to leap or require a bridge. Leaps in sequence change are irrational because the search space is too large and the target too small.

The presumption is that there is an unknown “bridge” that allows proteins to make the transition from one peak to another. That bridge has yet to be found (or even adequately hypothesised), and without it proteins are trapped on local peaks. Meaning evolution is limited to variety of what is, with no access to cool new stuff. Micro but not macro.

The premise that evolution is a fact allows for the presumption that “we don’t know yet” is a valid placeholder for the bridge. A glaring “god of the gaps”. My “dilemma” is how can evolution be called a fact, when the facts exist to challenge it? It can only be reckoned that belief is the “Jesus nut” that keeps it from flying apart.

Anyone who is a materialist will naturally, and justifiably, search for that bridge. Dualists can as well, but it’s discovery isn’t an imperative. For the theist, that bridge may well be agency. In any case, agency is no worse than “we don’t know yet” as a filler.

My question is, on what basis do you declare the materialist ontology correct and the dualist ontology false? The inability to test is a feature, not a test in itself.

What does it matter if the problem was before Eukaryotes? Evolution covers the first cell to everything. From what I’ve read, the Cambrian Explosion is where the problem is most evident with many new protein families that have no observed precursors. All within a tiny fraction of evolutionary time.

“A protein family is a group of proteins that share a common evolutionary origin, typically reflected in their similar amino acid sequences, structural features, and often their biological functions. These proteins are usually derived from a single ancestral gene that has undergone duplication and divergence over time, leading to variations within the family. Members of a protein family may differ in their specific roles or expression patterns but retain enough similarity to be classified together.” -Grok (I trust AI is allowed for definitions?)

I understand the standard hypothesis. Gene duplication allows one to remain stable while the other continues on down the evolutionary trail. I also understand there is a vast leap required for a protein to diverge into a new family. Recombination is most commonly considered for large leaps, though no evidence exists it can be done.

I understand the standard hypothesis. Gene duplication allows one to remain stable while the other continues on down the evolutionary trail. I also understand there is a vast leap required for a protein to diverge into a new family. Recombination is most commonly considered for large leaps, though no evidence exists it can be done.

I also understand that proteins are intolerant of big change. That paper by Axe estimated that only 1 in 10^63 random sequences fold right. Leaps mean a big change which hits that small target.

On the other hand, incremental changes enjoy a similar problem of losing functionality (which can kill all progress), while also facing time constraints. There isn’t enough time for evolution to search out functional sequences. Even a nice new protein with a stable fold must break the barrier of epistasis.

Finally, I’m talking about entirely new families. Think Superfamily. Like a transporter to the first protease. The information hurdle is massive, and the serendipity required makes Powerball look like a sure bet.

Evolution is not really varying allele frequencies. That works for HS kids but it falls short. Evolutionary theory is the explanation for those varying frequencies. Theories explain HOW, not what.

So we talked for a while about this silly claim. As Aron points out this is just the old show me a cat giving birth to a dog creationist claim translated to show me a transport protein evolving into a protease. It’s the same thing and the same answer. We can trace the ancestry of cats and dogs and see that they converge on a common ancestor in the distant past; we can trace the ancestry of various proteins and follow them back to a distant duplication event to the modern diverse pattern. The creationist wants to argue that the process is simply impossible by throwing around various sciencey terms. He uses the old creationist claim that the probability of a particular functional sequence is only 1 in 1063, a calculation built on faulty premises. He invokes the barrier of epistasis…what barrier is that? I don’t think he knows what epistasis is, let alone the nature of his imagined barrier. He throws around the term rugged fitness landscapes without recognizing that landscapes are an explanatory metaphor, not an actual physical entity.

If you don’t want to listen to us babble, I sent Aron a link to a paper by Tomoko Ohta that summarizes it all.

In eukaryote genomes, there are many kinds of gene families. Gene duplication and conversion are sources of the evolution of gene families, including those with uniform members and those with diverse functions. Population genetics theory on identity coefficients among gene members of a gene family shows that the balance between diversification by mutation, and homogenization by unequal crossing over and gene conversion, is important. Also, evolution of new functions is due to gene duplication followed by differentiation. Positive selection is necessary for the evolution of novel functions. However, many examples of current gene families suggest that both drift and selection are at work on their evolution.

The creationist says that all of that is inconceivable, of course. Never mind that we have evidence of each incremental step and can see intermediates in the process preserved in the genome.

Then he falls back on free will and morality as obstacles to evolution, somehow.

Do spiders count?

My new experimental animal?

A couple of Republicans have introduced a bill in congress to ban all research on animals. All animals, although I’m not sure they understand the breadth of that term. They do helpfully declare that The term ‘‘animal’’ does not include a human. So, according to the ‘Safeguard Pets, Animals, and Research Ethics Act’, we’re going to have to shut down all research involving any kind of animal, except humans. They don’t have the first clue what an “animal” is, or how devastating this would be to biomedical research.

Specifically, this legislation would ban animal testing in federal labs, establish a three-year phase-out, rehabilitate and re-home former lab animals, saving taxpayer dollars while enhancing research outcomes, and ensuring accountability and transparency. American taxpayers spend an estimated $20 billion funding experiments here in the US and overseas including in countries with subpar safety conditions in China, Russia, and Iran.

“I am proud to work alongside Congressman Aaron Bean to end the cruel and unnecessary spending on animal experiments that have wasted billions of tax dollars and inhumanely kept hundreds of thousands of innocent animals in captivity to be tortured and sentenced to painful death,” said Congresswoman Malliotakis. “From administering transgender hormone therapy to monkeys to infesting beagles with fleas and drilling into cats’ skulls for so-called ‘research purposes,’ the American taxpayer would be outraged to learn how their money has been spent. As Co-Chair of the Congressional Animal Protection Caucus and the Cosmetics Caucus, I am committed to advancing our legislation, promoting humane research alternatives, and ensuring taxpayer dollars are spent responsibly.”

“What Fauci did to beagles and other animals is disgusting. The federal government needs to get out of the business of torturing Snoopy. I am proud to join Congresswoman Malliotakis in introducing the SPARE Act.” said Congressman Bean.

Of course she brought up transgender hormones, Fauci, and saving money, the current Republican shibboleths. I can’t believe this would ever pass into real legislation, but I don’t know…congress and the president have been pushing some insane stuff lately. If it did become the law of the land, you can kiss most biological research goodbye.

Welp, I guess I better go release my spiders and all those fruit flies. Then I’ll go raid the local orphanages for small children I can still legally use in my experiments, before my colleagues get the same clever idea.

What would you tell people who want to gut basic research?

In 1997, Arthur Kornberg wrote an article for the Nobel Foundation, Basic research, the lifeline of medicine. It’s a good read.

The pursuit of curiosity about the basic facts of nature has proven, with few exceptions throughout the history of medical science, to be the route by which the successful drugs and devices of modern medicine were discovered. Though it seemed unreasonable and impractical, counterintuitive even to scientists, to solve an urgent problem of disease by exploring apparently unrelated questions in biology, chemistry and physics, these basic studies proved time and again to be utterly practical and cost-effective.

Then he goes on to give the examples of x-rays, penicillin, polio vaccine and genetic engineering.

The lessons to be learned from these four histories and so many others should be crystal clear. No matter how counter-intuitive it may seem, basic research has proven over and over to be the lifeline of practical advances in medicine. Without advances, medicine regresses and reverts to witchcraft. As in biomedical science, pioneering industrial inventions have not been mothered by necessity. Rather, inventions for which there was no commercial use, only later became the commercial airplanes, xerography and lasers on which modern society depends. Curiosity led to the inventions that became the source of industrial strength. It is imperative for a nation, a culture, a university and a company to understand the nature of the creative process and to encourage its support.

It’s too bad that we have a government that rejects this idea.

Reminder: the Stand up for science rally is taking place next week. The St Paul rally is from 3-5pm on Friday at the state capitol — I’ll be there.

I’m going to have to make a sign this weekend. Any suggestions for what I can put on it? I’m not going to put a copy of Kornberg’s paper on it — I need something short, pithy, and catchy.

Get ready for the Resistance

Nature has noticed that the United States is destroying its research infrastructure. The Trump administration is blocking research grants by hook and crook.

bout a month after Donald Trump took office as the 47th US president, almost all grant-review meetings remain suspended at the US National Institutes of Health (NIH), preventing the world’s largest public funder of biomedical research from spending much of its US$47 billion annual budget.

These review panels are suspended because the Trump administration has barred the agency from taking a key procedural step necessary to schedule them. This has caused an indefinite lapse in funding and led scientists to make difficult decisions about the future of their research programmes.

The Trump administration issued an order on 27 January freezing payment on all federal grants and loans, but lawsuits challenging its legality were filed soon after, placing the order on hold. The fact that payments still aren’t going out because Trump’s team has halted grant-review meetings is exploiting a “loophole” in the process, says Aaron Hoskins, an RNA biochemist at the University of Wisconsin-Madison who has had to reconsider hiring graduate students because of a frozen grant application. “It’s really quite nefarious.”

Getting a research grant has never been a process of pushing a button and the cash pops out. Writing grants is an arduous process, and after you submit it, the NIH brings in a large team of scientists from a relevant field to read them and review them and make comments and rate the proposal. It’s a big deal, and it’s not a process that can be bypassed. The trick they’re pulling is to prevent the NIH from scheduling review meetings, so the money is all bottled up. It’s devious and dishonest. Illegal, even.

Some legal scholars say this ‘backdoor’ approach to freezing funding is illegal. That’s because the US Constitution gives Congress, not the president or his team, the power to appropriate funds, says David Super, an administrative-law specialist at Georgetown University Law Center in Washington DC. Blocking “advisory-committee meetings that are legally required to make payments is no different in effect than simply refusing to sign contracts or issue checks”, he says.

My fellow Americans — we all remember those grade school civics classes, where we all learned about the tripartite division of powers, checks and balances, all that bullshit that Trump just ignores. Maybe we should try enforcing those principles?

How about marching on the state? Stand up for science!

March 7. We all need to get out there and make some noise. I can’t make it to the national event in DC, but there are local events all around the country, look up your nearest rally site. I’ll be in St Paul at noon that Friday!

Will I see you all there?

Back to the Miocene

It’s getting harder and harder to find something optimistic about. Seeing science knee-capped and obnoxious snots under Musk’s employ rifling through the IRS files and plotting to destroy Social Security (Hey! That’s my money! It’s not for billionaires to steal) is incredibly discouraging. I found something that looks on the bright side of climate change, though. The Miocene might be a good model for our future.

The Miocene, roughly 5-20 million years ago, had CO2 levels similar to where we’re going as we blast past recommended limit. It was generally warmer and wetter! That has some appeal as I sit here in a region at -30°C. It wasn’t a terrible world at all — primates were diverse and thriving, we had all these interesting mammals, “From Dryopithecus, a lineage of extinct primates that included forerunners of humans, to the toxodonts, large-hoofed mammals with long, curved incisors, to mammals similar to sloths, armadillos and anteaters, to marsupial carnivores”…it was great!

Significantly, the Miocene was a nearly 18 million year epoch full of change, albeit far slower change than ours. It started with a period of glaciation that must have been a chilly change from the greenhouse-like Oligocene, and ended with a prolonged period of glaciation, too. But through much of the Miocene, it was a warm world compared to today’s, a high CO2 planet that gradually cooled over millions of years until ice sheets developed in the Northern Hemisphere and Antarctica.

Around the middle of the epoch, we reached what is called the Miocene Climate Optimum (MCO), a roughly two million year-long greenhouse period when the world experienced its last period of sustained warmth, and the CO2 level was at least 500 ppm. This is the period we’re talking about, most specifically, when we talk about the Miocene as a proxy for our future, although changes throughout the Miocene are relevant: basically, from the middle Miocene Earth went through a process roughly opposite the one we are experiencing (and causing) today.

See? How can you dislike something called a “Climate Optimum”? It looks like paradise! Sign me up — these Minnesota prairies would be so exciting with little horses and hippos and Thylacosmilusand chalicotheres gamboling about in the lush vegetation.

The plants are going to love it.

Carbon dioxide levels affect plants by allowing for greater photosynthesis rates, and by increasing water use efficiency, in that plants can achieve the same amount of photosynthesis with less loss of water through the pores in their leaves, because higher availability of CO2 absorbed through open pores means they can keep them closed more of the time. Thanks to all this, it was also “a globally greener Miocene world,” as Reichgelt and West write in the 2025 paper. Various forms of evidence suggest that the biosphere was more productive during the Miocene compared to now, and that at higher latitudes, this effect was more pronounced.

Except for one major problem: evolution does not run backwards. No chalicotheres await us, especially since we’d be entering a neo-Miocene with a depauperate fauna.

Sadly, the taxodonts will not grace our future world. The long-armed, horsey Chalicotheriidae, reminiscent of Bojack Horseman, won’t be joining us at the bar. Smilodon, the catty predator whose ancestors emerged in the early Miocene, will not smile on us again. Nor the “bizarrely specialized” family of carnivorous marsupials, Malleodectidae, which used their massive ball peen-like third premolars to crush snails. Not the dog bears, Hemicyoninae, who emerged before and lived through the Miocene, nor the bear dogs, Amphicyonidae, which died out by the late Miocene. Evolution doesn’t work like that. Barring the odd de-extinction attempt, what’s lost is gone forever (that includes, thank goodness, the terror birds.)

Expect wild pigs and deer, already doing well, and novel species exploring new environments: I expect the descendants of raccoons and rats to thrive. Humans, not so much. We don’t do so well in the face of widespread environmental disruption, we like nice stable tame-able places where we can rely on crops to come in dependably. We’ll be starting with ecological wreckage and then amplifying the swings of climate and weather, which is a recipe for radical destabilization.

It’s also possible that we’re being seduced by the idea that the Miocene might represent a “happy medium.” As Steinthorsdottir and colleagues write, “More pessimistic scenarios of unmitigated greenhouse gas emissions quickly move us beyond the Pliocene state, pushing Earth’s systems into a potentially vulnerable position where many of its ‘tippable’ subsystems such as glaciers, sea ice, forest biomes, deserts and coral reefs will be permanently destabilized […] an ‘intermediate’ deep-time climate analog, where boundary conditions are close to modern but extreme climate changes occurred, is therefore of great interest.”

As humans we have a notorious tendency to believe that whatever’s in the middle of two given extremes is moderate, cozy, all around OK. (In politics, this results in the Overton Window.) But Miocene-style hydrological or water cycles favor high altitude wind events, like cyclones and hurricanes, that transport heat and moisture evaporating from the tropics to higher latitudes, or California’s intense seasonal rainstorms. The future may be lush, sure, but it’ll also be erratic and dangerous for us. And the “tippable” subsystems Steinthorsdottir mentions may have tipping points that occur well within a Miocene-like context, as scientists have warned.

Whenever a paleoclimatologist tells you a scenario is “of great interest”, it’s time to run.

Sorry. I told you it’s hard to find anything to be optimistic about.

How bad is it?

The situation is dire. Here’s a good overview.

Zach is not being hysterical. Everything he said is objective fact and an accurate prediction.

It’s hitting me personally now. I was benefitting from an HHMI grant written with the hard work of two of my colleagues. It wasn’t big money, I was mainly part of an effort to improve teaching in the university, in a project that paired me with another faculty member for an exercise in peer evaluation.

It was part of a category titled “Inclusive Excellence“. Oops. Forbidden word.

I used the past tense there, because I learned just today that the funding had been pulled, thanks to Trump’s anti-DEI nonsense.

I also have a student trying to get into a graduate program for next year. I’m hoping she gets accepted somewhere — she’s an excellent student with a lot of promise for a research career — but so far, we’re waiting for something. In a normal year, I’d expect grad schools to jump at her, she’s that good. But either nobody has any money, or they’re waiting to hear if their funding has been annihilated, so who knows what will happen? Maybe I should encourage her to apply to Mexican or Canadian schools.

All it took was one election to demolish the American scientific enterprise.

When an idiot is in charge of science’s purse strings…

Here’s a fantasy for you: a rich man uses his immense wealth to alleviate poverty, fund science that benefits all, or decides to distribute all of his money to worthy institutions. It never happens. Instead, we get the world’s richest man using his clout to get a job he isn’t qualified to do, who then uses his unwarranted power to do the opposite, and kill the research enterprise of the United States with one stupid stroke of his pen.

I’m not being dramatic. US research is the product of years of investment. There was a conscious decision to build up a more effective program of research and development after WWII, built upon the existing foundation of expertise in our universities (thanks, Vannevar Bush!). The government knew it would take long-term training and money and resources to create, and part of that was a system of federal grants to researchers with additional funds to the research institutions to build and maintain their infrastructure, which are called indirect costs. You don’t get anything for free! You want to encourage biologists to study the genome, well, you’re going to have to ask a university to maintain a large animal care facility, and hire people to keep an eye on the ethics of such research, and hire accountants to manage the expenses, and veterinarians to keep the animals healthy, and secretaries to help write up the work, and you’re going to have to pay publishers to disseminate it. It’s not cheap.

It’s true that there is some administrative bloat — Harvard is filthy rich, and I think they’ve been gaming the system to inflate those indirect costs — and the article at the link points out that there are a lot of regulations that could be streamlined, but to do that streamlining in a way that retains the useful necessities requires detailed analysis and careful pruning. Only an idiot would think you can just slash all indirect costs to the bone in one crude, extreme cut without totally disrupting all research at American universities.

Enter the idiot.

Musk doesn’t have the slightest clue what he is doing.

Yes, he is cutting funding for cancer research. He’s imposing a blanket, indiscriminate cut for all research. He’s going to gut a whole generation of scientists, a wound it would take decades to recover from, if there was any recovery possible. I suspect that instead of repair what’s going to happen is we’re going to replace universities with bible colleges, pandering to the populist idea that we can pray cancer away.