New depths in pseudoscience

Creationists have been playing a game for about 60 years. Their claims can’t get published in legitimate scientific journals, so they have created their very own boutique journals that mimic the real things: Answers in Genesis has the Answers Research Journal, which, surprisingly, always comes up with the same answer. The Discovery Institute has Bio-Complexity. The oldest of the bunch is Creation Research Society Quarterly, which proudly announces that it is Peer-reviewed by degreed scientists…with the caveat that in order to be involved in the journal at all, you must be a Christian who subscribes to their statement of belief.

It doesn’t need to be pointed out that real scientists don’t publish in any of those ‘journals’, only kooks who are in the business of rationalizing their superstitions.

But there’s one thing that they haven’t done, as far as I know, and that is creating their own Institutional Review Board to legitimize experiments. One good reason is that they don’t do experiments, especially not experiments on animals or people, so they don’t have to bother. You know who does have to pretend to do experiments? Anti-vaxxers.

They’ve gone and done it. They already have their own fake journals, but now they’ve gone and created a fake IRB so they can rubber-stamp horrible experiments with ridiculous reagents on living people. Orac has the low-down.

Recently, a longtime reader made me aware of a recent podcast episode in which an antivaxxer about whom I’ve written a number of posts over the years, James Lyons-Weiler, revealed a “surprise” announcement a little over halfway through the podcast that his antivax “research” organization, the Institute for Pure and Applied Knowledge (IPAK), is planning on forming his own institutional review board (IRB).

Lyons-Weiler has a fake organization and a fake journal, so why not go all the way and create a fake IRB to approve fake experiments?

IRBs are important for maintaining ethical standards and getting expert review of experimental protocols — setting up a fake IRB is a declaration that you want to work around those requirements. Orac has a specific idea of what Lyons-Weiler wants to do — not actual research of his own, but an opportunity to data mine other studies.

In the interview, Lyons-Weiler inadvertently reveals what is likely to be the true impetus and purpose for his IRB when he points out that states are refusing to release public health data, particularly record-level data, to researchers because they don’t have an IRB-approved protocol. My first thought was: How much do you want to bet that the “researchers” to which Lyons-Weiler refers are antivax “researchers” who want to data mine state public health databases in order to seek “findings” that attribute horrific harms to vaccines, particularly COVID-19 vaccines? In other words, how much do you want to bet that Lyons-Weiler’s IRB will exist to rubber-stamp antivax human subjects research protocols, so that antivax researchers can get their hands on that sweet, sweet state record-level public health data on vaccines?

I should confess that for many years I avoided having to get IRB approval, despite working on vertebrate animals, because there was a loophole that allowed experimentation on anamniote embryos — when you’ve got an animal that spews out hundreds of eggs per day, most of which will be cannibalized if they aren’t harvested, it’s hard to justify detailed animal care protocols for embryos (for adult animals, that’s a different story…but I didn’t do experiments on adult animals.) Now, of course, I’m working with spiders and flies, and no one cares what horrible crimes against God and nature I commit on them. I wouldn’t worry if the IRB decided that spiders need protection, because I’m doing entirely ethical work on them…I would just hate all the additional paperwork.

But it’s frightening to think this guy believes he can get approval to do whatever he wants to humans by recruiting a compliant board. Or that he can somehow escape data privacy requirements.

Nobody calls it the “gender chromosome”

Wow. Answers in Genesis falls back on the old simplistic notion that chromosomes determine sex (and gender!) in this video. It’s an amazingly bad clip.

OK, in 40 years of genetics experience, I’ve never heard the Y chromosome called the “gender chromosome” until now. Her absolutist, rigid definition of sex based on chromosome complement is archaic and ignorant. At one point, she rhetorically asks Can you change your chromosomes? Can you change what God knit you to be in the womb of your mother? You cannot “change your chromosomes”, but the pattern of gene activity changes throughout your life. God didn’t do any knitting in anyone’s womb, but you definitely can change — these Biblical ‘literalists’ are denying the reality of biological change, not just over evolutionary timescales, but on developmental timescales. What she is claiming is repulsively stupid.

You may wonder what Jennifer Rivera’s qualifications are. She holds an education doctorate in curriculum and instruction — it’s kind of odd how many creationists hold advanced degrees in education, which is nice, since it means they know how to teach, but they lack any knowledge of what content they should teach. She also has a BA in criminal justice, so AiG has her lecturing on forensic science.

I hope her understanding of fingerprints is better than her understanding of genetics and sex, but I’m afraid to look.

This is some real super-villain shit, you know

Neuralink has begun human trials, we think. The problem is that all we know about it is an announcement made by head jackass Musk on Twitter, which isn’t exactly a reputable source. That doesn’t stop Nature from commenting on it. I’m not used to seeing rumors published in that journal, and if you think about it, this is basically a condemnation of the experiment.

…there is frustration about a lack of detailed information. There has been no confirmation that the trial has begun, beyond Musk’s tweet. The main source of public information on the trial is a study brochure inviting people to participate in it. But that lacks details such as where implantations are being done and the exact outcomes that the trial will assess, says Tim Denison, a neuroengineer at the University of Oxford, UK.

The trial is not registered at ClinicalTrials.gov, an online repository curated by the US National Institutes of Health. Many universities require that researchers register a trial and its protocol in a public repository of this type before study participants are enrolled. Additionally, many medical journals make such registration a condition of publication of results, in line with ethical principles designed to protect people who volunteer for clinical trials. Neuralink, which is headquartered in Fremont, California, did not respond to Nature’s request for comment on why it has not registered the trial with the site.

So…no transparency, no summary of the goals or methods of the experiment, and no ethical oversight. All anyone knows is that Elon Musk’s team sawed open someone’s skull and stuck some wires and electronics directly into their brain, for purposes unknown, and with little hope of seeing the outcome published in a reputable journal. OK.

Besides the science shenanigans, I’m also curious to know about what kind of NDAs and agreements to never ever sue Neuralink the patients/victims had to sign. There has got to be some wild legal gyrations going on, too.

Elon has gone and done it

Musk has stuck a Neuralink device into a person’s head. His announcement isn’t particularly informative.

The first human received an implant from @Neuralink
yesterday and is recovering well.
Initial results show promising neuron spike detection.

…promising neuron spike detection? Do you realize how meaningless that is? I’ve jammed steel pins into a cockroach’s butt and gotten “promising neuron spike detection”. I’ve stuck sharpened tungsten wires into a zebrafish’s hindbrain and gotten “promising neuron spike detection”. This is a trivial accomplishment. Living brains are big sparking balls of continuous electrical activity, it’d be stunning if you put a wire in one and couldn’t get some measure of current.

This being Elon Musk, he continues with promises for the future rather than giving any details on what his company has actually accomplished.

In follow-up tweets sent in between arguing about video games and bantering with far-right influencers, the businessman said the first Neuralink product was called Telepathy.

”It enables control of your phone or computer, and through them almost any device, just by thinking,” he wrote. “Initial users will be those who have lost the use of their limbs. Imagine if Stephen Hawking could communicate faster than a speed typist or auctioneer. That is the goal.”

Musk has a long history of bold promises but a spottier record of fulfilling them. In 2016, he wrongly predicted that within two years it would be possible for a Tesla to drive autonomously from New York to Los Angeles. That year he said his SpaceX rocket company would fly to Mars in 2018 – it still has not.

Don’t forget the Hyperloop!

So can we expect this patient to be making calls to the press with his mind? Musk is not going to say, but I will boldly predict that…no, they will not. I will further guarantee that it will do none of the things Tesla PR promises.

Willy Ley would be proud of this kind of hyper-optimistic space nonsense

I wonder what role Jeff Bezos played in getting this tripe published in the Washington Post? It’s an article talking about setting up concert halls in space — you know, small cozy venues in which musicians can play, surrounded by vacuum and radiation. It sounds like a gimmicky, expensive conceit, and while I do want to see the arts supported to the same degree as science and technology, this is just a weird idea. We can only keep people alive out there at great expense and great risk, with serious medical issues with long term residence, and this writer thinks it would be great to do one-shot shows in space?

It got me daydreaming about what it might be like to one day watch a live musical performance in space. Not in the void, where sound waves cannot travel, but within built habitats in near-Earth orbit — such as the International Space Station (ISS). Forget U2 in the Las Vegas Sphere. Take me to a real concert in the round, where I can float 360 degrees around the stage, watching a guitarist shred from the perspective of a fly and inventing dance moves that Earth’s gravity would forbid.

It is amusing that she had to make an aside about not doing it in a vacuum — gotta squeeze a little science in there. But this sounds like the worst concert ever, with some vain people floating around trying out their flamboyant, jinky dance moves and trying to put all the attention on themselves. The article is even illustrated with a cartoon of her egotistical fantasy.

That must be extremely strong radiation proof glass around that giant dome. Isn’t it funny how NASA isn’t making space stations or space craft out of it? Also, why is the floating musician wearing a helmet and no one in the audience is? Do they know something the rubes don’t? Maybe it’s a trick to get a bunch of rich parasites into a floating bubble for a thorough irradiation.

But the author thinks this isn’t really a rich person’s idea of a wonderful way to flaunt their wealth. No, us peons who can barely afford a concert on Earth will be able to take advantage of this!

Before you dismiss this as a hallucination, consider that we’re on the cusp of a new era of space travel. Engineer and space architect Ariel Ekblaw, founder of MIT’s Space Exploration Initiative, says that within a decade, a trip off the planet could become as accessible as a first-class airline ticket — and that, in 15 or 20 years, we can expect space hotels in near-Earth orbit. She’s betting on it, having founded a nonprofit to design spherical, modular habitats that can assemble themselves in space so as to be lightweight and compact at launch, much like the James Webb Space Telescope that NASA vaulted into deep space two years ago. “The first era of space travel was about survival,” she told me as I recently toured her lab. “We’re transitioning now to build spaces that are friendlier and more welcoming so that people can thrive in space as opposed to just survive.” There’s no reason, Ekblaw said, that a concert hall can’t be one of those structures.

How many of you routinely buy first-class airline tickets for a quick jaunt to a show? Is Ticketmaster going to be in charge of pricing the seats? After you’ve spent, optimistically, $10,000 on your night in space, are you going to be pleased when Bina Venkataraman floats in front of you, gyrating and wiggling and trying out her dance moves?

At least she’s making some specific predictions. Within 10 years, you’ll be able to buy a ticket to space for a few hundred to thousands of dollars. Within 20 years, there will be “space hotels” in orbit, no doubt to capitalize on the hundreds of thousands of space tourists. You’ll have to let me know if any of that comes true. I rather doubt it.

For a scientific source, she cites Ariel Ekblaw, a smart, creative person who has been promoting theoretical space habitats in collaboration with Blue Origin (there’s a Bezos connection), and the best endorsement the author can get is “there’s no reason a concert hall can’t be one of those structures.” Yeah, I can use my imagination, too, and there’s no reason a giant shark-filled swimming pool can’t be one of my imaginary structures. Sure, why not? We’re not actually building any of that, but maybe someday…

By the way, the nonprofit the author links to is The Coalition for Deep Space Exploration, a pie-in-the-sky group that endorses more scientific exploration (good for them!) but is all about deep space, not space hotels in near-Earth orbit, and mainly writes reports and press releases that are sent to congress and to defense contractors. They don’t actually do anything.

While the WaPo laid off 20 journalists and got bought out by Jeff Bezos for $250 million, this is the kind of ascientific PR fluff they publish now…alongside a fine collection of conservative idiots as op-ed writers. It’s a real shame. Maybe they’ll be putting an astrology column on the front page next?

He’s done: Rebecca Watson takes on Avi Loeb

Loeb gets a quick filleting from Rebecca.

I know exactly how Loeb would respond, if he were to even notice, because he posted a rant 4 days ago.

The culture of superficial toxicity poses an existential threat to curiosity-driven innovation in science. This culture is fueled by social-media mobs, whose members use the megaphone of blogs and tweets to amplify hate towards professional scientists who are following the traditional practice of evidence-based research. Why would the critics do that? Because of jealousy at the public’s attention to novel ideas.

One might naively argue that there is nothing to worry about because scientific innovation was always about “survival of the fittest” in the realm of ideas. However, the professional test of innovative ideas is empirical evidence, and following it requires extensive work. In contrast, the opinion of superficial critics is easier to come by. It involves raising ash and claiming that they do not see anything. Toxic critics often use personal attacks to nip innovation in the bud. They poison the well of novel ideas by creating fear among young scholars who, as a result of witnessing trauma, hesitate to come up with new ideas because of the damaging repercussions to their job prospects.

Snrk. The traditional practice of evidence-based research and empirical evidence — things Loeb does not have. Evidence always has a context and a theoretical foundation. You can’t just pull something out of your ass, hold it up, and claim you’ve found evidence for your astonishing radical idea, and that’s basically what he’s got: he pulled up some tiny metallic spheres from the sea floor, and is claiming that they came from a meteor that wasn’t even of extrasolar origin, and he can’t even say with confidence that they came from a meteor at all, especially given that expert analysis suggests that it’s from terrestrial coal ash.

Man, I suspect that every night Loeb goes to bed angry and has a tough time getting to sleep because he’s busy building resentful retorts in his head.

Assembly Theory pops up again

This morning I was surprised to see Assembly Theory popping up all over in my social media. Did somebody find evidence for it? Did the authors clarify what their babble meant? No, nothing so interesting: another evolutionary biologist took a hard look at the original paper, and tried to figure out what Cronin was talking about.

In October, a paper titled “Assembly theory explains and quantifies selection and evolution” appeared in the top science journal Nature. The authors – a team led by Lee Cronin at the University of Glasgow and Sara Walker at Arizona State University – claim their theory is an “interface between physics and biology” which explains how complex biological forms can evolve.

The paper provoked strong responses. On the one hand were headlines like “Bold New ‘Theory of Everything’ Could Unite Physics And Evolution”.

On the other were reactions from scientists. One evolutionary biologist tweeted “after multiple reads I still have absolutely no idea what [this paper] is doing”. Another said “I read the paper and I feel more confused […] I think reading that paper has made me forget my own name.”

As a biologist who studies evolution, I felt I had to read the paper myself. Was assembly theory really the radical new paradigm its authors suggested? Or was it the “abject wankwaffle” its critics decried?

He highlights some of the weird stuff in the paper, like this observation that leapt out at me when I read it.

In the words of one Nature commenter: “Why so many creationist tropes in the first few sentences?”

Yeah, that was odd: either the author was so totally unaware of how creationists make really bad arguments, so he made one himself (the generous interpretation), or it was intentional, and he’s underhandedly trying to sneak creationist nonsense in the literature (the uncharitable interpretation). Either way it was a warning sign.

So the critic works through the paper, trying to answer the question, is it “abject wankwaffle” or not? The answer is phrased politely.

However, as a sweeping new paradigm aiming to unify evolution and physics, assembly theory appears – to me and many others – to be addressing a problem that does not exist.

“abject wankwaffle” it is!

Assembly Theory is Ontogenetic Depth relabeled, nothing more, and is just as useless

How exactly did this dreck, Assembly theory explains and quantifies selection and evolution, get published in Nature?

It’s a stunningly bad paper to be published in such a prestigious journal. Let’s dissect that abstract, shall we?

Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics.

This makes no sense. Evolutionary biologists have not had any problem with physical laws — it has always been assumed, as far as I know, that biology fits within the framework of chemistry and physics. What grappling? Have biologists been proposing theories that violate physics, and they didn’t tell me?

The citations to back up that outré claim are Stuart Kauffman, who can get a little weird but not that weird, and Ryan Gregory, whose papers I’ve used in class, and is probably a bit annoyed at being told his work supports that ridiculous claim.

These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena.

Sure. Emergent properties exist. We know you can’t simply derive all of biology from Ideal Gas Law. So far, nothing new.

Evolutionary theory explains why some things exist and others do not through the lens of selection.

Uh-oh. Just selection? Tell me you know nothing of evolutionary biology without saying you don’t know anything about evolutionary biology.

To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary3,4,5.

Here it comes, more bad theorizing. It is implicit in evolution that there is no “inherent design blueprint,” so where did these authors get the idea that design was a reasonable alternative? They don’t say. This is simply another imaginary controversy they’ve invented to make their theory look more powerful.

We don’t need a new approach to selection. To support that, they cite Charles Darwin (???) and Sean B. Carroll, and a fellow named Steven Frank, whose work I’m unfamiliar with. A quick search shows that he applies “evolutionary principles to the biochemistry of microbial metabolism,” which doesn’t sound foreign to standard biology, although he does throw the word “design” around a lot.

But here we go:

We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an ‘object’ on which these laws act. AT conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units.

Again, what biological theory has ever been proposed that alters the laws of physics? They keep touting this as a key feature of their model, that it doesn’t break physics, but no credible theory does. This talk of formation histories is nothing revolutionary, history and contingency are already important concepts in biology. Are they really going to somehow quantify “assembly”? They’re going to try.

We introduce a measure called assembly (A), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly.

I’ve heard this all before, somewhere. A new term invented, a claim of a novel measure of the complexity of a pathway, a shiny new parameter with no clue how to actually measure it? This is just ontogenetic depth! Paul Nelson should be proud that his bad idea has now been enshrined in the pages of Nature, under a new label. I did a quick check: Nelson is not cited in the paper. Sorry, Paul.

Here is all assembly theory is: You count the number of steps it takes to build an organic something, and presto, you’ve got a number A that tells you how difficult it was to evolve that something. That’s it. Biology is revolutionized and reconciled with physics. It’s just that stupid.

a–c, AT is generalizable to different classes of objects, illustrated here for three different general types. a, Assembly pathway to construct diethyl phthalate molecule considering molecular bonds as the building blocks. The figure shows the pathway starting with the irreducible constructs to create the molecule with assembly index 8. b, Assembly pathway of a peptide chain by considering building blocks as strings. Left, four amino acids as building blocks. Middle, the actual object and its representation as a string. Right, assembly pathway to construct the string. c, Generalized assembly pathway of an object comprising discrete components.

I told you, it’s just ontogenetic depth, with basic math. Here’s how to calculate A:

All you have to do is recursively sum the value of A for each object in the series, and you get the value of A for the whole! How you calculate the value of A for, say, acetate or guanine or oxaloacetic acid or your nose or a lobe of your liver is left as an exercise for the reader. It is also left as an exercise for the reader to figure out how A is going to affect their implementation of evolutionary biology.

By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists.

I read the whole thing. I failed to see any new aspect of physics, or any utility to the theory at all. I don’t see any way to apply this framework to evolutionary biology, or what I’d do if I could calculate A for one of my spiders (fortunately, I don’t see any way to figure out the A of Steatoda triangulosa, so I’m spared the effort of even trying.)

The primary author, Leroy Cronin, a chemistry professor at the University of Glasgow, acknowledges that the work was funded by the John Templeton Foundation. Quelle surprise!

I honestly don’t understand how such a steaming pile managed to get past the editors and reviewers at Nature. It should have been laughed away as pure crank science and tossed out the window. There has to have been a lot of steps where peer review failed…maybe someone should try to calculate the assembly value for getting a paper published in Nature so we can figure out how it happened.

Sharma, A., Czégel, D., Lachmann, M. et al. Assembly theory explains and quantifies selection and evolution. Nature (2023). https://doi.org/10.1038/s41586-023-06600-9

It’s your lucky day!

The Neuralink Patient Registry is now open! You too can now apply to have a robot operate on your brain (if you meet the requirements: you must be a quadriplegic over the age of 22 who has no other implants and is not prone to seizures.) It’s the most horrendously awful lottery ever.

Not only must the victims patients have experienced extreme tragedy and trauma, but they will be subject to intense, invasive surgery with no guaranteed outcome, and the procedure is entirely experimental with the goal of not restoring any function, but simply to test whether their surgical robot works without scrambling your brain.

Best case, if it works, you will be able to play Pong with your mind, at least until the scar tissue disables the whole device, or it triggers dangerous seizures. Also consider the implications of the requirements to enroll: no other implants allowed. When the new, improved MkII Neuralink comes out, that means MkI recipients will be undesirable. They’re always going to want fresh, untrammeled brains to hack into.

If I were in such dire straits to qualify, I wouldn’t apply. I wouldn’t need to make my situation worse, with such feeble promise of reward.

The Muslim fly studies are back!

Stop me if you’ve heard this before…oh wait. If you’ve read this blog before you’ve encountered this phenomenon in the past. There is a strange cottage industry among Muslim fanatics to demonstrate the infallibility of Mohammed by testing one of his weirder claims. This one:

Over a thousand years ago Prophet Mohammed (Peace Be Upon Him) said “if a fly falls down on your vessel, drown it then remove it, for one of its wings has the ailment and other has the cure” narrated by Al-Bokhari. In this study 4 flies of (Musca domestica) species were collected to investigate the antibacterial and antifungal activity of their wings. The obtained result showed that all media cultivated with right wing extract were free of bacterial and fungal growth however the bacterial and fungal growth for the left wing were observed. It could be concluded that the right fly wing is considered as new revolution of antibiotic recommended for further researches to find more antibiotics from right fly wing.

That’s from an article with the ungrammatical title, Microbiological Studies on Fly Wings(Musca domestica) Where Disease and Treat. I guess the World Journal of Medical Sciences does not exercise any editorial oversight at all, and their review process is a bit of a joke. The paper itself is incredibly bad, of a quality that would earn a failing grade if it were presented as a middle school science fair project. I mean, seriously — here’s the entirety of the results section (with a bit of the introduction and methods).

Pic. (1), (2) and (3) illustrated that there were no bacterial or fungal growth in test tubes containing the right fly wing extract however there were microbial growth in 4 test tubes for left wings extract indicated by turbidity which had been confirmed by microscopical examination, the slides for the right wings extract were free for the presence of any microbe although the slides for the left ones showed presence of both bacteria (cocci and bacilli) and fungi (hyphea)

That’s it. That’s all. Do you believe any of it? It’s not just the lack of believable data, but the introduction is full of obvious nonsense.

Entomologist latest research, certify that there is very little difference between a human and a fly-heart where biggest similarity is that both have heart disease as a result of getting older. Studied flies in order to produce cardiac medications

I know what both a fly heart and a human heart look like — and no, the only similarity is in some of the molecules that initiate differentiation.

I guess the only thing we can learn here is that the World Journal of Medical Sciences is not a trustworthy source. It’s a dumping ground for bad science and is nothing but a tool for incompetent pseudoscientists to pad their résumé.