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

Can somebody explain this to me?

The Palestinians have a tiny amount of territory, the Gaza Strip and the West Bank, that has been under Israeli control since 1968. Israel controls the air space, all of the entry points, and is allowed to let its military freely enter. All utilities, water, electricity, communications, etc. in these territories is completely controlled by Israel. Israeli settlers have been colonizing the territories. The Palestinians are treated as residents of a vassal state, with limited freedoms, and occasionally Israeli soldiers bulldoze a home or shoot a citizen.

The US has given Palestine $235 million in aid, mostly dedicated to supporting refugees. The US has given Israel almost $4 billion in aid, virtually entirely dedicated to propping up their military.

The US has responded to a terrorist attack in Israel by promising to send more aid, more arms, to Israel. They’re also moving an aircraft carrier to the coast in support.

This is insane.

Israel does not need more money, arms, and encouragement to continue their oppression of the Palestinian people. It is inarguably horrible and criminal that Hamas militants murdered civilians, and I cannot excuse that; but neither can I excuse the decades of brutal oppression of Palestinians by Israel. These are criminal acts all around, and none can be forgiven.

The only reasonable answer, though, is to give Palestinians greater freedom and autonomy. They’re turning to violent assholes in Hamas because there is no alternative, and because Israel has become increasingly tyrannical. The US ought to be working to moderate the relationship, not giving Israel the tools and the encouragement to commit genocide. That’s all the current pattern of behavior can end in, in the violent, bloody destruction of an entire people.

Current US policy is enabling that genocide.

Nightmare nest

This thing is hanging in a tree near where I walk on the way to the lab. It’s bigger than my head!

That’s actually what I think when I walk by: “What if that fell off and landed on my head and I had to run around waving my arms?” A childhood watching Saturday morning cartoons has given me that expectation.

Don’t trust self-driving cars

I think I can scratch a self-driving car off my Christmas list for this year…and for every year. I can always use more socks, anyway. The Washington Post (owned by another tech billionaire) has a detailed exposé of the catastrophic history of so-called autonomous vehicles.

Teslas guided by Autopilot have slammed on the brakes at high speeds without clear cause, accelerated or lurched from the road without warning and crashed into parked emergency vehicles displaying flashing lights, according to investigation and police reports obtained by The Post.

In February, a Tesla on Autopilot smashed into a firetruck in Walnut Creek, Calif., killing the driver. The Tesla driver was under the influence of alcohol during the crash, according to the police report.

In July, a Tesla rammed into a Subaru Impreza in South Lake Tahoe, Calif. “It was, like, head on,” according to a 911 call from the incident obtained by The Post. “Someone is definitely hurt.” The Subaru driver later died of his injuries, as did a baby in the back seat of the Tesla, according to the California Highway Patrol.

Tesla did not respond to multiple requests for comment. In its response to the Banner family’s complaint, Tesla said, “The record does not reveal anything that went awry with Mr. Banner’s vehicle, except that it, like all other automotive vehicles, was susceptible to crashing into another vehicle when that other vehicle suddenly drives directly across its path.”

Right. Like that ever happens. So all we have to do is clear the roads of all those other surprising vehicles, and these self-driving cars might be usable. That’s probably Elon Musk’s end goal, to commandeer the entirety of the world’s network of roads so that he can drive alone.

Speaking of Musk, he has a long history of lying about the capabilities of his autopilot system.

Tesla CEO Elon Musk has painted a different reality, arguing that his technology is making the roads safer: “It’s probably better than a person right now,” Musk said of Autopilot during a 2016 conference call with reporters.

Musk made a similar assertion about a more sophisticated form of Autopilot called Full Self-Driving on an earnings call in July. “Now, I know I’m the boy who cried FSD,” he said. “But man, I think we’ll be better than human by the end of this year.”

Lies. Lies, lies, lies, that’s all that comes out of that freak’s mouth. If you want more, Cody has a new video that explains all the problems with this technology. I know, it’s over an hour long, but the first couple of minutes contains a delightful montage of Musk making promises over the years, all of which have totally failed.

Can we just stop this nonsense and appreciate that human brains are pretty darned complex and there isn’t any AI that is anywhere near having the flexibility of a person? Right now we’re subject to the whims of non-scientist billionaires who are drunk on the science-fantasies they read as teenagers.

Now the spiders are leaving

Oh no. I was laughing at this very silly woman who claims the emergency phone alert system test the other day made everyone’s menstrual flow start. She has an n of 1, herself, and she admits that she doesn’t track her periods, so I don’t see the point. She doesn’t have any evidence at all for this claim, and I don’t see how a cell phone signal could trigger menstruation, so she lacks even a hypothetical mechanism.

And then we get to her chilling last line…

I checked the lab. No, they’re all there and are fine.

I’m also not menstruating.

Give her all the moneys

Never read the comments at Fox News. Here’s a sampling of the reaction to the news that a woman is suing Disney for injuries she received on a ride. The good folks commenting are torn; some think it’s great that “woke Disney” is getting sued, others are offended that anyone would sue a capitalist enterprise, and want to blame the woman.

I’m pretty sure this is a frivolious lawsuit. They planned it.

In the liberal world, there is no such thing as personal responsibility.

How predictable. The lawsuit doesn’t say they didn’t warn her. It’s says they didn’t tell her WHY she needed to cross her legs.

Then you read what happened to this woman.

(I’m going to put it below the fold because it’s rather horrific.)

[Read more…]

I’m not interested in promoting your Xian book

Smug twit

I’ve never had any respect for Alister McGrath, but apparently he thinks I’m a credible source on atheism. He has a book titled Coming to Faith Through Atheism, containing 12 essays about how people returned to religion after a dalliance with atheism, driven by how much they disliked Dawkins and the New Atheism. That sounds incredibly cliched — it’s practically a joke how often theists claim that they used to be an atheist, but then they saw the light.

Fine. More pedestrian pablum from a conventional Christian who doesn’t like Dawkins. I even have some sympathy with the thesis that Dawkins has become a detriment to atheism. However, an argument against one particular flavor of atheism is not an argument for the ridiculous Christianity McGrath favors. I also mildly resent that he cites me (and Ashley Miller) some kind of supporter of his ideas.

Yet it wasn’t just that Dawkins and others set out to make religious faith a badge of shame. The “New Atheism” encouraged a discriminatory rhetoric of denunciation and demonisation directed not primarily against religious ideas, but against religious people. Many were alarmed at this trend. The feminist atheist blogger Ashley Miller distanced herself from those who suggested that “people who are religious aren’t worthwhile and are certainly too stupid to be respected”. The debate ought to be about assessing ideas, she insisted, not about publicly ridiculing religious people: “We dehumanize people who disagree with us instead of arguing about ideas.” It didn’t exactly help with the public face of atheism.

Today, the “New Atheism” is generally regarded as having imploded, increasingly (though perhaps unfairly) being seen as the crystallisation of the cultural prejudices of old white Western middle-class males. Many of its former members, disenchanted by its arrogance, prejudice, and superficiality, have distanced themselves from the movement and its leaders.

Of course he’d think it unfair to view the failure of the New Atheism as a result of the cultural prejudices of old white Western middle-class males, since he is one, and his stodgy Christianity is the epitome of Western middle-class bullshit. His religion is not an improvement on atheism!

What he doesn’t acknowledge is that neither Ashley nor I have abandoned atheism, which is something rather different than the peculiarly assertive, aggressive style of Dawkins’ atheism. We aren’t Christians! It’s a little rude to pose two people who oppose his position as somehow backing up his new book.

Why didn’t he link to my assessment of Alister McGrath?

That’s McGrath. Incoherent and contradictory, vacuous and vapid, and bumbling along, triumphantly making fallacious arguments that he thinks are irrefutable.

Jebus, but I love “sophisticated theology”. It makes its practitioners look like such hopeless dolts.

I’m still a bit assertive and aggressive, and I still categorically reject McGrath’s weird beliefs.

Is Eric Hovind trying to provoke me?

He’s succeeding. He has this new series of videos titled “Beyond Darwin,” in which he tries to claim that fossils disprove evolution. It’s warmed-over Harun Yahya bullshit. You know, show a picture of a fossil, then show a picture of a modern animal, and declare, A-ha! There’s no difference between them!

It’s all perfectly ignorable nonsense, except he roused me from my slumber with this: SPIDERS DISPROVE EVOLUTION!

What a pitiful effort. Let’s scrutinize his example of failed evolution, shall we?

On the right, that’s a familiar beast: that’s a modern Araneus diadematus, or European garden spider, a big ol’ common orb weaver. It is most definitely a true spider.

On the left is a grainy photo of a fossil. It took me a moment to figure out what that is — you might look at it and notice that it seems to have only 6 legs. Actually, it has 8, but the 2nd pair is thin and attenuated. It also has a segmented abdomen, unlike most modern spiders, and there’s something going on with it’s mouthparts. It’s an arachnid all right, but it’s not a spider. That’s a fossil whip scorpion, Weygoldtina. Here’s a reconstruction that will clarify the details.

So here’s dumbass Hovind showing us a photo of two animals with radically different morphology, coming from two different distinct orders, the Araneae and the Amblypygi, and trying to tell us they look completely the same. Then he says Maybe evolution didn’t work on that one, or it just evolved as high as it can go, two excuses that aren’t valid evolutionary concepts. He riffs absurdly, pointing out that spiders still die, as if that’s something that wouldn’t happen under evolution.

Hey, Eric, does the fact that you’re still ignorant mean that education doesn’t exist? Do you think The Atlas of Creation is a biology textbook, rather than a religious scam written by a convicted con man? This approach didn’t work out so well for him, or your dad, you know.

I guess the rotting apple hasn’t fallen far from the dying corrupted tree, I guess.

Wait! I just watched the full video from Eric Hovind (the clip above is just an excerpt), and would you believe…he comes right out and cites The Atlas of Creation at the 21 minute mark and credits it for his ideas!

He is literally pulling out examples and photos from that discredited and blatantly silly book and quoting them as evidence that we have to move beyond Darwin. (Here’s a hint, Eric: we have. Darwin didn’t have genetics or molecular biology as tools.)

I thought the cacophony was bad…

My cell biology class is held from 1-2:05pm. Today was the monthly test of the tornado warning system, so we got sirens for the start of the hour, and then 20 minutes later everyone’s cell phones started ringing for the big national emergency alarm test. Fun. But we recovered quickly.

Except now I apparently have to worry about the long-term effects.

I thought it was just my lectures that turned students into zombies! If they start snarling and moaning about “braaaains,” I’ll let you all know.

I don’t like Star Trek anymore

I have a terrible confession to make, one that may drive away many readers: I am tired of Star Trek. I was a kid when the original series aired, I watched them religiously, I still have nothing but fond memories of it all. By the time Star Trek: The Next Generation rolled around, though, I was at the point where I was watching reruns to mainly groan at the bad science and the cheesy special effects, and ST:TNG didn’t help — more bad acting, more terrible writing, more ludicrous plots written by people who seemed to have more of a background in soap operas than in science fiction. All those other series that were subsequently shat out? I didn’t even watch them.

I know. I should be drummed out of the old SF nerd club. I feel terrible for not being able to share in the pleasure so many people still get out of the series, but you all go right ahead. Have a good time, while I roll my eyes at all the Trek worship.

I would rather see something with a fresh take. Something that is genuinely about ideas, rather than milking a comfortable old story to death.

But still, here’s something I did enjoy: a site that catalogs all the reused props from Star Trek. You need a strange futuristic device on a desk? Add some odd lighting to a CD rack. Glue random geometric shapes together, spray paint them silver, and done–we’ll find a use for it. Rearrange the shapes, you’ve got something new.

Nothing goes to waste. You can use them same props in different series!

Kudos to the props department for their creativity and economy. This I could enjoy reading, even as I’ve lost all interest in the plots of the stories they support.