Michael J. Behe's Blog, page 85

More depths to the bacterial flagellum: Mysterious protein FliL now better understood

FliL as seen with cryo-electron tomography/Jun Liu lab

The researchers hope to work on this “for decades”:

How bacteria move around, survive, and cause infection in the body has fascinated scientists, but the roles of certain key players involved in the mechanism of motility are still poorly understood. Now, for the first time, Yale researchers have visualized a unique ring structure that stabilizes the motor of the flagellum and enhances bacterial movement. The researchers published their findings in Proceedings of the National Academy of Sciences on March 7…

“Before, we didn’t know what the stators do exactly to rotate the motor,” says Shuaiqi Guo, Ph.D., associate research scientist and first author of the study. In 2020, the team found that the stators not only experience a conformational change but also rotate, like gears driving the belt of a motor. These slender, flexible structures need to rotate very fast, and without stabilization this rapid spinning would introduce instability to the whole motor. The members of the Liu lab wanted to figure out how the stators stay in place as they rotate, and in their latest studies, they found that this ability is made possible by a protein called FliL.

“This protein has been very mysterious in the field for thirty years,” says Guo. “It’s very important for bacterial motility in complex environments, but scientists have been heatedly debating its function and structure.” …

“We’ve made incremental progress in understanding this fascinating machine,” says Liu. “We hope to continue to work on this for decades to solve how the flagella of different bacteria uniquely evolved. We’ve just touched the tip of the iceberg of understanding this beautiful structure.”

Isabella Backman/Yale University, “How bacteria swim: Researchers discover new mechanisms” at Phys.org (April 4, 2022)

These researchers hardly sound like they are very committed to the Darwinian “it all just gradually evolved” camp, even if they must — at times — say that to keep their jobs.

The paper requires a fee or subscription.

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As the Babylon Bee still awaits rescue from Twitter jail…

The Dumpster Fire Is Saved: 9 Positive Changes Coming To Twitter: Including “9) Anyone who doesn’t like the changes will be offered the chance to leave and start their own social network: Conservatives are currently practicing their “smug” faces in the mirror for when they get a chance to say this.”

Revealed: What Your Morning Beverage Says About Your Politics

Twitter Workers Worried Elon Musk Will Turn Their Free Speech Platform Into Platform That Allows Free Speech “Others are concerned that Musk’s influence may cause the social network to allow unfettered social networking, and millions of people to use the platform to platform themselves even though they are yucky and have weird opinions that shouldn’t be platformed.”

Wife Turned To Pillar Of Salt After Looking Back While Fleeing Disneyland “”She didn’t even make it out of the park,” said distraught 37-year-old father Tim Lott. “She took one last look at the castle and—” He broke down, unable to further explain to authorities what had happened to his wife.”

Not To Be Outdone, Bill Gates Buys 9.2% Of MySpace “Gates confirmed he will be making some much-needed changes to the site—adding helpful information on the latest vaccines and boosters, a “Clippy” virtual assistant, and handy information on the benefits of subdermal microchip technology.”

Sad: Florida Students Ranked Last In The Nation In Subject Of ‘Teacher’s Sex Life “”This is all thanks to DeSantis’s bigoted ‘Don’t Say Gay’ bill,” said local kindergarten teacher Jimbo Pandy (he/him) to reporters. “I am no longer allowed to describe my sexual encounters from last weekend to my 5-year-old students, which has greatly crippled their sexual exploration. I thought this was America! What happened to freedom of speech?””

Costco Now Offering Convenient Payment Plans On Ground Beef “At publishing time, Costco announced you can now pay off the rest of your grocery bill by signing up for a reverse mortgage with them today.”

You may also wish to read: Will Elon Musk get the Babylon Bee out of Twitter Jail? The most significant thing to see about all this is that the Bee is doing what late night comics used to do but now dare not. Someone needs to fix that.

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What about the idea that cells were once much simpler? But how much simpler?

Introducing the third vid in the Long Story Short series (on cell membranes) Rob Stadler comments:

First, scientists have been working for decades to simplify existing life, trying to arrive at a minimal viable life form by jettisoning anything that is not essential from the simplest extant cells. The success of Craig Venter’s group is well known. Building on their efforts to produce synthetic life (“Synthia” or “Mycoplasma labritorium”) in 2010,1,2 in 2016 they introduced the current record holder for the simplest autonomously reproducing cell (JVCI Syn3.0).3 With a genome of only 473 genes and 520,000 base pairs of DNA, JVCI Syn3.0 can reproduce autonomously, but it certainly isn’t robust. Keeping it alive requires a coddling environment — essentially a life-support system. To arrive at a slightly more stable and robust organism that reproduced faster, the team later added back 19 genes to arrive at JVCI Syn3A.4 When combined, this work provides an approximate boundary for the simplest possible self-replicating life. We are clearly approaching the limit of viable cell simplicity. It seems safe to conclude that at least 400 genes (and approximately 500,000 base pairs of DNA) are the minimum requirements to produce a self-replicating cell.

(April 6, 2022)

Rob Stadler, “[article title]” at Evolution News and Science Today

Here are earlier episodes of Long Story Short, an education you actually have time for.

The critical question is viability. Anything can be a lot simpler, at least in principle, if it does not also need to be alive.

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Some things never change: Ridiculous attack on the surgeon author of an article on scientific gatekeeping

Readers will recall a story we ran on Tuesday about a surgeon, Jeffrey Singer, who protests scientific gatekeeping. Gatekeeping’s an obvious problem in any field.

But those who imagine themselves in charge of the gates (they’re usually not) in the case of science are, in themselves, a mildly interesting study. Get a load of this:

A surgeon attacks “scientific gatekeeping” over COVID-19 in Reason. It goes so poorly that I might have to resurrect an old shtick that I used to use with creationist surgeons.

Longtime readers might remember a humorous (I hope) shtick that I used to employ from time to time when I encountered a fellow physician—or, worse, a fellow surgeon—spewing science denial. The vast majority of the time, back in those early heady days of this blog, what provoked this shtick was seeing a surgeon spew creationist nonsense denying the theory of evolution. So what was this shtick? In brief, I had a running gag that involved highly extravagant descriptions (based on old Looney Tunes) of how I wanted to hide my face behind a paper bag in sheer embarrassment over the antiscience antics of fellow physicians, particularly . Over time, the gag evolved to my expressing a mock desire to hide my visage behind a metal Doctor Doom-style mask, again, over sheer embarrassment over the antiscience stylings of one of my colleagues. In most cases, it was evolution, because there are a depressingly large number of creationist physicians out there. (Anyone remember the creationist neurosurgeon Dr. Michael Egnor?) I retired the shtick many years ago, but every so often a physician or surgeon seriously tempts me to resurrect it. Thus far, I’ve resisted, but I failed when I encountered an article in Reason by a fellow general surgeon entitled Against Scientific Gatekeeping. As if to goad me further into resurrecting the paper bag, its subtitle read: Science should be a profession, not a priesthood.

Orac, “A risible attack on the “priesthood” of “scientific gatekeeping”” at Respectful Insolence (April 6, 2022)

Let’s just say, 1) the author goes on at some length and 2) readers may find it useful to know that gate defenders are out there and some of them would appear to have a lot of time on their hands.

You may also wish to read: A surgeon protests scientific “gatekeeping” Singer: “… a problem arises when some of those experts exert outsized influence over the opinions of other experts and thereby establish an orthodoxy enforced by a priesthood. If anyone, expert or otherwise, questions the orthodoxy, they commit heresy. The result is groupthink, which undermines the scientific process.”

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Someone out there is actually defending junk DNA

Can someone please tell them, the Titanic has sunk — its seaworthiness is no longer an issue?:

With the discovery of the double helical structure of DNA, a shift occurred in how biologists investigated questions surrounding cellular processes, such as protein synthesis. Instead of viewing biological activity through the lens of chemical reactions, this new field used biological information to gain a new profound view of how biological systems work. Molecular biologists asked new types of questions that would have been inconceivable to the older generation of researchers, such as how cellular machineries convert inherited biological information into functional molecules like proteins. This new focus on biological information also gave molecular biologists a way to link their findings to concepts developed by genetics and the modern synthesis. However, by the late 1960s this all changed. Elevated rates of mutation, unsustainable genetic loads, and high levels of variation in populations, challenged Darwinian evolution, a central tenant of the modern synthesis, where adaptation was the main driver of evolutionary change. Building on these findings, Motoo Kimura advanced the neutral theory of molecular evolution, which advocates that selection in multicellular eukaryotes is weak and that most genomic changes are neutral and due to random drift. This was further elaborated by Jack King and Thomas Jukes, in their paper “Non-Darwinian Evolution”, where they pointed out that the observed changes seen in proteins and the types of polymorphisms observed in populations only become understandable when we take into account biochemistry and Kimura’s new theory. Fifty years later, most molecular biologists remain unaware of these fundamental advances. Their adaptionist viewpoint fails to explain data collected from new powerful technologies which can detect exceedingly rare biochemical events. For example, high throughput sequencing routinely detects RNA transcripts being produced from almost the entire genome yet are present less than one copy per thousand cells and appear to lack any function. Molecular biologists must now reincorporate ideas from classical biochemistry and absorb modern concepts from molecular evolution, to craft a new lens through which they can evaluate the functionality of transcriptional units, and make sense of our messy, intricate, and complicated genome.

Alexander F. Palazzo* and Nevraj S. Kejiou, Non-Darwinian Molecular Biology, Front. Genet., 16 February 2022 | https://doi.org/10.3389/fgene.2022.83...

The paper is open access.

Tim Standish writes to say,

I’m intrigued by people who want to argue stuff like this, as if what they personally believe must be reflected in reality rather than the other way around. The argument that I make is that the assumption of meaning, function and purpose has proven to be productive, while the assumption that everything is most likely meaningless, functionless and lacks purpose is a science killing, depressing and often demonstrably wrong exhibition of prejudice. Does that mean that function for everything has been proven? Of course not, but logic that goes, “I don’t know what this does, therefore it does nothing,” is arrogance, not knowledge. Anyone who embraces it should be embarrassed.

You may also wish to read:

New use for “junk DNA”: Controlling fear Okay, why, until recently, did researchers think that “the majority of our genes were made up of junk DNA, which essentially didn’t do anything”? Because that vast sunken library of dead information (sheer randomness and waste) was a slam dunk for Darwinism, as politically powerful theistic evolutionist Francis Collins was quick to point out in The Language of God. (2007). If that’s not true, an argument for Darwinism is disconfirmed.

and

Ah, a real-world term for former “junk DNA.” And the winner is “genomic dark matter”: “Most DNA in the human genome still has unknown functions and is referred to as “genomic dark matter.”

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Trust the Science!: Woke edition

Apparently, a quite competent panel was Canceled recently at North Carolina State because the participants were just Wrong, sexually, ethnically, and so forth:

The science community clearly recognizes the value of public outreach, yet some prominent figures and institutions within it seem to have a higher priority—virtue signaling their social justice bona fides. Just last week, NC State’s Genetic Engineering and Society (GES) Center abruptly canceled a panel discussion designed to teach graduate students how to engage the public. The decision was fueled by a wave of complaints on Twitter alleging that the event featured an “all-white-male panel.”

The controversy and subsequent cancellation would have been perfectly justified if GES had selected panelists in a discriminatory fashion. After reviewing the tweets, the University’s rationale for halting the discussion, and speaking with one panelist willing to comment on the specifics of the situation, it’s clear to me that no such scandal occurred.

This entire affair was just another example of a broader, disturbing trend: academic institutions comprising their educational mission to appease abusive political activists.

Cameron English, “Silencing Science: NC State Cancels Panel Discussion To Appease Woke Activists” at American Council on Science and Health (April 5, 2022)

It is hitting medicine too:

Fat-acceptance advocates say medical terms like “obesity” and “overweight” stigmatize fat people and should be eliminated from our vocabulary. They’re putting public health at risk to promote a misguided ideology…

This thinking originated in a field known as “fat studies,” which maintains that the mainstream definition of “obesity” was socially constructed to oppress overweight people. Besides the fact that someone named Aubrey Gordon says so, Buzzfeed didn’t explain why we have to accept this conclusion. Appeals to authority don’t work in science, unless that authority has evidence to justify their views.

But even if we assume Gordon is correct for the sake of argument, it cannot be denied that the risk for serious disease increases with BMI. There isn’t an ideal weight we should all strive to achieve, but weight clearly influences our long-term health outcomes.

Cameron English, “Woke Science Denial: Social Justice Comes For ‘Obesity,’ And Other Harmful Language” at American Council on Science and Health (March 30, 2022)

How is a family doctor supposed to both tell and not tell a patient that being fifty pounds overweight (mmmph! mmmph! mmmph!) is a serious health danger? Why isn’t the patient entitled to that information? Of course it makes the patient feel bad. But is feeling bad worse than losing out on a chance to avoid being prematurely chronically ill or dead?

The Woke don’t care about that, of course. Family medicine is just another science-based discipline they get to throttle.

Another Woke enterprise in medicine:

Health Affairs, dubbed by a Washington Post columnist as “the bible of health policy,” represents something much more ambitious than woke virtue signaling. Its February issue reflects the effort of newly empowered “anti-racist” scholars to transform concepts that are still considered speculative and controversial – and some say unprovable – into scientific fact. This growing effort to document, measure, and quantify racism is being advanced by other high-profile publications, including The New England Journal of Medicine, The Journal of the American Medical Association, and Scientific American, which last year ran articles entitled “Modern Mathematics Confronts Its White, Patriarchal Past” and “Denial of Evolution Is a Form of White Supremacy.”

But this scientific aspiration faces major challenges. Science demands verification, testability, and replicability, whereas race is a social construct that can be difficult to separate from factors like class or culture, and explaining the data often remains dependent on academic theories about systemic racism. The articles in Health Affairs indicate that elevating the concept of systemic racism from moral certitude to scientific fact will require developing new tools and methods – and even more theories – in the face of skepticism and resistance from dissenters who view this direction in research as unscientific and ideological.

For example, five co-authors of the Health Affairs article “Improving the Measurement of Structural Racism to Achieve Antiracist Policy” observe that “there is a disconnect between the conceptualization and measurement of structural racism in the public health literature” – that is to say that acceptance of the idea outpaces the evidence for it.

John Murawski, “Medicine’s Got a Tricky Operation Coming Up: Grafting ‘Systemic Racism’ Onto Hard Science” at RealClearInvestigations (April 5, 2022)

When “acceptance of the idea outpaces the evidence for it,” expect to see many papers providing “evidence” that, analyzed, amounts merely to talking points decked out in statistics. But none dare analyze the methodology closely. Indeed, in some cases, it might be impossible to make sense of it.

In Murawski’s piece, professional (and usually) unidirectional skeptic Michael Shermer gets a look-in: He got dumped from Scientific American after 18 years for questioning all this:

“They’re saying we already know the answer – the answer is racism,” Shermer said in a phone interview with RealClearInvestigations. “We’re going to ignore all the other variables. They’re just reducing complex problems to one variable.”

John Murawski, “Medicine’s Got a Tricky Operation Coming Up: Grafting ‘Systemic Racism’ Onto Hard Science” at RealClearInvestigations (April 5, 2022)

One thing Wokeness does is this: In an age when a huge gulf yawns between the billionaires who fund the Woke and the rest of us — it stifles discussion of “class,” the truly relevant factor in many different life outcomes, in favor of “race,” with which the Woke can do whatever they want.

The billionaires who fund the Woke wouldn’t be billionaires if they weren’t smart enough to see the advantages of dividing their underlings in order to rule.

Summary: The people who carried on in the past about “science denial!” either 1) never really cared about science denial and were merely using it as a term of convenience or 2) they will rise to the occasion and do something about this stuff now. Any takers on a bet as to how that will go? If science is rescued at all, it will probably be rescued by its supposed enemies.

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Interesting new PNAS paper casts doubt on universal common ancestry

Paul Nelson has the story:

1. Back in the day, the best evidence for a single Tree of Life, rooted in the Last Universal Common Ancestor (LUCA), was the apparent biochemical and molecular universality of Earth life…

For [Theodosius] Dobzhansky, as for all neo-Darwinians (by definition), the apparent molecular universality of life on Earth confirmed Darwin’s prediction that all organisms “have descended from some one primordial form, into which life was first breathed” (1859, 494) — an entity now known as the Last Universal Common Ancestor, or LUCA. So strong is the pull of this apparent universality, rooted in LUCA, that any other historical geometry seems unimaginable.

Paul Nelson, “Sara Walker and Her Crew Publish the Most Interesting Biology Paper of 2022 (So Far, Anyway)” at Evolution News and Science Today (April 5, 2022)

Universal common ancestry was a religion, really. Create a religion, birth a heretic:

The “Laws of Life”

Theoretician Sara Walker and her team of collaborators, however, are looking for an account of what they call (in Gagler et al. 2022) the “laws of life” that would apply “to all possible biochemistries” — including organisms found elsewhere in the universe, if any exist. To that end, they wanted to know if the molecular universality explained under neo-Darwinian theory as material descent from LUCA (a) really exists, and (b) if not, what patterns do exist, and how might those be explained without presupposing a single common ancestor.

And a single common ancestor, LUCA? That’s what they didn’t find.

Paul Nelson, “Sara Walker and Her Crew Publish the Most Interesting Biology Paper of 2022 (So Far, Anyway)” at Evolution News and Science Today (April 5, 2022)

Imagine Sara Imari Walker and her team having the guts to just admit that they didn’t find that a single common ancestor was the best explanation — instead of just making something up, like so many people, faced with such a challenge, would do.

Also:

It is interesting to note that this paper was edited (for the PNAS) by Eugene Koonin of the National Center for Biotechnology Information. For many years, Koonin has argued in his own work that the putative “universality due to ancestry” premise of neo-Darwinian theory no longer holds, due in large measure to what he and others have termed “non-orthologous gene displacement” (NOGD). NOGD is a pervasive pattern of the use of functional synonyms — enzyme functions being carried out by different molecular actors — in different species.

Paul Nelson, “Sara Walker and Her Crew Publish the Most Interesting Biology Paper of 2022 (So Far, Anyway)” at Evolution News and Science Today (April 5, 2022)

But then, if there is no simple Tree of Life, what is the Darwin-in-the-schools lobby going to raise Cain about?

The paper is open access.

You may also wish to read: As evolutionary biologists slowly kill off Darwinism… hacking down the Tree of Life, even. Species merging. Julie Berwald: What I didn’t know then was that, even as I ambivalently placed the overhead film on the projector, the concept of the tree of life had begun to wilt. Four decades on, it’s morphed entirely.

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Researchers: The development of Earth’s inner core coincided with the Cambrian Explosion

We’re only learning about the inner core:

Earth’s magnetic field, nearly as old as the planet itself, protects life from damaging space radiation. But 565 million years ago, the field was sputtering, dropping to 10% of today’s strength, according to a recent discovery. Then, almost miraculously, over the course of just a few tens of millions of years, it regained its strength—just in time for the sudden profusion of complex multicellular life known as the Cambrian explosion.

… Once the inner core was born, possibly 4 billion years after the planet itself, its treelike growth—accreting a few millimeters per year at its surface—would have turbocharged motions in the outer core, reviving the faltering magnetic field and renewing the protective shield for life. “The inner core regenerated Earth’s magnetic field at a really interesting time in evolution,” says John Tarduno, a geophysicist at the University of Rochester. “What would have happened if it didn’t form?”

ALL THIS COMPLEXITY appears to be geologically recent. Scientists once placed the inner core’s birth back near the planet’s formation. But a decade ago, researchers found, using diamond anvils at outer core conditions, that iron conducts heat at least twice as fast as previously thought. Cooling drives the growth of the inner core, so the rapid heat loss combined with the inner core’s current size meant it was unlikely to have formed more than 1 billion years ago, and more than likely came even later. “There’s no way around a relatively recent appearance of the inner core,” says Bruce Buffett, a geodynamicist at UC Berkeley.

Paul Voosen, “The Planet Inside” at Science (March 31, 2022)

Sounds like a rollout, really.

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Ethan Siegel on where it all came from…

Setting aside crackpot theories about what happened before the Big Bang:

Although we can state with confidence where our observable Universe came from, and explain the origin of a great many phenomena within it, the questions of where things like space, time, energy, or the laws of physics came from in the first place, or whether they even began at all, remain unanswered.

Despite all that we know, we can be certain that all we ever will know is finite. There are a finite number of particles, encoding a finite amount of information, that have existed for a finite amount of time within our visible Universe. While questions like why our Universe is filled with matter and not antimatter, why we have dark matter and dark energy, and why the constants of nature have the values they do may someday be answered, there is no guarantee that what remains in the Universe, today, gives us sufficient information to find the answers. Whether we’ll ever answer these questions remains unknown, but the instant we decide we can’t and give up the search, we’ll be right.

Ethan Siegel, “Where did the Universe come from?” at Big Think (March 29, 2022)

One way of looking at it is that, if we are characters in the story, we can’t meet the author.

You may also wish to read: The trouble so many brilliant people have gone to in order to refute the Big Bang Overall, the anti-Big Bang quests tend to make one believe, if nothing else did, that there must be something in the Big Bang. A useful summary by Brian Miller.

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At Mind Matters News: Evolutionary psychologist argues that worms feel pain. But how?

Wait. David P. Barash’s hypothesis overlooks the fact that suffering is more than an alarm system. An alarm could be going off in an empty building:

He offers an evolutionary hypothesis:

Barash reasons that a less intelligent creature would need more pain than a more intelligent one, in order to teach it to avoid risk and harm:

The dummies, accordingly, would benefit more than the smarty-pants from an especially potent stimulus, a blast of something deeply unpleasant—call it “pain”—more likely to evoke whatever passes for memory and learning in their admittedly dim minds. If so, then they would benefit from a particularly loud alarm bell: More pain rather than less.

DAVID P. BARASH, “EVEN WORMS FEEL PAIN” AT NAUTILUS (MARCH 2, 2022)

Thus he concludes, “Pain would have been among the most fundamental traits to have emerged.”

Given the adaptive value of pain, that sensation would not only be conserved over evolutionary time, but ancestral, among the earliest and most fundamental traits to have emerged. This makes it, well, pretty much insufferable to deny other animals the experience of pain that we know all too well.

DAVID P. BARASH, “EVEN WORMS FEEL PAIN” AT NAUTILUS (MARCH 2, 2022)

Wait. Barash’s hypothesis overlooks the fact that suffering is more than an alarm system. An alarm could be going off in an empty building.

If a fire alarm went off in an empty building, a built-in fire safety protocol might seal all the windows, turn off some systems, and send a message to the firehall, copying the maintenance crew’s mailbox, without anyone experiencing anything. Life forms are fully capable of much more complex responses than these, even without any apparent self-awareness. Tests for the self-awareness that would cause them suffering cannot depend only on identifying a response to pain.

To “feel” pain, a life form must have a unified self, that is, be a subject of experiences. We all know that a dog experiences pain or rejection as happening to him as the subject of the experience. But does an earthworm experience pain that way?

Essentially, experiencing pain (sentience) can mean either of two things: the ability to react to pain or the perception of the pain as happening to one’s unified self. Or both.

We risk trivializing the question of suffering — and impeding humane reforms — if we cast the net too widely.

News, “Evolutionary psychologist argues that worms feel pain. But how?” at Mind Matters News (April 5, 2022)

Takehome: If some invertebrates show much more self-awareness than expected, it hardly follows that all do. We risk impeding humane reforms if we cast the net too widely.

You may also wish to read:

Can crabs think? Can lobsters feel? What we know now. In Switzerland, it is now illegal to boil a lobster alive. Are the Swiss right? Is it cruel? How does a self that feels pain come to exist? And how do we distinguish information use — computer style — from self-awareness?

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