Michael J. Behe's Blog, page 105

February 18, 2022

Devolution in a flower is remarketed as “sudden evolutionary change”

The mutant (left) and wild-type Colorado blue columbine are so different that a taxonomist might assign them to different genera at first glance. Credit: Zachary Cabin

The new columbine doesn’t look as nice but may have a survival advantage:

Hodges, doctoral student Zachary Cabin and their colleagues just have identified a case of a sudden evolutionary change. In the journal Current Biology, the scientists describe a population of columbines that have lost their petals, including the characteristic nectar spurs. A drastic change caused by a mutation in a single gene. The finding adds weight to the idea that adaptation can occur in large jumps, rather than merely plodding along over extended time spans…

Enter the Colorado blue columbine. In one population, a mutation has caused many of the plants to lose their petals with the iconic nectar spurs. While not an uncommon occurrence in columbines, spurlessness seems to have stuck around in this area: About a quarter of the plants lack the distinctive feature.

The team plumbed the plant’s genome to find the source of the unusual morphology. They considered a gene, APETALA3-3, known to affect spur development. They found that this single gene controlled the entire development of the flower’s spurs and nectarines.

“The gene is either on or off, so it’s about as simple of a change you can get,” said lead author Zachary Cabin. “But that simple difference causes a radical change in morphology.”

It turned out the mutant plants actually produced more seeds than their counterparts, much to the team’s surprise. They began combing through their observations, searching for an explanation…

And as the data built up, a clear trend emerged: Deer and aphids preferred flowers with nectar spurs.

University of California Santa Barbara, “Examining sudden evolutionary change” at Phys.org (February 16, 2022)

The team reckons that it has vindicated Goldschmidt’s once widely ridiculed “hopeful monster” thesis.

Reality check: Devolution, as described in Michael Behe’s book, Darwin Devolves, just means that a type of life form may survive better by losing complex equipment. Many examples are available and this sounds like one of them. But it reverses the meaning of “evolution,” which usually refers to increases, not decreases in complexity.

It’s a useful find but if a lineage of peacocks lost the showy tails due to a transmissible genetic defect — but was thus better able to flee predators — that could also be marketed as “sudden evolutionary change.” But what question about the origin of complex life would such terminology engineering really answer?

The paper is open access.

You may also wish to read: Devolution: Getting back to the simple life

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Published on February 18, 2022 06:29

E. O. Wilson and racism: The smoking gun is found

When we first started hearing the scuttlebutt about the recently deceased founder of sociobiology, we tended to think, oh, yeah, he’s a racist, just like all those (black) creationist pastors… yawn.

But now some new information has emerged: Interesting material from a box of Wilson’s letters in the Library of Congress:

Now, two separate pairs of researchers, drawing from Wilson’s papers at the Library of Congress, have published details of correspondence in which Wilson privately supports a psychologist known for his racist work. “It doesn’t surprise me at all,” said Joseph Graves, Jr., an evolutionary biologist at North Carolina Agricultural and Technical State University who has written extensively about scientific racism, and who reviewed some of the new archival work before it was published. What’s important about the new research, he added, “was coming up with the smoking gun.”

Michael Schulson, “New Evidence Revives Old Questions About E.O. Wilson and Race” at Undark (February 16, 2022)

It was a fluke of the COVID-19 pandemic , actually:

One pair of researchers who surfaced those connections, Howard University evolutionary biologist Stacy Farina and her husband, Matthew Gibbons, began reading sections of “Sociobiology” while stuck at home during the Covid-19 pandemic. They were taken aback by what they found.

Michael Schulson, “New Evidence Revives Old Questions About E.O. Wilson and Race” at Undark (February 16, 2022)

Stuck for regular work to do, they decided to go through boxes of Wilson’s correspondence at the Library of Congress. There. they discovered that he had an amicable relationship with an undoubted racist psychologist, Canadian J. Philippe Rushton. Rushton, who was something of a pariah in Canada, headed up a eugenics outfit, the Pioneer Fund, from 2002 util his death in 2012.

The letters, Farina said, demonstrate a warm relationship between Wilson and the psychologist. In the correspondence, which dates from the 1980s and ’90s, Wilson expressed support for Rushton’s work, and lamented a stifling culture that, he suggested, had prevented him from speaking more freely, referring in one note to a “leftward revival of McCarthyism.” When Rushton’s university seemed poised to sanction him for academic misconduct, Wilson sent letters in his defense. He also sent letters to drum up support for Rushton from colleagues at Harvard and at the conservative National Association of Scholars.

Michael Schulson, “New Evidence Revives Old Questions About E.O. Wilson and Race” at Undark (February 16, 2022)

Two historians, David Sepkoski and Mark Borello, happened to be combing the same files, unbeknownst to Farina and Gibbons:

The correspondence, Sepkoski and Borrello now say, suggests that Wilson was carefully managing his public persona — even as he quietly continued his dispute with his left-wing critics.

Providing comments on one Rushton paper — which applied a famous Wilson theory, meant to examine reproductive differences between different species, to argue that Black and non-Black people pursue different reproductive strategies — Wilson was effusive. “This is a brilliant paper,” he wrote, “one of the most original and heuristic written on human biology in recent years.”

“Whether it can even be published in this or some other journal devoted to human sociobiology,” Wilson wrote later in his comments, “will be a test of our courage and fidelity to objectivity in science.”

Michael Schulson, “New Evidence Revives Old Questions About E.O. Wilson and Race” at Undark (February 16, 2022)

Some have dismissed the findings but others say they fit a pattern:

“I don’t really care that Wilson had racist ideas, because I know pretty much all of the people that I dealt with, when I was coming up through the science system, had racist ideas,” said [evolutionary biologist Joseph] Graves, who in 1988 became the first Black American to receive a Ph.D. in evolutionary biology. “Wilson was just one of many.”

Michael Schulson, “New Evidence Revives Old Questions About E.O. Wilson and Race” at Undark (February 16, 2022)

Oh. So what does that mean for the future of Darwinism? It appears from Schulson’s article that zealous witch hunts are now in progress.

You may also wish to read: Evolutionary biologist Jerry Coyne defends “Darwin’s heir” from accusations of racism Unfocused claims of “racism” are a familiar Woke tactic for destroying careers and reputations and they are only beginning to hit Darwinians. (Neither Jerry Coyne nor we knew about this stuff at the time the article was written. Coyne is currently airbrushing Wilson’s legacy.)

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Published on February 18, 2022 01:01

Here’s the webinar on topoisomerase, the complex ,specified “untangling” enzyme in our cells

That’s “topo-eye-SO-merase” (to pronounce it), a classic in design in nature:

On Darwin Day (February 12, 2022), Casey Luskin of the Center for Science and Culture interviewed biochemist Joe Deweese on topoisomerase:

Biochemist Joe Deweese explains the topoisomerase molecular machine and answers questions submitted by viewers from around the world. The interview is conducted by Casey Luskin, Associate Director of the Center for Science and Culture at Discovery Institute.

Topoisomerase II is an extremely important enzyme in your cells that is designed to untangle knots and supercoils in DNA strands that arise during replication and transcription. It does this by grabbing two tangled DNA segments, holding one steady while it breaks the other segment in two, and then passing the first segment through the break. The second segment is then reconnected, and the two DNA segments are released, having been successfully untangled. Without topoisomerases, chromosomes would become an impossible mess, making DNA replication, transcription, and cell duplication impossible.

The carefully orchestrated untangling activity of topoisomerase II doesn’t happen by accident. This enzyme is a molecular machine that only works because its amino acid sequence is highly specified to provide a special shape and structure necessary for its function. In other words, topoisomerase enzymes contain high levels of complex and specified information—a hallmark of intelligent design.

Joe Deweese received his BS in Biochemistry from Freed-Hardeman University and his PhD in Biochemistry from Vanderbilt University. For twelve years, he taught in the Department of Pharmaceutical Sciences at Lipscomb University. His teaching included biochemistry, molecular biology, genetics, anticancer pharmacology, and cellular physiology. Deweese is starting a new role in August, 2021 as Professor of Biochemistry and Director of Undergraduate Research at Freed-Hardeman University. His research interests include characterizing the mechanism of anti-cancer agents, especially those that target topoisomerase II. Recent studies from his lab have focused on etoposide metabolites, thiosemicarbazones, and natural product derivatives. Currently, his work is focused on examining the differences between the two versions of topoisomerase II found in humans. He and his wife, Liz, have two children.

Here’s the animation:

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Published on February 18, 2022 00:18

February 17, 2022

The Galapagos finches as fractured icons of Darwinian evolution

Physicalist philosopher Daniel Dennett likes to say that natural selection is the single best idea anyone ever had.

From Jonathan Wells’s series on the fractured fairytales of schoolbook Darwinism, here’s what’s wrong (assuming you don’t need natural selection in order to prop up physicalism):

Darwin had no real evidence for natural selection as a driver of evolutionary change, to produce all the variety of life, as he claimed. Later followers have tried many lines of evidence, including the famous, and reverenced, Galapagos finches:

Better evidence for natural selection came from finches in the Galápagos Islands in the 1970s. The islands were home to what biologists listed as 13 different species of finches, and biologists Peter and Rosemary Grant and their colleagues studied one of these on a single island. The Grants and their colleagues kept detailed records of each finch species’ anatomy, including the length and depth of their beaks. When a severe drought in 1977 killed many of the islands’ plants, about 85 percent of the birds died. The Grants and their colleagues noted that the survivors had beaks that were, on average, 5 percent larger than the population average before the drought, presumably because the surviving birds were better able to crack the tough seeds left by the drought. In other words, the shift was due to natural selection. The Grants estimated that if a similar drought occurred every ten years, the birds’ beaks would continue to get larger until they would qualify as a new species in 200 years.

The Arrival of the Fittest

When the drought ended and the rains returned, however, food was plentiful, and the average beak size returned to normal. No net evolution had occurred. Nevertheless, “Darwin’s finches” found their way into most biology textbooks as evidence for evolution by natural selection.

So there is evidence for natural selection, but like domestic breeding, it has never been observed to produce anything more than microevolution. As Dutch botanist Hugo de Vries wrote in 1904, “Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest.”

Jonathan Wells, “Top Scientific Problems with Evolution: Natural Selection” at Evolution News and Science Today (February 15, 2022)

You may also wish to read: Jonathan Wells rates homology as one of the top scientific problems with evolution theory. Similarity of features is taken to be due to common descent. Wells: “Yet animals and plants possess many features that are similar in structure and position but are clearly not derived from a common ancestor with those features. The camera eye of a vertebrate and the camera eye of a squid or octopus are remarkably similar, but no one thinks they were inherited from a common ancestor that possessed a camera eye.”

and

Jonathan Wells: Why molecular phylogeny is a problem in evolution. Wells: If two sequences can be aligned in more than one way, then any comparison will depend heavily on what alignment the investigator chooses. And when many sequences are compared, as they are in molecular phylogenies, the problem becomes much worse.

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Published on February 17, 2022 02:07

As 24 nonsense papers are retracted, Daily Sceptic asks, What happened to peer review?

It’s as if they are not even trying any more:

Last August, a cluster of fake scientific papers appeared in the journal Personal and Ubiquitous Computing. Each paper now carries a notice saying that it’s been been retracted “because the content of this article is nonsensical”…

If you’re a long-time reader of the Daily Sceptic, computer-generated gibberish being presented as peer-reviewed science won’t come as a surprise because this has happened several times before. Last year Springer had to retract 463 papers, but the problem isn’t restricted to one publisher. In July it was discovered that Elsevier had published a stream of papers in the journal Microprocessors and microsystems that were using nonsensical phrases generated from a thesaurus, e.g. automatically replacing the term artificial intelligence with “counterfeit consciousness”. This was not a unique event either, merely the first time the problem was noticed – searching Google Scholar for “counterfeit consciousness” returns hundreds of results spanning the last decade…

But why don’t these papers get caught by human editors? Scientific publishers like Springer and Elsevier appear to tolerate zombie journals: publications that look superficially real but which are in fact brain dead. They’re not being read by anyone, not even by their own editors, and where meaningful language should be there’s only rambling nonsense. The last round of papers published by this tech+sports group in the Arabian Journal of Geosciences lasted months before anyone noticed, strongly implying that the journal doesn’t have any readers at all. Instead they have become write-only media that exist purely so academics can publish things.

Publishers go to great lengths to imply otherwise…

Given these goals, why does Springer tolerate the existence of journals within their fold that repeatedly publish auto-generated or irrelevant articles? Put simply, because they can. Journals like these aren’t really read by normal people looking for knowledge. Their customers are universities that need a way to define what success means in a planned reputation economy. Their function has been changing – no longer communication but, rather, being a source of artificial scarcity useful for establishing substitute price-like signals such as h-indexes and impact factors, which serve to bolster the reputations and credentials of academics and institutions.

Mike Hearn, “Publisher Retracts 24 Scientific Papers for Being “Nonsensical” – What Happened to Peer Review?” at Daily Sceptic (February 14, 2022)

That’s what “Trust the Science” does. It enables a superstitious reverence for nonsense at best and corruption at worst. And only occasionally does anyone in charge need to pretend to reform anything.

Hat tip: Ken Francis, co-author with Theodore Dalrymple of The Terror of Existence: From Ecclesiastes to Theatre of the Absurd

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Published on February 17, 2022 01:32

At Mind Matters News: Why would a purely physical universe need imaginary numbers?

Our computers and the entire modern world depend on them, says science writer Michael Brooks in an excerpt from his new book:

In an excerpt from his new book, The Art of More: How Mathematics Created Civilization, science writer Michael Brooks offers the intriguing idea that the modern world arose from imaginary numbers:

But what does his claim that the numbers are “not some deep mystery about the universe” leave us? Recent studies have shown that imaginary numbers — which we can’t really represent by objects, the way we can represent natural numbers by objects — are needed to
describe reality. Quantum mechanics pioneers did not like them and worked out ways around them:

In fact, even the founders of quantum mechanics themselves thought that the implications of having complex numbers in their equations was disquieting. In a letter to his friend Hendrik Lorentz, physicist Erwin Schrödinger — the first person to introduce complex numbers into quantum theory, with his quantum wave function (ψ) — wrote, “What is unpleasant here, and indeed directly to be objected to, is the use of complex numbers. Ψ is surely fundamentally a real function.”

Ben Turner, “Imaginary numbers could be needed to describe reality, new studies find” at LiveScience (December 10, 2021)

But recent studies in science journals Nature and Physical Review Letters have shown, via a simple experiment, that the mathematics of our universe requires imaginary numbers.

News, “Why would a purely physical universe need imaginary numbers?” at Mind Matters News (February 16, 2022)

Takehome: The most reasonable explanation is that the universe, while physical, is also an idea, one that cannot be reduced to its physical features alone.

You may also wish to read:

Why the unknowable number exists but is uncomputable. Sensing that a computer program is “elegant” requires discernment. Proving mathematically that it is elegant is, Chaitin shows, impossible. Gregory Chaitin walks readers through his proof of unknowability, which is based on the Law of Non-contradiction.

Most real numbers are not real, or not in the way you think. Most real numbers contain an encoding of all of the books in the US Library of Congress. The infinite only exists as an idea in our minds. Therefore, curiously, most real numbers are not real. (Robert J. Marks)

and

Can we add new numbers to mathematics? We can work with hyperreal numbers using conventional methods. Surprisingly, yes. It began when the guy who discovered irrational numbers was—we are told—tossed into the sea. (Jonathan Bartlett)

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Published on February 17, 2022 01:01

When the Centers for Disease Control abandon science…

The CDC, we are told, is, in part, a scientific agency but fundamentally a political one, and it shows:

The director is appointed by the president of the United States, and the CDC’s guidance often balances public health and welfare with other priorities of the executive branch.

Throughout this pandemic, the CDC has been a poor steward of that balance, pushing a series of scientific results that are severely deficient. This research is plagued with classic errors and biases, and does not support the press-released conclusions that often follow. In all cases, the papers are uniquely timed to further political goals and objectives; as such, these papers appear more as propaganda than as science. The CDC’s use of this technique has severely damaged their reputation and helped lead to a growing divide in trust in science by political party. Science now risks entering a death spiral in which it will increasingly fragment into subsidiary verticals of political parties. As a society, we cannot afford to allow this to occur. Impartial, honest appraisal is needed now more than ever, but it is unclear how we can achieve it…

Masking is not the only matter in which the CDC’s stated policy goal has coincided with very poor-quality science that was, coincidentally, published in their own journal. Consider the case of vaccination for kids between the ages of 5 and 11. COVID vaccination in this age group has stalled, which runs counter to the CDC’s goal of maximum vaccination. Interestingly, vaccinating kids between 5 and 11 is disputed globally; Sweden recently elected not to vaccinate healthy kids in this age group, and some public health experts believe that it would be preferable for kids to gain immunity from natural exposure instead. Stalling U.S. uptake therefore reflects a legitimate and open scientific debate, regardless of whether the CDC’s policy goal would like to consider it closed.

Enter the CDC’s new study. Widely covered in news outlets, the January 2022 study claims that kids below the age of 18 who get diagnosed with COVID are 2.5 times more likely to be diagnosed with diabetes. “These findings underscore the importance of COVID-19 prevention among all age groups,” the authors write, “including vaccination for all eligible children and adolescents.” But a closer examination of the study again reveals problems.

First, it does not adjust for body mass index. Higher BMI is a risk factor for COVID, prompting hospitalization and diabetes, and yet the CDC analysis does not adjust for weight at all. Second, the absolute risks the study finds are incredibly low. Even if the authors’ finding is true, it demonstrates an increase in diabetes of up to 6 in 10,000 COVID survivors. Third, the CDC’s analysis uses billing record diagnoses as a surrogate for COVID cases, but many kids had and recovered from COVID without seeking medical care. Without a true denominator that conveys the actual number of COVID cases, the entire analysis might be artifact. As the former dean of Harvard Medical School Jeffrey Flier told The New York Times, “The CDC erred in taking a preliminary and potentially erroneous association and tweeting it to specifically create alarm in parents.” Some might view it as a mistake, but after observing these matters for almost two years, I believe it was the entire point of the study: Alarm might boost flagging vaccine uptake in kids. (Already, a better study out of the United Kingdom finds no causal link between COVID and diabetes in kids.)

Vinay Prasad, “How the CDC Abandoned Science” at Tablet (February 14, 2022)

After a while, the public will catch on. The reputation of science is not going to do well out of the “Trust the Science!” phase.

Right now, we are still in this stage: At Mind Matters News: We trust nonsense from lab coats more than from gurus. It’s hard to understand why the researchers take comfort from finding that, worldwide, people will believe absolute nonsense if it comes from scientists.

Note: They will believe it until it begins to cost themin ways they understand. After that, they may not believe good sense either.

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Published on February 17, 2022 00:46

February 16, 2022

Jonathan Wells: Why molecular phylogeny is a problem in evolution

It should have been a solution:

The word phylogeny refers to the evolutionary history of an organism. The word was coined by German Darwinian biologist Ernst Haeckel several years after the publication of On the Origin of Species. Evolutionary biologists have proposed phylogenies based on homologies in fossils, but as we have seen, there are problems with both fossils and homology. With the rise of modern molecular biology, evolutionary biologists have increasingly sought to base phylogenies on molecules such as proteins and DNA.

Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)

And then what happened?

Molecular comparisons are complicated by the problem of alignment. DNA sequences in living things typically contain repeated and/or deleted segments, so it is often unclear where to line them up. If two sequences can be aligned in more than one way, then any comparison will depend heavily on what alignment the investigator chooses. And when many sequences are compared, as they are in molecular phylogenies, the problem becomes much worse.

Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)

So discrepancies were feature, not a bug:

And the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.”5 In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”

Jonathan Wells, “Top Scientific Problems with Evolution: Molecular Phylogeny” at Evolution News and Science Today (February 14, 2022)

We can assume common ancestry as a starting point for from molecular phylogenetics but we can’t use such a system to prove it.

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Published on February 16, 2022 00:52

Prof: There are evolutionary advantages to pedophilia

Well, in venues where evolution is a sort of religion, this had to happen:

Dr. Stephen Kershnar, a SUNY Fredonia professor, has been suspended after an investigation into video of Kershnar asserting that opposition to pedophilia is “a mistake” and that there are “evolutionary advantages to child/adult sex.” Kershnar teaches libertarian philosophy (no surprise) and applied ethics (you’ve got to be kidding me). His comments provoked a massive backlash from students that contributed to his suspension.

Kerhsnar actually believes that sexual relationships between children an adults can be a good thing…

It is difficult to exaggerate the vileness of Kershnar’s remarks. “[Attraction to minors is] fairly widespread among young men, particularly young men in our society,” Kershnar stated. There could, he averred, be “evolutionary advantages” to permitting this, and noted that in his view, it is society’s reaction to pedophilia that is problematic rather than pedophilia itself. He does, however, state that he still thinks pedophilia should be illegal, although is not entirely clear how this correlates with his other views.

It is not the fact that a professor holds such repulsive views that concerns me the most. He is not, of course, the first… It is the fact that he has been publicly defended by 153 other professors, who noted that while they might disagree with Kershnar’s conclusions, his academic freedom should allow him to explore this subject.

Jonathan Van Maren, “Ethics professor at New York public university praises ‘evolutionary advantages’ of pedophilia” at Lifesite News (February 10, 2022)

Well, a lot depends on how the prof intends to explore the subject. It would be interesting to see whether the same profs would have supported Eric Hedin looking into intelligent design theory at Ball State University.

Anyway, in the late stages of Darwinism, things come out of the woodwork that would have been smacked back into it early on. The classical Darwinians no longer seem to own the story.

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Published on February 16, 2022 00:32

At Mind Matters News: The remarkable things we’re learning about bird intelligence

These findings are only among birds that have actually been studied; most birds have not been studied:

● African grey parrots have been observed to share tokens — given to them by humans — that they associated with a treat (walnuts) with other parrots by way of exchange or just helpfulness:

Parrots, it seems, don’t just have the ability to comprehend metal rings as currency for food, but they also “understand the consequences their actions can have on another individual,” says Christina Riehl, an expert in bird behavior at Princeton University who wasn’t involved in the research. “That’s pretty sophisticated reasoning.”

Katherine J. Wu, “Parrots Will Share Currency to Help Their Pals Purchase Food” at Smithsonian Magazine (January 9, 2020) The paper is open access.

Is this an instance of abstract comprehension of the concept of currency? It’s more likely a learned series of steps: Give a token, get a walnut. Or anyway, get social interaction with a neighbor. But it’s pretty complex anyway. And apparently, blue-headed macaws couldn’t — or anyway didn’t — do it.

…

The main thing to see here is that problem-solving intelligence peaks among some life forms that are not at all closely related. Crows and chimpanzees are thought to have last had a common ancestor 300 million years ago. Bees are thought to have had a common ancestor with them 600 million years ago. But crows, chimpanzees, and bees are all much more closely related to life forms that have not attracted attention for their intelligence. Are we just missing their intelligence? Or perhaps the question of unusual intelligence in some birds and other life forms but not others is one of the fruitful mysteries of science that invites further study.

Denyse O’Leary, “The remarkable things we’re learning about bird intelligence” at Mind Matters News (February 15, 2022)

You may also wish to read: Crows can be as smart as apes. But they have quite different brains. The intelligence doesn’t seem to reside in the details of the mechanism. Studying animal intelligence has taught us many things. But in some ways, it has deepened the mystery of intelligence.

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Published on February 16, 2022 00:12

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