Michael J. Behe's Blog, page 97

Charming bacteria set off virus bombs in their neighbors

At least in the lab:

Certain E. coli strains can engage in a form of bacterial warfare by producing colibactin, a chemical that can awaken long-dormant viruses inside neighboring cells’ DNA, sometimes resulting in their destruction, according to a new study published February 23 in Nature.

“It’s an interesting strategy, and it’s also a dangerous strategy,” Heather Hendrickson, an evolutionary microbiologist at the University of Canterbury in Christchurch, New Zealand, who was not involved in the work, tells Science News…

The researchers don’t yet know whether colibactin can trigger prophages when bacteria are in their natural habitats, such as human and other animal intestines. And perhaps awakening the viruses is an accident, Balskus tells Science News. She says she and her colleagues are continuing to work toward finding out whether that’s the case.

Natalia Mesa, “Bacteria Set Off Viral “Bombs” Inside Neighbors” at The Scientist (March 7, 2022)

If it is the case, then it is another example of a life form having strategy that raises the question, “Could it really have randomly evolved with no underlying intelligence in nature?” Lot of those questions piling up.

The paper is open access (via a sharing token).

You may also wish to read: Why do many scientists see cells as intelligent? Bacteria appear to show intelligent behavior. But what about individual cells in our bodies?

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Amber fossil shows 100 million-year stasis in plant genus

It creates an odd naming situation in the process:

Today, naming a mid-Cretaceous angiosperm as a modern genus is unusual and controversial. But in the current issue of Nature Plants, Shi et al.1 do just that. With evidence from multiple exquisitely preserved plant parts, they identify the modern genus Phylica in an amber that they date to 99 million years old1. While an extraordinary claim today, it is one that would not have surprised Charles Darwin. Fossils of angiosperms (often known as ‘flowering plants’) are well known to appear suddenly and in great diversity in Cretaceous rocks. In 1879, Darwin famously wrote: “The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.” …

For Darwin, the only plausible solution to this set of problems was that angiosperms had originated and diversified in long ages before the Cretaceous…

The apparent discovery by Shi et al.1 of a modern genus in the mid-Cretaceous, with evidence from multiple plant parts, now calls us to reconsider this issue. Great care is needed to verify their claim, as the stakes are high. If they are correct, Phylica is unlikely to be alone. In current phylogenies, Phylica is not an early diverging angiosperm lineage but is highly nested within the rosid eudicots. If Phylica was present in the mid-Cretaceous, then a large number of other modern genera were likely to have been present too. If this turns out to be the case, our view of the fossil record could be restored to one similar to that of Charles Darwin when he wrote about the abominable mystery. Buggs, R.J.A. Reconfiguring Darwin’s abominable mystery. Nat. Plants (2022). https://doi.org/10.1038/s41477-022-01...

This most interesting article makes very heavy weather out of partly confirming something Darwin mused on. Perhaps that’s the price of publication of the fact that little or no evolution appears to have happened in all that time. Which is not even unusual:

Stasis: Life goes on but evolution does not happen

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What makes a law of nature a “law,” exactly?

Marc Lange, author of Because Without Cause, offers some thoughts:

Scientists discover laws of nature by acquiring evidence that some apparent regularity is not only never violated but also could never have been violated. For instance, when every ingenious effort to create a perpetual-motion machine turned out to fail, scientists concluded that such a machine was impossible – that energy conservation is a natural law, a rule of nature’s game rather than an accident. In drawing this conclusion, scientists adopted various counterfactual conditionals, such as that, even if they had tried a different scheme, they would have failed to create a perpetual-motion machine. That it is impossible to create such a machine (because energy conservation is a law of nature) explains why scientists failed every time they tried to create one.

Laws of nature are important scientific discoveries. Their counterfactual resilience enables them to tell us about what would have happened under a wide range of hypothetical circumstances. Their necessity means that they impose limits on what is possible. Laws of nature can explain why something failed to happen by revealing that it cannot happen – that it is impossible.

Mark Lange, “What is a law of nature?” at Psyche (March 10, 2022)

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At ID The Future: Debunked transitional fossils with Gunter Bechly

Gunter Bechly

The podcast is here.

On today’s ID the Future Casey Luskin hosts distinguished German paleontologist Gunter Bechly to discuss Bechly’s essay in the recent Harvest House anthology, The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos (2021).

Darwinian evolution predicts a gradually branching tree of living forms, with one form shading into another over long periods of evolution, with each transitional step almost too modest to notice. Does the fossil record suggest such a pattern? Quite the opposite, Bechly says. Instead the pattern of the fossil record is consistently one of sudden appearance, and evolutionists have yet to successfully construct a single robustly populated series of gradually transitioning fossils that move chronologically from one form to a distinctly different morphology. Darwinism would lead us to expect such transitional sequences all over the fossil record, and yet evolutionists, searching assiduously for more than 160 years, have yet to construct a single one of these. Bechly debunks the hype around some fossil sequences, such as that said to have been assembled from ape-like to human. He explains the difference between “transitional forms” as paleontologists generally use the term and the meaning of the term for evolutionists attempting to defend modern Darwinism. And he and Luskin also discuss fossil forgeries, how to tell real from fake fossils, and four explosions of morphological novelty in the history of life. [25:19 min]

Note: If you are following our updates on the “Trust the Science!” COVID Crazy, new stuff just went up.

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Researchers: Some genes are unique to humans

You’ve heard endlessly about humans as the 98% or 99% chimpanzee (and rightly discounted it if you have any capacity to analyze an argument). One group of students decided to look at the human genes that are different:

A team of student researchers from John Jay College of Criminal Justice has discovered human microRNA genes not shared with any other primate species and which may have played an important role in the unique evolution of the human species. The students, under the direction of John Jay Professors Dr. Hunter R. Johnson and Dr. Nathan H. Lents, found at least three families of microRNA genes on chromosome 21…

Although the team found that the long arm of human chromosome 21 aligns well with that of other extant ape species, the short arm aligned poorly, suggesting that this region of the human genome has recently and substantially diverged from that of other primates.

According to their analysis of prehistoric human genomes, these changes predate the divergence of Neanderthals and modern humans. The genes also show little to no sequence-based variation within the modern human population. The team therefore theorized that the microRNA (miRNA) genes found in that region [miR3648 and miR6724] likely evolved in the time since the chimpanzee and human lineages split, sometime in the last seven million years, and are specific to humans.

The City University of New York, “Student researchers discover genes unique to humans in search for source of our evolutionary distinctiveness” at ScienceDaily (March 8, 2022)

The authors attribute the differences to de novo genes (genes that just suddenly appear):

“Understanding the genetic basis for human uniqueness is an important undertaking because, despite sharing nearly 99% of our DNA sequences with the chimpanzee, we’re remarkably different organisms,” said student researcher José Galván. “Small post-transcriptional regulatory elements like miRNAs and siRNAs [small interfering RNA] are under-appreciated and often misunderstood in the effort to understand our genetic differences.”

Thanks to their small size and structural simplicity, miRNA genes have fewer barriers to de novo creation than other gene types. MicroRNA genes can be extremely prolific in their regulation of other genes, meaning that modest changes to DNA sequence can result in wide-ranging impacts to the human genome. The creation of miR3648 and miR6724 serve as excellent examples of this process. This study revealed a new possible mechanism for the creation of new miRNA genes through duplications of rRNA genes, which calls for further research on how general this phenomenon may be.

The City University of New York, “Student researchers discover genes unique to humans in search for source of our evolutionary distinctiveness” at ScienceDaily (March 8, 2022)

The paper is closed access.

Note: One of the faculty advisors is Nathan Lents, known to many readers as the author of a book, Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, claiming that humans are poorly designed. Perhaps we will soon hear that these unique, de novo genes were poorly designed.

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At Mind Matters News: Science writer: Explain-away-the-mind book doesn’t succeed

In a departure from an all-too familiar approach to science writing, Philip Ball offers constructive criticism of the “nothing but” approach to the mind:

At eminent science journal Nature, science writer Philip Ball reviews a book offering to explain how the mind arose from the mud. And he departs from the script.

The book is Journey of the Mind: How Thinking Emerged from Chaos by neuroscientists Ogi Ogas and Sai Gaddam. One would expect a conventional science writer to announce that this new book is an important contribution to the quest to naturalize the human mind — to show that the mind is a mere adaptation that enabled the tailless ape to survive the savannah. Such a belief needn’t be true (and isn’t); it’s a placeholder for a better-founded purely naturalist belief.

Yet Ball looks at the claims made in Journey of the Mind, and offers actual criticism:

Ogas and Gaddam take a very broad view of mind as “a physical system that converts sensations into action”. At face value, this grants a mind to thermostats and robots as much as to living entities. “A mind responds. A mind transforms. A mind acts,” they write. But the same is true of many machines. What, then, distinguishes a mind? If it’s sentience or awareness, the authors give a confusing picture. They say the “self-awareness” of an amoeba is “piddling” — and later seem to deny this quality to all organisms except vertebrates.

Many assertions go beyond the facts. The discussion of consciousness rests on the belief that the problem has been solved by cognitive scientist Stephen Grossberg (whom the authors thank for “guidance and support”). Since the late 1960s, Grossberg has developed the idea that consciousness arises from ‘resonance’ between specific modules of the brain. Ogas and Gaddam are vague about what resonance means here, beyond saying that the modules amplify and prolong each other’s outputs, and they give the reader little indication of what empirical evidence exists to support the idea. Grossberg’s theory is provocative and stimulating, but, couched in the abstract mathematical framework of dynamical systems theory, it remains contingent on his supposition that “all conscious states are resonant states”. I’m not convinced it amounts to the revolution that the authors assert.

PHILIP BALL, “A TOUR OF THE EVOLUTION OF MINDS” AT NATURE (MARCH 7, 2022)

Ball is right, of course. Popular science literature on the mind touts many claims that we are on the brink of reducing it to a material substrate. Meanwhile, professional approaches to the subject have been described in the Chronicle of Higher Education as bizarre. Repeated rebuffs from the evidence teach nothing in most cases except to keep trying.

News, “Science writer: Explain-away-the-mind book doesn’t succeed” at Mind Matters News (March 8, 2022)

Takehome: Ball notes that the Journey of the Mind authors’ (phantom) reductionist revolution relies on a single cognitive scientist’s work.

It’s not that he thinks it’s a terrible book. But he supposes (unusually in this area) that critical standards matter and that he should apply them.

You may also wish to read:

It’s not even clear how the mind relates to the brain Journalist and editor Ken Francis asks a series of skeptical questions of those who claim that the mind is really just the brain. The placebo effect — we start getting better because we believe we will, before any meds have kicked in — is a classic demonstration of the mind at work.

and

Your mind vs. your brain:
Ten things to know

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How Darwinians deal with the lack of evidence for gradualism

Casey Luskin notices a pattern:

Years ago I began to recognize a repeating phenomenon in the rhetoric of evolutionary literature: Scientists, echoed by science journalists, would only admit a problem with their models or a challenge to their ideas once they thought they had found a solution. I’ve called these “retroactive admissions of ignorance.” We now have another example of this, from a paper just published in Nature Communications purporting to demonstrate Darwinian gradualism: “General statistical model shows that macroevolutionary patterns and processes are consistent with Darwinian gradualism.” Retroactive admissions of ignorance, weakness, or other problems typically come in the first sentences of the abstract or introduction of a paper. The rest of the paper is then supposed to show why the admission no longer applies, as the weakness has been cleared up. This paper is no exception to the pattern.

Casey Luskin, “Nature Communications Retroactively Concedes a Lack of Evidence for Darwinian Gradualism” at Evolution News and Science Today (March 8, 2022 )

The supposedly slam dunk paper deals with body size in mammals. Trouble is, it’s too easy a topic. Body size is — everyone agrees — easily malleable, compared to say, the development of vision:

The point is that while this recent Nature Communications paper purports to find evidence of gradual evolutionary change in mammalian body size, that’s not something that would surprise anyone in light of the diverse spectrum of body sizes that often exist even within a species at any given time. Change in body size, even gradual evolutionary change, does not represent the kind of novel body plans or novel phenotypic traits that the neo-Darwinian model struggles to explain.

Casey Luskin, “Nature Communications Retroactively Concedes a Lack of Evidence for Darwinian Gradualism” at Evolution News and Science Today (March 8, 2022 )

And then that very week, Luskin tells us, another paper came out: “The paper concludes that tuataras (lizard-like reptiles from New Zealand) have experienced stasis and virtually no change over at least the last ~190 million years” Now that’s gradual.

The paper is open access.

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Whales have developed a unique sleep solution: Shut down only half the brain at a time

If they became fully unconscious while asleep, whales, dolphins, and porpoises would drown:

So [whales] have solved the problem with unihemispheric sleep: that is, they shut down only one half of the brain at a time, keeping one-half conscious and breathing.”

Whales have some of the largest brains on the planet. Sperm whales and killer whales in particular have the biggest brain of any living mammal. This means they can actively decide which part of their brains to use at a given time.

Rose said this peculiar way of sleeping can be seen most clearly in captive whales, as they are easier to see. When whales are “sleeping” they can be seen keeping one eye closed while the other remains open.

Robyn White, “How Do Whales Sleep?” at Newsweek (March 4, 2022)

So whales just “solved the problem”? In reality, without any underlying intelligence in nature, their lifestyle just would not have existed.

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Sabine Hossenfelder: Did the early universe really inflate rapidly?

Thirty orders of magnitude in a fraction of second? Contrary to what we sometimes read, that’s only a hypothesis:

In the popular science media, inflation is sometimes presented as if it was established fact. It isn’t. Its status is similar to that of particle dark matter. They are both unconfirmed hypotheses. But while most physicists agree that particle dark matter has yet to be empirically confirmed, opinions about inflation are extremely polarized.

On the one hand you have people like Alan Guth, one of the inventors of inflation theory, arguing that the theory has made many correct predictions and that evidence speaks for it. On the other hand, you have people like Paul Steinhardt, interestingly enough also one of the inventors of inflation, who argue that inflation doesn’t make any predictions and isn’t even science. In an essay some years ago, Steinhardt together with Anna Ijjas and Avi Loeb wrote “inflationary cosmology, as we currently understand it, cannot be evaluated using the scientific method.”

Sabine Hossenfelder, “Did the early universe inflate?” at BackRe(Action) (March 5, 2022)

Her conclusion?

So to summarize. Guth is right in saying that inflation is good science. But he is wrong with the reason for why that’s the case. Steinhardt is right with pointing out that Guth’s argument doesn’t hold up. But his conclusion is wrong because there are other reasons for why inflation is good science.

However, that doesn’t mean inflation is right. Physicists have proposed many other theories for the early universe, for example cyclic cosmology, and those can also explain observations. And maybe in the end one of those other theories will be the better explanation.

Sabine Hossenfelder, “Did the early universe inflate?” at BackRe(Action) (March 5, 2022)

It’s the part in between that’s the most fun.

You may also wish to read:

Sabine Hossenfelder asks: Will the Big Bang repeat? Hossenfelder: I am not sure that CCC actually solves the problem it was supposed to solve. Remember we are trying to explain the past hypothesis. But a scientific explanation shouldn’t be more difficult than the thing you’re trying to explain. And CCC requires some assumptions, about the conformal invariance and the erebons, that at least to me don’t seem any better than the past hypothesis.

and

At Mind Matters News: Theoretical physicist: Quantum theory must be replaced
Sabine Hossenfelder can live with the neutrinos that are inconsistent with the Standard Model of physics but quantum uncertainties are beyond the pale. We might conclude that the universe is a stranger place than we have sometimes been led to suspect and that the amount and type of strangeness each of us can tolerate depends, to some extent, on prior commitments. But it is what it is anyway.

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Neil Thomas on “Evolutionary Theory as Magical Thinking”

Neil Thomas, author of Taking Leave of Darwin (2021), talks about the need to invoke a sort of magic to account for the changes that Darwinism requires, without any intelligence in the process whatsoever:

The shaky logical basis of Darwin’s thinking has not gone entirely unremarked. The notion of a supposedly unintelligent yet remarkably independent “self-evolving” biosphere (like the postulation of a self-creating cosmos) presents, when dispassionately considered, an offense to logic great enough to invite attempts to square the circle.  A fairly recent publication which accepts this challenge came in the form of Simon Powell’s Darwin’s Unfinished Business: The Self-Organizing Intelligence of Nature (Rochester: Park Street Press, 2012). Powell willingly concedes that “to state nonchalantly that evolution just happens and that it involves no more than changes in a gene pool over time, or that it is simply descent with modification, is really not good enough. Nature is crying out for a more decent appraisal.” (p. 18)

Indeed so, yet Powell’s ambition to attribute what he terms “bio-logic” to nature, now declared by him to be intelligent, can hardly be said to advance a fresh naturalistic explanation or make convincing his claim that “this new paradigm can be delivered without recourse to supernatural forces.” (p. 26) 

For the contention begs the question of the origin of such intelligence. 

Neil Thomas, “[article title]” at Evolution News and Science Today

This is the sixth article in Thomas’s Victorian Crisis of Faith series. Read all the articles to date here.

You may also wish to read:

\At Evolution News: Darwin and the ghost of Epicurus. 3 March 2022One way of looking at it: Darwinism enabled thinkers to retain the thought of Epicurus and Lucretius when, in general, the thinkers themselves were forgotten.

and

Neil Thomas on Darwinism’s place in the Victorian culture wars. Anyone familiar with popular science writing on evolution will see what Thomas means here. Darwinism is introduced as a hypothesis/theory but then treated as a dogma/article of faith — and (this is emotionally very important) a way of segregating the Smart People from the Yobs and Yayhoos. Appeals to science-based analysis fall on deaf ears because the dogma has become what “science” now means.

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