Michael J. Behe's Blog, page 69

May 22, 2022

At Evolution News: Natural Machinery Operates Without Intervention; But How?

David Coppedge’s article was originally pulished in 2015 but is even more relevant now:

Paley’s “watch on a heath” was only an analogy in 1805. Now, we can see real biological clocks of amazing design and precision in the cells of life. Current Biology talks about “unexpected biochemical cogs” in a cyanobacterium, freely using the word “clock” as well as “oscillator,” “regulator,” and “switch.” The circadian clock runs on a much slower schedule than most cellular reactions. It’s calibrated to the 24-hour day-night cycle, and keeps constant time even when the temperature changes. It would have been astonishing to Paley or Bacon to learn that a three-protein oscillating machine is found in such a tiny organism. In higher vertebrates, biological clocks are even more elaborate.

David Coppedge, “Natural Machinery Operates Without Intervention; But How?” at Evolution News (May 13, 2022)

David Coppedge offers many similar examples, noting

Those are a few recent examples of the “machine talk” pouring out of labs around the world. This is not just metaphorical language for “nature” like the Victorians used. It’s observation and description of realities the early mechanical philosophers could not have imagined. And it’s everywhere. Machine talk is driving an explosion of discovery in science.

The old mechanical philosophy is hopelessly inadequate for these realities. The reason? We know from our experience that unguided natural law does not produce machinery, factories, and quality control. Something else is required: information.

David Coppedge, “Natural Machinery Operates Without Intervention; But How?” at Evolution News (May 13, 2022)

And he has a suggestion:

Willaim Dembski’s book Being as Communion would serve as a fine discussion starter. [David] Wolpert comes so close, but is still so far from explaining what he set out to explain: why the moon differs from the earth. He talks about information flow through the system, but the moon gets exactly the same sunlight the earth does. And he never defines what information is, or where it comes from. Here is where intelligent design can offer real, substantive insight.

Information is the key to a “mechanical” philosophy for the 21st century. We know, because we have a great deal of experience producing information and imposing it on matter. We build computers. We make robots. We make clocks and trucks and factories. Indeed, we can even make machines that make other machines, and robots that increasingly look and act like us.

David Coppedge, “Natural Machinery Operates Without Intervention; But How?” at Evolution News (May 13, 2022)

You may also wish to read: Casey Luskin: ID as a fruitful approach to science The trouble is, many people would just as soon that research into evolutionary computation anatomy and physiology, and bioinformatics, however fruitful, not be done if it undermines a comfortable Darwinism.

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Published on May 22, 2022 18:24

Debate: Theism vs. Naturalism: Which is a Better Account of Reality?

The May 16 debate featured apologist Jonathan McLatchie vs “Cosmic Skeptic” Alex O’Connor, an influential New Atheist:

Some hope he’ll resurrect New Atheism.

You may also wish to read: How did new atheism,/a> become the “godlessness that failed”?

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Published on May 22, 2022 17:41

May 21, 2022

Sabine Hossenfelder on the closest we have to a theory of everything

She argues that the principle of least action is the closest we have to a theory of everything but, of course, along comes quantum mechanics and…

What’s with quantum mechanics? In quantum mechanics, the principle of least action works somewhat differently. In this case a particle doesn’t just go one optimal path. It actually goes all paths. Each of these paths has its own action. It’s not only that the particle goes all paths, it also goes to all possible endpoints. But if you eventually measure the particle, the wave-function “collapses”, and the particle is only in one point. This means that these paths really only tell you probability for the particle to go one way or another. You calculate the probability for the particle to go to one point by summing over all paths that go there.

This interpretation of quantum mechanics was introduced by Richard Feynman and is therefore now called the Feynman path integral. What happens with the strange dependence on the future in the Feynman path integral? Well, technically it’s there in the mathematics. But to do the calculation you don’t need to know what happens in the future, because the particle goes to all points anyway.

Except, hmm, it doesn’t. In reality it goes to only one point. So maybe the reason we need the measurement postulate is that we don’t take this dependence on the future which we have in the path integral seriously enough.

Sabine Hossenfelder, “The closest we have to a Theory of Everything” at BackRe(Action) (May 21, 2022)

Quantum mechanics keeps the world interesting and reminds us that this is not a deterministic world after all.

You may also wish to read: Sabine Hossenfelder asks, did the W-boson break the Standard Model? Hossenfelder: Is it correct? I don’t know. It could be. But in all honesty, I am very skeptical that this result will hold up. More likely, they have underestimated the error and their result is actually compatible with the other measurements.

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Published on May 21, 2022 19:39

At Mind Matters News: Could the dinosaurs have had a now-lost civilization?

Geoscientist Dirk Schulze-Makuch argues that it is more possible than we might think.

But the really interesting find here is palaeobiologist Simon Conway Morris on how dinosaurs might have evolved into humanlike creatures:

Conway Morris almost sounds like an ID theorist. No wonder the BBC had to bring a bunch of people on toward the very end to imply that he is an idiot.

Conway Morris is a prominent proponent of convergent evolution — from very different starting points, life navigates to similar solutions. There asre only so many solutions to basic survival problems that actually work, which is why very different life forms converge on the same ones.

News, “Could the dinosaurs have had a now-lost civilization?” at Mind Matters News

Takehome: Prominent Cambridge palaeobiologist Simon Conway Morris thinks that, had the dinosaurs not been wiped out, they would have developed human-like intelligence.

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Published on May 21, 2022 19:06

Are all those codes used by cells really “codes”?

One biologist thinks that only DNA is really a code. David Coppedge disagrees.

Biologist Jonathan Wells has listed six codes used by cells: the genetic code, the epigenetic code, the membrane code, the sugar code, the RNA splicing code, and the bioelectric code. Geoffrey North, on the other hand, writing for Current Biology, contends that there is only one code, because all the others ultimately derive from DNA. Who’s right?

“As each eager new candidate comes along, it is invariably dubbed a new second genetic code — never a third or fourth genetic code…. Why is this? In the contemporary parlance of the internet age, a kind of crowd-sourced opinion is being made, a thumbs down to the claim, which, if truly meaningful and useful, would surely be taken up into general usage, to become the second genetic code. I would suggest we accord the one, universal genetic code its deserved special place by not nominating others to join it in a list.”

So is multiplying codes a taxonomic trick, a violation of Occam’s razor? Lest we be accused of standing by our ID colleague regardless, let’s look at some other information about codes in living things and then reason about what makes a code a code.

David Coppedge, “In Life, Not One Code but Many” at Evolution News (May 19, 2022)

Meanwhile, other codes are being found all the time, as Coppedge notes, listing some.

Bioelectric code:

Responding to Geoffrey North’s view, he notes,

But it seems fair to categorize codes separately if they contain unique information and produce unique results. Even if histones are built from DNA, once they are assembled, they no longer rely on the genetic code. They follow their own rules of tagging genes with “tails” made of other molecules. Transcription factors and their pulsations, similarly, act apart from the language of DNA triplet codons. How much more the sugar code, membrane code, and bioelectric codes that are not even made up of amino acids?

David Coppedge, “In Life, Not One Code but Many” at Evolution News (May 19, 2022)

You may also wish to read: Researchers: Cells organize themselves in our organs by increasing in volume when tissues bend. “The fact that this increase in volume is staggered in time and transient also shows that it is an active and living system,” adds a researcher. Once again, we are expected to believe that such a system can just develop in a gradual Darwinian fashion.

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Published on May 21, 2022 18:48

Epigenetics: Editing epigenome decreased alcoholism in rats

Let’s start this one by saying that they shouldn’t have given the rats alcohol in the first place. Seriously, the target is teenagers:

Specifically, alcohol exposure during adolescence reprograms the epigenome at an enhancer region called SARE (synaptic activity response element) that regulates the expression of a gene called Arc (activity-regulated cytoskeleton-associated protein). This decreases Arc expression in both rodent and human amygdala, a region of the brain important in regulating emotional behaviors. How epigenomic changes at Arc SARE, upon adolescent exposure to alcohol, results in anxiety and drinking disorders in adulthood is unclear.

A new study on animal models by researchers from the University of Illinois Chicago published in the journal Science Advances (“Targeted epigenomic editing ameliorates adult anxiety and excessive drinking after adolescent alcohol exposure“) suggests gene editing may treat anxiety and alcohol use disorder in adults who were exposed to binge drinking in their adolescence…

In the current study, the researchers showed that this epigenetic reprogramming due to alcohol exposure in adolescence, which persists throughout life, can be reversed using CRISPR/Cas9 mediated gene editing in rat models.

News, “CRISPR Edits Brain Epigenome to Reset Anxiety and Excessive Drinking in Rats” at Genetic Engineering and BioTechnology News (May 11, 2022)

Fine for rats, maybe, but for humans, Alcoholics Anonymous and Smart Recovery make more sense than gene editing.

Epigenetics chips away at the Darwinian edifice in the sense that the question of whether one “inherits” a tendency to drink too much alcohol may be obviated if epigenetics change cements the tendency long after fertilization.

The paper is open access.

You may also wish to read: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Published on May 21, 2022 18:20

May 20, 2022

Some species thought to be extinct may simply be “lost”

That is, they haven’t been seen by anyone in more than 50 years. But are they really gone for good?

Researchers reviewed information on 32,802 species from the International Union for Conservation of Nature Red List of Threatened Species (IUCN Red List) and identified 562 lost species. Their findings appear in the journal Animal Conservation.

The IUCN Red List defines extinct as ‘when there is no reasonable doubt the last individual of a species has died,’ which can be challenging to verify. According to Simon Fraser University biodiversity professor and study co-author Arne Mooers, the Red List categorizes 75 of these 562 lost species as ‘possibly extinct.’ The researchers note the existence of many species with an uncertain conservation status may become increasingly problematic as the extinction crisis worsens and more species go missing.

A total of 311 terrestrial vertebrate species have been declared extinct since 1500, meaning 80 per cent more species are considered lost than have been declared extinct.

Reptiles led the way with 257 species considered lost, followed by 137 species of amphibians, 130 species of mammals and 38 species of birds. Most of these lost animals were last seen in megadiverse countries such as Indonesia (69 species), Mexico (33 species) and Brazil (29 species).

While not surprising, this concentration is important, according to researchers. “The fact most of these lost species are found in megadiverse tropical countries is worrying, given such countries are expected to experience the highest numbers of extinctions in the coming decades,” says study lead author Tom Martin from the UK’s Paignton Zoo.

Mooers, who anchored the study, says: “While theoretical estimates of ongoing ‘extinction rates’ are fine and good, looking hard for actual species seems better.”

Simon Fraser University, “Lost or extinct? Study finds the existence of more than 500 animal species remains uncertain” at Eurekalert (May 19, 2022)

The paper has “limited shared access.”

Apart from loss of habitat due to human encroachment, it would be interesting to know whether there is much study of patterns that govern extinctions — that is, natural extinctions. Paleontologist David Raup (1933–2015) wrote quite a good book on the topic, Extinction: Bad Genes or Bad Luck in 1991 but it’s not clear how much has been done since then.

While we’re here:

A species of moth, not seen since 1912, was found inside a passenger’s luggage at the Detroit Metropolitan Airport.

U.S. Customs and Border Protection found larvae and pupae from the moth last September inside a bag arriving from the Philippines.

Sheri Walsh, “Moth last seen 110 years ago found at Detroit airport” at UPI (May 18, 2022)

The moth larvae and pupae were destroyed, as a potential agricultural pest.

You may also wish to read: At Mind Matters News: Did small brains doom the mammoth and the giant armadillo? Before we decide, let us hear a word in defense of small brains. The topic is not as simple as many think.

and

Extinction (or maybe not): New Scientist offers five “Lazarus species”

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Published on May 20, 2022 18:56

Evolution News: In His New Book, Denton Shows How Science Leads the Charge to Theism

Neil Thomas writes:

William Paley once quipped that observation of the complexity of the human eye (which, it will be recalled, was wont to give Darwin uncomfortable doubts about the efficacy of natural selection) supplied an assured “cure for atheism.” Extending Paley’s quip, I would add that if the eye doesn’t do it for you, the brain with its quadrillions of synchronized electro-chemical operations almost certainly will. There seems to be little exaggeration in claiming that cytology, the microscopic study of cells enabled by the ultra-high magnifications of the electron microscope, has led to a wholly unexpected revival of the fortunes of Paley’s once derided natural theology.

Recent advances in biological science, a subject formerly proclaimed to be corrosive of metaphysical beliefs1, have somewhat unexpectedly become a stimulus to the emergence of new advances which endorse many of the older observations of natural theology. As astronomer Paul Davies remarked some four decades ago, “It may seem bizarre, but in my opinion science offers a surer path to God than religion.”2 Supporting this contention — that science itself leads the charge toward a fresh theistic turn — Michael Denton makes the firm observation in his new book, The Miracle of Man: The Fine Tuning of Nature for Human Existence, that recent studies of the way the terrestrial environment appears to be fine-tuned for humankind are “not based on the Judeo-Christian scriptures or classical philosophy but on evidence derived from advances in our scientific understanding of nature.” (p. 208)

Gifts from the Gods

Providing chapter and verse for his views, in convincing detail with an enviably multi-disciplinary command, Denton elaborates on ways in which the properties of light, carbon, water, and metals contribute to the fitness of nature for humankind, providing substantial circumstantial evidence that the world we inhabit was “pre-adapted” for our use.

The notion that we are simply an “epiphenomenon” of mindless processes cast adrift in a cosmos configured by pure chance has in the last half century or so been challenged by a new scientific landscape, Denton argues — with some understatement. For as Michael Behe comments in his advance praise of Denton’s work, the philosopher Bertrand Russell’s notorious contention that “Man is the product of causes which had no prevision of the end they were achieving” has turned out to be “the most spectacularly wrong-headed pronouncement of the 20th century.”

Cosmologists make no bones about the fact they can see no logical pathway to how we all came to be here on this planet. The cosmological constants which create conditions favorable to life are on any statistical reckoning improbable to an extreme, even prohibitive degree. The same goes for the genesis and proliferation of life forms: the whole phenomenon remains stubbornly unamenable to rational decipherment.

Evolution News

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Published on May 20, 2022 17:44

New complexities discovered in how plants protect themselves against microorganisms

CCO/Public Domain

A novel biochemical mechanism is involved:

Key players in these plant immune responses are so-called immune receptors, which detect the presence of molecules delivered by foreign microorganisms and set in motion protective responses to repel the invaders.

A subset of these immune receptors harbors specialized regions known as toll-interleukin-1 receptor (TIR) domains and function as enzymes, special proteins that break down the molecule nicotinamide adenine dinucleotide (NAD+), a highly abundant, multi-functional small molecule found in all living cells. Breakdown of NAD+, in turn, activates additional immune proteins, ultimately culminating in the so-called “hypersensitive response,” a protective mechanism that leads to the death of plant cells at sites of attempted infection as an effective way to protect the plant as whole. However, studies have shown that breakdown of NAD+, while essential, is not sufficient for plant protection, suggesting that additional mechanisms must be involved…

Using structural analysis, the authors could show that TIR proteins form different multi-protein structures for breakdown of NAD+ or RNA/DNA, explaining how one and the same protein can carry out two roles. To cleave the RNA/DNA molecules, the TIR proteins follow the contours of the RNA/DNA strands and wind tightly around them like pearls on a string. The ability of TIR proteins to form two alternative molecular complexes is a characteristic of the entire immune receptor family. The exact shape of the TIR proteins thus dictates the respective enzyme activity.

The authors went on to show that this function itself was not enough for cell death, suggesting that specific small molecules generated by the breakdown of RNA and DNA were responsible. Using analytical chemistry, the scientists could identify the molecules as cAMP/cGMP (cyclic adenosine monophosphate/cyclic guanosine monophosphate), so-called cyclic nucleotides that are present in all kingdoms of life. Intriguingly, rather than the well-characterized 3 ,5 -cAMP/cGMP, the authors analysis showed that the TIR domains were triggering the production of the so-called non-canonical 2 ,3 -cAMP/cGMP, enigmatic “cousins,” whose precise roles have thus far been unclear. When they reduced TIR-mediated production of 2 ,3 -cAMP/cGMP, cell death activity was impaired, demonstrating that the 2 ,3 -cAMP/cGMP molecules are important for the plant immune response. Max Planck Society, “Function follows form in plant immunity” at Phys.org (May 20, 2022)

The paper requires a fee or subscription.

We keep discovering these novel mechanisms that all work together like an exquisitely designed system. And it is all supposed to have just happened by natural selection. Yet we never see that working in any situation where we try it.

You may also wish to read: Did the dinosaurs’ departure change plants? Researchers: Defensive features such as spines regressed and fruit sizes increased. The research has demonstrated this using palm trees as a model system…

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Published on May 20, 2022 17:23

At Mind Matters News: Did small brains doom the mammoth and the giant armadillo?

A recent study showed that survivors had brains that were 53% larger, which was perhaps useful in avoiding predators. The problem is, it is genuinely unclear what role brain size plays in intelligence:

According to one study, lemurs, with brains 1/200th the size of chimps’ brains, passed the same IQ test.

Sometimes a small brain is actually an advantage. This is especially true of flighted life forms like birds and insects. Consider the gnat ogre fly, with a brain “smaller than the period at the end of this sentence”: “The researchers attribute the fly’s ability to adjust its trajectory so rapidly to its small size, which allows signals to travel rapidly from eye to brain to flight muscles.”

Small brains can be highly organized for survival: “ … researchers say, fly brains may be organized so as to make predictions based on universal design aspects of animal nervous systems, to avoid the swat.” Thus, the fact that the fly has only 100,000 to a million neurons depending on species, and you have 86 billion doesn’t improve your chances of a successful swat because the fly’s neurons are organized with only a few goals (like anti-swat), not thousands of them (as you have).

Of course, it is possible that the Quaternary megafaunas’ brains were not particularly well organized but that would be a challenge to study with the materials we currently have.

News, “Did small brains doom the mammoth and the giant armadillo?” at Mind Matters News (May 20, 2022)

Takehome: Before we decide, let us hear a word in defense of small brains. The topic is not as simple as many think.

You may also wish to read: Can largely rearranged genomes explain why octopuses are smart? Even compared to each other, the genomes of three cephalopods studied had been broken up and extensively reorganized. The relationship between massive genome rearrangement and very high intelligence in an invertebrate remains unclear but it is a promising research avenue.

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Published on May 20, 2022 16:02

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