Michael J. Behe's Blog, page 219

How cells signal that they should be killed

And why this cell death or “apoptosis” is essential for survival:

“Every day, ten billion cells die and are engulfed by blood cells called phagocytes. If this didn’t happen, dead cells would burst, triggering an auto-immune reaction,” explains iCeMS biochemist Jun Suzuki, who led the study. “It is important to understand how dead cells are eliminated as part of our body’s maintenance.”

Scientists already know that dead cells display an ‘eat me’ signal on their surface that is recognized by phagocytes. During this process, lipids are flipped between the inner and outer parts of the cell membrane via a variety of proteins called scramblases. Suzuki and his team have already identified several of these lipid-scrambling proteins, but some of their activation mechanisms have been unclear…

Specifically, the scientists found that cell death signals lead to a nuclear protein, called XRCC4, getting cut by an enzyme. A fragment of XRCC4 leaves the nucleus, activating Xkr4, which forms a dimer: the linking of identical pieces into configurations. Both XRCC4 binding and dimer formation are necessary for Xkr4 to ultimately transfer lipids on the cell surface to alert phagocytes.

Kyoto University, “Eat Me: The Cell Signal of Death” at Neuroscience News

Again, a complex signalling system that supposedly just so happened and in this case it doesn’t function for the protection of the cell but for it’s elimination — look, if Darwinism really worked, many gravel pits would be full of newly forming life. They probably have all the ingredients. So why doesn’t survival of the fittest work its magic in creating massive complexity today?

The paper is closed access.

See also: 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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Fifty different genes for eye color?

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You’ve heard this one before. From the study group: Eye color is “much more complex than previously thought.” If we’d thought of trademarking that phrase, we wouldn’t be asking for money from our readers at Christmas. On the other hand, it’s just as well used for free; it’s needed so often now.

Researchers have identified 50 new genes for eye color in a study involving the genetic analysis of almost 195,000 people across Europe and Asia.

An international team of researchers led by King’s College London and Erasmus University Medical Center Rotterdam have identified 50 new genes for eye colour in the largest genetic study of its kind to date. The study, published today in Science Advances, involved the genetic analysis of almost 195,000 people across Europe and Asia…

In addition, the team found that eye colour in Asians with different shades of brown is genetically similar to eye colour in Europeans ranging from dark brown to light blue…

This study builds on previous research in which scientists had identified a dozen genes linked to eye colour, believing there to be many more. Previously, scientists thought that variation in eye colour was controlled by one or two genes only, with brown eyes dominant over blue eyes.

Co-senior author Dr Pirro Hysi, King’s College London, said: “The findings are exciting because they bring us to a step closer to understanding the genes that cause one of the most striking features of the human faces, which has mystified generations throughout our history.

King’s College London, “Eye color genetics not so simple, study finds” at ScienceDaily (March 11, 2021)

Some of us recall learning in school that eye color was strictly a one-off. Brown eyes were represented by a capital B and blue eyes by a small b. Only one square in the diagram had two bb’s. That, we were told, was why blue eyes were rare…

Not that they were at all rare in our community. But hey, it was science! Who were we to argue?

Well, fast forward: Trust the science? It’s a good thing no one needed to take that one very seriously. It’s another thing when they’re dogmatically wrong about the stuff that really matters.

By the way, all this stuff supposedly came about purely by natural selection acting on random mutations (Darwinism)? Naw.

The paper is open access.

Hat tip: Philip Cunningham

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Are Darwin’s loyalists dwindling in number and cultural attractiveness?

That’s how it seems, from recent news events, including the decline of New Atheism:

I’ve been following the intelligent design controversy for over twenty years now. I had assumed that Darwinism would last forever. It’s the perfect materialist explanation of everything! As the most famous of the new atheists, Richard Dawkins, said in 1986: “Although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist” (The Blind Watchmaker, 1986).

But now, not only is new atheism collapsing, but, if we go by recent developments at New Scientist, so is Darwinism.

Okay, first let’s talk about new atheism. Last year, we learned that new atheism had begun to feel like “a movement certain of its own victory burning out spectacularly over the course of a few short years, followed by mysterious yet near-total contempt from the very people it thought it had convinced.”

That was a startling admission from a supporter. But it makes sense. Who cares any more about the Church of the Flying Spaghetti Monster? (You can look that up on the internet if you are not sure what it means. On the other hand, maybe you needn’t bother.)

Denyse O’Leary, “The passé scientist” at Mind Matters News

The article goes on to talk about events at New Scientist and The Economist and reasons for a decline.

See also: Dawkins’s claim: “every gene delivers approximately the same tree of life” contested at Nature journal You know, Dawkins may be losing his shine. New Scientist was making similar types of noise last October. It’s now okay to say when there’s something wrong with this stuff.

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When psychology tries to be a science instead of a mythology…

After a hundred and fifty years, this is what they got:

But isn’t psychology different from mythology in that it can be falsified? No doubt, since 1879, psychologists have devised methods to empirically investigate the mind, ranging from introspectionism to behaviourism, cognitive modelling, connectionism, and more. For example, as a cognitive psychologist, I am trained in the theory of how the mind works and the use of statistical instruments to pursue investigations of behaviour. Yet, our field is currently in a crisis due to issues with replication, ecological validity, the cultural limits of experimental subject populations, and some ethical peccadilloes. Frankly, for more than 100 years of research, we don’t have as much to show as the physical sciences do; so far, psychology is not very effective at tracing general laws. Sigmund Freud’s theories were largely unfalsifiable, and the promissory note that the mind is the brain has yet to be cashed in. It might be best to conceive of empirical psychology as a set of pragmatic methods to develop discursively helpful metaphors of the mind and hold out in hope that we slowly secure a set of reliable correlations between neuroanatomy and function.

Conceiving of psychology as a mythology enables us to perceive that psychology is an explicit portrayal of what we want to understand about reality and the ultimately pragmatic forms that such knowledge has taken. The emotional need to possess explanations worthy of the commitment of belief is greater than what we can ever know.

Rami Gabriel, “Myth and the mind” at Aeon

Gabriel encourages us to see psychology as a mythology and, of course, he is right: “Sigmund Freud’s theories were largely unfalsifiable, and the promissory note that the mind is the brain has yet to be cashed in.” The idea that the mind is just the brain is unfalsifiable too. Beliefs that do not originate in fact are impervious to evidence.

See also: Back to school briefing: Seven myths of social psychology: Many lecture room icons from decades past are looking tarnished now. (That was 2014 and it has gotten worse since.)

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More evidence of fine-tuning in DNA replication

The Origin Recognition Complex (ORC) is a group of proteins required to be fully assembled for the first step in DNA replication. One component of the ORC, ORC1 (visible in this image as bright green dots), is sequestered into droplets in the nucleus of the cell, and allowed to move briefly and assemble with other proteins at the right moment in the cell cycle. Credit: Manzar Hossain/Stillman lab/CSHL, 2021

Not that they call it that, of course.

Throughout most of the cell division cycle, ORC1 and CDC6 amounts oscillate in the cell. Stillman explains that “both high and low amounts of ORC1 lead to severe consequences for cell viability. So, you have to have just the right amount” of each protein throughout the cell cycle. Stillman and his colleagues have shown that CDC6 recruits other regulatory proteins that control the activity and levels of ORC1 in both space and time. They published their findings in Molecular Cell.

Cold Spring Harbor Laboratory, “How human cells coordinate the start of DNA replication” at Phys.org

From the caption: “required to be fully assembled for the first step in DNA replication.” Hmm.

“Just the right amount” over and over in a cascade is still just a big accident, right? That’s if you still want your job at the lab…

The paper is closed access.

See also: Dawkins’s claim: “every gene delivers approximately the same tree of life” contested at Nature journal You know, Dawkins may be losing his shine. New Scientist was making similar types of noise last October. It’s now okay to say when there’s something wrong with this stuff.

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Is the mind just a program run by the brain?

Neurosurgeon Michael Egnor thinks that much modern neuroscience can be characterized as a collection of weak metaphors about the mind and brain. The Computational Theory of Mind (CTM) is one of them:

I believe that the computational model of the mind is fatally flawed. Here are some reasons:

The most obvious reason is that all mental states have meaning — that is, they are intentional. Intentionality means that our thoughts are about something — there is always an object to which a thought points. I think about my vacation, or about politics or about my dog. But computation, understood as manipulation of symbols, is never intrinsically about anything. A computer matches a set of configurations of electrons to another set of configurations of electrons. What those configurations of electrons are about is not inherent to the computation — the meaning of this post as I type it is not inherently in the patterns of electrons on my screen but in the thoughts in my mind…

Michael Egnor, “Why “the mind is just a computation” is a fatally flawed idea” at Mind Matters News

Summary: The mind is the opposite of computation. Mental states are always intentional and computation, by its nature, is never intentional.

You may also enjoy: A reader asks, Is it true that there is no self? (Michael Egnor) The assertion that self is an illusion is not even wrong — it’s self-refuting, like saying “I don’t exist” or “Misery is green.”

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Dawkins’s claim: “every gene delivers approximately the same tree of life” contested at Nature journal

It’s just not like that, says a Queen Mary U prof. He points to this vid:

and writes,

The lay-person reading this, or watching the video above, is given the clear impression that every gene or pseudogene in every living organism gives essentially the same phylogenetic tree, when analysed with its homologs from other species. This is simply not true.

If this were true, then phylogeny building in the genomic era would be a walk in the park. But, as many of my readers will know from personal experience, it is not.

If this were true, terms like horizontal gene transfer, incomplete lineage sorting, introgression, and molecular convergence would be rare curiosities in the genomic literature. But they are common (click on the links in the previous sentence to see searched for these terms on Google Scholar).

If this were true, commonly-used phylogenetic software like ASTRAL, ASTRID and BUCKy, designed to deal with gene tree incongruence, would be seldom used. But they are used often.

I hardly need to labour my point to the present audience. Dawkins’ statements are simply wrong. Gloriously and utterly wrong.

Richard Buggs, “Obsolete Dawkinsian evidence for evolution” at Nature: Ecology & Evolution

You know, Dawkins may be losing his shine. New Scientist was making similar types of noise last October. It’s now okay to say when there’s something wrong with this stuff.

See, for example: The Selfish Gene is no longer cool. At New Scientist: “Some researchers think the solution lies in an idea called cultural group selection. Forget shared genes, they argue: selection can favour cooperative groups if the people within them share enough culture.” Darwin has left the building and returned to his estate.

This is New Scientist we’re talking about. And that’s Dawkins’s Selfish Gene.

So maybe science really is self-correcting. We’ve had lots of reasons to wonder if that’s just a myth. You know, nonsense drop-kicked from one journal article to the next doesn’t inspire confidence.

If they can set the record straight about the Tree of Life stuff, maybe a lot of other things would start getting straightened out.

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We are urged to believe in the “facts” of science yet, historically, these facts often change

From 2014 but still pungent:

The “scientific” label comes freighted with assumptions that a matter is factual, proven, and settled. Yet the dust-bin of science is filled with once-settled “facts” that stand as reminders that scientific conclusions can be wrong—very wrong; think of geocentrism, spontaneous generation, luminiferous aether, and the fixity of time and space, to name but a few. They should give us pause anytime we hear that some current conclusion—global warming, Darwinian evolution, overpopulation, fill-in-the-blank—is a settled scientific fact beyond dispute. As someone once quipped, he who is wedded to the science of the day will soon find himself a widower.

In some cases, scientific error is due to inadequate testing and verification. For example, the Aristotelian belief that heavy objects fall faster than lighter ones was the scientific consensus until Galileo actually tested it, 2,000 years later!

In other cases, ideology and researcher bias are to blame. Take the fossil record. Ian Tattersall, curator of the American Museum of Natural History, once confessed that “the [evolutionary] patterns we perceive are as likely to result from our unconscious mindsets as from the evidence itself.” Likewise, Richard Leakey disclosed that his father, paleontologist Louis Leakey, had the habit of fitting fossils into a pre-conceived line of descent.

Regis Nicoll, “Unsettling Science” at Salvo

Note: Enjoy this piece while you can. Stories from Salvo have been known to disappear behind a paywall at some point. Of course, the subscription is well worth the money.

See also: Honeybees, astonishingly, are not going extinct Science writer Hank Campbell vs. the apocalypse industry: Instead of dying out, there are now 10 honeybees for every human on the planet – more than 25 years ago. And that is just in one species. There are over 25,000 species of bees, we just don’t try to count them all because the others are not part of a billion dollar industry, like sending honeybees around in trucks to pollinate almond farms.

Dang. Another apocalypse shot to hell.

and

Horizontal gene transfer as a serious blow to claims about universal common descent. Trust our stalwart physics color commentator Rob Sheldon to draw the logical conclusion about horizontal gene transfer between plants and insects: If plants and insects can exchange genes (and who knows what else can?), what are we to make of dogmatic claims about universal common descent?

Another great moment in Cancel Culture threatened…

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Researchers: Watery worlds may be common rather than rare

Note: The Earth-like exoplanet illustration is a stock image with elements furnished by NASA, © sdecoret / stock.adobe.com

The researchers offer a thesis of planet formation according to which watery planets should be more common than some scientists think: If planets’ water resources came from accretions of tiny carbon and ice particles, rather than icy asteroid hits, many would have lots of water, and maybe life.

A common assumption among exoplanet experts is that most planets got their water via a chance hit early on from an icy asteroid. But researchers from the GLOBE Institute at the University of Copenhagen offer an alternative scenario, based on the millimetre-sized particles of ice and carbon that orbit all the young stars in our Milky Way galaxy.

If masses of these particles are incorporated into a planet from its beginning, it isn’t a matter of chance whether the planet has water. It is a matter of chance if it loses water, which seems to have happened, for example, to Mars.

News, “Could the universe be swimming in watery planets?” at Mind Matters News

You may also enjoy:

Is intelligent life in the universe living in interior oceans of planets and moons? The Ocean Planets Hypothesis is that intelligent beings may flourish in the interior oceans of the moons of gas giant planets — or within exoplanets — but they are trapped there. If intelligent life forms are trapped in the interior oceans of rocky moons and planets, Earth is a special planet—much better suited to space exploration.

and

We won’t find ET on ocean planets, researchers say. We will see few extraterrestrials if a great many promising exoplanets are Waterworlds. Prominent astrobiologists doubt that intelligent life could develop in an entirely aquatic environment. But are they right?

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The rarity of bonobo adoption as an argument for human exceptionalism

At Nature, a recent report of bonobo females adopting outgroup babies was hailed as a primate first. But this story is not what it seems. Let’s cut through some pop science assumptions (video footage provided):

Among dogs and cats, adoption, including interspecies adoption, has often been documented…

Tomcats also adopt kittens… So will male dogs… Not only will tomcats adopt a kitten but at least one tomcat adopted a guinea pig…

Could this be a clue?: Most animal whose adoption behavior we have catalogued were domestic animals cared for by humans. They were not especially (or anyway not immediately) worried about survival. For them, food is found in the cupboard by pleading, not the wilderness by hunting or foraging. Perhaps they can afford to show qualities that they would not otherwise show, as a result of living with humans.

In a way, the willingness of our domestic animals to adopt other animals’ offspring — relative to that of the bonobos, according to researchers — is an argument for human exceptionalism. Given a chance, we break nature’s rules. We do things differently.

Denyse O’Leary, “At Nature: Bonobo chimpanzees adopt orphans, a first for great apes” at Mind Matters News

The willingness of our pets to adopt other animals’ offspring — relative to that of the wild chimpanzees — is an argument for human exceptionalism. The real story is a reason that humans are not just animals.

You may also wish to read:

In what ways are dogs intelligent? There is no human counterpart to some types of dog intelligence.

In what ways are cats intelligent? Cats have nearly twice as many neurons as dogs and a bigger and more complex cerebral cortex.

And

The real reason why only human beings speak. Language is a tool for abstract thinking—a necessary tool for abstraction—and humans are the only animals who think abstractly

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