Michael J. Behe's Blog, page 100

March 2, 2022

At Mind Matters News: Eric Holloway asks, Is AlphaZero Actually Superior to the Human Mind?

He thinks that comparing AI and the human mind is completely apples and oranges:

… we all know that computer processing time is not the same as human thinking time. For example, according to the paper, AlphaZero evaluates 63 thousand moves in a second, whereas a human can only evaluate at most a couple, or not even one. Not even in the same ballpark! So once we start looking at the raw processing numbers for the AI engine, it becomes very clear that comparing AI and the human mind is completely apples and oranges.

If we were to limit AlphaZero to human level processing capabilities, it would completely flounder. What is actually remarkable is the shear amount of processing power needed to bring computers up to the level of even the most basic human player! This indicates the human mind is doing something totally different and extraordinarily more efficient than the best AI algorithms we have today.

Rather than demonstrating the superiority of algorithms over thinking, these AI game engines instead show the ever-widening gap between computation and cogitation, with the advantage clearly in the human court.

Eric Holloway, “Is AlphaZero actually superior to the human mind?” at Mind Matters News (February 28, 2022)

Takehome: What is actually remarkable is the sheer amount of processing power needed to bring computers up to the level of even the most basic human player!

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Published on March 02, 2022 13:19

Researchers: Bacteria provided plants with genes to colonize land

Challenging conventional views:

Genes jumping from microbes to green algae hundreds of millions of years ago might have driven the evolution of land plants, researchers report March 1 in the journal Molecular Plant. Their analysis reveals that hundreds of genes from bacteria, fungi, and viruses have been integrated into plants, giving them desirable traits for a terrestrial life.

“Our study changes the conventional view on land-plant evolution,” says senior author Jinling Huang, a biologist at East Carolina University. “I have suspected that horizontal gene transfer helped plants to move from water to land, but we didn’t know how big of a role it played until now.” …

Conventionally, scientists thought eukaryotic genes move only via vertical gene transfer, during which genes pass down from parents to offspring and mutations can occur to give rise to new genes and traits. But Huang and his colleagues, including plant biologist Chun-Peng Song at Henan University, have found evidence from prior studies that HGT in plants might be common.

Cell Press, “Bacteria genes gave ancient plants traits to colonize land” at ScienceDaily (March 1, 2022)

Again, we ask, if so, in a world where horizontal gene transfer is this extensive and significant, what becomes of all the carefully structured Darwinian tales of the gradual development of selective advantage? Aren’t they just evolutionary fiction, a form of historical fiction?

The paper is open access.

You may also wish to read: Animal DNA modifier captured from bacteria 60 million years ago The obvious question this raises is, what about all the detailed Darwinian narratives that a horizontal gene transfer could obviate?

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Published on March 02, 2022 08:06

Zoom call with biochemist James Shapiro on the re-release of Evolution: A view from the 21st century

James Shapiro, author of Evolution: A view from the 21st century is holding a zoom meet March 8, 1:00 PM – 3:00 PM PST (Time zones.), celebrating the re-release of his 2011 book on natural genetic engineering:

From the classroom to the laboratory, conventional wisdom still paints evolution as the passive result of mutational accidents and natural selection. A modern vision of evolution recognizes that all living beings, from the simplest organisms to humans, actively modify their read-write (RW) genomes as they evolve.

In an unpredictable world, the ability to evolve actively is essential to survival. Today, understanding evolution is equally critical to our shared future…

James A. Shapiro, Professor in the University of Chicago’s Department of Biochemistry and Molecular Biology, is a leading bacterial geneticist, the discoverer of transposable elements in bacteria, and the key researcher involved in first organizing the field of mobile genetic elements. The earliest proponent of “natural genetic engineering” as a basic feature of evolution, he has been a leading scientific critic of orthodox evolutionary theory for 20 years.

A friend writes to say that’s good because it’s hard to get a copy of the 2011 edition new and even the second-hand copies are expensive.

You may also wish to read: University of Chicago biochemist: All living cells are cognitive James Shapiro’s recent paper points out, with examples, that bacteria meet the Oxford English Dictionary’s definition of “cognitive.”
Future debates over origins of intelligence, consciousness, etc., may mainly feature panpsychists vs. theists rather than materialists vs. theists.

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Published on March 02, 2022 01:49

How can an intestinal system have an “innate memory”?

Increasingly, researchers must confront intelligence in nature, whatever they may choose to call it.

The innate immune system plays a crucial role in regulating host-microbe interactions, and especially in providing protection against pathogens that invade the mucosa. Using an intestinal infection model, scientists discovered that innate effector cells — group 3 innate lymphoid cells — act not only during the early stages of infection but can also be trained to develop an innate form of immunological memory that can protect the host during reinfection…

The gut mucosa harbors a complex defense system that allows it to combat pathogen infection while maintaining tolerance to commensal microbiota, which are essential for the normal bodily function. This constant surveillance is performed by the innate immune system, which provides early defense in the initial hours after infection. The adaptive immune system then develops a memory for the pathogens that it encounters by activating specific receptors expressed at the surface of B and T lymphocytes, thereby enabling the production of protective antibodies and inflammatory cytokines. Unlike the clearly established function of the adaptive system in long-term tolerance and protection, the role of the innate system in immune memory remains to be determined.

Institut Pasteur, “Discovery of an innate immunological memory in the intestine” at ScienceDaily (February 28, 2022)

So there’s a lot we still don’t know about how it works.

The paper is closed access.

It was easier to be a Darwinian naturalist when cells were just little blobs.

With so much information packed into nature, it is easy to see why some prominent researchers start talking like panpsychists, not naturalists. It’s the best they can do to be honest with what they actually know.

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Published on March 02, 2022 01:24

March 1, 2022

A media bias takedown by the Frontline Doctors

If you needed a case study on loaded language driven slanted reporting, here is a case study that deserves to be headlined:

yay, it works . . .

For context, see the de-spin chart:

Remember, this has been with lives on the line. END

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Published on March 01, 2022 11:18

Animal DNA modifier captured from bacteria 60 million years ago

By the bdelloid rotifer:

Epigenetic marks are modifications to DNA bases that don’t change the underlying genetic code, but “write” extra information on top of it that can be inherited along with your genome. Epigenetic marks usually regulate gene expression — turn genes on or off — particularly during early development or when your body is under stress. They can also suppress “jumping genes” — transposable elements that threaten the integrity of your genome.

In humans and other eukaryotes, two principal epigenetic marks are known. A team from the Marine Biological Laboratory (MBL) has discovered a third, novel epigenetic mark — one formerly known only in bacteria — in bdelloid rotifers, small freshwater animals. This fundamental and surprising discovery is reported this week in Nature Communications.

“We discovered back in 2008 that bdelloid rotifers are very good at capturing foreign genes,” said senior author Irina Arkhipova, senior scientist in the MBL’s Josephine Bay Paul Center. “What we’ve found here is that rotifers, about 60 million years ago, accidentally captured a bacterial gene that allowed them to introduce a new epigenetic mark that was not there before.” This is the first time that a horizontally transferred gene has been shown to reshape the gene regulatory system in a eukaryote.

“This is very unusual and has not been previously reported,” Arkhipova said. “Horizontally transferred genes are thought to preferentially be operational genes, not regulatory genes. It is hard to imagine how a single, horizontally transferred gene would form a new regulatory system, because the existing regulatory systems are already very complicated.”

“It’s almost unbelievable,” said co-first author Irina Yushenova, a research scientist in Arkhipova’s lab. “Just try to picture, somewhere back in time, a piece of bacterial DNA happened to be fused to a piece of eukaryotic DNA. Both of them became joined in the rotifer’s genome and they formed a functional enzyme. That’s not so easy to do, even in the lab, and it happened naturally. And then this composite enzyme created this amazing regulatory system, and bdelloid rotifers were able to start using it to control all these jumping transposons. It’s like magic.”

Marine Biological Laboratory, “New DNA modification system discovered in animals, captured from bacteria more than 60 MYA” at ScienceDaily (February 28, 2022)

The obvious question this raises is, what about all the detailed Darwinian narratives that a horizontal gene transfer could obviate?

The paper is open access.

You may also wish to read: Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more.

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Published on March 01, 2022 07:50

At Mind Matters News: Detecting BS data: If it’s too good to be true, it probably is

This is just as true in science as in other disciplines:

Two Johns Hopkins economists recently wrote a Wall Street Journal opinion piece titled, “Jerome Powell Is Wrong. Printing Money Causes Inflation.” Their argument is that Federal Reserve chair Powell is mistaken in his assertions that there is not a close relationship between money and inflation.

[The economists offered a chart … ]

I learned of this WSJ nonsense via an e-mail from Jay Cordes. Jay is not an economist, but he does know data and he knows that predictions of human behavior are never as precise as indicated in the WSJ:

“Okay, I’m calling bullcrap on that chart below. No “predictions” ever match up that well with reality. What’s the trick?”

The moral is that if you encounter empirical claims that are implausible (like Asian-Americans being prone to heart attacks on the fourth day of every month or hurricanes being deadlier if they have female names), or results that are too good to be true, they probably aren’t true.

Gary Smith, “Detecting BS data: If it’s too good to be true, it probably is” at Mind Matters News (February 28, 2022)

Takehome: Business prof Gary Smith: A recent Wall Street Journal article shows a near-perfect link between inflation and money. But a link that near-perfect raises suspicions. Precise predictions of human behavior are implausible and rarely match up to the far more complicated reality

Oh, while we are here anyway, about the Asian American heart patients and also the hurricanes, see:

The British Medical Journal’s top picks in junk medical science. In its legendary Christmas edition, the Journal highlights the worst offenders. The publicized studies have twisted and tortured data to come up with suspicious or ridiculous conclusions. Here’s how they did it.

and

Female hurricanes: How a mass of hot air became a zombie study. When a reporter first asked me about a study claiming that “Female Hurricanes are Deadlier than Male Hurricanes,” I was sceptical. Do sexist humans die because they don’t take hurricanes with female names seriously? No, the study is seriously flawed.

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Published on March 01, 2022 07:35

Paradox: Why wasn’t our planet frozen solid in the early solar system?

There was significantly less sunlight, we are told, due to planet-forming detritus floating around (like a smoke-filled room, sort of):

Not much is known about what was happening on Earth at that time, but what little we do know suggests that there was some amount of liquid water present at or near the surface starting in the Hadean, and there is evidence that life itself began in the Archean (4.0–2.5 billion years ago). If modern Earth were suddenly to receive 25% less sunlight today, it would quickly freeze over, so how did early Earth manage to avoid it for 2 billion years?

Kimberly M. S. Cartier, “The Young Earth Under the Cool Sun” at Eos (February 22, 2022)

The only thing current researchers are sure of is that they do not like the term “paradox.” That said, they do not have a clear answer, just a number of evidence-based speculations:

Beyond a boost in geophysical data, there is an almost unanimous call for better and faster 3D models of the interconnected Earth system: mantle and crust, sea ice and lower atmosphere, solar radiation and upper atmosphere. Each component of the system plays a key role in solving this early Earth puzzle. Arriving at a consensus solution will require a holistic and interdisciplinary approach that leverages the strengths of each field—paleoclimatology, geochronology, astronomy.

“Whenever there is a paradox or a problem of this type, people look for that one glorious solution which does it all,” Feulner mused. “But there’s probably no silver bullet. [The solution] is probably a mixture of many factors contributing to the warming…just a mix of more CO2, less clouds, you name it. It’s probably messier than many people think.”

Kimberly M. S. Cartier, “The Young Earth Under the Cool Sun” at Eos (February 22, 2022)

So it’s still a paradox until the word itself gets Cancelled.

You may also wish to read: Did giant mountain ranges provide nutrients in early Earth’s history? According to the new thesis, the erosion of mountains provided nutrients that were hitherto unavailable, that helped life forms get started. Sounds like a rollout, actually.

and

Researchers: Poisonous cyanide may have been a harbinger of life 4 billion years ago Note the “may have” and “could have been.” That’s where a lot of origin of life studies are, really. Nothing wrong with that, of course, as long as it is not mistaken for “the findings of science.” It’s speculation, pure and simple. It would be a great hard sci-fi novel, maybe a flick. And fun for chemistry students!

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Published on March 01, 2022 06:58

Remember when cells were random blobs?

Now they are a tightly orchestrated dance:

For decades, biologists had assumed that activity in the cytoplasm was essentially random; the cellular world churned with such dramatic speed that the right proteins would eventually bump into one another. But it turned out that some molecules in the cytoplasm weren’t randomly circulating. They were swirling in ways that brought related parties together. Suppose an important reaction involved five proteins out of ten thousand; the five tended to hang around one another, loosely attracted. (They sometimes had floppy regions that exerted a mutual pull, and which had been missed in images made of the proteins when they were in crystallized form.) Brangwynne and others found that, under the right conditions, groups of proteins could “phase separate,” like bubbles of oil in a salad dressing, forming structures. For decades, researchers had known that complex biochemical reactions tended to happen faster in living cells than in test tubes. Now they knew why: the lava-lamp-like conditions inside a living cell allow chemicals to take advantage of subtle attractive forces more efficiently than is possible in the looser and more uniform environment of a tube or a dish. We’ve long imagined a spark of life—but it could be the physical structure of cytoplasm that’s the key.

This new understanding has begun to open doors. In 2017, Glass helped found the Build-a-Cell consortium—a steering committee for hundreds of labs that are trying to build a working cell from scratch. Researchers in the consortium began combining nonliving parts—proteins, ribosomes, RNA, and other molecular constructions—into membranes that resembled cells, hoping that the mixture would come to life by expressing genes, doing metabolic work, and eventually dividing. Drew Endy, a professor of bioengineering at Stanford who is one of Glass’s co-founders, described the group as trying to solve the Humpty Dumpty problem: could the parts add up to a whole? Such artificial cells could be used as living factories for the production of biofuels or drugs, or as hyperefficient sites of artificial photosynthesis. But although the right parts are there, none have crossed the border from nonliving to living. Endy’s group was experimenting with slightly different ingredients; if that failed, the problem might be in how they’re physically arranged. He told me, “I think there’s a milestone right in front of us. I don’t think it’s that far away.”

James Somers, “A Journey to the Center of Our Cells” at New Yorker (February 28, 2022)

But if the researchers do create living cells, that’s intelligent design, not natural selection acting on random mutations (Darwinism).

Another friend draws our attention to this effort to create a minimal cell (depiction by David Goodsell).

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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Published on March 01, 2022 00:55

February 28, 2022

Sabine Hossenfelder asks: Will the Big Bang repeat?

Roger Penrose’s theory that argues that the Big Bang will repeat is called “conformal cyclic cosmology” and Hossenfelder has her doubts about it. After summarizing the theory, she says, in part,

If the previous eon leaves information imprinted in the next one, then it isn’t obvious that the cycles repeat in the same way. Instead, I would think, they will generally end up with larger and larger fluctuations that will pass on larger and larger fluctuations to the next eon because that’s a positive feedback. If that was so, then Penrose would have to explain why we are in a universe that’s special for not having these huge fluctuations.

Another issue is that it’s not obvious you can extend these cosmologies back in time indefinitely. This is a problem also for “eternal inflation.” Eternal inflation is eternal really only into the future. It has a finite past. You can calculate this just from the geometry. In a recent paper Kinney and Stein showed that this is also the case for a model of cyclic cosmology put forward by Ijjas and Steinhard has the same problem. The cycle might go on infinitely, alright, but only into the future not into the past. It’s not clear at the moment whether this is also the case for conformal cyclic cosmology. I don’t think anyone has looked at it.

Finally, 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.

Sabine Hossenfelder, “Will the Big Bang repeat?” at BackRe(Action)

You may also wish to read: The Big Bang: Put simply, the facts are wrong.

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Published on February 28, 2022 00:05

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