Michael J. Behe's Blog, page 83

April 12, 2022

Changing the genetic code — and still enabling life — would be a challenge

Some think they know how to do it:

in a new study published last month in eLife, a group of researchers at the Massachusetts Institute of Technology and Yale University showed that it’s possible to tweak one of these time-honored rules and create a more expansive, entirely new genetic code built around longer codon words. In principle, their discovery points to one of several ways of expanding the genetic code into a more versatile system that synthetic biologists could use to create cells with novel biochemistries that make proteins found nowhere in nature. But the work also showed that an extended genetic code is hampered by its own complexity, becoming less efficient and even surprisingly less capable in some ways — limitations that hint at why life may not have favored longer codons in the first place.

It’s uncertain what these findings mean for how life elsewhere in the universe could be encoded, but it does imply that our own genetic code evolved to be neither too complicated nor too restrictive, but just right — and then ruled life for billions of years thereafter as what Francis Crick called a “frozen accident.” Nature opted for this Goldilocks code, the authors say, because it was simple and sufficient for its purposes, not because other codes were unachievable.

Yasemin Saplakoglu, “Life With Longer Genetic Codes Seems Possible — but Less Likely” at Mind Matters News (April 11, 2022)

The basic message is that we can’t improve on all the things that just happen to work by accident in exactly the right way. Yet in just about any area of life other than evolution theory we find a completely different picture. Why is Darwinism allowed to be such a big exception to the general rule?

The paper is open access.

You may also wish to read: In Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, Nathan Lents wrote the book, literally, on what some think could be done to improve the human body. The human eye, for example.

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Published on April 12, 2022 20:45

Neil Thomas comments on the difficulty of accommodating Darwinism to sudden origin of life

Neil Thomas, author of Taking Leave of Darwin (2021) comments on a curious fact about Darwinism:

The greatest problem for the acceptance of Darwinism as a self-standing and logically coherent theory is the unsolved mystery of the absolute origin of life on earth, a subject which Charles Darwin tried to bat away as, if not a total irrelevance, then as something beyond his competence to pronounce on. Even today Darwinian supporters will downplay the subject of the origins of life as a matter extraneous to the subject of natural selection. It is not. It is absolutely foundational to the integrity of natural selection as a conceptually satisfactory theory, and evolutionary science cannot logically even approach the starting blocks of its conjectures without cracking this unsolved problem, as the late 19th-century German scientist Ludwig Buechner pointed out…

In what was shaping up to become the largely post-Christian 20th century in Europe, the untenability of the abiogenesis postulate was resisted by many in the scientific world on purely ideological grounds. The accelerating secularizing trends of the early 20th century meant that the outdated and disproven notion of spontaneous generation was nevertheless kept alive on a form of intellectual life-support despite the abundant evidence pointing to its unviability.

Neil Thomas, “Considering “Abiogenesis,” an Imaginary Term in Science” at Evolution News and Science Today (April 11, 2022)

Now that Thomas mentions it a remarkable literature has been produced in the last century offering explanations of the origin of life and — it is fair to say — none of them work.

Here’s a thought: If your origin of life theory works, can we reverse engineer the conditions to produce life from non-life today? If we can’t, that doesn’t prove your theory false. After all, it is very difficult to demonstrate that something “couldn’t have” happened under any circumstances whatever. But you must now rejoin the queue in your previous place…

The rest of the series to date is here.

You may also wish to read: Could life have started in the depths of the Earth? It’s controversial. Talk about an extremophile deep in the Earth! Trouble is we don’t know that life started out like audaxviator. It could just as easily be that one late-arriving microbe could inhabit that territory but nothing else could.

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Published on April 12, 2022 19:50

Could life have started in the depths of the Earth? It’s controversial.

The question originated with Cornell astronomer Thomas Gold in a 1992 paper and was developed in a book, Underground (2019) by Will Hunt.

As science writer Ross Pomeroy explains at Real Clear Science, much of the controversy revolved around claims made by Hunt that oil and gas dated to Earth’s formation…

The main effect was to encourage looking deep in Earth for life forms. If you don’t mind that they are all microbes, it has been a rich haul:

Microbes have been found as far as 2.8 kilometers underground, munching on a range of minerals for “food” and generally subsisting at a much slower pace compared to life up above. Some are so different from surface microbes that they’ve garnered a catchy nickname: “intraterrestrials”. Crucially, in regards’ to Gold’s bold hypotheses that deep microbes could have started life and may exist in the interiors of far-flung planets, scientists have found a bacterium that seems to exist totally independent from Earth’s surface. Candidatus Desulforudis audaxviator was found under a deep gold mine in South Africa and exists at temperatures as high as 140 degrees Fahrenheit in the absence of organic compounds, light, and oxygen.

Ross Pomeroy, “Did Life Start Deep Below Earth’s Surface?” at RealClearScience (April 12, 2022)

Talk about an extremophile deep in the Earth! Trouble is we don’t know that life started out like that. It could just as easily be that one late-arriving microbe could inhabit that territory but nothing else could.

Some hope to find evidence of life forms like audaxviator on exoplanets.

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Published on April 12, 2022 18:36

At Mind Matters News: Does information have mass? An experimental physicist weighs in

Physicist Melvin Vopson argues that information has mass; Eric Holloway replies that, if so, the mass must come from outside the universe.

Meanwhile, our physics color commentator Rob Sheldon offers,

For numbers less than 4, geometrical series win, but for 4 and greater the exponential series win out.

So as soon as we are talking about real world information, the more information we have, the less the bits weigh, until at very large amounts of information they weigh almost nothing.

The only way Vopson could be vindicated is if we store all that information serially on magnetic tape. But if the bits are not indistinguishable serial QM bits, then in the infinite limit they weigh nothing at all.

News, “Does information have mass? An experimental physicist weighs in” at Mind Matters News

(You need to visit the OP to see the mathematical demo.)

Takehome: Rob Sheldon notes that the more real-world information we have, the less the bits weigh until, at very large amounts of information, they weigh almost nothing.

Here are Eric Holloway’s reflections on whether information has mass:

Does information weigh something after all? What if it does? At the rate we create information today, one physicist computes that in 350 years, the energy will outweigh the atoms of Earth. Vopson’s idea that creating information also creates mass and energy is fascinating — and it promises even bigger mysteries than the ones we address now.

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Published on April 12, 2022 17:58

Asked at Space.com: Could gravity itself be the origin of dark matter?

In as proposed model, dark matter came first:

A new model of the very early universe proposes that the graviton, the quantum mechanical force carrier of gravity, flooded the cosmos with dark matter before normal matter even had a chance to get started.

The proposal could be a way to connect two of the biggest outstanding puzzles in modern cosmology: the nature of dark matter and the history of cosmic inflation.

Paul Sutter, “Is the origin of dark matter gravity itself?” at Space.com (April 10, 2022)

Commenting on an article at open-access ArXiv, Stony Brook astrophysicist Paul Sutter adds,

The physicists tuned their model to create the right amount of dark matter that observations of the cosmos demand. However, it’s still theoretical work. Most important, physicists aren’t exactly sure how gravity interacts with particles. This is the regime of quantum gravity, a theory of strong gravity at small scales, which is the current holy grail of modern physics. So, for their work, the co-authors of the paper had to make a lot of assumptions as to how gravity operated at these scales.

Still, the idea is interesting because it provides a way for the early universe to produce significant amounts of dark matter and for that dark matter to (essentially) never talk to normal matter ever again.

Paul Sutter, “Is the origin of dark matter gravity itself?” at Space.com (April 10, 2022)

Well, dark matter is bound to be fascinating:

You may also wish to read: Dark Matter as Fermi balls? Rob Sheldon offers a question.

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Published on April 12, 2022 08:48

Ultra-In mag New Yorker: “For our nation and our species, the future depends” on Francis Collins’s success…

And that of others like him:

Collins was able to work for three Presidential Administrations in part because he could inhabit multiple identities—scientist, physician, Christian, musician, communicator, advocate—and speak to the concerns of the people in front of him. He might have talked genomic discoveries with one lawmaker and the overlap between science and religion with another. “I probably met a thousand times one-on-one with congressional members,” he told me. “I always tried to come across as someone who doesn’t just want to talk but who wants to listen. I tried to understand what’s important to them—what are they interested in?”

Speaking to Collins, I felt that his openness was more than a strategy. It seemed sincere. I wondered whether his sincerity flowed from the fact that he is genuinely part of the two tribes that he hopes to connect. He speaks both languages, understands both cultures, and feels acutely the rift between them. He must know that his insistence on bringing them together could make him less welcome in either. But, for Collins, this pursuit is not an abstract ideal or a political goal. It is, in some sense, a higher calling. For our nation and our species, the future depends on its success.

Dhruv Khullar, “Faith, Science, and Francis Collins” at New Yorker (April 7, 2022)

If the “future depends” on Francis Collins’s success, the future must then cope with this:

At Evolution News And Science Today: The appalling moral failure of Francis Collins. John West provides a, er, surprising and enlightening picture of the theistic evolution great. Not for the faint of heart.

and

Collins’s role in an experiment on premature babies: “Medical ethicists were appalled. “The word ‘unethical’ doesn’t even begin to describe the egregious and shocking deficiencies in the informed-consent process for this study,” said Michael Carome, MD, the director of the Health Research Group at the nonprofit (and politically liberal) group Public Citizen. “Parents of the infants who were enrolled in this study were misled about its purpose. … They were misled to believe everything being done was in the ‘standard of care’ and therefore posed no predictable risk to the babies.”

One way of looking at it: In light of the appalling treatment of infants under Collins’s regime, he is just the sort of individual that the New Yorker would want to represent evangelical Christians — or any other group that its staff despise.

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Published on April 12, 2022 07:24

Researchers shed light on how horizontal gene transfer triggers antibiotic resistance

“Jumping genes” that jump between species spread the resistance:

Biomedical engineers at Duke University believe they have discovered the physical mechanism that causes high doses of antibiotics to promote the spread of antibiotic resistance between bacteria.

The culprit, they say, is an overabundance of “jumping genes,” called transposons, that carry the genetic instructions for resistance from the cell’s source code to plasmids that shuttle between cells.

“There’s a lot of evidence that suggests human pathogens likely pick up antibiotic resistance from other species living in the natural environment,” said Lingchong You, professor of biomedical engineering at Duke. “Intuitively, it makes sense that high levels of antibiotics in these environments are facilitating the jumping of resistance genes from chromosomes to plasmids so that they can spread, but the underlying mechanism never been directly tested. That’s where our work comes in.” …

“Yi’s experiments were designed to test this possible pathway that explains how different pathogens actually get resistance from environmental species,” You said. “And he demonstrated that not only is this possible, it’s also very likely.”

Transposons are tiny pieces of DNA that constantly jump around the inside of a cell. They can jump from place to place within a cell’s central genetic database, and they can jump from the database of the DNA to the larger plasmids capable of traveling between cells, or vice versa. This can lead to chromosomes or plasmids that contain many copies of the same genetic blueprints.

Duke University, “Tiny jumping genes fingered as culprit in rise of antibiotic resistance” at ScienceDaily (April 5, 2022)

A bit like an arms race but with plasma?

The paper requires a fee or subscription.

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Published on April 12, 2022 00:19

April 11, 2022

Eric Holloway: Does information weigh something after all? What if it does?

At the rate we create information today, one physicist computes that in 350 years, the energy will outweigh the atoms of Earth. Eric Holloway responds:

Is Vopson’s theory justified? I am a bit skeptical, but the reversing of Landauer’s Principle appears sound. If we assume the opposite, that creating information does not increase the energy and mass in the system, then we end up with a situation where we create infinite negative energy and mass by constantly creating and destroying information.

Let’s take one more little step off Vopson’s idea. Let’s accept that creation of information can indeed increase the amount of energy and mass in a system. But, according to the conservation of energy, the energy in a closed system remains constant. So, if Vopson is correct we now have a mystery because his theory is in tension with the conservation of energy. The only solution is that the system is not closed. So where is the opening in the system? If the system is physically closed, then the influx of information must come from outside the physical realm.

Eric Holloway, “Does information weigh something after all? What if it does?” at Mind Matters News (April 11, 2022)

The paper is open access.

Takehome: Vopson’s idea that creating information also creates mass and energy is fascinating — and it promises even bigger mysteries than the ones we address now.

You may also wish to read: Is GPT-3 the “reborn doll” of artificial intelligence? Unlike the reality doll collectors, GPT-3 engineers truly believe that scaling up the model size will suddenly cause GPT-3 to think and talk like a real human. If we doubt that the reborn dolls will ever become real babies, why should we expect a different outcome with the GPT-3 language model? (Eric Holloway)

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Published on April 11, 2022 18:33

Neil Thomas on “The Dawkinsian Mythology”

Richard Dawkins is, for popular science media, one of the “world’s smartest scientist” types and therefore big enough to have a mythology:

With reference to the biological world, in the aftermath of the 1976 publication of Richard Dawkins’s The Selfish Gene, philosopher Mary Midgely pointed out the fatuousness of the “meme” hypothesis in painfully direct terms which are doubtless well-known to readers of her articles. Her critique has since been reinforced by others. Philosopher David Stove subjected the Dawkinsian conjecture to the most comprehensive critique. Latterly, John Gray, with habitual trenchancy, has written of “the cod-science of memes” — those supposed “replicating” forces postulated by Dawkins which have no more referent in the real world, Gray fulminates, than the non-existent substance of phlogiston.

In the course of opposing Dawkins’s attempt to extend further the Darwinian imperium into the realm of “universal Darwinism,” philosopher Anthony Flew even disputed whether the term “natural selection” had any genuine meaning at all, questioning the selective power Darwin claimed for it. His British colleague Richard Spilsbury concurred, writing in regard to the question-begging term “complexification” (postulated as a process leading — by intermediate steps wholly unknown — from unicellular species to the eventual evolution of homo sapiens) that “to say that these developments might have come about through the selection of chance variation is not evidence that they did.”5

To establish a conceptual possibility was far from advancing a concrete proof, Spilsbury objected. To assent to that proposition was as futile as it would be to support Charles Darwin’s long disproved theory of pangenesis and the associated idea of “gemmules” in heredity.6

Neil Thomas, “The Dawkinsian Mythology” at Evolution News and Science Today April 9, 2022)

The Selfish Gene undergirded the careers of a thousand evolutionary psychologists, undergirded in turn by popular science media recycling secular beliefs. Facts, in such a case, must necessarily be largely irrelevant unless they are cherrypicked to support Dawkins’s conclusions. That gene was one of those things that just couldn’t not be true.

Neil Thomas is the author of Taking Leave of Darwin (2021).

Note: Thomas’s article is part of a series, Why Words Matter: Sense and Nonsense in Science, which can be read, to date, here.

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Published on April 11, 2022 07:30

At Skeptic mag: Colleague defends Darwinian great E. O. Wilson from accusations of racism

Well, what goes around comes around, as they say:

And now this from Skeptic Magazine, from a long-time collaborator with E. O. Wilson:

The point is I never found one statement in his writings that would indicate that Ed Wilson followed a racist ideology. This was the invention, or rather the falsehood, created by the International Committee Against Racism (INCAR), members of which physically attacked Ed at the beginning of an invited lecture he was to deliver at a meeting of the AAAS (American Association for the Advancement of Science). This is intellectual fascism. In fact, even Lewontin made clear that Wilson is not a racist. As Lewontin said in an interview with The Harvard Crimson on December 3, 1975: “Sociobiology is not a racist doctrine, but any kind of genetic determinism can and does feed other kinds, including the belief that some races are superior to others. However, this is very far from Wilson’s intuition. Because Wilson is concerned with the universals of human nature — his chief point is that we are all alike.”

Bert Hölldobler, “Self-Righteous Vigilantism in Science” at Skeptic Magazine (April 5, 2022)

Wait. Excising racism from Darwinism is like trying to get the wet out of water. If we are all merely evolved apes, some may indeed be more evolved than others. The traditional stories preclude that by declaring that “all have sinned and fallen short of the glory of God.” But all that involves precisely what Darwinism denies.

And about Wilson’s support for genuine racist, Canadian Philippe Rushton (1943–2012)?

Having now looked at the work by Rushton with greater attention, it is clear to me that Ed could not have paid much scrutiny to Rushton’s work but rather was motivated by the impression he got from Rushton’s own description of his plight, namely, that he was being persecuted by far-left wing ideologues, as Wilson himself had been after publication of Sociobiology. Note too that Rushton had strong academic credentials as a former John Simon Guggenheim Fellow and a fellow of the Canadian Psychological Society. Nevertheless, Ed’s recommendation of a manuscript submitted by Rushton to the journal Ethology and Sociobiology, in which Rushton wrongly applied Wilson’s r-K selection model, was in my opinion a serious misjudgment. When Wilson encouraged Rushton to pursue this line of investigation and advised him not to be discouraged, at one point warning him “the whole issue would be clouded by personal charges of racism to the point that rational discussion would be almost impossible,” my guess is that Wilson’s response was colored by his own and painful experience and decision to continue with his work despite vicious attacks from Science for the People, rather than an in-depth examination of the of Rushton’s paper. If we could ask Ed today, I am sure he would say: “I made a mistake, I was wrong.” But a misjudgment made when reviewing a paper for a journal does not make Ed Wilson a racist or a promoter of race science!

Bert Hölldobler, “Self-Righteous Vigilantism in Science” at Skeptic Magazine (April 5, 2022)

But again, wait. Racism wasn’t an incidental, culturally conditioned element in Rushton’s work. It appears to have been the point of it. If the great E. O. Wilson couldn’t see that, the likely explanation is that elements in Darwinism blinded him to what was pretty obvious to most of Rushton’s fellow Canadians. And why is that?

Anyway, if interested, you might wish to read the above in light of:

People who doubt “evolution” are more likely to be racist? Reader’s comment on the study: The principle that isolation breeds prejudice against the “other” is a truism. And you could find evidence supporting this truism from very different groups. If you surveyed attitude of ivory tower types you’d find similar prejudiced against conservative religious groups you’d find similar discriminatory attitudes. Why? Because those evolutionary secular academic types who accept human evolution have very little contact with conservative religious people.

and

E. O. Wilson and racism: The smoking gun is found. Some have dismissed the findings but others say they fit a pattern. From Schulson’s story: “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.” Oh. And remember, Wilson was supposed to be the second Darwin. Funny no one talks about that now.

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Published on April 11, 2022 06:31

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