Michael J. Behe's Blog, page 145

A friend says this paper illustrates that universal common descent is untestable

Abstract:

Protein post-translational modifications (PTMs) add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than one billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared to products of likely endosymbiont gene transfer, mitochondrial proteins and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.

Thomas F M Cummings, Kevin Gori, Luis Sanchez-Pulido, Gavriil Gavriilidis, David Moi, Abigail R Wilson, Elizabeth Murchison, Christophe Dessimoz, Chris P Ponting, Maria A Christophorou, Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria, Molecular Biology and Evolution, 2021;, msab317, https://doi.org/10.1093/molbev/msab317

From the paper: “Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies…Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria.”

So the clade consists of animals and blue-green algae…

If any assumption can be made as long as it supports universal common descent, universal common descent will always work.

The paper is open access.

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New book focuses on animal intelligence as not product of pure randomness

The just-released book is Animal Algorithms. Author Eric Cassell’s areas of expertise include flight navigation systems:

How do blind mound-building termites know passive heating and cooling strategies that dazzle skilled human architects? What taught the honeybee its dance, or its hive mates how to read the complex message of the dance? How do monarch butterflies known to fly thousands of miles to a single mountainside in Mexico, to a place they’ve never been before?

The secret, according to author Eric Cassell: behavioral algorithms embedded in their tiny brains.

The Problem for Darwinists

But how did these embedded programs arise in the history of life? There’s the problem for evolutionists. “Specified complexity, irreducible complexity, and the Cambrian explosion are inexplicable from a Darwinian viewpoint,” comments Baylor University computer engineer and intelligent design theorist Robert J. Marks. “In this book, Cassell masterfully adds animal algorithms to the list.”

Several other specialists have praised the book, including an entomologist, a paleoentomologist, and a neurobiologist.

Jonathan Witt, “New Book, Animal Algorithms, Spells Fresh Trouble for Darwinism” at Evolution News and Science Today(November 1, 2021)

Another riff on the question of how intelligence arises from sheer randomness (of course, it doesn’t) but this time with animals.

The algorithms idea is certainly worth using as a model.

From the publisher at Amazon:

How do some birds, turtles, and insects possess navigational abilities that rival the best manmade navigational technologies? Who or what taught the honey bee its dance, or its hive mates how to read the complex message of the dance? How do blind mound-building termites master passive heating and cooling strategies that dazzle skilled human architects? In The Origin of Species Charles Darwin conceded that such instincts are “so wonderful” that the mystery of their origin would strike many “as a difficulty sufficient to overthrow my whole theory.” In Animal Algorithms, Eric Cassell surveys recent evidence and concludes that the difficulty remains, and indeed, is a far more potent challenge to evolutionary theory than Darwin imagined.

You may also wish to read: Neuroscientist: Even viruses are intelligent. Antonio Damasio says, in the excerpt from his new book, that — based on the evidence — we cannot deny viruses “some fraction” of intelligence. Researchers who study viruses, including the one that causes COVID, note similarities between viral strategies and those of insects and animals.

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At Mind Matters News: How information becomes everything, including life

Without the information that holds us together, we would just be dust floating around the room:

In Define information before you talk about it, neurosurgeon Michael Egnor interviewed engineering prof Robert J. Marks on the way information, not matter, shapes our world (October 28, 2021). In the first portion, Egnor and Marks discuss questions like: Why do two identical snowflakes seem more meaningful than one snowflake?

News, “How information becomes everything, including life” at Mind Matters News

Michael Egnor

Michael Egnor: What fascinates me is not only that living things quite obviously containing enormous amounts of information but even just the ordinary laws of nature, manifest information and manifest an intelligent cause. That I think you can see information in snowflakes and the laws of physics, all sorts of things.

Robert J. Marks: Yes, exactly. In fact, one of the interesting things is that things with high Shannon, or even Kolmogorov information happen all the time. We know, for example, that the generation of a single snowflake, as you mentioned, requires a lot of information in terms of either bits or the description length of Kolmogorov…

Robert J. Marks

I think a more interesting question is, What is the meaning of two identical snowflakes? Then all of a sudden, you get into the idea of meaning — two identical snowflakes has a greater meaning than a single observation of a single snowflake.

Takehome: As computer engineer Robert J. Marks explains, our DNA is fundamentally digital, not analog, in how it keeps us being what we are.

You may also wish to read: How information realism subverts materialism Within informational realism, what defines things is their capacity for communicating or exchanging information with other things.

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First recipient of the Lysenko Award was one of Dorian Abbot’s Cancellers

The award is, of course, named after Trofim Lysenko, the bogus Soviet scientist whose agronomy caused many to starve:

MTC’s Lysenko Award is for those in academia who promote or advocate the silencing of academic inquiry and speech, especially where the motive for doing so is based on political disagreement. Nominees for future awards can be sent to Managing Editor David Acevedo (acevedo@nas.org).…

While also involved in l’affaire Abbot, she is not on the MIT faculty or in its administration, so unlike Prof. van der Hilst, she was not thrust into the fray. Nevertheless, this Williams College department chair helped lead the keyboard warriors demanding that Prof. Abbot be disinvited from giving the Carlson Lecture—not because his science was unsound, or that he was unqualified, or that he had broken the law or committed a tort, but because he believes that individuals in higher education should be evaluated based on their individual merit rather than their membership in an identity group. Scandalous, I know. Apropos to the purpose of our award, when interviewed by the New York Times, our winner justified her actions thusly:

What, she was asked, of the effect on academic debate? Should the academy serve as a bastion of unfettered speech?

“This idea of intellectual debate and rigor as the pinnacle of intellectualism comes from a world in which white men dominated,” she replied.

Trofim Lysenko would be pleased, although he likely would have formulaically dismissed the need for academic rigor and debate as being the product of fascist-bourgeois-imperialist-capitalist culture, instead of the current wokeism of “straight white men” as the source of the world’s problems.

So congratulations, Williams College Professor Phoebe Cohen, you are the first recipient of the Minding the Campus Lysenko Award for the Suppression of Academic Speech.

Louis K. Bonham, “Introducing the Minding the Campus Lysenko Award” at Minding the Campus (October 28, 2021)

Why go to Williams College except to say that you have a degree from Williams College? But what if that stops being worth as much? Employers are not paying so much attention any more.

You may also wish to read: Is online learning poised to replace universities? Perhaps sooner than we think, if present trends continue. A degree may confer only social status — which depends on others’ acceptance.
Venture capitalist Peter Thiel doubts that a degree is a good investment today — he has called college administrators subprime mortgage brokers. Learn why.

and

Canceled exoplanets prof Dorian Abbot at the Wall Street Journal The thing is, in 2017, it was ultra-progressive places like Evergreen where the liberal biology teachers could be run off campus. Now it’s MIT, folks. Either Woke goes or science does. But bureaucrats find it easier to cater to Woke than to resist. The more bureaucrats there are, the less university there will be.

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At Nature: The Cambrian Explosion just got more Bang

Bryozoan life forms’ origin is pushed back by 35 million years:

Bryozoans (also known as ectoprocts or moss animals) are aquatic, dominantly sessile, filter-feeding lophophorates that construct an organic or calcareous modular colonial (clonal) exoskeleton1,2,3. The presence of six major orders of bryozoans with advanced polymorphisms in lower Ordovician rocks strongly suggests a Cambrian origin for the largest and most diverse lophophorate phylum2,4,5,6,7,8. However, a lack of convincing bryozoan fossils from the Cambrian period has hampered resolution of the true origins and character assembly of the earliest members of the group. Here we interpret the millimetric, erect, bilaminate, secondarily phosphatized fossil Protomelission gatehousei9 from the early Cambrian of Australia and South China as a potential stem-group bryozoan. The monomorphic zooid capsules, modular construction, organic composition and simple linear budding growth geometry represent a mixture of organic Gymnolaemata and biomineralized Stenolaemata character traits, with phylogenetic analyses identifying P. gatehousei as a stem-group bryozoan. This aligns the origin of phylum Bryozoa with all other skeletonized phyla in Cambrian Age 3, pushing back its first occurrence by approximately 35 million years. It also reconciles the fossil record with molecular clock estimations of an early Cambrian origination and subsequent Ordovician radiation of Bryozoa following the acquisition of a carbonate skeleton10,11,12,13.

Zhang, Z., Zhang, Z., Ma, J. et al. Fossil evidence unveils an early Cambrian origin for Bryozoa. Nature (2021). https://doi.org/10.1038/s41586-021-04...

Less time for that Darwinian famous claim:

It may be said that natural selection is daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, wherever and whenever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.

The paper is open access.

You may also wish to read: Gunter Bechly on the discontinuous fossil record. Bechly: “Darwin’s doubt” did not get smaller over time but bigger, and if he were still alive, he would likely agree that the evidence simply does not add up, since he was much more prudent than many of his modern followers.

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Gunter Bechly on the discontinuous fossil record

Darwin believed strongly that evolutionary change happened gradually, a point he repeated six times in On the Origin of Species. The fact that the history of life doesn’t look that way was explained by “gaps” in the fossil record. But, says Gunter Bechly,

If the gaps and discontinuities in the fossil record were just artifacts, they should more and more dissolve with our greatly increasing knowledge of the fossil record. But the opposite is the case. The more we know, the more acute these problems have become. “Darwin’s doubt” did not get smaller over time but bigger, and if he were still alive, he would likely agree that the evidence simply does not add up, since he was much more prudent than many of his modern followers.

Günter Bechly, “The Discontinuous Fossil Record Refutes Darwinian Gradualism” at Evolution News and Science Today (November 2, 2021)

A good point. Many of the followers are just reiterating what they take to be a Truth. Patterns of evidence don’t really come into it.

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At Mind Matters News: Neuroscientist: Even viruses are intelligent in some sense

Antonio Damasio says, in the excerpt from his new book, that — based on the evidence — we cannot deny viruses “some fraction” of intelligence:

Neuroscientist Antonio Damasio says that some sort of intelligence can also we credited to viruses, in an excerpt from his recent book, Feeling & Knowing (Penguin Random House, 2021):

News, “Neuroscientist: Even viruses are intelligent in some sense” at Mind Matters News

For what it is worth, people who study and work with viruses can compare their behavior to that of insects and animals. Here’s a sample from the last twenty-five years:

1998: Coronaviruses attract attention for their “intelligence:” “Researcher teases out secrets from surprisingly ‘intelligent’ viruses”: …

2021: We are told that “Adaptation of SARS-CoV-2 virus to the immune system not purely random”:

Research shows that the emergence of mutations in SARS-CoV-2 are not purely random. Rather, the virus has repair and adaptation mechanisms in its genome that can accelerate the occurrence of particularly dangerous mutations. In the light of these findings, it appears that the most effective strategies to combat the pandemic are those that aim to achieve the lowest possible incidence rates… Systems capable of solving problems with a higher rate of success than might be expected with random processes, can indeed be called ‘intelligent’, even if the virus is not actually ‘thinking’ or ‘planning’.

News, “Coronavirus: “intelligent” mutants” at Test Biotech (25 February 2021)

So… the problem-solving systems of the virus that causes COVID can be called “intelligent” even though the virus itself is not doing any thinking? That points to an intelligence underlying or within nature that the viruses did not themselves create…

Takehome: Researchers who study viruses, including the one that causes COVID, note similarities between viral strategies and those of insects and animals.

Panpsychism is not theism (the universe was created by God). At the same time, it is not materialism, which seeks to show either that consciousness does not really exist or that it is a state of matter. The implausibility of materialism has caused many scientists to lean more toward panpsychism.

The clash between panpsychism and materialism will make for an interesting watch.

You may also wish to read:

Neuroscientist: Nervous systems alone do not cause consciousness. Antonio Damasio, author of Feeling & Knowing (2021), points to the whole body as involved in consciousness. One-celled intelligence aside, it’s unclear how Antonio Damasio’s ladder of consciousness, built on self-balancing and death avoidance, gets us the human mind.

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.

and

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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A Whole Host of Mechanisms of Directed Mutation

I’m doing a series of videos on mechanisms of directed mutations that you all may be interested in. I have trouble how there remains adherents to the modern synthesis in light of all of the data to the contrary that has come out over the last 20 years. More videos to come, too.

Biology Roughcuts

Anyway, any comments/criticisms of the video content are welcome, here or on the videos themselves. (note – I don’t care about video *quality* – these are all done live via OBS with extremely minimal preplanning).

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Jerry Coyne on Cancel Culture’s hit on medical science

Darwinian evolutionary biologist Jerry Coyne, at one time a Cancel Culture zealot himself (see the Ball State story, where Coyne himself instigated the Cancellation of Eric Hedin’s course ) is now becoming a useful source of information on the latest shutdown of civilization.

This time it’s Medspeak (courtesy American Medical Association) – insisting that physicians use only Woke terminology in describing problems. For example,:

“Advancing Health Equity: A Guide to Language, Narrative and Concepts,” a strange document that calls for doctors to insert progressive politics into even plain statements of fact…

3/ For example, the word ‘vulnerable’ is out. You’re not supposed to say “vulnerable groups,” because this doesn’t communicate progressive political beliefs. Try “Groups that have been economically/socially marginalized.”

4/ The document doesn’t have any guidelines for doctors who don’t think each and every instance of ‘vulnerability’ can be tied direcly to injusice, but that sort of seems to be the point: to expurgate any language that *could be interpreted* as anything but progressive.

Jerry Coyne, “Jesse Singal: The AMA jumps the Woke Shark, introduces Medspeak” at Why Evolution Is True (November 1, 2021)

The new terminology would make it hard for most family doctors to talk plainly about typical health issues around, say, obesity or substance abuse very clearly. One doesn’t get the impression from any of the Woke rhetoric that the patient can decide to make changes that lead to better health. Yet people in all social groups do that every day.

Anyway, Coyne is way more useful fighting this than fighting design in nature.

You may also wish to read: It begins at last… T. H. Huxley, Darwin’s bulldog, about to be Cancelled – other early Darwinists to get the chop soon, we hear. W. D. Hamilton, Ronald Fisher, and J. B. S. Haldane are also threatened. We never thought it would happen but it is happening… so fast.

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Casey Luskin on the unique origins of humanity in the fossil record

Uploaded today:

Does the fossil record prove humans developed from ape-like ancestors? Or does it reveal that humans had a unique origin? In this lecture, geologist Casey Luskin offers some surprising evidence about the fossil history of humanity.

Dr. Luskin is co-author of the book Science and Human Origins, and an editor of The Comprehensive Guide to Science and Faith.

This talk was originally offered as part of the 2021 Dallas Conference on Science and Faith sponsored by Discovery Institute.

Hat tip: Philip Cunningham

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