Michael J. Behe's Blog, page 463

Why some biologists are beginning to question the “biological species concept”

Because it hasn’t made sense for quite some time and some are beginning to notice the problem.

The problem that Hejnol sees with the whole system is that the ranks don’t mean anything specific or uniform across all groups of life. Even though species is arguably the most important rank across multiple fields of biology, there are dozens of species concepts in use — and biologists working with different groups of organisms can’t seem to agree on just one. You might think that the other end of the hierarchy would be more settled, but it wasn’t so long ago that domains simply didn’t exist — the three domains we use today (Archaea, Bacteria and Eucarya) were only proposed in 1990. At that time, the top rank was kingdom, and there were five of those; now there are at least six, though some say there should be as many as 32. Similar ambiguities plague all the taxonomic ranks in between — even those often considered to be major, distinct and unambiguous, like phyla.

Perhaps this could all be resolved if the scientific community simply agreed upon a definition for each rank, but there’s no consensus for that.

Christie Wilcox, “What’s in a Name? Taxonomy Problems Vex Biologists” at Quanta

If modern biology began with “On the Origin of Species,” many may be willing to live with chaos to protect the sacred history.

See also: A physicist looks at biology’s problem of “speciation” in humans

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Can one apply the “Goldilocks Principle” of fine-tuning to DNA structure?

From ScienceDaily:

Inspired by ideas from the physics of phase transitions and polymer physics, researchers in the Divisions of Physical and Biological Sciences at UC San Diego set out specifically to determine the organization of DNA inside the nucleus of a living cell. The findings of their study, recently published in Nature Communications, suggest that the phase state of the genomic DNA is “just right” — a gel poised at the phase boundary between gel and sol, the solid-liquid phase transition.

Think of pudding, panna cotta — or even porridge. The consistency of these delectables must be just right to be ideally enjoyed. Just as the “sol-gel” phase transition, according to the scientists, seems just right for explaining the timing of genomic interactions that dictate gene expression and somatic recombination.

“This finding points to a general physical principle of chromosomal organization, which has important implications for many key processes in biology, from antibody production to tissue differentiation,” said Olga Dudko, a theoretical biophysicist and professor in the Department of Physics at UC San Diego, who collaborated with colleague Cornelis Murre, a distinguished professor in the Section of Molecular Biology, on the study. Paper. (open access) – Nimish Khanna, Yaojun Zhang, Joseph S. Lucas, Olga K. Dudko, Cornelis Murre. Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-10628-9 More.

From what these researchers report, yes, one can definitely apply the principle. But then one must accept that biology shows evidence of design. “Just right” is rarely an accident.

See also: Carbon dioxide and the Goldilocks Principle

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A new bug for Darwin’s finches: Mating disrupted by parasite

Remember how Darwin’s finches proved Darwinism – and then the story collapsed in a heap of uncertainty about how different all those “new species” were/are?

Invasive parasites in the Galápagos Islands may leave some Darwin’s tree finches singing the blues.

c The nonnative Philornis downsi fly infests the birds’ nests and lays its eggs there. Fly larvae feast on the chicks’ blood and tissue, producing festering wounds and killing over half of the baby birds. Among survivors, larval damage to the birds’ beaks may mess with the birds’ songs when they’re older, possibly affecting their appeal to potential mates, researchers report June 12 in Proceedings of the Royal Society B. …

For medium tree finches, the deformity meant they sounded similar to a small tree finch with a healthy beak. That may explain why scientists had previously had observed female medium tree finches choosing small male tree finches as partners, instead of males from their own species. The researchers did not observe female small tree finches choosing medium tree finch mates.

Carolyn Wilke, “Parasites ruin some finches’ songs by chewing through the birds’ beaks” at ScienceNews

One evolutionary biologist predicts the “extinction” of the medium tree finch as a result. The insect is thought to have arrived in the Galapagos in about 1960.

The whole story leaves one wondering what role incidental factors played, over many centuries, in the constant, reversible micro-evolution of the once-iconic Darwin’s finches.

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See also: Epigenetics may explain how Darwin’s finches respond to environment

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Cooking with starches 100 000 years ago and more

Humans over 100,000 years ago, lived in caves along South Africa’s coastline and cooked with starches:

Small pieces of charred tubers found at the Klasies River site in South Africa date back 120,000 years, making them the earliest-known evidence of H. sapiens cooking carbs, according to recent research published in the Journal of Human Evolution…

Cynthia Larbey, an archaeologist at Cambridge University in the United Kingdom and lead author of the new study, suspects that roasting tubers provided critical nutrition to our species. “It was the way we were able to continue feeding ourselves as we moved and migrated,” she says. Hunting was difficult and unreliable, so “it was a skill to be able to find food as they moved to different ecologies.”…

“This is really a very nice find,” says Simcha Lev-Yadun, a paleobotanist at the University of Haifa in Israel. Lev-Yadun was part of the team that discovered evidence of hominins roasting nuts and tubers 780,000 years ago. Sarah Wild, “Scientists Find First Evidence of Humans Cooking Starches” at Sapiens

As cooks know, starches are much easier to keep and more versatile than meats.

The article is noteworthy for not claiming that starches explain human brain development.

See also: See also: Eating fat, not meat, led to bigger human type brains, say researchers. Theories of the evolution of the human brain are a war of trivial explanations that no one dare admit are too trivial for what they purport to explain. It’s like blaming World War II on indigestion, only monstrously bigger.

Earlier discussion of the fat theory.

Starchy food may have aided human brain development

Do big brains matter to human intelligence?

Human evolution: The war of trivial explanations

and

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Darwinism must have bypassed Chernobyl

In 2011, it was noted that Chernobyl, forbidden to humans due to radiation after the nuclear accident, had not shown signs of new species evolving by natural selection acting on random mutations (Darwinism), as hoped. But it was simply teeming with usual wildlife.

A recent article updates the theme:

Most Chernobyl Animals Don’t Look Any Different from Their Non-Chernobyl Counterparts.

Tour guides tell visitors not to pet Chernobyl animals due to potential radioactive particles in their fur, but some biologists have been surprised that the incidence of physical mutations appears lower than the blast of radiation would have suggested. There have been some oddities recorded within the area—such as partial albinism among barn swallows—but researchers think that the serious mutations mostly happened directly after the explosion. Today’s wild animals are sporting their normal number of limbs and aren’t glowing.

Claudia Dimuro, “8 Facts About the Animals of Chernobyl” at Mental Floss

Insects suffered a drop in numbers though.

See also: Is there anything city life can’t do? We are now told it is affecting evolution.

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Cells from a billion years ago remarkably preserved

And undergoing study, after northwest Scotland find:

What’s more, the microscopic fossils were preserved so remarkably that the researchers were able to see distinct cellular structures inside …

Inside the cells, Wacey and his team saw shapes called intracellular inclusions (ICIs) that could have been cytoplasmic storage granules or even distinct organelles, but the researchers couldn’t be certain.

Ross Pomeroy, “Scientists Gaze Inside 1 Billion-Year-Old Cells” at RealClearScience

Apparently, the rare minerals they take up fossilized them. Far older cells have been found but these were better preserved.

If researchers find cells in a really clear state of preservation, who will be surprised if it turns out that they are a lot like modern cells but somehow that fact doesn’t point to anything. Darwinism, after all, can just happen in the twinkling of an eye…

Paper. (open access)

See also: Researchers: Multicellular animals started out complex

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Why scientists tend to dismiss well-supported ideas that lie outside the paradigm

A science writer looks at a number of examples from physics:

“The way in which a community behaves is constructed over a long social progress, made by power structures, years of training, reward systems, rules of competition and collaboration between and within different groups,” says Roberto Lalli, research scholar at the Max Planck Institute for the History of Science. He says that history has shown that subcultures within physics—such as theoretical or particle physics—are relatively stable, and that it’s likely that places like CERN and ideas within the paradigm will continue to be considered the most plausible.

“This attitude is not only due to authority bias, but also has to do with first-hand knowledge of the internal reviewing systems within experimental groups,” Lalli said. “This creates a system of trust, which will not change in a sudden way.” Social pressures, like the continual fight for funding and university positions, also make communities more unwilling to accept those from outside the mainstream.

But a case still can, and should, be made for seeking new standards for the system. A sterling reputation can be hard to come by in a digital world, where obtaining visibility can be like shouting over a million voices, and the difficulty of the academic job market has spread talent widely beyond the most well-known institutions. Additionally, outsider ideas can help break the echo chamber that comes of only speaking to those within a relatively closed community.

Claudia Geib, “How Much Should Expectation Drive Science?” at Nautilus

The problem is that people can come to think of approved stagnation as a duty and stagnating as a virtue. Correct procedures are followed without much result and everything is fine. Maybe things simply must stay that way until a new genius comes along and shakes it all up.

But what if people find that they cannot listen to the genius in principle?

See also: Sabine Hossenfelder: Don’t Expect Too Much From New Proposals To Detect Dark Matter

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Is a 3-D printer alive?

Can information theory help us understand origin of life? A mid-length essay sponsored by the Santa Fe Institute touches on many of the main points, asking what if a 3-D printer could reproduce itself? Would that be life?

But let us look at the functional information that makes us. Some was acquired around 4 billion years ago when life got started, but most was acquired over evolutionary time. We learned how to build our bodies around 540 million years ago, and to digest cooked food maybe in the past million years. We are a bundle of information, acquired at different stages, some acquired by the bacteria in our gut, and some acquired through culture. From the lineage viewpoint, the 3D printers were always life, there was no nonlife/life transition in our thought experiment. But something did change over the course of their evolution – they acquired functional information over millions of years on Mars, and were able to use this information to do novel things – that is, they came closer to what we would call alive. It is in this sense that we might consider the 3D printers to represent new examples of alive things, each generating new possibilities for life…

Although you care deeply for your creation, your insurance company worries about the unfavourable losses if Eve ever takes over the Earth. So, you figure out a way to get your little autonomous 3D printer sent on the next mission to Mars as a stowaway. Imagine Eve has a happy existence in a hidden valley on Mars, and goes on to produce many copies of itself. Humanity discovers the valley a few million years later to find the process of evolution on 3D printers generated a wide variety of them that are quite different from your original design – small ones, big ones, blue ones, red ones, ones that hunt other 3D printers for resources, and so on.

The value of this thought experiment is that it allows us to play with the notions of life and alive. Intuitively, we feel that life emerged, or maybe that the new robots are even alive. Did the 3D printers become life? If so, at what point did they become life? Are they alive?

Michael Lachmann and Sarah Walker, “Life ≠ alive” at Aeon

Clearly, we have come a long way in thinking up new ways to explore the origin of life problem.

See also: The Science Fictions series at your fingertips – origin of life What we do and don’t know about the origin of life.

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At one time, witchcraft was considered a Halloween hoot…

Yet it is taken increasingly seriously among people we are expected to listen to:

Writing for Time.com, Pam Grossman explains, “Today, more women than ever are choosing the way of the witch, whether literally or symbolically. They’re floating down catwalks and sidewalks in gauzy black clothing and adorning themselves with Pinterest-worthy pentagrams and crystals. They’re filling up movie theaters to watch witchy films and gathering in back rooms and backyards to do rituals, consult tarot cards and set life-altering intentions. They’re marching in the streets with HEX THE PATRIARCHY placards and casting spells each month to try to constrain the commander-in-chief. Year after year, articles keep proclaiming, ‘It’s the Season of the Witch!’ as journalists try to wrap their heads around the mushrooming witch ‘trend.'”

Michael Brown, “The resurgence of the feminist witch” at Charisma News

Wait till you catch one of them also fronting the idea that we should all trust science. You can at least enjoy a sense of the ridiculous.

See also: Skeptic asks, why do people who abandon religion embrace superstition? Belief in God is declining and belief in ghosts and witches is rising

and

Which side will atheists choose in the war on science? They need to re-evaluate their alliance with progressivism, which is doing science no favours.

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But how can evolution be “wrong”?

Concluding a review of Felipe Fernández-Armesto’s Out of Our Minds: What We Think and How We Came to Think It,
philosopher John Gray writes,

Most puzzling in this fascinating compendium of ideas is Fernández-Armesto’s own idea that human imagination is an immaterial faculty. “Human intelligence,” he avers, “is probably fundamentally unmechanical: there is a ghost in the human machine.” Again, he is not the first to suggest that the human mind may not be wholly explicable in mechanical terms. Alfred Russel Wallace, the co-discoverer with Darwin of modern evolutionary theory, believed the human animal emerged via natural selection but at some point acquired higher mental powers from a non-natural source. Having studied animal minds and emotions, Darwin was horrified by Russel Wallace’s suggestion. What was at stake for Darwin was not just his own theory, which was meant to include the human mind. It was the idea of science itself, which – though he never unequivocally rejected theism – he thought meant explaining events in the world by reference to natural processes within it. Whether Fernández-Armesto rejects this idea of science is unclear.

The puzzle is deepened by his observation that most ideas are bad or wrong or both. If what makes humans unique is the power of seeing what is not there, what makes them so destructive is that they believe what they have seen to be real. Untold millions have killed and died for the sake of dreams – gods, utopias, visions of the past or future – conjured up in the imagination. The ancient Gnostics, discussed by Fernández-Armesto when he considers the origins of Christianity, believed a malignant deity or “demiurge” had consigned human beings to a lower world of ghosts and phantasms. It’s an entertaining metaphysical speculation. But perhaps we should consider the more mundane possibility that in the course of its evolution something went badly wrong with the human brain. The destructive power of ideas may have a natural explanation. There may be no ghost in the human machine, simply some crossed wires we cannot untangle.

John Gray, “The perils of the human imagination” at New Statesman

Well, it’s important to know whether there is a “ghost in the human machine” vs. “crossed wires we cannot entangle” because the ghost may be acting badly. But evolution caan’t go “badly wrong.” Ain’t no such animal.

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