Michael J. Behe's Blog, page 148

Scientists’ reaction to ever more of the cell’s complexity in its own environment

In mind-boggling detail:

For a few weeks in 2017, Wanda Kukulski found herself binge-watching an unusual kind of film: videos of the insides of cells. They were made using a technique called cryo-electron tomography (cryo-ET) that allows researchers to view the proteins in cells at high resolution. In these videos, she could see all kinds of striking things, such as the inner workings of cells and the compartments inside them, in unprecedented detail. “I was so overwhelmed by the beauty and the complexity that in the evenings I would just watch them like I would watch a documentary,” recalls Kukulski, a biochemist at the University of Bern, Switzerland.

In recent years, imaging techniques such as cryo-ET have started to enable scientists to see biological molecules in their native environments. Unlike older methods that take individual proteins out of their niches to study them, these techniques provide a holistic view of proteins and other molecules together with the cellular landscape. Although they still have limitations — some researchers say that the resolution of cryo-ET, for example, is too low for molecules to be identified with certainty — the techniques are increasing in popularity and sophistication. Researchers who turn to them are not only mesmerized by the beautiful images, but also blown away by some of the secrets that are being revealed — such as the tricks bacteria use to infect cells or how mutated proteins drive neurodegenerative diseases such as Parkinson’s.

Diana Kwon, “The secret lives of cells — as never seen before” at Nature (October 26, 2021)

No wonder panpsychism is catching on, among those who are forbidden to think in terms of design.

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Free index to world’s research papers a boon to vast literature searches

About time, too:

In a project that could unlock the world’s research papers for easier computerized analysis, an American technologist has released online a gigantic index of the words and short phrases contained in more than 100 million journal articles — including many paywalled papers. The catalogue, which was released on 7 October and is free to use, holds tables of more than 355 billion words and sentence fragments listed next to the articles in which they appear. It is an effort to help scientists use software to glean insights from published work even if they have no legal access to the underlying papers, says its creator, Carl Malamud. He released the files under the auspices of Public Resource, a non-profit corporation in Sebastopol, California that he founded.

Holly Else, “Giant, free index to world’s research papers released online” at Nature 26 October 2021

Malamud isn’t breaching copyright, he says, because his quotations are only five words or so. In the article, Else warns that publishers might question how he could have created the index in the first place.

Some of us are left wondering why, iogven that the public generally pays for science, the public isn’t allowed to read it for free.

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At Mind Matters News: Why just anything can’t happen given an infinite sum of universes

Baylor engineering prof Robert J. Marks says, we can figure out why, using simple mathematical reasoning in this universe:

Can anything happen if there are an infinite number of universes each with an infinite number of possibilities in each? Can you be bald in one universe and fully haired in another? Can you have two eyeballs in this universe and three in another? The answer is no. In a nutshell, the reason is that some infinities are bigger than other infinities. (And this is not a claim like infinity plus one is bigger than infinity. Infinity plus one is still infinity.)

The number of points on a line segment from, say zero to one, is a bigger infinity than the number of counting numbers {1,2,3,…}. We can label the infinite number of universes in the multiverse as universe #1, #2, #3, etc. Because they can be counted, this infinity is said to be countably infinite. This looks to be the smallest infinity. (“Smallest infinity” sounds like an oxymoron but isn’t.) And, no, true infinity is not the same as the symbol ∞. In mathematics, ∞ typically means “increasing without bound.” And no matter how high you count, you still have infinity to go.

Robert J. Marks, “Why just anything can’t happen given an infinite sum of universes” at Mind Matters News

By now, you can guess where this is heading, re claims about a multiverse: to Hilbert’s infamous Hotel:

Infinity is conceptually weird. Assuming that it is a reality leads to absurdities as illustrated by Hilbert’s hotel. Hilbert’s hotel has an infinite number of rooms labeled 1,2,3, etc. There is no vacancy in the hotel. All the rooms are occupied. Nevertheless, a room can be made available by moving the lodger in room 1 to room 2, the lodger in room 2 to room 3, 3 to 4, etc. Doing so leaves room 1 unoccupied for a new guest. In Hilbert’s hotel, there is literally always room for one more.

In fact, a hundred rooms can be vacated in Hilbert’s fully occupied hotel. Move the occupant of room 1 to room 101, the occupant of room 2 to 102, 3 to 103, etc. Doing so vacates the first 100 rooms.

But here’s the real surprise. A countably infinite number of rooms can be vacated in Hilbert’s fully occupied hotel. Every occupant looks at their room number, doubles it, and moves to that room. So room 1’s occupant is moved to room 2, room 2’s occupant is moved to room 4, room 3 to room 6, 4 to 8, etc. This leaves all of the odd numbered rooms, (1,3,5,…), empty so Hilbert’s hotel, despite being totally full, can still accept a countably infinite number of new guests! More.

Takehome: It can be shown mathematically that the infinite does not exist in reality, only in our minds. Thus an infinite number of universes cannot exist.

You may also wish to read:
Yes, you CAN manipulate infinity — in math. The hyperreals are bigger (and smaller) than your average number — and better! Hyperreal numbers are a new type of number that was developed to simplify and rethink the way that we deal with very large and very small numbers. It reduces the complexity of the task and allows us to use our well-honed high-school algebra skills to solve complex problems easily. (Jonathan Bartlett)
and
The jump of Chaitin’s Omega number Gregory Chaitin explains, “For any infinity, there’s a bigger infinity, which is the infinity of all subsets of the previous step.” Chaitin tells us, “In the mathematics that I would say is discovered not invented, you feel you’re touching a reality beyond normal reality.”

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It begins at last… T. H. Huxley, Darwin’s bulldog, about to be Cancelled – other early Darwinists to get the chop soon?

At Western Washington University. Darwinian evolutionary biologist Jerry Coyne has the story: (with Imperial College London also poised to Cancel)

Over at Western Washington University (WWU) in Bellingham, WA, 19th-century biologist Thomas Henry Huxley is poised for cancellation in December, for the administration has contemplated (and will surely enact) changing the name of its well known Huxley College of the Environment, listed as one of the Unversity’s “notable degree programs“. In an ill-conceived, erroneous, and poorly written critique of Huxley as a racist, a document on the website of the President of WWU made the case to rename the college. (A better case for renaming was that Huxley really didn’t have anything to do with WWU, but if the name’s there, presumably there was a reason—possibly to honor the man.)

The case for cancelling Huxley is weak, and vanishes when you take into account the good he did. Later in his life he was an abolitionist, reformer of education, and a lecturer on science to working people, as well as a crack scientist. You can read my pieces pieces on Huxley and WWU here, here,  and especially  which links to Nick Matzke’s terrific defense of Huxley and critique of WWU’s shameful and ignorant cancellation.

Jerry Coyne, “T. H. Huxley about to be cancelled at Imperial College London” at Why Evolution Is True (October 27, 2021)

 

W. D. Hamilton, Ronald Fisher, and J. B. S. Haldane are likewise threatened.

The Cancellers are, of course, protesting that they do respect free speech… Coyne isn’t buying it.

We never thought it would happen but it is happening… so fast.

A couple of notes on the fly:

Can Darwin really survive Cancel Culture when all his messengers are Unpersons?

Coyne’s defense of Thomas Henry Huxley (1825–1895) as not really racist and on account of all the good he did is ham-handed. First, Huxley was really racist. Almost all educated Brits were in those days, more or less. The environment of the Empire on which the Sun Never Set and America rising!, encouraged that vice. If the Woke succeed in Cancelling it all, there will be little left of English-speaking culture. Maybe that’s a feature, not a bug…

Second, for heaven’s sakes, the Woke don’t care about “good.” They need a level playing field in which to safely enjoy the rewards of mediocrity, with no expectation of achievement other than obedient Correctness. That’s all they can aspire to. Racism is their battering ram.

They use that ram because it works. Look how many True Believers in Darwin’s and Huxley’s message just surrendered. Coyne had better get used to fighting alone and becoming the victim of vile, false aspersions.

Third, the decision of the big Darwin-in-the-Schools lobby, the National Council for Science Education, to go big into anti-climate change politics was prescient. So far, anything barked in the name of opposing climate change is likely to be safe. If they have to, they can denounce Darwin too and still keep their funding – to fight climate change, mainly.

And lastly, of course, the Darwinists themselves helped create and maintain the culture in which they now squirm. Given the circumstances, we’d even help them – if we could. We warned them a long time ago to take the racism seriously while rational discussion was still possible. But they sneered.

Story developing…

You may also wish to read: Darwin reader: Darwin’s racism

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Flim flam? Flash in the pan? Paleontologists find “possible” dinosaur DNA from 125 million years ago

Almost Jurassic:

A team has extracted what could be DNA molecules from a 125-million-year-old fossil dinosaur, according to a study published last month (September 24) in Communications Biology. But other experts have voiced caution or outright skepticism about the findings…

In the new study, paleontologists from the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) of the Chinese Academy of Sciences and Shandong Tianyu Museum of Nature extracted and decalcified femur cartilage from a 125-million-year-old Caudipteryx dinosaur, which lived in the Jehol Biota—in what is now the coastal province of Liaoning in northeast China—during the Early Cretaceous period.

Chloe Tenn, “ Paleontologists Find Possible Dinosaur DNA” at The Scientist (October 26, 2021)

The oldest extant DNA is from a 1 million-year-old woolly mammoth.

Paleogeneticist Love Dalén from the Centre for Palaeogenetics in Sweden was part of the team that extracted million-year-old mammoth DNA. He calls the notion of DNA enduring in dinosaur remains almost “impossible,” adding in an email to Gizmodo, “We know from both massive empirical studies and theoretical models that even under completely frozen conditions, DNA molecules will not survive more than ca 3 million years.”

Chloe Tenn, “ Paleontologists Find Possible Dinosaur DNA” at The Scientist (October 26, 2021)

Maybe file under: Wouldn’t THAT be fun?

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Wokeness isn’t new: Apparently there was such a thing as Marxist astronomy

At least for Dutch astronomer Anton Pannekoek (1873–1960) , also a Marxist thinker, and council communist:

In the many drawings that Dutch astronomer, Marxist thinker, and council communist Antonie (“Anton”) Pannekoek (1873–1960) made of the Milky Way over the course of his life, it is not immediately clear what we are looking at. The band of stars appears like a smudged backbone, sometimes in “true” colour (white stars on a black background), and sometimes inverted, with the stars as dark points and the “milk” of the Milky Way made inky. They are simultaneously vague and precise — something between a charcoal rubbing and an X-ray.

In fact, the drawings are not technically of the Milky Way at all, because according to Pannekoek, such a thing was not actually accessible as a purely objective entity. While it was widely understood in Pannekoek’s time that even highly-skilled astronomers fall prey to observational bias during stargazing (a phenomenon known as “the personal equation”), Pannekoek went further, theorising that what we perceive as the Milky Way is actually a visual trick that emerges at the intersection of the stars and the people on earth who perceive them. During an article published in an 1897 issue of Popular Astronomy, Pannekoek discussed the well-known problem of the Milky Way’s ocular inconsistency, wondering if “the character of the galactic phenomenon precludes its being fixed by delineation”.2 This was not just a failing of observational science; it reflected what the Milky Way actually was: a kind of optical illusion that changed its shape depending on the lived experiences of the observer, their historical period, and how these experiences informed the patterns that the mind constructed out of the fluid nature of reality. Pannekoek’s drawings, then, are of the act of perception itself — an approach informed by his political beliefs.

Like Marx and Engels — who drew on Feuerbach, Hegel, and Heraclitus — Pannekoek understood material reality to be a “continuous and unbounded stream in perpetual motion”.3 He also believed that the human brain had a tendency to generate fixed, abstract patterns from this fluidity, patterns that are always socially and historically contingent.

Lauren Collee, “Marxist Astronomy: The Milky Way According to Anton Pannekoek” at Public Domain Review (October 27, 2021)

Pannekoek would have been a stalwart, had he lived in our day, in the war on math.

You may also wish to read: Further dispatches from the war on math (September 14, 2021) Discussions of social policy where math is relevant can be useful. But a student who does not understand how an equation works will fail at both math AND social policy.

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New animated short on the origin of life is a lot of fun

10:17 min. Here’s an interview by Eric Anderson with Rob Stadler, who helped create the vid:

Today’s episode of ID the Future spotlights a new origin-of-life video showing that researchers aren’t anywhere close to creating life from non-life, despite the fact most Americans seem to believe otherwise. In the episode, host Eric Anderson interviews Stairway to Life co-author Rob Stadler, who helped create the latest Long Story Short animated video. Stadler and Anderson explore how origin-of-life papers and popular media reports have misled the public, evidenced by a survey underscored by Rice University synthetic organic chemist James Tour.

Jonathan Witt, “New Animated Video Dismantles Origin-of-Life Hype” at Evolution News and Science Today

Here’s the podcast (22:58 min)

Here are other episodes in the Long Story Short shorts series.

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The Big Bang of flowers, 50–100 million years ago

A new open-access paper discusses the “explosive boost” — massive changes generated by angiosperms (most flowering plants):

Biodiversity today has the unusual property that 85% of plants and animal species live on land rather than in the sea, and half of these in tropical rainforests. An explosive boost to terrestrial diversity occurred from ca. 100–50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their (1) flowers and efficiencies in reproduction, (2) coevolution with animals, especially pollinators and herbivores, (3) photosynthetic capacities, (4) adaptability, and (5) ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

Benton, M.J., Wilf, P. and Sauquet, H. (2021), The Angiosperm Terrestrial Revolution and the origins of modern biodiversity. New Phytologist. Accepted Author Manuscript. https://doi.org/10.1111/nph.17822 (October 26, 2021)

From the concluding portion:

In sum, despite several outstanding and data-rich examples such as the PETM, the data are far Angiosperm evolution from the Early Cretaceous onward seems to have driven the diversification of life on land in four ways: (1) ongoing evolutionary radiations of hugely diverse lineages with a dizzying variety of structural, chemical, vegetative, and reproductive novelties providing niche opportunities; (2) pollinator and herbivore opportunities often through intricate plant-animal mutualistic relationships, with cascading biodiversity effects through the food web; (3) increased productivity allowing for a greater flux of energy into the fauna; and (4) increasing the geographic extent of wet tropical biomes through their hydrological effects. Therefore, many insect groups owed their biodiversity boost to eating plant parts, pollinating flowers, or preying on the insects that did so. Others, such as fungi, liverworts, ferns, frogs, and angiosperms themselves benefited from new habitats in expanding angiosperm-dominated everwet tropical forests. Angiosperm innovations continue to the present day with ongoing evolutionary radiations, as shown by the Neogene expansion of important biomes such as seasonal tropical forests, temperate forests, and grasslands.Preceding and underlying all these physiological and ecological changes, angiosperms underwent genomic revolutions that enabled them to diversify and evolve in different ways from other plants, as a consequence of new pathways through whole genome duplication and post-polyploidization diploidization. It is not just that angiosperms are species-rich, but many individual angiosperm families show more morphological variety than all other seed plants combined, a distinction that reflects the dynamics of their genomes.

An episode we never heard before from the history of life. Is this the new Cambrian Explosion?

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Useful reflections on the Cancel Culture everyone faces now

Including self-Cancelation. Used to just be ID types and some others who knew about this stuff up close:

Cancel culture operates on at least three different levels: the personal, the corporate, and the political. Each is more troubling than the next, because each casts a broader net and eliminates more and more options. It’s one thing for me to cancel my Twitter account after being attacked as morally obtuse, worse to be permanently kicked off the site because its moderators have decided I am beyond redemption, and more troubling still to have the government shut down Twitter because it allowed my awful speech.

It’s tempting to single out that last level because the other two involve individuals or private entities who ultimately should be free to do whatever they want. Only the government can engage in true censorship, surely. But the three layers work synergistically to increase the cultural and political regulation of thought and expression. To build as free and open a society as possible, we need to challenge the precepts of cancel culture at all levels…

Nick Gillespie, “Self-Cancellation, Deplatforming, and Censorship” at Reason (September 7, 2021)

and self-Cancelation?

Self-cancellations, in which individuals take the initiative to put themselves out of the public’s misery, are in many ways the purest manifestation of cancel culture, because they reveal the religious-cum-totalitarian sensibility undergirding the process. From the Spanish Inquisition through Mao’s struggle sessions, it wasn’t enough simply to damn the accused. The goal was to make them testify to their moral and ideological failings, to show they were “doing the work” and owning their sins. This move was on display when the banjoist for the fading hipster-retro band Mumford & Sons announced in March that he “was taking time away from the band to examine [his] blindspots” after he unforgivably endorsed a book that purports to unmask “antifa’s radical plan to destroy democracy.” Winston Marshall’s crime was to tweet “Finally had the time to read your important book. You’re a brave man” at the controversial journalist Andy Ngo, whose Unmasked spent time on the New York Times bestseller list and is still available for purchase at Amazon, the new arbiter of what is and isn’t hate speech. “I have offended not only a lot of people I don’t know,” wrote Marshall, “but also those closest to me, including my bandmates and for that I am truly sorry.” I’ll come back to Marshall, who announced in June that he was leaving Mumford & Sons for good. For now, let’s just note that when he apologized for his wrongthink, he felt a need to insist he was not just sorry, but truly sorry.

Nick Gillespie, “Self-Cancellation, Deplatforming, and Censorship” at Reason (September 7, 2021)

Baring your throat to the wolf is not really a good survival tactic.

The incidents are also distracting from more serious threats to freedom of expression, particularly the continuous narrowing of acceptable discourse on social media platforms such as Twitter and Facebook and shopping platforms such as Amazon and eBay. After the Dr. Seuss Foundation made its announcement, for instance, Amazon and eBay quickly banned sales of used copies of the canceled Seuss books, the sort of prohibition more commonly applied to Nazi memoribilia. What kind of simulation are we living in where Mein Kampf is easier to purchase than McElligot’s Pool?

Nick Gillespie, “Self-Cancellation, Deplatforming, and Censorship” at Reason (September 7, 2021)

Oh, that’s easy to answer. It will be as fully an authoritarian culture as the Third Reich but with different authoritarians in charge. And that’s the way Cancel Culture supporters want it.

You may also wish to read: Berkeley Scientist and center director resigns over MIT’s deplatforming of exoplanet scientist Note how little difference facts of science make in these matters — whether Abbot has anything to say that contributes to our knowledge does not matter of the Woke are displeased. Darwinism was the original Wokeness in science — immune to fact-based critique. The people who thought that that didn’t concern them are now formally wrong. It’s everywhere now.

Science always loses in these wars because a high proportion of important new ideas are misunderstood or controversial. Perhaps actual science will only survive on the fringes.

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Insect parasite replaces fish’s tongue — and it all works

The tongue-eating louse is the only known parasite to completely replace an organ in another animal:

An unknown person working at Galveston Island Sate Park, Texas Parks and Wildlife, has posted a picture of a unique fish that was caught at the park on Facebook—it has no natural tongue. Instead, it has a tongue made up of a group of parasites known as a tongue-eating louse. In the picture, the fish is held up to the camera with its mouth wide open showing the strange foreign ‘tongue’ inside …

It makes its way into the fish’s mouth through its gills—only the female replaces the tongue, while the males remain in the gills. He also notes that until now, he had never seen it in an Atlantic croaker. He adds that the louse is the only known parasite to completely replace an organ in another creature. Oddly, the new tongue does not seem to harm the fish, or the people who may catch it, though it is not known what would happen if a person were to eat the parasitic tongue. Fisher notes that not enough research has been done on the parasite to understand how it pulls off such a feat. Prior research has shown that the parasite does not survive by eating the food taken in by the fish but instead consumes the mucus that forms on the inside of the fish’s mouth.

Bob Yirka, “Parasite that replaces a fish’s tongue caught at Texas state park” at Phys.org (October 26, 2021)

The takehome point is that devolution (shedding independent characteristics in order to survive, perhaps symbiotically) leads the history of life forms down some strange paths.

You may also wish to read: Devolution: Getting back to the simple life.

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