Michael J. Behe's Blog, page 205
April 29, 2021
Project to map 70,000 vertebrate genomes already turning up more bad news for “junk DNA”
After only 25 genomes, along with other interesting discoveries:
The team’s improved accuracy shows that previous genome sequences are seriously incomplete. In the zebra finch, for example, the team found eight new chromosomes and about 900 genes that had been thought to be missing. Previously unknown chromosomes popped up in the platypus as well, as members of the team reported online in Nature earlier this year. The researchers also plowed through, and correctly assembled, long stretches of repetitive DNA, much of which contain just two of the four genetic letters. Some scientists considered these stretches to be non-functional “junk” or “dark matter.” Wrong. Many of the repeats occur in regions of the genome that code for proteins, says Jarvis, suggesting that the DNA plays a surprisingly crucial role in turning genes on or off.
Howard Hughes, “Project to read genomes of all 70,000 vertebrate species reports first discoveries” at ScienceDaily
Wethinks the Darwinians are going to regret junk DNA>
Also:
The new information also may boost efforts to save rare species. “It is a critically important moral duty to help species that are going extinct,” Jarvis says. That’s why the team collected samples from a kākāpō parrot named Jane, part of a captive breeding program that has brought the parrot back from the brink of extinction. In a paper published in the new journal Cell Genomics, of the Cell family of journals, Nicolas Dussex at the University of Otago and colleagues described their studies of Jane’s genes along with other individuals. The work revealed that the last surviving kākāpō population, isolated on an island off New Zealand for the last 10,000 years, has somehow purged deleterious mutations, despite the species’ low genetic diversity. A similar finding was seen for the vaquita, with an estimated 10-20 individuals left on the planet, in a study published in Molecular Ecology Resources, led by Phil Morin at the National Oceanic and Atmospheric Administration Fisheries in La Jolla, California. “That means there is hope for conserving the species,” Jarvis concludes.
Howard Hughes, “Project to read genomes of all 70,000 vertebrate species reports first discoveries” at ScienceDaily
“The work revealed that the last surviving kākāpō population, isolated on an island off New Zealand for the last 10,000 years, has somehow purged deleterious mutations, despite the species’ low genetic diversity.” Hmm.
Both of the first two papers are open access: Here and here.
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Do antimatter stars anti-twinkle?
Here’s something you won’t read every day: It’s possible, researchers report, that fourteen stars consist of antimatter:
These antistar candidates seem to give off the kind of gamma rays that are produced when antimatter — matter’s oppositely charged counterpart — meets normal matter and annihilates. This could happen on the surfaces of antistars as their gravity draws in normal matter from interstellar space, researchers report online April 20 in Physical Review D.
“If, by any chance, one can prove the existence of the antistars … that would be a major blow for the standard cosmological model,” says Pierre Salati, a theoretical astrophysicist at the Annecy-le-Vieux Laboratory of Theoretical Physics in France not involved in the work. It “would really imply a significant change in our understanding of what happened in the early universe.”
Maria Temming, “Stars made of antimatter could lurk in the Milky Way” at ScienceNews
The universe is believed to have started with equal amounts of matter and antimatter but just what happened to almost all of the latter is not currently known. In theory, as the vid below says, the universe shouldn’t exist.
Before we worry too much about the fate of the Standard Model of the universe, it’s worth noting that we are also told that it would be “extremely difficult” to prove that a star is really an anti-star. It’s mainly just an intriguing idea at this point.
The paper is open access.
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Best depiction yet of the bacterial flagellum
Which, you will recall, is not supposed to be irreducibly complex:
Released today @EMDB_EMPIAR & @PDBeurope, & published @CellCellPress, the awesome 3.9 Å #CryoEM structure of the #Flagellar #Motor-Hook complex, the molecular machine that drives rotation of the #Flagellum for #Bacterial motility by Tan et al. from @ZJU_China
— EMDB – EMPIAR @EBI (@EMDB_EMPIAR) April 28, 2021
1/2 pic.twitter.com/R4CSFd9Sdt
More visuals here.
The paper is closed access but a friend swatched these graffs to us:
“Although the flagellum has been proposed to be the evolutionary ancestor of T3SSs, the structure of the flagellar motor is significantly different from that of the T3SS basal body (Figure S7I). The rod in the basal body of the Salmonella T3SS consists of two proteins, PrgJ and PrgI, and adopts a relatively simple helical structure. In contrast to the tight contacts of the T3SS rod with the secretin channel and the inner membrane ring, the flagellar rod has few contacts with the LP ring to facilitate its high-speed rotation and torque transmission. In addition, unlike the C24-symmetric inner membrane ring assembled by PrgH and PrgK in the Salmonella T3SS, the MS ring of the flagellar motor is composed of 34 FliF subunits with mixed internal symmetries. Therefore, the flagellar motor has evolved special structural elements for bacterial motility.
The flagellar motor is a rotary engine for torsional force transmission to enable bacterial motility. In contrast, the rotation of F/V-type ATPases, another type of natural rotational machinery (Kühlbrandt, 2019), transmits torque force to induce conformational changes of the enzymatic domain for ATP synthesis or hydrolysis. The torque transmission mechanism from the rotary ring structure to the axial rod in the flagellar motor (Figure S7J) is different from that utilized by F/V-ATPases, in which the membrane-bound rotary ring forms a perpendicular surface attachment with the central stalk via salt bridges for planar-to-axial torsional force transmission. Thus, this work presents the structural basis for assembly and torque transmission of the flagellar motor and indicates the diversity of torque transmission mechanisms of natural rotary protein machineries.” Jiaxing Tan, Xing Zhang, Xiaofei Wang, Caihuang Xu, Shenghai Chang, Hangjun Wu, Ting Wang, Huihui Liang, Haichun Gao, Yan Zhou, Yongqun Zhu, Structural basis of assembly and torque transmission of the bacterial flagellar motor, Cell, 2021, , ISSN 0092-8674, https://doi.org/10.1016/j.cell.2021.0....
As more of this type of information becomes available, expect the topic of irreducible complexity to be no longer discussable. When it can’t be debunked, it can be ruled undiscussable.
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Someone finally got around to classifying science papers correctly
And of course it had to be XKCD. Here’s the first page (don’t miss the rest):

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April 28, 2021
Genetic Literacy Project tackles Critical Race Theory
Some would suggest that that’s equivalent to playing footsie with a bomb but Patrick Whittle dives in and offers a thoughtful critique of some of the overheated nonsense one can read in many science media:
If Black is not a meaningful category, why is “white”?
As Reich suggests, there is more than irony at work here. At the same time that critical race theorists and their supporters caution against “the myth of biological race,” the broad yet ill-defined racial term ‘white’ is used repeatedly — as in the SciAm article, for example: “white supremacy”, “white centering”, “white academics”, “white researchers”, “white people”.
This even extends, so the article suggests, to a “white perspective” (and a contrasting “non-white perspective”) on science and the world. Such an idea, though, is itself problematic: it implies that all white people share a single point of view, while all non-white people share another. That whiffs of race essentialism — the historically pernicious idea that each different ‘race’ has unique traits and characteristics distinguishing them from others.
A similar denial of race and yet fixation with race identity is central to modern CRT, which can be broadly defined as the belief “that race itself, instead of being biologically grounded and natural, is a socially constructed concept that is used by white people to further their economic and political interests at the expense of people of color”.
Patrick Whittle, “Is science racist? Genetics, evolutionary human differences and ‘critical race theory’” at Genetic Literacy Project
The problem with Whittle’s long, thoughtful, and informative piece is that he seems determined to be reasonable and make sense. In the age of the war on math and the war on science, the Twitter mob is the new sanity and acting out is evidence of Virtue.
Note: He offers some entertaining as well as useful information on how much the Irish were despised in the 19th century. Yes, yes, but then, “No Irish Need Apply” became a music hall hit…
See also: American Humanist Association underbuses Richard Dawkins As a reader puts it: From anti-God hero to trans-racist zero… But the thing is, who cares about the American Humanist Association without people like Dawkins?
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Why are statements about “evolution” so often just filler?
A reader draws attention to a recent media release from U South Australia positing that future drones will resemble 300 million-year-old dragonflies:
A team of PhD students led by UniSA Professor of Sensor Systems, Javaan Chahl, spent part of the 2020 COVID-19 lockdown designing and testing key parts of a dragonfly-inspired drone that might match the insect’s extraordinary skills in hovering, cruising and aerobatics…
Describing the dragonfly as the “apex insect flyer,” Prof Chahl says numerous engineering lessons can be learned from its mastery in the air.
“Dragonflies are supremely efficient in all areas of flying. They need to be. After emerging from under water until their death (up to six months), male dragonflies are involved in perpetual, dangerous combat against male rivals. Mating requires an aerial pursuit of females and they are constantly avoiding predators. Their flying abilities have evolved over millions of years to ensure they survive,” Prof Chahl says.
“They can turn quickly at high speeds and take off while carrying more than three times their own body weight. They are also one of nature’s most effective predators, targeting, chasing and capturing their prey with a 95 per cent success rate.” …
“Their long abdomen, which makes up about 35 per cent of their body weight, has also evolved to serve many purposes. It houses the digestive tract, is involved in reproduction, and it helps with balance, stability and manoeuvrability. The abdomen plays a crucial role in their flying ability.”
University of South Australia, “Future drones likely to resemble 300-million-year-old flying machine” at ScienceDaily
The paper is open access.
The reader notes that the release would read just as meaningfully if the text was shortened to “Their flying abilities ensure they survive,” Prof Chahl says.” and “Their long abdomen, which makes up about 35 per cent of their body weight, serves many purposes”.
Our philosopher and photographer friend Laszlo Bencze had a look at it and writes to say,
I have written about this issue myself several times. It’s so annoying. But the purpose of dropping these meaningless nods to evolution into articles is to dress them up as highly scientific.
Unfortunately, I think it works. If you say, “Most people prefer vanilla ice cream,” you’ve just made a trivial claim of no great significance. But if you say, “People have evolved to prefer vanilla ice cream,” well now you’ve made an insightful and fascinating statement backed by years of scientific research, no doubt about it. I’m sure that’s how most people respond to these evolution genuflections.
I know I certainly did. How could anyone make these claims unless they were backed up with rigorous studies? There had to be reams of papers, PhD theses, articles in Nature magazine for every such mention.
When I learned in 1983 from an article by Tom Bethell, published in Harper’s Magazine that there were no such studies, no not even one, I was shocked. Also I was angry at having been lied to for years. Those nods to evolution are not trivial. They are harmful in creating an aura of respectability about evolution that has no right to be there.
If an editor removed the genuflections, you can bet that the authors would be outraged and would pillory that unfortunate who would never again possess any scientific credibility. As hollow as it is, these evolution words puff up writers allowing them to believe that they are themselves, “highly scientific.” You can’t divest an author of such profound power without severe repercussions.
Well, if they can’t have the cattle, they are going to insist on the Big Hat, right?
Bethell noted the same tendency in Darwinian language in 2005:
That phrase–”it was selected for”–is regarded as a sufficient explanation for . . . everything. The same mundane phrase is given as the explanation for everything under the sun. How did the bats get sonar? “It arose by an accidental mutation of the genes and was selected for. Next question?” How did the eye develop? “Piecemeal. There was a random mutation and it conferred an advantage so it was selected for. Then the same thing happened over and over again. Next question?” How did the camel get its hump? “Random mutations conferred some advantage and so they were selected for. Next question?”
Tom Bethell, “Don’t Fear The Designer” at National Review (December 1, 2005)
We should write more parodies of that stuff, really. Anyone have friends at the Babylon Bee.
Presumably the ancient dragonfly was something like this:
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Interesting finding: COVID-19 populations show high convergent evolution
A paper on SARS-CoV-2 sequencing around the globe reports:
We find that two particular mutation rates, G →U and C →U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. While previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
Nicola De Maio, Conor R Walker, Yatish Turakhia, Robert Lanfear, Russell Corbett-Detig, Nick Goldman, Mutation rates and selection on synonymous mutations in SARS-CoV-2, Genome Biology and Evolution, 2021;, evab087, https://doi.org/10.1093/gbe/evab087
The paper is open access.
Evolution appears to converge on goals—but in Darwinian terms, is that possible?
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April 27, 2021
Scientist says philosophy helps with science thinking
Rasha Shraim had taken an undergrad degree in biology and philosophy:
… my study of formal logic turned out to be very helpful in my transition from a wet-lab undergraduate scientist to a computational scientist on my master’s programme as I learnt coding languages, which involve elements such as logical operators and if-then reasoning. It also helped me to understand inference, the process of arriving at conclusions from evidence and reasoning. None of my science classes has formally taught the difference between induction (these frogs are all from this pond and they are all green: therefore all of the frogs in the pond are green) and deduction (all frogs in this pond are green and this frog is from this pond: therefore this frog is green), nor have any of them taught how to methodically evaluate arguments. Reading, studying and evaluating philosophical arguments as premises and conclusions has shaped my ability to scrutinize evidence and conclusions in research reports.
Rasha Shraim, “How philosophy is making me a better scientist” at Nature (April 23, 2021)
This is a far cry from Stephen Hawking’s famous denunciation of philosophy in 2011 as “dead” because it was out of step with theoretical physics. From Cardiff U philosopher Christopher Norris at Philosophy Now:
This brings us back to the point likely to provoke the most resistance from those scientists – chiefly theoretical physicists – who actually have the most to gain from any assertion of philosophy’s claim to a hearing in such matters. It is that scientists tend to go astray when they start to speculate on issues that exceed not only the current-best observational evidence but even the scope of what is presently conceivable in terms of testability. To speak plainly: one useful job for the philosopher of science is to sort out the errors and confusions that scientists – especially theoretical physicists – sometimes fall into when they give free rein to a speculative turn of mind. My book Quantum Theory and the Flight from Realism found numerous cases to illustrate the point in the statements of quantum theorists all the way from Niels Bohr – a pioneering figure but a leading source of metaphysical mystification – to the current advocates (Hawking among them) of a many-worlds or ‘multiverse’ theory. To adapt the economist Keynes’ famous saying: those scientists who claim to have no use for philosophy are most likely in the grip of a bad old philosophy or an insufficiently thought-out new one that they don’t fully acknowledge. (2011)
Yes. Most of the denunciators could have used some philosophy themselves.
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Rob Sheldon offers some thoughts on Richard Dawkins getting canceled by the American Humanist Association
Our physics color commentator Rob Sheldon recalls,
Dawkins was part of the cancel culture 30 years ago “Christianity is like smallpox only harder to eradicate”. So the fact that the cancel culture turns on its own, is not surprising. Indeed, since anything Dawkins said in his 60 year career is fair game, cancel culture cancels everything, including itself. Soon we will see people being cancelled for having cancelled in the past. When, like the French Revolution, the pace of rolling heads reaches a climax, the whole affair will be over with some authoritarian in charge again. It is, as some political scientists argue, the reason democracies are never stable.
Maybe Cancel Culture is a cancer in society. Unable to stop, it metastasizes until it dies along with its victim. Who or what then will Cancel the American Humanist Association? Is there some reason they should be among the few survivors?
See also: Dawkins deplatformed by American Humanist Association — but who still retains AHA awards?
Soave: “The AHA gave Humanist of the Year awards to the author and activist Alice Walker—who promoted anti-Semitic conspiracy theories—and also to Margaret Sanger, the founder of Planned Parenthood who promoted eugenics and white supremacy. Sanger’s legacy is so complicated that her own organization is currently disowning her.” Apparently, Rebecca Goldstein and Steven Pinker, also AHA award winners, have written an open letter, asking the AHA to reverse course.
American Humanist Association underbusses Richard Dawkins As a reader puts it: From anti-God hero to trans-racist zero… But the thing is, who cares about the American Humanist Association without people like Dawkins?
and
Planned Parenthood now denouncing Margaret Sanger — a bit late maybe. Cancel Culture is basically fascism,, tweeted. But the way Darwinism and Social Darwinism sponsored racism — because in that scheme of things, someone always needs to be the lesser human — should have been dealt with a long time ago. There are certainly plenty of other reasons for doubting Darwin and denouncing Sanger today.
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Planned Parenthood now denouncing Margaret Sanger — a bit late maybe
Maybe she’s like an old queen bee who, having done her work, gets killed or kicked out:
Black pro-life leaders condemned Planned Parenthood’s “hollow” denunciation of Margaret Sanger after Planned Parenthood President Alexis McGill Johnson distanced the organization from Sanger’s “association with white supremacist groups and eugenics.”
Human Coalition vice president Benjamin Watson, a former NFL athlete, said Sunday that Planned Parenthood’s denunciation of its founder rang “hollow” in light of the organization’s current work…
“I am glad that Alexis McGill Johnson is finally acknowledging what many black leaders have said for decades — Margaret Sanger harbored racist and eugenicist views,” Human Coalition Action Executive Director Rev. Dean Nelson said in a statement. “The problem with Margaret Sanger is more than just her ‘association’ with white supremacist groups and eugenics, it’s the implementation of those views in creating the largest abortion provider in America targeting people of color.”
Mary Margaret Olohan, “Planned Parenthood’s Denunciation of Founder Rings ‘Hollow’ to These Black Pro-Life Leaders” at The Stream
Some relevant facts about Planned Parenthood and Black Americans:
“According to recent Centers for Disease Control (CDC) statistics, while African-Americans constitute 32.2 percent of Georgia’s population, 62.4 percent of abortions in Georgia are performed on African-American women. By contrast, whites constitute 60.8 percent of the Georgia population, but only 24.7 percent of abortions were performed on white women. Even pro-abortion groups like the Guttmacher Institute admit that “black women are more than 5 times as likely as white women to have an abortion.” – Arthur Goldberg, “Abortion’s Devastating Impact Upon Black Americans” at Witherspoon Institute (February 11, 2019)
Abortion is also made easy for Black American women: “Eighty percent of Planned Parenthood’s abortion clinics are within easy walking distance of minority neighborhoods and 60 percent are in minority zip codes.” – Carol M. Swain, First Things, (February 5, 2021)
News, “Is there bias in terms of which babies are aborted?” at Mind Matters News
Some, like Politico’s Bill Scher, hope to explain it away using “isms”/“-ists”:
He waves off her embrace of eugenics (quoting historian Thomas C. Leonard) because it was “mainstream; it was popular to the point of faddishness; it was supported by leading figures in the still-emerging science of genetics; it appealed to an extraordinary range of political ideologies, not least to the progressives.” So, yes she was “ableist,” but not racist!
Wesley J. Smith, “Planned Parenthood Founder Margaret Sanger Boosted Racism by Embracing Racists” at National Review
Such defenses are not consistent with the things Sanger actually said and did. But never mind. In a Woke environment, Sanger’s guilt or innocent will not be decided on conventional grounds anyway. The question is, would it be better for Woke politics to dump or defend her? Dump won, it seems.
Smith puts it like this: “Sanger enabled racists. Sanger gave them respectability. Sanger befriended them. Sanger viewed them as valued colleagues. Her wicked social Darwinism would have had a devastating and disproportionate impact on minority communities.”
The situation is strikingly similar to what we find with Darwin’s racism. Darwin and his colleagues and followers made racism “scientific” and, in turn, they have always been largely exempted from the current pushback. But now, if it’s not working for Sanger, maybe the magic dust on others is also wearing thin…
Note: Cancel Culture is basically fascism, tweeted. But the way Darwinism and Social Darwinism sponsored racism — because in that scheme of things, someone always needs to be the lesser human — should have been dealt with a long time ago. There are certainly plenty of other reasons for doubting Darwin and denouncing Sanger today.
See also: American Humanist Association underbuses Richard Dawkins. As a reader puts it: From anti-God hero to trans-racist zero… But the thing is, who cares about the American Humanist Association without people like Dawkins?
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