Michael J. Behe's Blog, page 585

Lysenko: The risks of politicizing science

Debate rages about whether scientists should get political. This story crossed the desk, and it might be food for thought: From Ian Goodwin and Yuri Trusov at the Conversation:

By the late 1920s, as director of the Lenin All-Union Academy of Agricultural Sciences, Vavilov soon amassed the largest seed collection on the planet. He worked hard, he enjoyed himself, and drove other eager young scientists to work just as hard to make more food for the people of the Soviet Union.

However, things did not go well for Vavilov politically. How did this visionary geneticist, who aimed to find the means for food security, end up starving to death in a Soviet gulag in 1943?

nter the villain, Trofim Lysenko, ironically a protégé of Vavilov’s. The notorious Vavilov-Lysenko antagonism became one of the saddest textbook examples of a futile effort to resolve scientific debate using a political approach.

We more or less know the Lysenko story, hauntingly recounted by Goodwin and Trusov:

In reality, Lysenko was what we might today call a crackpot. Among other things, he denied the existence of DNA and genes, he claimed that plants selected their mates, and argued that they could acquire characteristics during their lifetime and pass them on. He also espoused the theory that some plants choose to sacrifice themselves for the good of the remaining plants – another notion that runs against the grain of evolutionary understanding.

Pravda – formerly the official newspaper of the Soviet Communist Party – celebrated him for finding a way to fertilise crops without applying anything to the field.

None of this could be backed up by solid evidence. His experiments were not repeatable, nor could his theories claim overwhelming consensus among other scientists. But Lysenko had the ear of the one man who counted most in the USSR: Joseph Stalin. More.

A perennial historical illusion is that if we were there, we would have seen through it all. Don’t be so sure. Ideologically, Lysenko was just the ticket.  He said what cool people wanted to believe.

Inviting the politician into the lab is one thing; safely ejecting him is another.

See also: New Scientist: EU green energy policies make global warming worse.

Geologist on why a scientists’ march on Washington is a bad idea

and

March for Science in Boston: Geek sign language to ponder

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Discovery of 7 times higher complexity of protein folding!

Can protein folding complexity be formed by stochastic processes? With 14 intermediate steps?

JILA Team Discovers Many New Twists in Protein Folding

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .

They fold into three-dimensional shapes that determine their function through a series of intermediate states, like origami. Accurately describing the folding process requires identifying all of the intermediate states.

The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.

“The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”

“If you miss most of the intermediate states, then you don’t really understand the system,” he said.

Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.

Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. 2017. H. Yu, M.G.W. Siewny, D.T. Edwards, A.W. Sanders and T.T. Perkins. Science. March 3. Vol. 355, Issue 6328, pp. 945-950, DOI: 10.1126/science.aah7124

Pulling apart protein unfolding

Elucidating the details of how complex proteins fold is a longstanding challenge. Key insights into the unfolding pathways of diverse proteins have come from single-molecule force spectroscopy (SMFS) experiments in which proteins are literally pulled apart. Yu et al. developed a SMFS technique that could unfold individual bacteriorhodopsin molecules in a native lipid bilayer with 1-µs temporal resolution (see the Perspective by Müller and Gaub). The technique delivered a 100-fold improvement over earlier studies of bacteriorhodopsin and revealed many intermediates not seen before. The authors also observed unfolding and refolding transitions between intermediate states.

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Maybe the speed of light isn’t constant?

From Stuart Clark at New Scientist:

The universe’s ultimate speed limit seems set in stone. But there’s good reason to believe it might once have been faster – and may still be changing now

Light’s constant, finite speed is a brake on our ambitions of interstellar colonisation. Our galaxy is 100,000 light years across, and it is more than four years’ light travelling time even to Proxima Centauri, the closest star to the sun and home, possibly, to a habitable planet rather like Earth. More.

Oddly, such a position was once widely derided as a young Earth creationist one.

It’s getting harder to be a respectable bigot these days. Just pounding the lectern in favor of a rock hard position and dumping insults on anyone who disagrees…

See also: Loophole in laws of physics enables light speed to increase?

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Astronomy text that privileges fine-tuning over flap doodle?

Avoiding flap doodle is becoming important today. We are living in an age of well-funded fake physics (space aliens could be hiding in dark matter and such). At the end of the day one would want to learn something…

A friend says that Luke Barnes’s A Fortunate Universe: Life in a Finely-Tuned Cosmos is a good resource:

Over the last forty years, scientists have uncovered evidence that if the Universe had been forged with even slightly different properties, life as we know it – and life as we can imagine it – would be impossible. Join us on a journey through how we understand the Universe, from its most basic particles and forces, to planets, stars and galaxies, and back through cosmic history to the birth of the cosmos. Conflicting notions about our place in the Universe are defined, defended and critiqued from scientific, philosophical and religious viewpoints. The authors’ engaging and witty style addresses what fine-tuning might mean for the future of physics and the search for the ultimate laws of nature. Tackling difficult questions and providing thought-provoking answers, this volumes challenges us to consider our place in the cosmos, regardless of our initial convictions. More.

Are students allowed to read it?

See also: 2016 worst year ever for “fake physics”?

and

Copernicus, you are not going to believe who is using your name. Or how.

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Kingdom of Speech: But is Everett wrong about Piraha?

Noel Rude, a specialist in native American languages,wrote to offer some thoughts on Tom Wolfe’s takedown of Noam Chomsky’s language theories in The Kingdom of Speech. Chomsky’s theories dominated linguistics for decades. His progressive politics, which were, strictly speaking, irrelevant to his work are often considered to play a role in his prominence.

Along the way, he clashed with linguist Daniel Everett who had, with an inexcusable lack of political correctness, found an apparent exception to Chomsky’s theories in a remote Brazilian language, Piraha.

Wolfe chronicles the conflict from both sides, making clear that current theories about the origin of human language are not useful.

Here is the perspective of Noel Rude, an ID-friendly linguist (a specialist in native American languages):

It’s been a bit since Tom Wolfe’s delightful book debuted, so maybe a few negative observations won’t detract. Wolfe, as I’ve said, describes the reaction of the literati to the present stand-off between Noam Chomsky and his most vociferous critics. In the Sixties and Seventies it was de rigueur to say that we are all alike–Noam Chomsky’s universal grammar fit that bill. Now it is politically correct to say that the only thing we share is that we differ–which is essentially what Daniel L. Everett claims.

Wolfe compares Chomsky to Charles Darwin and Everett to Alfred Russel Wallace. The comparison is apt. Chomsky is no field worker whereas Everett exudes the aura.

But Wallace, as Wolfe shows, had second thoughts about a materialistic theory of evolution whereas Darwin never did. Chomsky and Everett, on the other hand, each have had second thoughts.

Chomsky started out a Darwin doubter (see Chomsky 1959, 1966, 1968; Denton 2016) but now embraces Darwinian gradualism (see Berwick & Chomsky 2016). Daniel L. Everett has moved from Christian missionary to full blown atheist.

Chomsky emphasized the unique creativity of all human languages. For him language is innate (biologically so if questioned on the matter). There is, therefore, a universal grammar. Children learn to speak regardless of “the poverty of the stimulus.” Steven Pinker agreed, but challenged Chomsky on Darwin. Now, sadly, Chomsky agrees with Pinker.

=====================================================================

There is no language that cannot distinguish cause from effect, temporal relationships, volitional agents, consciousness, intention and purpose–even though elite materialists demean all this as merely “subjective” and not part of the reality they envision.

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One of the impressions, I’m afraid, that Wolfe’s book might leave is that Everett is right about language. Pirahã really is a primitive language lacking recursion, and if one language out of thousands lacks recursion then Chomsky must have been wrong. Language is not innate–it’s just another human invention. Nothing to see here. Linguistics is of no interest to ID.

I checked with an Amazonian linguist, one well within the Darwinian “cog-ling” camp and no supporter of Chomsky. He says that Everett is wrong about Pirahã.

Pirahã has more phonemes than Hawaiian. Unlike Hawaiian, it also has complex lexical tones some of which may be grammatical. The grammar is already complex:

There are, yes, primitive cultures lacking vocabulary we consider essential. Sometimes even numbers are unnamed (though these cultures generally count on their fingers). A few decades ago R. M. W. Dixon (1972, 1977, etc.) introduced linguists to such languages and their exotic grammars. We were all impressed.

There is no language that cannot distinguish cause from effect, temporal relationships, volitional agents, consciousness, intention and purpose–even though elite materialists demean all this as merely “subjective” and not part of the reality they envision.

One might conclude from Wolfe’s book that linguistics has failed to discover much at all. Chomsky strove for a theory of universal syntax that did not appeal to function, but other than acknowledging the fact that all languages are structured hierarchically, many now think the enterprise failed. But this does not mean there are no universals of grammar. There are many.

There are absolute universals, implicational universals, universal tendencies, and so on. Linguistics is like biology. There is no comprehensive “theory” of biology. Biology is more observational than theoretical. And structure is linked to function much as in the typological-functional (now called “cognitive”) school of linguistics.

Nevertheless, Chomsky was right that grammar is instinctive. Children seem programmed to learn it. It is, in fact, children who create grammar.

In learning a language, adults typically focus on words and miss the grammar. Little children do not parrot what they hear. They say, “Daddy goed store.” They grasp for grammatical regularities and learn later to incorporate irregularities. We are programmed to speak just as we are programmed to walk. We are empowered to invent and create and advance technology. We are not programmed to invent and create—hence “primitive” cultures with sophisticated grammars.

Whence then this language facility? Likely, let me suggest, all the following:

1. Grammar is biologically innate

2. Grammar adapts to reality

3. Grammar is Platonic

The study of stroke victims proves that the brain is involved. Cross-language studies reveal how grammar adapts to the environment. And if you are a mathematical realist, then why wouldn’t the mind of a child be attuned to logic that is “out there”? Maybe Michael Denton,’s “laws of biology?” Rupert Sheldrake’s “morphic resonances” perhaps also play a role. Adults have conscious access to vocabulary, and know when a foreigner gets pronunciation and grammar wrong, but adults mostly do not have conscious access to their grammars. Only little children have that.

Language is not the mind–it is the principle code the mind uses. It is a window into the soul.

[*Noel Rude’s notes below]

See also: Andrew Ferguson reviews Wolfe’s Kingdom of Speech at Commentary

Daniel Everett finally speaks for himself, just wants academic freedom

Can we talk? Language as the business end of consciousness

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* Noel Rude’s notes:

Berwick, Robert C., Angela D. Friederici, Noam Chomsky, and Johan J.

Bolhuis. 2013. Evolution, brain, and the nature of language. Trends in

Cognitive Sciences 17 (2): 89-98.

http://www.sciencedirect.com/science/...

Berwick, Robert C., and Noam Chomsky. 2016. Why Only Us: Language and

Evolution. The MIT Press. https://mitpress.mit.edu/books/why-on...

Bethell, Tom. 2016. Darwin’s House of Cards: A Journalist’s Odyssey

Through the Darwin Debates. Seattle: Discovery Institute.

Chomsky, Noam. 1959. Reviews: Verbal behavior by B. F. Skinner. Language

35 (1): 26–58. http://chomsky.info/1967____/

Chomsky, Noam. 1966. Cartesian Linguistics: A Chapter in the History of

Rationalist Thought. New York: Harper and Row.

Chomsky, Noam. 1968. Language and Mind. New York: Harcourt, Brace &

World. http://chomsky.info/mind01/

Chomsky, Noam, and Marcel-Paul Schützenberger. 1963. The Algebraic Theory

of Context-Free Languages. In P. Braffort and D. Hirschberg, eds., Computer

Programming and Formal Systems, pp. 118–161. Amsterdam: North-Holland.



http://www-igm.univ-mlv.fr/~berstel/M...

Denton, Michael J. 1998. Nature’s Destiny: How the laws of biology reveal

purpose in the universe. New York: Free Press.

Denton, Michael J. 2016. Evolution: Still a Theory in Crisis. Seattle:

Discovery Institute Press.

Dixon, R. M. W. 1972. The Dyirbal Language of North Queensland. Cambridge

Studies in Linguistics, 9. Cambridge University Press.

Dixon, R. M. W. 1977. A Grammar of Yidiny. Cambridge Studies in

Linguistics, 19. Cambridge University Press.

Pinker, Steven. 1994. The Language Instinct: How the Mind Creates

Language. William Morrow & Company.

Pinker, Steven. 2003. The Blank Slate: The Modern Denial of Human Nature.

Reprint edition. Penguin Books.

Sheldrake, Rupert. 1995. Seven Experiments That Could Change the World: a

do-it-yourself guide to revolutionary science. New York: Riverhead Books.

Wolfe, Tom. 2016. The Kingdom of Speech. New York: Little, Brown and

Company.

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Richard Dawkins needs to lie down

No, really. See this:

PLEASE read https://t.co/vEUBmgqcwL Terrifying. Sinister social-media bots read minds & manipulate votes. Explains mystery of Trump & Brexit

— Richard Dawkins (@RichardDawkins) February 27, 2017 

Dawkins now appears to be channelling persons who cannot handle the new non-gatekeeper world of online media, who think it must all be a big plot involving fake news, the alt right, the Russians, and all things that scare them.

 

 

Memo

From: UD News

To: UD News Robotics Dawkinsbot II Special Project

Re: Retooling needed for Dawkinsbot II – urgent

Our revamped Dawkinsbot has been performing fabulously to date.* But AI experts are warning that our introduction of a ramped-up politics algorithm could endanger the entire mechanism.

We have not worked out a protocol for what happens if the bot just plain goes nuts.

Remember, our goal is to damage the Darwin brand. We will succeed in doing so if the bot merely sounds off-base. Not if it sounds like it is in meltdown! Look, in the worst-case scenario, someone might see connectors sticking out…

Plus there is always the risk that the real Richard Dawkins, hard at work in his cottage on his lifetime masterpiece, How Darwinism Explains Absolutely Everything, might be tipped off by a friend as to what we are doing.

[image error]

Our legal counsel advises that the real Dawkins could sue us for portraying him as far more foolish than he can possibly be.

A joke’s a joke, but … Okay, you get the picture, guys: Our advisory board wants you to scale back that politics algorithm and get him back to bashing religion in really tasteless ways. You could probably do it in a couple of days.

As we all know, Brexit and US 2016 were normal political events and the main problem was the inability of conventional mainstream media to understand and report on them accurately in the internet age.

Our Corner Historian points out that the same thing happened at the dawn of the printing press, and probably with the dawn of writing (maybe 7 millennia ago?). Media based in earlier technologies and the establishment figures associated with them usually fail to read the moods rightly because they aren’t part of the critical conversations. They don’t even want to be part of them. The situation naturally feels like an apocalypse to them.

Can one of you guys generate a rough schedule and cost estimate for this project? Soon.

* See: Memo November 3,2016: Earnings watch for UD News shareholders: Dawkinsbot disliked by scientists, no longer a hot property Note: Our fix worked but it might have gone too far in a different direction.

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Earliest evidence of life on Earth found at 3.77 bya?

From Sarah Kaplan at Washington Post on a recent find in northern Canada:

The straw-shaped “microfossils,” narrower than the width of a human hair and invisible to the naked eye, are believed to come from ancient microbes, according to a new study in the journal Nature. Scientists debate the age of the specimens, but the authors’ youngest estimate — 3.77 billion years — would make these fossils the oldest ever found.

Some apparent finds in recent years have not been found to be the residue of life, but in this case:

But the scientists behind the new finding believe their analysis should hold up to scrutiny. In addition to structures that look like fossil microbes, the rocks contain a cocktail of chemical compounds they say is almost certainly the result of biological processes.

If their results are confirmed, they will boost a belief that organisms arose very early in the history of Earth — and may find it just as easy to evolve on worlds beyond our own.

“The process to kick-start life may not need a significant length of time or special chemistry, but could actually be a relatively simple process to get started,” said Matthew Dodd, a biogeochemist at University College London and the lead author of the paper. “It has big implications for whether life is abundant or not in the universe.” More.

Dodd’s spin on the find is so familiar now that few pause to notice what underlies it: Pushing the origin further back (the authors’ oldest estimate is s 4.28 billion years) leaves ever less time for a random natural origin of life. And we still simply have no idea whether life is abundant in the universe, as he suggests, because conditions can be so different elsewhere. Bringing the idea up avoids the obvious conclusion that current proposed accounts can’t work.

See also: Origin of life requires “a privileged function?”

What we know and don’t know about the origin of life

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Doug Axe: The culture of engineering vs. the culture of biology, and what Hidden Figures can tell us about that

From Douglas Axe, author of Undeniable, at The Stream:

Hidden Figures — the true story of three brilliant African-American women who proved themselves in a 1960s NASA culture dominated by white men — is sure to inspire. The film is filled with emotive lessons, most powerfully a vindication of the hope that those who persevere honorably for a just cause will not be disappointed.

Another lesson, more pragmatic, occurred to me as the drama unfolded. Having migrated in my own career from the measurable-fact culture of engineering to the more descriptive culture of biology, I felt a tinge of nostalgia as I watched a roomful of nerds with their calculators and chalk boards working together to find the answer to a pressing question: How can we bring an orbiting astronaut back safely to Earth?

Notice the very pre-post-truth essence of that phrase find the answer. Engineers have always taken for granted that clearly posed questions have uniquely correct answers — there to be found by anyone with the skill to find them, and unambiguously recognized as correct when found. The joy of Hidden Figures is that it sweeps away our prejudicial attitudes as to who might have these requisite skills.

Evolutionary biology would have a hard time recognizing that kind of skill set. Darwin, born into the privileged life of English gentry, didn’t really have to solve practical problems. He had the luxury of concerning himself more with persuasion and influence than calculation or invention. More.

Nothing has changed, as it happns. Unlike the hidden figures, Darwin’s followers can arrange the facts to suit their convenience and the call in traditional media to admire them. Although the latter, come to think of it, are an ever-diminishing ally. Thee’s one cange that might prefigure other changes.

See also: Nature: “Unhelpful to exclude conservative voices from debate”

and

The alt right, popular media, and Darwin

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Will the universe’s expansion put an end to science as we know it?

Well, that’s what some cosmologists fear. Call it a futurist’s dystopia if you like.

Big Bang/NASA

Sci-tech writer Geoff Manaugh explains at BLDGBLOG:

As the universe expands over hundreds of billions of years, Reynolds explained, there will be a point, in the very far future, at which all galaxies will be so far apart that they will no longer be visible from one another.

Upon reaching that moment, it will no longer be possible to understand the universe’s history—or perhaps even that it had one—as all evidence of a broader cosmos outside of one’s own galaxy will have forever disappeared. Cosmology itself will be impossible.

…

There would be no reason to theorize that other galaxies had ever existed in the first place. The universe, in effect, will have disappeared over its own horizon, into a state of irreversible amnesia.More.

For Manaugh, these thoughts riff off a recent article on the “crisis brewing in the cosmos” (the universe seems to be expanding too fast).

Hmmm. We could probably put off worry about it for a little, especially because we don’t seem to have anything like a program yet for the  End of All Things. Keep the file open.

See also: Crisis in cosmology: Universe expanding too fast?

Now fierce debate over universe expansion speed

New physics? Conflict in universe’s expansion data

and

Universe expansion speed just right for life?

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Researchers: Pre-mammalian reptile evolved venom 100 million years before snakes

[image error]

artist’s impression of Euchambersia/Wits University

From ScienceDaily: Euchambersia was a dog-sized pre-mammalian reptile living 260 million years ago in a deadly South African environment:

Living in the Karoo, near Colesberg in South Africa, the Euchambersia developed a deep and circular fossa, just behind its canine teeth in the upper jaw, in which a deadly venomous cocktail was produced, and delivered directly into the mouth through a fine network of bony grooves and canals.

“This is the first evidence of the oldest venomous vertebrate ever found, and what is even more surprising is that it is not in a species that we expected it to be, ” says Dr Julien Benoit, researcher at the Bernard Price Institute for Palaeontological Research at the University of the Witwatersrand in South Africa.

“Today, snakes are notorious for their venomous bite, but their fossil record vanishes in the depth of geological times at about 167 million years ago, so, at 260 million years ago, the Euchambersia evolved venom more than a 100 million years before the very first snake was even born. ” Paper. (public access) – Julien Benoit, Luke A. Norton, Paul R. Manger, Bruce S. Rubidge. Reappraisal of the envenoming capacity of Euchambersia mirabilis (Therapsida, Therocephalia) using μCT-scanning techniques. PLOS ONE, 2017; 12 (2): e0172047 DOI: 10.1371/journal.pone.0172047 More.

The venom, which probably flowed directly into the animal’s mouth, is thought to have been used primarily for hunting.

The fact that venom might be useful to the animal does not really explain how it comes to have it. But we are learning a lot about how complex mechanisms develop much earlier than thought.

See also: Evolution appears to converge on goals—but in Darwinian terms, is that possible?

and

Stasis: Life goes on but evolution does not happen

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