Michael J. Behe's Blog, page 568

Researchers: Ribosome translational system dates back to earliest Earth

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The ribosome in relation to other cell parts/ Nicolle Rager, National Science Foundation

From ScienceDaily:

So audacious was Marcus Bray’s experiment that even he feared it would fail.

In the system inside cells that translates genetic code into life, he replaced about 1,000 essential linchpins with primitive substitutes to see if the translational system would survive and function. It seemed impossible, yet it worked swimmingly, and Bray had compelling evidence that the great builder of proteins was active in the harsh conditions in which it evolved 4 billion years ago.

The experiment’s success reaffirmed the translational system’s place at the earliest foundations of life on Earth.

Every living thing exists because the translational system receives messages from DNA delivered to it by RNA and translates the messages into proteins. The system centers on a cellular machine called the ribosome, which is made of multiple large molecules of RNA and protein and is ubiquitous in life as we know it.

“There’s nothing alive without ribosomes,” said Loren Williams, a professor at the Georgia Institute of Technology’s School of Chemistry and Biochemistry. “The ribosome is about the oldest and most universal part of biology, and its origins go very far back to a time not too long after Earth had formed and cooled.”

…

Amazingly, the atomic swaps barely changed the shape of the ribosome.

“It’s totally unbelievable this would work because biology makes very specific use of things. Change one atom and it can wreck a whole protein,” Williams said. “When we probed the structure, we saw that all three metals do essentially the same thing to the structure.”

…

“Surrounding the ribosome is also a huge cloud of magnesium atoms. It’s called an atmosphere, or shell, and engulfs it completely. I replaced everything, including that, and the whole system still worked.”Paper. (open access) – Marcus S. Bray, Timothy K. Lenz, Jay William Haynes, Jessica C. Bowman, Anton S. Petrov, Amit R. Reddi, Nicholas V. Hud, Loren Dean Williams, Jennifer B. Glass. Multiple prebiotic metals mediate translation. Proceedings of the National Academy of Sciences, 2018; 201803636 DOI: 10.1073/pnas.1803636115 More.

So the system is flexible enough to work despite substitutions of parts.

Note: The “experiment corroborates translational system’s place at earliest foundations of life on Earth”? What are the chances of evolving it randomly by a series of steps? And if that could happen, why isn’t it happening all the time, everywhere (spontaneous generation)?

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See also: Mitochondria have their own ribosomes as well as their own DNA

and

Ribosome precisely structured for cell growth

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PBS’s American Experience: The Eugenics Crusade

A friend writes to recommend it:

American Experience: The Eugenics Crusade is one of the best documentaries I have ever seen and I have watched many hundreds of them. As the movie documents, it started with Darwin, then moved on to Galton who spent his life developing the science of eugenics, then the American eugenics movement is covered in detail. Next is many leading, Harvard and other elite school educated scientists took it up, and Congress passes laws to end over 90 percent of immigration, and it moved on to Nazi Germany, and the Holocaust, noting at the Nuremberg Nazi trial the lawyers defending the Nazis cited the Bell v. Buck U.S. Supreme court case to justify their eugenics program. Along the way, the documentary covered the abuse of IQ tests, and racism in the mix and, last, showed how people uncritically relied on science and the scientists to justify their acts. Science turned out to sound reasonable but, in the end, was horribly wrong. Could the same problem be true with Darwinism? It sounds good, but as evidence, as is accumulated, it may turn out to be horribly wrong. There is clearly a lesson here. More.

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See also: A note on eugenics, social darwinism and evolutionary theory (kairosfocus)

From the Edge: Another reason not to like evolutionary psychology –support for Chinese eugenics

and

Eugenics: How consensus science can be dead wrong

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John Sanford on claims about brand new nylonase genes

Recently, we noted that John Sanford was speaking at NIH on human health and mutations. Philip Cunningham writes to mention a 2017 paper by Sanford and S. T. Cordova, Nylonase Genes and Proteins – Distribution, Conservation, and Possible Origins on whether the ba cteria that digest nylon evolved new genes:

We began this work hoping to better understanding the various claims regarding the de novo origin of certain nylonase genes. The idea that nylonases would have arisen very recently, de novo, was based upon the widely-held assumption that nylonases would have been essentially non-existent prior to the artificial manufacture of nylon. This basic assumption would not be justified if there were any nylonlike polymers in nature, or if nylonase activity required very low specificity, such that enzymes with other functions might also possess or acquire nylonase activity.

Our analyses indicate that nylonase genes are abundant, come in many diverse forms, are found in a great number of organisms, and these organisms are found within a great number of natural environments. We also show that nylonase activity is easily acquired through mutation of other enzymes, which strongly suggests that nylonase activity has very low specificity of the active site. These findings refute the widely held assumption that nylonases were essentially non-existent before 1935. In this light, there is no reason to believe that any nylonase emerged since 1935, and so there is no solid basis for invoking any de novo nylonase genes. Therefore, it seems only reasonable to reexamine the earlier claims of de novo genes. More.

More from the Biologic Institute about nylon-eating bacteria.

Hat tip: Philip Cunningham

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See also: John Sanford gives lecture at NIH on mutations and human health

John Sanford: Darwin a figurehead, not a scientist

and

John Sanford: Accepting Darwinism’s collapse is a matter of scientific integrity

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Darwinian biologist Jerry Coyne denounces Michael Behe’s forthcoming book unread

Of course, just now, one suspects that it is mainly the editors in Frisco who have pored over it. But now, Darwinian evolutionary biologist Jerry “Why Evolution Is True” Coyne  tells us,l

Michael Behe, author of the intelligent-design (ID) creationist books Darwin’s Black Box and The Edge of Evolution, has a new book coming out next February, Darwin Devolves: The New Science about DNA that Challenges Evolution. (Let me point out here that the phrase “that challenges evolution” has an unclear antecedent, either the new science that challenges evolution—what he clearly means—or the DNA itself that challenges evolution. Bad title!)

The construction that offends Dr. Coyne is a clause, not a phrase; however, why be picky and it will doubtless be clear enough to most people. Maybe too clear. But now,

I realize that I’ve just given Behe publicity, but how many people who would buy an ID book read this website? Anyway, I’ll have more to say about it after I’ve read it. More.

Might be an idea, that, to read it first. But, to answer the rhetorical question, thanks to UD, possibly a number of people will read that post and order the book.

Let’s see how the book does.

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See also: A peek at Mike Behe’s new book Darwin Devolves We’re told that the basic thesis is, The First Rule of Adaptive Evolution: Break or blunt any functional gene whose loss would increase the number of offspring.

and

Huge study shows yeasts evolve by reducing their complexity If losing complex traits is a reliable and successful form of evolution, how did successful life forms acquire great complexity in the past, when there was less time to evolve?

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Democracies Fail Without Adult Supervision

Pure democracies are inherently unstable.  Exhibit A for why that is so:

Progressive Democrat Alexandria Ocasio-Cortez

The reason for the fiscal instability of a pure democracy was captured in a widely circulated quotation usually attributed to Alexander Fraser Tytler:

A democracy cannot exist as a permanent form of government. It can only exist until the majority discovers it can vote itself largess out of the public treasury. After that, the majority always votes for the candidate promising the most benefits with the result the democracy collapses because of the loose fiscal policy . . .

 

Ocasio-Cortez has a list of goodies she wants the federal government to dispense, including Medicare for all, jobs guarantees, student loan forgiveness, free college, paid family leave, and Social Security expansion.  The price tag is $40 trillion (with a “t”) over the next 10 years.  We would have to more than double federal taxes to pay for it all.

When asked how she proposes to pay for all of this she responded, “the same way you pay for anything; you just pay for it.”  It is truly frightening that someone as aggressively stupid as Ocasio-Cortez was not only elected to the United States House of Representatives, she was elected easily by a very wide margin.

The glory of the American system of government established by the Constitution is that it provides for majority rule with distinctly anti-majoritarian checks.  It is, as it were, “democracy with adult supervision.”  Ocasio-Cortez needs adult supervision.  It does not take a genius to realize that if she ran the House and Sanders ran the Senate the county would go bankrupt so fast your head would spin.

Keep this in mind the next time you hear some pundit whine about how insufficiently democratic our federal government is.  The Constitution did not establish a democracy.  To which I say, thank God.

And , yes, this post has nothing to do with ID.

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New life form more different from others “than animals are from fungi”

two identified types, Spironema, and Hemimastix kukwesjijk/Yana Eglit, Nature

Hemimastigotes:

Like animals, plants, fungi and ameobas — but unlike bacteria — hemimastigotes have complex cells with mini-organs called organelles, making them part of the “domain” of organisms called eukaryotes rather than bacteria or archaea.

About 10 species of hemimastigotes have been described over more than 100 years. But up until now, no one had been able to do a genetic analysis to see how they were related to other living things. Emily Chung, “Rare microbes lead scientists to discover new branch on the tree of life” at CBC

 

Eglit watched carefully as it hunted. Hemimastix shoots little harpoons called extrusomes to attack prey such as Spumella, a relative of aquatic microbes called diatoms. It grasps its prey by curling its flagella around it, bringing it to a “mouth” on one end of the cell called a capitulum “as it presumably sucks its cytoplasm out,” Eglit said. Emily Chung, “Rare microbes lead scientists to discover new branch on the tree of life” at CBC

Note: “But Simpson noted that discoveries like this one are pretty rare: ‘It’ll be the one time in my lifetime that we find this sort of thing.’”

Just a minute here. The new organisms “were found in dirt collected on a whim” on a hike. Why should we assume that they are rare, as opposed to unsought? One can only wonder what new insights we would gain if there were less Darwin in our system and more open-minded exploration.

We are also told at CBC, “ … you’d have to go back a billion years — about 500 million years before the first animals arose — before you could find a common ancestor of hemimastigotes and any other known living things.”

Hmmm. Half a billion years is a long time. Why start by assuming that we even have a common ancestor?: Who decided that that should be our main focus just now when everything else has been a century-long mystery?

Two types of these organisms were found (and who knows how many others there may be?):

Opening sentences of the Letter to Nature Almost all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics1–4. The ‘phylum’ Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture5–7; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here we report phylogenomic analyses based on high-coverage, cultivation-independent transcriptomics that place Hemimastigophora outside of all established eukaryote supergroups. They instead comprise an independent supra-kingdom-level lineage that most likely forms a sister clade to the ‘Diaphoretickes’ half of eukaryote diversity (that is, the ‘stramenopiles, alveolates and Rhizaria’ supergroup (Sar), Archaeplastida and Cryptista, as well as other major groups). The previous ranking of Hemimastigophora as a phylum understates the evolutionary distinctiveness of this group, which has considerable importance for investigations into the deep-level evolutionary history of eukaryotic life—ranging from understanding the origins of fundamental cell systems to placing the root of the tree. We have also established the first culture of a hemimastigote (Hemimastix kukwesjijk sp. nov.), which will facilitate future genomic and cell-biological investigations into eukaryote evolution and the last eukaryotic common ancestor. (open access) More.

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The story reminds some of us a bit of new findings about viruses.

See also: Virus expert highlights the conflict over whether viruses are alive In short, it is an open question. The question relates to the role viruses can play in evolution, among other things. Are they precursors of life, detritus of life, or something in between? Or all three? Keep the file open.

Viruses invent their own genes? Then what is left of Darwinism?

Why viruses are not considered to be alive

Another stab at whether viruses are alive

Phil Sci journal: Special section on understanding viruses

Should NASA look for viruses in space? Actually, it’s not clear that RNA came first. Nor is it clear that viruses precede life. A good case can doubtless be made for viruses being part of the scrap heap of existing life. But no matter. If you think you can find viruses in space, boldly go.

Why “evolution” is changing? Consider viruses

The Scientist asks, Should giant viruses be the fourth domain of life? Eukaryotes, prokaryotes, archaea… and viruses?

Viruses are alive.

and

Are viruses nature’s perfect machine? Or alive?

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You are conscious? But so what? Maybe your coffee mug is too

A survey of materialist (naturalist) theories of consciousness would require you to keep an open mind on the topic. At Mind Matters,

In an academic article,  Kastrup identified the available materialist options, as he sees them. Picture, if you will, you, an amoeba, and a coffee mug. How much does each of you participate in consciousness?

a) physicalism (everything is a physical reality)

you 0  amoeba 0  coffee mug 0

On this view, consciousness is an evolved illusion.

b) bottom-up pan-psychism

you 1  amoeba 1  coffee mug 0

You and the amoeba both evolved consciousness as you evolved life but the coffee cup (and, we presume, its associated electrons) did not.

amoeba

c) cosmopanpsychism

you + amoeba + coffee mug = 1

You, the amoeba, and the mug are one indivisible consciousness.

d) dissociated alters (multiple personality disorder)

you 1  amoeba 1  coffee mug 0

This d) view, which Kastrup favors, sees you and the amoeba as dissociated selves of the universe as a whole. The universe is thus seen as a victim of multiple personality disorder. But Kastrup’s view allows for a fundamental difference between the living and the non-living. Only the living are seen as personalities. Sorry, mug, you are not a dissociated self, a subject of experience, after all.  More.

But never mind. In some materialist systems, the mug wins.

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See also: Does your brain construct your conscious reality? Part I  A reply to computational neuroscientist Anil Seth’s recent TED talk (Michael Egnor)

Does your brain construct your conscious reality? Part II In a word, no. Your brain doesn’t “think”; YOU think, using your brain (Michael Egnor)

A short argument against the materialist account of the mind (Jay Richards)

and

What great physicists have said about immateriality and consciousness

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There will be cyborgs on Mars! says well-known astronomer

Martin Rees

From Sir Martin Rees at NBC:

AI apocalypse is certainly in the air. Elon Musk, Henry Kissinger, and the late Stephen Hawking have all predicted an AI doomsday. Industry professionals’ doubt and disparagement don’t seem to register with the media in the same way.

Rees, who is former president of the Royal Society, goes further, however. He also predicts in his book that “a physics experiment could swallow up the entire universe.” When he received the Templeton Prize in 2011, he was noted for speculating that we could be living in a giant computer simulation. In 2017, he suggested that our universe may be lost in an “unbounded cosmic archipelago,” a multiverse where “we could all have avatars.” As for universes, “Ours would belong to the unusual subset where there was a “lucky draw” of cosmic numbers conducive to the emergence of complexity and consciousness. Its seemingly designed or fine-tuned features wouldn’t be surprising.”

The only type of universe we do not seem to be living in, on that view, is the simpler one we observe, about which we have at least some information.More.

Reality check: It’s unfortunate that the public is taught by legacy media to take seriously the claims of prominent people like Sir Martin who don’t have day-to-day knowledge of what is happening in machine learning, while ignoring professionals who say, well, um, no, not really… And it’ll be more than just unfortunate, if out gassing politicians get the whole landscape wrong when they promote and vote on legislation.

See also: See also: AI machines taking over the world? It’s a cool apocalypse but does that make it more likely?

Software pioneer says general superhuman artificial intelligence is very unlikely The concept, he argues, shows a lack of understanding of the nature of intelligence

and

Machines just don’t do meaning And that, says a computer science prof, is a key reason they won’t compete with humans

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Huge study shows yeasts evolve by reducing their complexity

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lab-grown yeast colony/Dana Opulente

Not by adding to it. Everyone seems to be talking about devolution (“reductive evolution”) these days. From ScienceDaily:

“This is the first large genome project like this that actually looks at hundreds of different eukaryotic species, not different individuals or isolates of the same species,” says Chris Todd Hittinger, a UW-Madison genetics professor and one of the senior authors of the study. “Budding yeasts, despite their phenotypic similarity, are very different from one another genetically. They’re as different from one another as all animals or all plants are from one another.”

Collecting such a deep pool of yeast types gave researchers enough information to use comparisons of the shifting genetics to redraw the budding yeast family tree into a dozen major branches and paint a detailed picture of their past.

The yeasts are thought to have got started about 400 million years ago.

The researchers examined their yeasts for 45 traits representing their ability to process a variety of yeast foods — different sources of carbon and nitrogen necessary to store energy and build cells. Tracking back the evolutionary paths of modern yeasts suggests the common ancestor yeast had a metabolism that could work with a varied diet.

“We have a more consistent picture now of the variations of carbon and nitrogen sources across the modern species,” says Dana Opulente, a postdoctoral researcher in Hittinger’s lab who redid much of the trait-testing work of a century of yeast researchers for the Cell study. “They show us that this ancestor yeast would have been able to use a wider array of sugars than modern budding yeasts.”

Modern yeasts have narrowed their appetites in a process called reductive evolution, losing quite a few of those 45 traits as they specialized to flourish in their particular niches.

“To pick on the model budding yeast, S. cerevisiae has one of the more reduced genomes,” Hittinger says. “It lacks many of the metabolic capabilities that other budding yeasts have.” Paper. (paywall) – Xing-Xing Shen, Dana A. Opulente, Jacek Kominek, Xiaofan Zhou, Jacob L. Steenwyk, Kelly V. Buh, Max A.B. Haase, Jennifer H. Wisecaver, Mingshuang Wang, Drew T. Doering, James T. Boudouris, Rachel M. Schneider, Quinn K. Langdon, Moriya Ohkuma, Rikiya Endoh, Masako Takashima, Ri-ichiroh Manabe, Neža Čadež, Diego Libkind, Carlos A. Rosa, Jeremy DeVirgilio, Amanda Beth Hulfachor, Marizeth Groenewald, Cletus P. Kurtzman, Chris Todd Hittinger, Antonis Rokas. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell, 2018; DOI: 10.1016/j.cell.2018.10.023 More.

If losing complex traits is a reliable and successful form of evolution, how did successful life forms acquire great complexity in the past, when there was less time to evolve?

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See also: John Sanford gives lecture at NIH on mutations and human health Sanford has a great deal to say about genetic entropy and devolution.

A peek at Mike Behe’s new book Darwin Devolves We’re told that the basic thesis is, The First Rule of Adaptive Evolution: Break or blunt any functional gene whose loss would increase the number of offspring.

Devolution: Worm gives up sexual reproduction, loses 7000 genes

Giant shipworm found alive is example of devolution

and

Devolution: Getting back to the simple life

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Brendan Dixon: Even the skeptical Deep Learning researcher left out one AI myth

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Brendan Dixon

Readers may remember Dixon from the time MIT tried building a universal moral machine. Here are some of his thoughts on one overlooked aspect of the “superintelligent AI” myth:

[Google AI researcher] Francois Chollet is right to recognize that we, like all animals, come pre-wired. Young deer stand, leap, and run within hours of birth. Birds build nests without prior instruction. Squirrels bury and find nuts. We speak and juggle abstract thoughts. But basic chemistry does not create language; while speaking may require chemical bonding and signaling, language rests on something more. Vision is another “chicken and egg” problem: The best human eye in the world is worthless without a nervous system to transmit the signals and a mind to interpret them. Chollet recognizes that these abilities are “required for human intelligence” so that it can make use of a human body. What he neglects to ponder is whence did they come? How does intelligence arise? Chollet raised the question without answering it.

He, unintentionally, introduces the same tension when he discusses feral children— children raised, literally, by animals in the wild. Unless rescued young, these children never develop into full, social humans; they remain unable to use human language. His point is that we require culture to develop culture and use our intelligence. I think you can see the problem: If we need culture to function, then whence came the culture in which we have all been raised? Which is the chicken and which is the egg?

I strongly support Chollet’s core observations. The super-intelligent AI myth is little more than a replacement “god” for those uncomfortable with traditional theism. It is an article of faith. And, like all uncritically held articles of faith, it induces blindness: blindness both to the real problems AI can cause (when we cede unwarranted control to the machines) and to the stunning magnitude of the human mind. More.

* Brendan Dixon is a Software Architect with experience designing, creating, and managing projects of all sizes. He first foray into Artificial Intelligence was in the 1980s when he built an Expert System to assist in the diagnosis of software problems at IBM. Though he’s spent the majority of his career on other types of software, he’s remained engaged and interested in the field.

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Also by Brendan Dixon: What Does It Mean to Be Intelligent? (Evolution News and Science Today:, 2016)

“Bob Dylan” is a mechanical mockingbird (Evolution News and Science Today:, 2017)

See also: Software pioneer says general superhuman artificial intelligence is very unlikely

and

There is no universal moral machine Brendan Dixon’s view of MIT’s Moral Machine is featured.

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