Michael J. Behe's Blog, page 506

March 23, 2019

One way viruses get spread “should never have evolved”?

Recently, we talked about how different segments of a virus genome can inhabit different cells but work together. Is this unimaginable? Sci-fi? No, just one reason why more attention should be paid to viruses if we want to understand life.

Here’s another take on it, explaining how the researchers got the idea of testing for distribution between cells:

These viruses have always been baffling, even to virologists who knew about them. Everyone assumed that they could only reproduce if all the segments infected the same host cell. But the risk of losing a piece, and so dooming the others, skyrockets as the number of pieces goes up. In 2012, two researchers calculated that the odds of successfully getting every segment in the same cell become too low with anything more than three or four segments. FBNSV, with its eight segments, “should never have evolved,” Blanc says. Its mere existence suggests “that something must be wrong in the conceptual framework of virology.”

Perhaps, he realized, these viruses don’t actually need to unite their segments in the same host cell. “If theory was saying that this is impossible, maybe the viruses just don’t do it,” he says. “And once we had this stupid idea, testing it was very easy.”Ed Yong, “A New Discovery Upends What We Know About Viruses” at The Atlantic

Maybe in some fields we need more “stupid” ideas that don’t depend on what “should have” evolved.

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See also: Reset! Different segs of virus genome can exist in different cells but work together. Researchers: “It has long been believed that all of the genome segments must move together from cell to cell to cause an infection. But the new study shows this is not the case.” We underestimate our viral overlords. They are making “it has long been believed” our enemy.

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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Published on March 23, 2019 13:35

Insectologists swat insects-are-doomed paper

Smack! Entomologists were bugged by the data errors, data-gathering methods, and editorializing tone in the paper:

To a trio of UK-based biologists at the University of York and Cardiff University, this doesn’t pass the smell test. “Trying to extrapolate from population or biomass declines over several decades, or from threatened species lists, in ‘developed’ temperate zone countries to, say, 100 year species level extinctions of undescribed endemics confined to the precipitous eastern flanks of the Andes does not wash,” these critics wrote in Global Change Biology earlier this month.

Finnish biologists at the University of Jyväskylä, writing in Rethinking Ecology this week, called out other issues, including the fact that local extinctions reported in some of the studies aren’t easily extrapolated to a broader scale, and at least one instance in which insects with the conservation designation “data deficient” were lumped in with those designated “vulnerable” and thus assumed to be declining when we can’t be sure.Maddie Stone, “Bug Scientists Squash ‘Insect Apocalypse’ Paper” at Gizmodo

The strongest point was made by the ecologist who said, ““We don’t know anything about most insect species on Earth.”(Maddie Stone, Gizmodo)

The temptation for some seems to be to resort to apocalypse voodoo to demonstrate a crisis, at the expense of the methods that make scientists worth listening to, as an alternative to supermarket tabloids. File this one with: The real reasons people don’t “trust science”

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See also: Insects In Decline? Science Writer Says It’s Myth

and

Alfred Russel Wallace’s Giant Bee Turns Out Not To Be Extinct

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Published on March 23, 2019 09:42

Are the best measurements to date deepening the “cosmological crisis”?

This image represents the evolution of the Universe, starting with the Big Bang. The red arrow marks the flow of time.

Big Bang/NASA

A continuing discrepancy between two measurements of the expansion of the universe is “forcing” a re-examination of the Standard Model, which physicists have hated for decades, mainly for philosophical reasons:

“The exciting thing is that if the discrepancy is due to new physics prior to recombination, it will almost certainly have distinctive signatures,” Lewis says. The signatures would show in the finer details of the CMB—something that the next generation of CMB telescopes, such as the upcoming Simons Observatory, could see.

Riess also thinks that the discrepancy is pointing fingers at cosmologists’ standard model. “At some point, you have to start saying the universe has another wrinkle in it, in the cosmological model—in the composition of the universe or in some feature of dark matter or dark energy—[that] could also potentially explain this,” he says. “You have to give that some serious consideration.”Anil Ananthaswamy , “Best-Yet Measurements Deepen Cosmological Crisis” at Scientific American

Two things many cosmologists would like to get rid of are the Big Bang and apparent fine-tuning of the universe. Telling a different story is difficult mainly due to lack of evidence for a different story but they can make do with discrepancies. But then maybe the years have made some of us cynical.

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See also: Sabine Hossenfelder: Is science harmed by an illusion of progress?Tellingly, Hossenfelder adds, “So here is the puzzle: Why can you not find any expert, besides me, willing to publicly voice criticism on particle physics? Hint: It’s not because there is nothing to criticize. ”

Discover: Even the best dark matter theories are crumbling

and

Researcher: The search for dark matter has become a “quagmire of confirmation bias” So many research areas in science today are hitting hard barriers that it is reasonable to think that we are missing something.

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Published on March 23, 2019 07:40

March 22, 2019

Please Pass the Blueprints

Were told that reproducibility is what endows evolution (i.e., NS+RM) with the necessary power for overcoming huge obstacles of complexity.

However, does this same argument apply to the structures that organisms construct? DNA can produce, and then reproduce, an ‘eye,’ but how, exactly, does DNA produce and reproduce an architectural plan?

For example, a group of biologists, engineers and other scientists, led by scientist from Imperical College, London have used 3D X-ray imaging to explore and understand the structure underlying nests built by termites. It’s really quite incredible.

A group of engineers, biologists, chemists and mathematicians lead by Imperial College London, the University of Nottingham, and CNRS-Toulouse have looked closer than ever before at how these nests work using 3-D X-ray imaging. They found small holes, or pores, in the walls of termite mounds which help them stay cool, ventilated, and dry.

Lead author Dr. Kamaljit Singh, from Imperial’s Department of Earth Science and Engineering, said: “Termite nests are a unique example of architectural perfection by insects. The way they’re designed offers fascinating self-sustaining temperature and ventilation controlling properties throughout the year without using any mechanical or electronic appliances.”

Who would have thought that termites, using random mutations, could turn themselves into master architects!! They’re creators of “architectural perfection”.

In fact, it’s such an outstanding design that the authors tell us this:

Dr. Singh said: “Not only do these remarkable structures self-ventilate and regulate their own temperatures—they also have inbuilt drainage systems. Our research provides deeper insight into how they manage this so well.”

The scientists say the newly found architecture within termite nests could help us improve ventilation, temperature control, and drainage systems in buildings—and hopefully make them more energy efficient.

They’ve out-designed humans! Bravo!

But there is this question: where are we to locate the architectural plans for these nests? IOW, are they found in some kind of organelle in some cell somewhere? Is there some kind of termite boarding school where all this fascinating archticture is taught and learned?

Or, is this “knowledge” contained in their DNA and copied in just the same way as all DNA is copied by the cell and then transmitted? Isn’t this the likely answer?

But this implies, does it not, that DNA can contain–is the respository of, “knowledge” simply as “knowledge”? And isn’t “knowledge” the work of ‘minds’? Isn’t it only the ‘mind’ that can discover, distinguish, appropriate and value “knowledge”? If so, then isn’t the conclusion we should take away from what termites are able to accomplish one of DNA being completely capable of harmonizing itself with the work of a ‘mind’?

I suspect there are a few evolutionary biologists (Darwinists) who might disagree with this notion.

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Published on March 22, 2019 18:10

Biologist responds to fretting over “denialism” at Nature

Biologist Wayne Rossiter, author of Shadow of Oz: Theistic Evolution and the Absent God, writes to offer his thoughts on the recent screed at Nature against “denialism”:

—–

There is much that could be said about this article. Science “denialism” is absolutely permitted within science, so long as the denier adheres to the larger mainstream views (which are often not scientific at all). One can blast Darwin, so long as the replacement is equally dysteleological (or worse).

The other presumed “denial” here is climate change. From my reading of the facts, the only things “scientists” mostly agree on are that 1) the climate changes and 2) we are exacerbating it. Details beyond those assertions are particularly fuzzy.

I’m not a climate change denier at all. But we must admit just how errant “scientific authority” has been. Dire predictions of catastrophic destruction have come and gone (I won’t list them all here, but my old digs in NJ are supposed to be completely inundated by now). Then you have the “fallibility” part of expert science:

Here’s what we know, and it doesn’t take more than an entry-level stats course to figure it out. The 150 year pattern of average global temperature shows a slight linear increase (something like 0.8 C). That is troubling, because even slight changes have greatly altered global and local processes. You’ll get no fight with me there. But, if we attempt to extract a relationship between that pattern and global atmospheric CO2 (which has increased geometrically), you won’t find one. Yet, CO2 is the central point of discussion. Falsely. (again, the rise of CO2 is worrisome for other reasons. We measure these global fluxes in gigatons, and right now, we think about 90 gigatons of CO2 move from the oceans to the atmosphere, but 92 gigatons move from the atmosphere to the oceans, and this is leading to acidification).

So, why should we trust “authority,” when it has been publicly embarrassed over and over?

The bigger problem I would point to (which isn’t mentioned by Crease is that “science” has become sensationalized to the point of being tantamount to “fake news.”

Outrageous claims, and modest findings. Big Science looks more and more like WWE wrestling or daytime television. I say that painfully, because it’s a true shame of our time.

——

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See also: At Nature: Waging war on the science deniers! Sadly, there is a war on science, of sorts, afoot. Social justice warriors, for example, are taking dead aim at math. And at objectivity generally. It’s as if, unable or unwilling to even name, let alone withstand the threat, establishment science types hope to distract themselves with a different story until it goes away. Good luck with that. SJWs see that science has funding. And they always need more money.

and

Why can top scientists get away with extraordinary claims?

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Published on March 22, 2019 14:17

New US free speech policy for universities miffs boffins at Nature

We were just talking about a recent piece in Nature, grousing about public doubts about science calling out Paul the Apostle, of all people. Now get a load of this:

Peter McPherson, president of the Association of Public and Land-Grant Universities in Washington DC, called the order “plainly unnecessary” in a statement. “Public universities are already bound by the First Amendment and work each day to defend and honor it,” he said. Sara Reardon, “Universities spooked by Trump order tying free speech to grants” at Nature

A guy has to be stone cold tone deaf to write something like that in the age of FIRE and Bret Weinstein. Universities across the Western world have made clear that they don’t respect intellectual freedom. Even Darwinian evolutionary biologist Jerry Coyne got the message recently and wants universities to sign the Chicago Statement.

News at Linked In

The universities are “spooked by” Trump, are they? Well, they brought him on themselves. They could have listened before, when someone nicer than he is was telling them.

Taxpayers should not be willing to support indoctrination centres run for the benefit of clueless mediocrities, where your prof can get thugged or your car torched by people who feel threatened by challenging ideas.

The big worry should be, nothing will come of it all. Okay then on to Stage 2: How many finishing schools for no-brain enforcers, as opposed to actual universities, does a country need? (Think of a number between -1 and 0… )

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and

Jerry Coyne Discovers The Lack Of Intellectual Freedom On Campus

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Published on March 22, 2019 12:03

At Nature: Waging war on the science deniers!

A philosopher, introducing his new book, The Workshop and the World: What Ten Thinkers Can Teach Us About Science and Authority, begins with an attack on the apostle Paul. Sure, that’ll help:

Hanging in the Louvre Museum in Paris is an imposing painting, The Preaching of St Paul at Ephesus. In this 1649 work by Eustache Le Sueur, the fiery apostle lifts his right hand as if scolding the audience, while clutching a book of scripture in his left. Among the rapt or fearful listeners are people busily throwing books into a fire. Look carefully, and you see geometric images on some of the pages.Robert P. Crease, “The rise and fall of scientific authority — and how to bring it back” at Nature

Paul is, of course, responsible for what someone painted over 1500 years later. For the record, St. Paul was a learned man but counted it all loss compared to believing that his sins were forgiven in Christ. Blaise Pascal had a similar experience. It’s not rare. Anyway, now that our author thinks he has established a common bond with his audience, he goes on to say,

Today, St Paul is making a comeback: the authority of science is again under attack. In areas of national and global consequence — from climate to medicine —political leaders feel confident that they can reject scientific claims, substituting myths and cherry-picked facts. I have spent five years investigating why this has happened and what can be done. Robert P. Crease, “The rise and fall of scientific authority — and how to bring it back” at Nature

Well, if Dr. Crease has not yet tumbled to the idea of avoiding dragging in historical figures who are, in reality, unrelated to the immediate problem, we can only wonder what solutions he will propose. He tells us that “Science denial, however, is like crime: combating it requires both short-term and long-term strategies.”

A friend offers a summary of the strategies implied by his comments:

“Preaching, denouncing or shouting ‘Science works!’ won’t help. Neither will throwing around statistics, graphs and charts.” He’s right, but it doesn’t follow that facts don’t convince anyone. When important, well-known facts are omitted from a discussion, their signal can be louder than the permitted signals.

“If the entire range of such vulnerabilities is not understood, attacking science denial is a frustrating game of whack-a-mole: it simply crops up elsewhere. To curb it, we have to comprehend what makes the whack-a-mole machine tick.” The metaphor of pointless conflict makes clear that the author does not come prepared to listen or learn anything; a bad beginning to a discussion between parties in conflict. “Contemporary science deniers have not one (religious) motive, but many — greed, fear, bias, convenience, profits, politics — to which they cling with various degrees of sincerity and cynicism.” Like all attacks on motives, this one causes a thoughtful reader to wonder about the author’s own co-belligerents’ motives. Given that they make a living out of science, would’;t many of them have roughly the same motives. It doesn;t hbear either way on who is more correct on the facts.“Science denial, however, is like crime: combating it requires both short-term and long-term strategies.” Implying that “science denial” is like crime could translate roughly as “It is a crime to disagree with my faction’s positions.” That approach has a history.“Only by retelling that story — of how the authority of the scientific workshop was promoted, attacked, defended, coupled with society and then diminished — can we have an idea of how to respond when it decouples.” Offhand, it sounds as though Crease is trying to make his patriotic history of science into a popular legend. But he has certainly gone about it the wrong way.

Dr. Crease certainly serves a purpose. Listening to him helps us understand why so many people doubt orthodox science.

Sadly, there is a war on science, of sorts, afoot. Social justice warriors, for example, are taking dead aim at math. And at objectivity generally. It’s as if, unable or unwilling to even name, let alone withstand the threat, establishment science types hope to distract themselves with a different story until it goes away. Good luck with that. They see you have funding. And they always need more money.

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See also: The war on math,

and

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

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Published on March 22, 2019 06:16

Would 3-D virtual fossils speed up research?

And would everyone think that was a good thing? They’re here but not as popular as you might think. Many paleontologists fear losing control of the story:

One of the characteristics of information is that, unlike matter and energy, it is not reduced by being shared. And when it is shared, it can generate new information. Of course, some well-sourced new information may contradict earlier ideas or even important beliefs. “Are 3-D Virtual Fossils a Boon or a Threat?” at Mind Matters

See also: Thousands of Cambrian fossils discovered in China, new to science We are told that this Qingjiang discovery is important for its diversity, especially of cnidarians (corals and jellies). The new fossils represent a different ecology from previous discoveries in China at Chengjiang. The Cambrian era seems to have been more complex than thought.

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Published on March 22, 2019 04:58

Thousands of Cambrian fossils discovered in China, new to science

Hallucigenia/ Matt Martyniuk
(CC BY-SA 3.0)

These animal groups lived in the ocean over half a billion years ago but were buried by a subterranean mudflow:

Paleontologists found thousands of fossils in rocks on the bank of the Danshui river in Hubei province in southern China, where primitive forms of jellyfish, sponges, algae, anemones, worms and arthropods with thin whip-like feelers were entombed in an ancient underwater mudslide. The creatures are so well preserved in the fossils that the soft tissues of their bodies, including the muscles, guts, eyes, gills, mouths and other openings are all still visible. The 4,351 separate fossils excavated so far represent 101 species, 53 of them new.Ian Sample, “‘Mindblowing’ haul of fossils over 500m years old unearthed in China” at The Guardian

We are told that this Qingjiang discovery is important for its diversity, especially of cnidarians (corals and jellies). The new fossils represent a different ecology from previous discoveries in China at Chengjiang. The Cambrian era seems to have been more complex than thought.

Paper. (paywall)

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See also: Surprise Superhighway: Cambrian Worms Lived In “Unsustainable” Ocean 500 Mya

and

Complex Worm Find From Cambrian (541-485 Mya) “Helps Rewrite” Our Understanding Of Annelid Head Evolution

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Published on March 22, 2019 04:42

March 21, 2019

Templeton winner Marcelo Gleiser endorses the Rare Earth principle

Earth/NASA, DSCVR That is, Earth is unusual rather than common. In an interview with Scientific American, which mainly wanted to talk about his view that atheism is inconsistent with the scientific method. But about Earth as rare:

Gleiser – Own work//CC BY-SA 4.0

Scientific American: So, a message of humility, open-mindedness and tolerance. Other than in discussions of God, where else do you see the most urgent need for this ethos?

You know, I’m a “Rare Earth” kind of guy. I think our situation may be rather special, on a planetary or even galactic scale. So when people talk about Copernicus and Copernicanism—the ‘principle of mediocrity’ that states we should expect to be average and typical, I say, “You know what? It’s time to get beyond that.” When you look out there at the other planets (and the exoplanets that we can make some sense of), when you look at the history of life on Earth, you will realize this place called Earth is absolutely amazing. And maybe, yes, there are others out there, possibly—who knows, we certainly expect so—but right now what we know is that we have this world, and we are these amazing molecular machines capable of self-awareness, and all that makes us very special indeed. And we know for a fact that there will be no other humans in the universe; there may be some humanoids somewhere out there, but we are unique products of our single, small planet’s long history.

The point is, to understand modern science within this framework is to put humanity back into kind of a moral center of the universe, in which we have the moral duty to preserve this planet and its life with everything that we’ve got, because we understand how rare this whole game is and that for all practical purposes we are alone. Lee Billings, “Atheism Is Inconsistent with the Scientific Method, Prizewinning Physicist Says” at Scientific American

Good chance they don’t like any of this.

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See also: Templeton winner: Atheism is inconsistent with scientific method Marcelo Gleiser: “Atheism is a belief in non-belief. So you categorically deny something you have no evidence against.”

Apparent non-crackpot physicist wins Templeton Prize Marcelo Gleiser sounds as though he thinks that the great mysteries of physics are about this universe, not space aliens, computer sim universes, cyborgs, and so forth (for another view, see 2011 Templeton winner Sir Martin Rees).

Hugh Ross: The fine-tuning that enabled our life-friendly moon creates discomfort Was it yesterday that we noted particle physicist Sabine Hossenfelder’s view that fine-tuning is “a waste of time”? Not so fast. If the evidence points to fine-tuning and the only alternative is the crackpot cosmology she deplores, it’s not so much a waste of time as a philosophically unacceptable conclusion. Put another way, it comes down to fine-tuning, nonsense, or nothing.

and

What becomes of science when the evidence does not matter?

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Published on March 21, 2019 14:28