Michael J. Behe's Blog, page 587

Prehistoric artists 38 kya used Van Gogh-type technique

detail demonstrates technique, in Paul Signac, Femmes au Puits, 1892/Musee d’Orsay, Paris

From Laura Geggel at LiveScience:

Archaeologists found 16 limestone tablets dating to the Aurignacian period, named for the first known people to settle in Europe. The tablets were engraved with pictures of horses, mammoths and aurochs (extinct wild cows). Most notably, the pictures were drawn using a series of dots and lines — or as archaeologists call the technique, pointillism.

Modern pointillism was invented in the 1880s by Georges Seurat and Paul Signac, who developed the technique by using small dots to create the illusion of a larger image. Other artists, including Camille Pissarro and Roy Lichtenstein, followed suit. More.

We know we are dealing with stasis in human evolution when we now find ourselves referring to “modern” pointillism.

See also: Possibly oldest European rock art to date found in France

The search for our earliest ancestors: signals in the noise

Stasis: Life goes on but evolution does not happen

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Big squawks over bird speciation?

From Andrew Jenner at

In July 2008, an American ornithologist named Bret Whitney was researching antbirds in the Brazilian Amazon when he heard a curious bird song. The sound, to his expert ear, clearly belonged a Striolated Puffbird––a big, streaky creature that looks like an owl crossed with a kingfisher. But it also had a smoother quality that struck him as “off-the-charts different” from the slightly warblier songs he knew from elsewhere in the region.

He divided the Puffbird into an additional three new species, based on this information but in the ensuing dispute the American Ornithological Society was willing to recognize only one new species:

Failing to see the logic behind this decision, Whitney regards it as “just nuts.” But it’s not unusual for things to get messy in the world of avian taxonomy, which addresses a fundamentally impossible task: the scientific imperative to label and sort amid the ever-evolving reality of life on Earth. An ostrich is definitely not a bald eagle, nor is a Canada goose a mallard. But the closer you zoom, the fuzzier things get. Are the Striolated Puffbirds of the western Amazon who stutter at the start of their songs different enough from other Striolated Puffbirds to merit full species status? What is a species, exactly, and where do the lines between one and another lie?

Sure, it’s messy. But there’s more going on here. Many fields are inherently messy.

I could tell you the word count that supposedly differentiates a novella from a novel.* But would you be surprised if a well-known novella were routinely classed as a novel? And who cares if it is? Nothing is at stake unless one is quoting on a rush job over the phone in the publishing industry.

Is there a “crisis” in cosmology or does it merely face “challenges”?

history of universe assuming cosmic inflation/Yinweichen

For the crisis, go here. For the “challenges,” see Anna Ijjas, Paul J. Steinhardt, and Abraham Loeb at Scientific American:

The latest astrophysical measurements, combined with theoretical problems, cast doubt on the long-cherished inflationary theory of the early cosmos and suggest we need new ideas. (paywall) More.

We remember when inflation was beyond dispute. It promised naturalists a multiverse. But science is now merely one expression of naturalism, so we can be sure that doubts about inflation will not cause doubts about the multiverse.

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

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Origin of life: Horizontal gene transfer “negligible” and endosymbiosis “wrong” as factors in earliest known life?

From science writer Suzan Mazur, author of Paradigm Shifters, continuing her interview at Huffington Post with Swedish deep evolution investigators Charles Kurland and Ajith Harish regarding

… their central position on deep evolution, which is that the most recent universal common ancestor (MRUCA) is complex not a simple bacteria and “is the root of eukaryote and akaryote lineages” containing “more than a thousand Superfamilies.” Kurland and Harish think MRUCA represents complex survivors from a now extinct biosphere.

On horizontal gene transfer as routine:

Charles Kurland: We have to remember there’s only a little background of horizontal gene transfer in bacterial populations. The simple reason is that bacteria eat DNA. So sequences are going in all the time. Most of them get chopped up.

However,

But I agree completely with what Jeff Errington said. We think that the most recent universal common ancestor [MRUCA] was the product of a lot of HGT and Carl Woese described the reasons for this.

On endosymbiosis:

The thing is once you see the phylogeny of the sort that we have, that Ernst Mayr predicted, where the akaryotes are separated in their descent from the eukaryotes, the obvious possibilities for akaryotes to make eukaryotes are just not there. But that’s the essence of the symbiosis hypothesis — the bacteria gets together with an archaea and it makes a eukaryote, the bacteria becomes the mitochondria and the archaea becomes the nucleus cytoplasmic host. That’s the theory. It’s very, very clearly specified that way.

It’s interesting because it was Lynn’s [Margulis] attempt to explain why DNA was found in the cytoplasm of eukaryotes, and it turned out to be DNA located in mitochondria. It turned out to be DNA located in chloroplasts. Her idea was that: Ah, the mitochondria, the chloroplast, certain kinds of flagella, were actually originally bacteria. Her idea was that if you look at mitochondria, the DNA that was there was the whole genome of that bacteria.

It turns out that it’s nothing like that. And we should have been much more suspicious of the hypothesis as soon as it was discovered that a minor fraction of information for mitochondria is coded in the mitochondria. We should have been very suspicious of that.

These models may, of course, reappear, refurbished with new evidence.

Later in the interview, Kurland notes that he is not an ardent fan of dogma in science:

It’s definitely a problem. It gets embedded in the education system. There’s no one who takes a biology course that does not believe archaea plus bacteria make eukaryotes. It’s a rule now. It’s beyond criticism now. Well, let’s see if we can change that.

His view is highly advisable:

Suzan Mazur: You’ve gotten some serious support there from the Royal Swedish Science Academy, from the Nobel Committee.

Charles Kurland: Yes. But I think if it were up to most molecular evolutionists, we would be starved to death. More.

Ah yes. Survival of the fittest really is true in some places.

Origin of life: We are all descended from a “complex” ancestor?

From science writer Suzan Mazur, author of Paradigm Shifters, at Huffington Post:

I recently had a three-way phone conversation with Swedish deep evolution investigators Charles Kurland and Ajith Harish about their phylogenomic Tree of Life (ToL) based on protein structure, which shows that we are descended from a “complex” ancestor — MRUCA (most recent universal common ancestor) — not a simple bacteria. Kurland and Harish think a ToL paradigm shift may be in order. What’s more, Kurland and Harish figure that MRUCA was not the first ancestor, but represents complex survivors of a now-extinct biosphere.

The findings of Kurland and Harish challenge not only mainstream ToL perspectives, but also those of endosymbiosis hypothesis fans, as well as the “HGT industry” — as Kurland describes the inflated role he sees assigned to lateral gene transfer in evolution.

…

Charles Kurland: There’s a commonality between archaea, bacteria and eukaryotes. The universal common ancestor is the root of eukaryote and akaryote lineages and it contains more than a thousand superfamilies!

The other really remarkable thing, the thing that really stunned us is that there were people before us who had seen this also and at the time were totally ignored. The people I have in mind are Christos Ouzounis and his collaborators from Cambridge. They recognized that the universal common ancestor was a very complex ancestor. It is apparently a very big genome. But, now I have to qualify that. We cannot say more than that the universal common ancestor is a population. We don’t know how it is structured. We have no idea how many species/populations are in that ancestor.

The researchers think that Snowball Earth was a key factor but…

Charles Kurland: It’s not simply Snowball Earth. It’s Snowball Earth that recovers in a volcanic period where temperatures go off-scale. It’s not clear what the crunch is, whether it’s the Snowball ice, per se, or what some people say is a Slushball. It’s not necessarily the low temperatures that are killing off the preexisting organisms. It can be the recovery. The volcanism can drive the temperatures up so high that much on this surface cannot survive.

The other thing is this. If you look at the fossil remains, at the micrographs that the paleontologists can produce — it’s very interesting. They have by microscopic examination what they very tentatively identify as bacterial groups. But actually identifying bacteria in rocks as fossils is a tough game, and I think that none of those identifications are worth the paper they’re printed on. More.

In the biosphere we know, there was probably never any such thing as a “simple” cell, which is the likely reason the innumerable “it all comes down to” theories of the origin of life don’t work. But now, how can we research pre-Snowball Earth?

Note: These excerpts are from Part I of Mazur’s interview, “Kurland & Harish Rethink Deep Evolution”.  Here is Part II.

See also: Origin of life: Do L-form bacteria hint at origin of primordial cells? So then the ability to switch back and forth is a form of stasis from earliest times?

Origin of life: Iceball Earth is back

Maybe if we throw enough models at the origin of life… some of them will stick?

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

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RNA self-editing: “It sounds simple, but in real life it was really complicated”

[image error]

RNA molecule graphic/Feldman, Wikipedia

From Kelly Rae Chi at Nature:

n 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs — the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ‘A-to-I editing’ can alter a protein’s coding sequence, and, in humans, is crucial for keeping the innate immune response in check. “It sounds simple, but in real life it was really complicated,” Rechavi recalls. “Several groups had tried it before and failed” because sequencing mistakes and single-nucleotide mutations had made the data noisy. But using a new bioinformatics approach, his team uncovered thousands of sites in the transcriptome — the complete set of mRNAs found in an organism or cell population — and later studies upped the number into the millions1.

Inosine is something of a special case: researchers can readily detect this chink in the armour by comparing DNA and RNA sequences. But at least one-quarter of our mRNAs harbour chemical tags — decorations to the A, C, G and U nucleotides — that are invisible to today’s sequencing technologies. (Similar chemical tags, called epigenetic markers, are also found on DNA.) Researchers aren’t sure what these chemical changes in RNA do, but they’re trying to find out.

…

That said, epitranscriptomics researchers are excited about the direction their field is taking. “Just as you wouldn’t think of DNA without thinking about how DNA is packaged, or epigenetically modified,” says geneticist Chris Mason at Weill Cornell Medical College in New York City, who has led m6A-mapping efforts, “I think now and in the future, no one will think of RNA without thinking ‘How is it modified?’” target=”another”>More.

As RNA joins DNA as an immensely complex language, information theory is likely to become more important and simplistic Darwinian thinking much less so. But don’t expect to hear the matter put plainly.

See also: Junk RNA helps embryos sort themselves out

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Education PhD candidate: Objectivity in science is sexist.

From Joy Pullmann at Federalist:

College science classes are hostile to women and minorities because they use the scientific method, which assumes people can find reliable truths about the natural world through careful and sustained experimentation, concludes a recent dissertation by a doctoral candidate at the University of North Dakota.

Laura Parson, a student in the university’s education department, reviewed eight science class syllabi at a “Midwest public university” and said she discovered in them a hidden hostility to women and minorities:

…

Instead of promoting the idea that knowledge is constructed by the student and dynamic, subject to change as it would in a more feminist view of knowledge, the syllabi reinforce the larger male-dominant view of knowledge as one that students acquire and use make [sic] the correct decision. More.

The dissertation’s abstract does not immediately signal the rottenness within:

Abstract: This study explored the gendered nature of STEM higher education institution through a feminist critical discourse analysis of STEM course syllabi from a Midwest research university. I explored STEM syllabi to understand how linguistic features such as stance and interdiscursivity are used in the syllabus and how language and discourses used in the syllabus replicate the masculine nature of STEM education. Findings suggest that the discourses identified in the syllabi reinforce traditional STEM academic roles, and that power and gender in the STEM syllabi are revealed through exploration of the themes of knowledge, learning, and the teaching and learning environment created by the language used in the syllabus. These findings inform and extend understanding of the STEM syllabus and the STEM higher education institution and lead to recommendations about how to make the STEM syllabus more inclusive for women. Dissertation.

But we go on to read,

Another aspect of the chilly climate is competitiveness, and the STEM syllabi were also framed as competitive courses, exemplified by grading on a curve, “The final grading scale may be curved based on class performance” (Lower level biology). Grading on a curve is one way that the literature has found to be competitive and discouraging to women and minorities (Shapiro & Sax, 2011). Finally, the competitive, difficult chilly climate was reinforced in the syllabi through the use of unfriendly and tough language, “Do not ask me to figure out your grade standing. I’ll be glad to show you how to do it yourself, but the homepage includes that explanation already” (Lower level geology). Like this statement, many of the syllabi used language that was unfriendly and reinforced the individualistic, difficult and competitive nature of the STEM classroom. Throughout the syllabi, the chilly climate was reinforced through language use and the selection of assessments and teaching methods.

So, if some can’t stand the heat, we just turn off the power to the kitchen!

At Federalist, Pullmann adds, regarding Parson’s claims,

In education theory this exhibits itself as a theory called “constructivism,” and teachers who subscribe to it say students should be set free to “construct their own knowledge” by exposing them to many different environments and giving them freedom to select their own courses of study and even lessons and reading material.

But cognitive research throws cold water over this outdated and ineffective theory about how people learn. It turns out that refusing to give students explicit instruction or set their course of study drastically increases minority achievement gaps. It also turns out that people do construct knowledge, but not independently; we develop knowledge best when it is directly and explicitly transmitted to us as an objective reality to digest. More.

But Pullmann, that’s a benefit, not a feature, as far as the education industry is concerned. For decades,  government will throw ever more money at educrats to “fix” the very problems that the industry now exists only to perpetuate. Discouraging objectivity in science students supports their goal.

And, overall, wow! This is right up there with Julie Shaw in Scientific American, on the benefits of post-fact science.  Let’s see now, we’ve also got a war going against falsifiability and Occam’s razor, plus a huge influx of feelgood fake physics stories and mounting scandals in peer review.

As we’ve noted, the real problem with all the “marchin, marchin” for science these days is that the troubles killing science are back at the desk. They are not caused by anti-science villains but by people the marchers would probably feel compelled to embrace and march alongside.

It’s like a drug. Get help, people, before you forget what sobriety felt like.

Note: I (O’Leary for News) am leaving it to whoever wants to jump in to make the point that women and minorities should be offended by the idea that they are not capable of thinking objectively. The main thing to ask here is not “Why is this idea stupid?” (But do go on and tell us, if you feel like it…)

No, the main thing to ask is, why is Parson’s view considered reputable and reasonable? If Big Science chooses to throw in its lot with educrats like these, it will have much to answer for.

See also: A scientist on the benefits of post-fact science

2016 worst year ever for “fake physics”?

Jason Rosenhouse: Multiverse is a “done deal,” Occam’s razor doesn’t apply

March for Science in Boston: Geek sign language to ponder

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Blowing up mathematics

From Jordana Cepelewicz at Nautilus, on mathematician Harvey Friedman:

The foundations of mathematics is also a field—in stark contrast to the casual and light tone of Friedman’s emails—that has been in crisis for nearly a century. In 1931, the Austrian mathematician and philosopher Kurt Gödel proved that any logical system adequate to develop basic arithmetic gives rise to statements that cannot be proven true or false within that system. One such statement: that the system itself is consistent. In other words, no system can ever prove itself to be free of contradiction. The result seemed to present an insurmountable problem for mathematicians, not so much because it prevented them from ever knowing whether the system their work is built on is consistent (so far there haven’t been inconsistencies), but because it meant their fundamental logic had significant limitations.

So mathematicians got by with a system called ZFC:

And so something odd happened: Mathematicians chose to move on. Incompleteness, they decided, had no direct bearing on their own work. The axioms commonly known as ZFC (the Zermelo-Fraenkel axioms plus the axiom of choice) that constitute today’s most commonly used foundation of mathematics provides a rigorous framework for proving theorems.

…

Friedman proved that for any set in the rational cube (from three to an arbitrary number of dimensions), there is a maximal emulation with drop symmetry between specific pairs of points. To prove that theorem and identify the points for which it holds, he had to rely on a system stronger than ZFC. That is to say, it cannot be refuted, nor can it be proven, in ZFC.

Showing the theorem is not refutable is a pretty standard (although certainly not simple) process: Demonstrate that it logically follows from the consistency of large cardinal axioms. Showing it’s not provable, on the other hand, is more difficult. He did this with a proof by contradiction: He began with the assumption that he could prove his theorem in ZFC, and then constructed from it a system of objects in which ZFC holds. Which means that if his theorem holds true, then ZFC is consistent—and, transitively, that ZFC has proven its own consistency. But by Gödel’s incompleteness theorem, that cannot possibly be the case. And so, the theorem cannot be proven in ZFC. He’s working to extend the theory to other types of symmetries, other definitions of “maximal,” and other types of objects.

…

With a broadened foundational diversity may come new opportunities to solve old problems. In his 1960 essay “The Unreasonable Effectiveness of Mathematics in the Natural Sciences,” physicist Eugene Wigner recalls a student asking a perspicacious question: “How do we know that, if we made a theory which focuses its attention on phenomena we disregard and disregards some of the phenomena now commanding our attention, that we could not build another theory which has little in common with the present one but which, nonetheless, explains just as many phenomena as the present theory.” Wigner goes on to note that the idea is a valid one—or, at least, that there’s never been any evidence to suggest this wouldn’t happen. More.

Mathematics is probably safe from Harvey Friedman if 2 + 2 continue to make 4.

See also: How was mathematics woven into reality?

and

Mathematics challenges naturalism, says math prof

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Do true believers hold back society?

An unexpectedly level-headed discussion from Tom Mahony at RealClearScience:

Ironically, true believers often moralize about the importance of facts and insist they’re the only ones who are “reality based.” However, in practice, they confuse facts with assumptions, beliefs, conjecture, and opinion. If you take an incorrect assumption, assume it as fact, and extrapolate from that assumption, even if the logic of the extrapolation is sound, the whole idea is wrong because the foundational assumption is wrong. Garbage in, garbage out. Yet, since true believers mistake their incorrect assumption for fact, and tout their impeccable extrapolation, you’re the kook. This is what passes for logic in the true-believer community.

True believers haunt any subject: science, religion, health, history, economics, politics. The distinction is not the subject matter, but the treatment of evidence and dismissal of same. True believers are not restricted to any particular political affiliation, ideology, culture, gender, age, metaphysical belief system, or education level. They can occur anywhere, but seem especially concentrated in partisan politics, dogmatic religion, and scientific materialism.

True believers include believers in scientific materialism? Yes, yes, everyone knows that what Mahony says is true and that it is drowning science in nonsense (cf crackpot cosmology). But the pop science media is a temple and, you know, death to unbelievers and all that …

Science has, for centuries, been vital to discovering evidence about the natural world and countering religious dogma. But calling yourself a “scientist” doesn’t inoculate you from true-believer status. Science is an empirical study that is both open minded and skeptical. Not all scientists practice this. Dogmatic adherents to scientific materialism, despite abundant evidence to the contrary, are a perfect example. (They will argue vehemently against this characterization, but present them with evidence countering materialism and see what happens.) More.

See what happens? When the smoke cleared, Uncommon Descent was still here. But yes, it was a blast.

See also: great physicists

and

Neuroscience tried wholly embracing naturalism, but then the brain got away

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Health sciences: But just what IS a medical myth?

Sugar: Current villain in human mortality

From Robin Nixon, Elizabeth Peterson and Karen Rowan (October 2016) at LiveScience:

25 Medical Myths that Just Won’t Go Away

Despite what you may have heard, drinking eight glasses of water a day isn’t the key to good health. Also, neglecting to wear a coat on a cold day won’t make you sick. And — you might want to sit down for this — pregnancy doesn’t last nine months.

Health-related myths are often repeated as fact, even though any diligent Google search will reveal the truth behind these fallacies. Here are 26 of the most common medical myths, debunked.More.

Hmmm. Some women distinctly recall pregnancy lasting a year and a half.