Michael J. Behe's Blog, page 561

Can beavers contribute to evolution by transforming the tundra?

That thing the beaver is sitting on is its paddle tail.

Anyone familiar with beavers will know that the big busy rodents can transform roads into ponds. They are making a comeback in Alaska:

Beavers may be infiltrating the region for the first time in recent history as climate change makes conditions more hospitable, says Ken Tape, an ecologist at the University of Alaska Fairbanks. Or maybe the expansion is a rebound after trapping reduced beaver numbers to imperceptible levels in the early 1900s, he says. Nobody knows for sure.

And the full range of changes the rodents are generating in their new Arctic ecosystems hasn’t been studied in detail. But from what Tape and a few other researchers can tell so far, the effects could be profound, and most of them will probably be beneficial for other species.Sid Perkins, “Beavers are engineering a new Alaskan tundra” at Science News

The main thing beavers will do is add to the biodiversity by creating ponds as habitat for fish, amphibians, and waterfowl and also, one suspects, producing kits for wolves and coyotes to stalk.

No surprise if some of the changes beavers introduce get classified as evolution in the sense that various lifeforms may produce offspring adapted to the new conditions that then get classified as new “species.” No one is likely to wait around to see if the changes are easily reversible potentials in the whole group, manifested in some.

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See also: Biogeography: Life before ecology, when Canadian beavers overran Tierra del Fuego

Researcher: Human impact is reshaping the tree of life

Devolution: African elephants survive by shedding their tusks (no interest to poachers) The trait (no tusks or else have tiny tusks) was there all along but became an asset when the main foe was attracted to, rather than deterred by, tusks. The double whammy may have meant even more rapid change.

John Sanford on claims about brand new nylonase genes

and

Beavers illustrate complex specified information, they don’t author it.

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Hi tech mogul tells campus autocrats to grow up or get lost

Well, PayPal’s Peter Thiel put it more politely but… that’s the bottom line. We don’t usually hear tech moguls talking this way. More frequent news is stuff like Is it Google-com or Google.gov? or Digital dictatorship.

But Thiel thinks the riot is over:

“The reformation is going to happen,” Thiel added, noting it won’t come from within, but from the “outside.”

Thiel made the comments in a keynote speech at the Intercollegiate Studies Institute’s Collegiate Network editors’ conference. The group funds independent and conservative-minded campus news outlets at universities across the nation, and Thiel is an alumnus of the 39-year-old nonprofit, founding the Stanford Review in the late 1980s.

…

In reality, higher education is in trouble, he said, citing the ballooning student debt crisis, the lack of instruction that translates into marketable skills, and the fact that even though universities have seemingly endless resources — “they’re not delivering in any way.” Jennifer Kabbany, “Peter Thiel predicts ‘reformation’ of higher education in speech to student journalists” at The College Fix

Who wants to fund a riot anyway?

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See also: Without free speech, science would be back in the Stone Age It makes as much sense to blame dead white guys for upending cozy sanctimonies about how the world works as to blame the person who tries to cross the bridge that collapsed for the fact that the bridge collapsed. True, some people are more likely to want to cross a bridge than others but the first foot is not the reason it collapsed.

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Media are flabby from a diet of junk science

Should we believe them when they tell us that the drinking four cups of coffee daily lowers our risk of death people with spouses live longer? A statistician and a physician team up to

explain why not:

A subtler manifestation of dishonesty in research is what amounts to statistical cheating. Here is how it works… If you try to answer one question – by asking about levels of coffee consumption, for example, to test whether drinking certain amounts a day are associated with more or less cancer; or whether being married is associated with increased longevity — and test the results with appropriate statistical methods, there is a 5% chance of getting a (nominally) statistically significant result purely by chance (meaning that the finding isn’t real).

If you try to answer two questions, the probability is about 10%. Three questions, about 14%. The more you test, the more likely you’ll get a statistical false positive, and researchers exploit this phenomenon. Researchers have thereby created what is for them a winning “science-business model”: Ask a lot of questions, look for associations that may or may not be real, and publish the result. Just how many questions are typical in a university research project? It varies by subject area, and researchers have become masters at gaming their methodology. Often, they ask thousands of questions. And they get away with it, because there are no scientific research cops … S. Stanley Young & Henry Miller, “Junk Science Has Become a Profitable Industry. Who Will Stop It?” at RealClearScience

A writer raises another point:

Science “journalists” are a huge part of the problem. If the talking points make for a good headline, like Young and Miller’s example about coffee, then the “research” will get written up, no questions asked.

Young and Miller ultimately ask what can be done to save science, and suggest the solution might fall on government funding agencies “to cut off support for studies with flawed design; and to universities, which must stop rewarding the publication of bad research.” But since so many studies these days just confirm preconceived notions, it seems unlikely that partisans at federal agencies or congressional appropriators will stop giving funds. Ashe Schow, “‘Junk Science’ Is Everywhere, And The Media Eat It Up” at Daily Wire

Not only that, one might add that many media feel a sense of virtue about running with this stuff. Unlike hearing the latest and greatest on a celeb bust-up, it’s supposed to be good for people’s health. But of course, the reality is that if it’s just misinformation, it could be worse for people’s health than hearing the latest about the bust-up.

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See also: From RealClearScience: No, we can’t trust government data on diet and nutrition. Censored researchers: Nutrition is a “degenerating” research paradigm. Also: The skinny on salt, veggie oil, skim milk, whole foods. Nutrition science is nearly baseless but it rules.

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Without free speech, science would be back in the Stone Age

Every new idea, good or bad, has had its establishment detractors who want Something To Be Done about the hateful people who make them uncomfortable. Joe Miller and guests talk about science and free speech at More Than Cake:

In the tradition of natural law theorists such as John Stuart Mill, Free Speech is considered one of the most fundamental of human rights, yet this right is attacked today as a vestige of racist white Western civilization that oppresses minorities and gender-equality warriors. Today the guys look at attacks on free speech happening on our college campuses and argue from a Christian worldview why protecting this right matters to all of us regardless of political affiliation.

It makes as much sense to blame dead white guys for upending cozy sanctimonies about how the world works as to blame the person who tries to cross the bridge that collapsed for the fact that the bridge collapsed. True, some people are more likely to want to cross a bridge than others but the first foot is not the reason it collapsed.

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See also: Do racial assumptions prevent recognizing Homo erectus as fully human?

J.R. Miller on Darwinism, racism, and human zoos

and

Was Neanderthal man fully human? The role racism played in assessing the evidence

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Quantum physicist: The particle itself does not know where it is

In this 2018 video, quantum physicist Anton Zeilinger explains the essence of quantum physics for a general audience:

The skinny, courtesy Philip Cunningham:

40 sec: Every object has to be in a definite place is not true anymore…

The thought that a particle can be at two places at the same time is (also) not good language.

The good language it that there are situations where it is completely undefined where the particle is. (and it is not just us (we ourselves) that don’t know where the particle is, the particle itself does not know where it is). This “nonexistence” is an objective feature of reality…

5:10 min:… superposition is not limited to small systems…

7:35 min:… I have given lectures on quantum physics to children, 6 and 7 years old, and they understand the basic concepts of quantum physics if you tell them the right way…

9:00 min:… the main issue (with quantum mechanics) is interpretation. What does it mean for our view of the world… “emotional” fights happen over what it means…

15:45 min:… the fact that some of the brightest minds in physics have been working on this issue, (i.e. The unification of General Relativity and Quantum Mechanics), for 80 years now at least, and have not found a solution means that the solution will be extremely deep. It will be extremely significant if somebody found it, and it will probably be in a direction where nobody expected it…

16:55:… Dark matter and Dark energy smell a little bit like the (fictitious) ether in the old electrodynamic theory…

17:30:… In quantum mechanics we have the measurement paradox (i.e. measurement problem)… I think it (the measurement paradox) tells us something about the role of observation in the world. And the role of information.,, Maybe there are situations where we have to reconsider the “Cartesian cut”*

* The Cartesian cut is a metaphorical notion alluding to Decartes’ distinction of res cogitans (thinking substance) and res extensa (extended substance). It plays a crucial role in the long history of the problem of the relationship between mind and matter and is constitutive for the natural sciences of today. While the elements of res cogitans are mental (non-material) entities like ideas, models, or concepts, the elements of res extensa are material facts, events, or data. The conventional referents of all natural sciences belong to the latter regime.

Hat tip: Philip Cunningham

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See also: Quantum mechanics: Pushing the “free-will loophole” back to 7.8 billion years ago (concerns Anton Zeilinger’s work)

and

Twisted light can carry arbitrarily large amounts of information – a find friendly to theism?

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Gene that controls for animal size may have been identified

mega-morph finch (really large beak)/Tom Smith, UCLA

From ScienceDaily:

The birder and biologist was Tom Smith, who has spent his career studying finches — specifically, black-bellied seedcrackers (Pyrenestes ostrinus) — in Cameroon and in his lab at the University of California-Los Angeles.

He and his colleagues have spent years investigating why some of these finches have small beaks while others have large beaks. Much of their original work identified differences in the hardness of the seeds they eat, a story quite similar to that of Darwin’s finches. Smith, who is a professor at UCLA as well as the founding director of the Center for Tropical Research, established a breeding colony of these finches to understand the inheritance of beak size.

The result was startlingly and elegantly simple: Mendelian genetics, best known to generations of high school students through Punnett squares. The larger beak was the dominant trait, so two small-billed parents could only have small-billed offspring, but if either parent had a large bill, their offspring would have a mix of large and small bills, perfectly matching the 3:1 pattern predicted by Gregor Mendel centuries ago.

“You never get this!” said vonHoldt with a laugh. “Traits rarely show such a clean pattern of inheritance, especially traits that are very central to fitness in a wild population.”

That Mendelian pattern was the key, said vonHoldt. With new technology to analyze the entire genome, combined with the Smith’s years of ecological data and insights, they had all the pieces to find and understand the genes behind this mystery.

Smith had found the Mendelian pattern in these Cameroonian birds through observation, but he hadn’t been able to identify the gene responsible for it. But when vonHoldt compared the genes of the large-beaked birds to those of their smaller-beaked counterparts, she found one stretch of DNA — 300,000 base pairs, apparently inherited as a chunk — that always varied between finches of large and small beak size. And right in the middle of that piece of chromosome was the gene IGF-1, familiar to vonHoldt from canine genetics.

“In dogs, this is a giant gene, literally and figuratively,” she said. “It’s a growth-factor gene. In dogs, if you change how it’s expressed, with just a few genetic changes you can change a normal-sized dog into a dwarfed, teacup-sized dog.”

The gene can affect a specific trait or a whole animal, depending where it’s located on the genome and when it is expressed. “If this gene is expressed more, you expect a larger trait: a larger body, a larger foot, a larger ear, whatever it is controlling. It then is easy to imagine that with a small change to this gene, traits could very easily change in size or shape. We suspect this is the story here, with these beaks,” vonHoldt said.

Smith and his colleagues had already determined that beak size affected diet — whether a finch lived on large or small seeds — but it didn’t seem to have any impact on mate selection. “Females don’t prefer males with a large beak, or vice-versa,” said vonHoldt.

In these birds, the bill was the only trait changing size; large-beaked and small-beaked black-bellied seedcrackers are otherwise identical. But Smith also discovered a third morph of these finches, which he called the “mega” variety, with an even bigger bill and a larger overall body size.

After examining the genes, vonHoldt discovered that the “mega” is genetically distinct from the small- and large-beaked morphs. Not only does it carry two copies of the large allele — like the large-beaked finches — but it also has other chromosomal changes, apparently the product of an additional evolutionary step. Paper. (open access) – Bridgett M. vonHoldt, Rebecca Y. Kartzinel, Christian D. Huber, Vinh Le Underwood, Ying Zhen, Kristen Ruegg, Kirk E. Lohmueller, Thomas B. Smith. Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nature Communications, 2018; 9 (1) DOI: 10.1038/s41467-018-07374-9 More.

Note: “You never get this!” said vonHoldt with a laugh. “Traits rarely show such a clean pattern of inheritance, especially traits that are very central to fitness in a wild population.” It may turn out to be a bit more complex than this but it’s nice to know that sometimes Mendelian genetics really does work.

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See also: Mammals get smaller when the climate heats up?

Researchers: Island rule of size evolution does apply to rodents

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Stephen Hawkings’ views outside physics were more noted than notable

That’s a common problem when we ask great figures their opinion about things they haven’t studied. From a review of Stephen Hawking’s (1942–2018) last book (or the last book that could be put together plausibly under his name), Brief Answers to the Big Questions:

Because of the likelihood of a nuclear confrontation or an environmental catastrophe, we should work out how to leave the planet and colonise space, Hawking reckons. “Spreading out,” he says, “may be the only thing that saves us from ourselves.” He concedes that move will involve abandoning the flora and fauna of Earth, but Hawking seems to believe that humans deserve more of a future than other species. Leaving all other life to fend for itself is something humanity will have to have “on our conscience”.

This is strange, since he has said elsewhere that “we will need to consider transporting several thousands of people, animals, plants, fungi, bacteria and insects”. And here we reach the slightly perplexing nature of this book. It was “in development” at the time of Hawking’s death, and has been pulled together from speeches, interviews and essays. It’s unclear where Hawking’s words end, and where the voice of colleagues, collaborators, family and the Stephen Hawking Estate begins. Michael Brooks, “The hawking of Stephen: is Brief Answers to the Big Questions more spin than science?” at New Statesman

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See also: Stephen Hawking’s final paper, just released, tackled the “information paradox”

Did the dying Stephen Hawking strengthen the case for God by reintroducing fine-tuning?

Stephen Hawking’s final theory scales back multiverse

Sabine Hossenfelder: Hawking’s final theory is just one of a thousand speculations

and

Did Stephen Hawking discover a means of detecting parallel universes just before he died?  This sounds a lot like grief talking but we’ll see.

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Can AI help scientists formulate ideas?

Yes, if you mean “dumb AI,” and there ain’t no “smart AI”:

Quantity is definitely a solved problem. STM, the “voice of scholarly publishing” estimated in 2015 that roughly 2.5 million science papers are published each year. Some are, admittedly, in predatory or fake journals. But over 2800 journals are assumed to be genuine. From all this, we can deduce that most scientists have not read most of the literature in their field, though they probably read immediately relevant or ground-breaking findings.

But the question has arisen whether, in some cases, scientists have even read papers in which they are listed as authors. A report in Nature (September 2018) revealed that “Thousands of scientists publish a paper every five days” or 72 papers a year:“Quantity vs. quality: Can AI help scientists produce better papers?” at Mind Matters

The sensible reaction, as one author put it, is, this is absurd…

See also: Who does the concept of “intellectual property” really benefit? Was traditional copyright law meant to protect algorithms that decide people’s financial fate?

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Mathematician: Our universe is really chaotic; we just don’t see it that way

Is it only selective attention that causes us to see order in the universe?

There is another, more interesting, explanation for the structure of the laws of nature. Rather than saying that the universe is very structured, say that the universe is mostly chaotic and for the most part lacks structure. The reason why we see the structure we do is that scientists act like a sieve and focus only on those phenomena that have structure and are predictable. They do not take into account all phenomena; rather, they select those phenomena they can deal with.

Some people say that science studies all physical phenomena. This is simply not true. Who will win the next presidential election and move into the White House is a physical question that no hard scientists would venture to give an absolute prediction. Whether or not a computer will halt for a given input can be seen as a physical question and yet we learned from Alan Turing that this question cannot be answered. Scientists have classified the general textures and heights of different types of clouds, but, in general, are not at all interested in the exact shape of a cloud. Although the shape is a physical phenomenon, scientists don’t even attempt to study it. Science does not study all physical phenomena. Rather, science studies predictable physical phenomena. It is almost a tautology: science predicts predictable phenomena. Noson S. Yanofsky, “Chaos makes the multiverse unnecessary” at Nautilus

If we stopped noticing the order, would it still be there?

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See also: The multiverse is science’s assisted suicide

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Human origins upended once again

We humans must have originated in some kind of a cement mixer, to judge from recent reports.

Making stone tools (Oldowan technology) is believed to have started in East Africa 2.6 million years ago and spread from there. But archaeologists recently found stone tools and butchered animals on a high plateau in Algeria:

The newly discovered limestone and flint tools are about 2.4 million years old — almost the same age as the oldest known such tools, which were found in Gona, Ethiopia, and are 2.6 million years old.

The discovery means that hominins were present in the Mediterranean fringe of North Africa around 600,000 years earlier than previously thought. Aisling Irwin, “Algeria fossils cast doubt on East Africa as sole origin of stone tools” at Nature

and

Abstract: East Africa has provided the earliest known evidence for Oldowan stone artifacts and hominin induced stone tool cutmarks dated to ~2.6 million years ago (Ma). The ~1.8 Ma stone artifacts from Ain Hanech (Algeria) were considered to represent the oldest archaeological materials in North Africa. Here we report older stone artifacts and cutmarked bones excavated from two nearby deposits at Ain Boucherit estimated to ~ 1.9 Ma, and the older to ~2.4 Ma. Hence, the Ain Boucherit evidence shows that ancestral hominins inhabited the Mediterranean fringe in Northern Africa much earlier than previously thought. The evidence strongly argues for early dispersal of stone tool manufacture and use from East Africa, or a possible multiple origin scenario of stone technology in both East and North Africa. (open access) – Mohamed Sahnouni1,2,3,*, Josep M. Parés1, Mathieu Duval4,1, Isabel Cáceres5,6, Zoheir Harichane2,7, Jan van der Made8, Alfredo Pérez-González1, Salah Abdessadok9,2, Nadia Kandi10, Abdelkader Derradji2,11, Mohamed Medig11, Kamel Boulaghraif2,12, Sileshi Semaw1,3 1.9-million- and 2.4-million-year-old artifacts and stone tool–cutmarked bones from Ain Boucherit, Algeria, Science 29 Nov 2018: eaau0008

DOI: 10.1126/science.aau0008 More.

From others: It’s not clear what human group created the tools. No human bones were found at the site:

The animal bones also provided clues. Many of them came from species of extinct pigs, horses, and elephants that only lived within certain time frames, which the team checked against the dates from their magnetic calendar. This work, which took most of the decade to do, revealed that the two areas the team dug up were 1.92 million years old and 2.44 million years old. Ed Yong, “2.4-Million-Year-Old Stone Tools Turn Up in an Unexpected Place” at The Atlantic

and

The bones came from the  ancestors of crocodiles and hippopotamuses too:

One hypothesis is that early ancestors of modern day humans quickly carried stone tools with them out of East Africa and into other regions of the continent.

Another is a “multiple origin scenario,” in which early hominids made and used tools in both East and North Africa. “2.4-million-year-old tools found in Algeria could upend human origin story” at Agence France Presse

See also: Complex stone tools from 160,000 to 170,000 years ago found in China

Stone tools found in Saudi Arabia from 300,000 years ago

How did stone tools get to the Philippines 700 kya?

Revolutionary stone tools found in India “much earlier than thought,” 385 kya

Stone tools confirmed from 3.4 mya?

and

Stone tools now dated to 3.3 million years ago

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