Michael J. Behe's Blog, page 507

March 21, 2019

Abandon statistical significance, learn to live with uncertainty, scientists demand

What’s hot? What’s not?/Niklas Bildhauer, Wikimedia

Nature reports that three statisticians and more than 800 signatories call argue for scientists to abandon statistical significance:

How do statistics so often lead scientists to deny differences that those not educated in statistics can plainly see? For several generations, researchers have been warned that a statistically non-significant result does not ‘prove’ the null hypothesis (the hypothesis that there is no difference between groups or no effect of a treatment on some measured outcome)1. Nor do statistically significant results ‘prove’ some other hypothesis. Such misconceptions have famously warped the literature with overstated claims and, less famously, led to claims of conflicts between studies where none exists. …

We must learn to embrace uncertainty. One practical way to do so is to rename confidence intervals as ‘compatibility intervals’ and interpret them in a way that avoids overconfidence. Specifically, we recommend that authors describe the practical implications of all values inside the interval, especially the observed effect (or point estimate) and the limits. In doing so, they should remember that all the values between the interval’s limits are reasonably compatible with the data, given the statistical assumptions used to compute the interval7,10. Therefore, singling out one particular value (such as the null value) in the interval as ‘shown’ makes no sense. Valentin Amrhein, Sander Greenland & Blake McShane, “Scientists rise up against statistical significance” at Nature

Retraction Watch interviewed statistician Nicole Lazar, who explains:

One such principle about which there has been contentious debate, especially in the Frequentist versus Bayesian wars, is objectivity. It is important to understand and accept that while objectivity should be the goal of scientific research, pure objectivity can never be achieved. Science entails intrinsically subjective decisions, and expert judgment – applied with as much objectivity and as little bias as possible – is essential to sound science.

Hold that thought when another flatulent editorial in a local news source extols the “objectivity of science” while recommending some bad policy or other based on a probably questionable study.

Let’s see where this goes. Will it lead to less magic with numbers or more and bigger magic?

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Published on March 21, 2019 13:42

Devolution or Evolution?

Today there’s a Press Release provided by the University of Bristol about comb jellies from the Cambrian, found outcrops south of Kunming in the Yunnan Province, South China by Professor Hou Xianguang, co-author of the study.

Of interest, given the recent release of Michael Behe’s new book, Darwin Devolves, is the following statement:

The study shows how comb jellies evolved from ancestors with an organic skeleton, which some still possessed and swam with during the Cambrian. Their combs evolved from tentacles in polyp-like ancestors that were attached to the seafloor. Their mouths then expanded into balloon-like spheres while their original body reduced in size so that the tentacles that used to surround the mouth now emerges from the back-end of the animal.

“With such body transformations, I think we have some of the answers to understand why comb jellies are so hard to figure out. It explains why they have lost so many genes and possess a morphology that we see in other animals,” added co-author Dr. Luke Parry.

So, to get a modern-day comb jelly, the organic skeleton has to be lost. Is this progress?

And what about the “[loss] of so many genes”? Is this evolution, or devolution?

The PR also says this:

Several amazingly preserved fossils have been unearthed from outcrops scattered among rice fields and farmlands in this part of tropical China in the last three decades.

It has been named Daihua after the Dai tribe in Yunnan and the Mandarin word for flower ‘Hua’, a cup-shaped organism with 18 tentacles surrounding its mouth. On the tentacles are fine feather-like branches with rows of large ciliary hairs preserved.

So, were the “fine feather-like branches” also ‘lost’?

So much evidence already points towards Behe’s “First Rule of Adaptation,” and this only adds further evidence substantiating Nature’s progression.

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Published on March 21, 2019 10:10

Sabine Hossenfelder: How you can help science out of a rut

With her publisher’s permission, Sabine Hossenfelder is making Appendix C of her book Lost in Math: How Beauty Leads Physics Astray, available at her blog: This bit of that excerpt is addressed to the science-minded public:

As a science writer or member of the public, ask questions:

● You’re used to asking about conflicts of interest due to funding from industry. But you should also ask about conflicts of interest due to short-term grants or employment. Does the scientists’ future funding depend on producing the results they just told you about?

● Likewise, you should ask if the scientists’ chance of continuing their research depends on their work being popular among their colleagues. Does their present position offer adequate protection from peer pressure?

● And finally, like you are used to scrutinize statistics you should also ask whether the scientists have taken means to address their cognitive biases. Have they provided a balanced account of pros and cons or have they just advertised their own research?

You will find that for almost all research in the foundations of physics the answer to at least one of these questions is no. This means you can’t trust these scientists’ conclusions. Sad but true. Sabine Hossenfelder, “Science has a problem. Here is how you can help.” More. – Reprinted from Lost In Math by Sabine Hossenfelder. Copyright © 2018. Available from Basic Books, an imprint of Perseus Books, a division of PBG Publishing, LLC, a subsidiary of Hachette Book Group, Inc
at BackRe(Action)

What if these standards were applied to biology? …

Whoops. That sound you just heard was three tenured Darwin trolls’ heads exploding. We almost wish.

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See also, featuring Sabine Hossenfelder: Cosmic inflation is overblown

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. ”

Physics Problems That Lead To Breakthroughs Arise From Inconsistencies In Data, Not Beautiful Math

and

Theoretical Physicist Sabine Hossenfelder Shares Her Self-Doubts About Exposing Nonsense In Cosmology

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Published on March 21, 2019 06:24

We are now informed that evolution can go backward

From ScienceDaily:

The study of evolution is revealing new complexities, showing how the traits most beneficial to the fitness of individual plants and animals are not always the ones we see in nature. Instead, new research by behavioral scientists shows that in certain cases evolution works in the opposite direction, reversing individual improvements to benefit related members of the same group.

Wow. They are trying to revive the heresy of a group selection over against the selfish gene. It doesn’t matter whether this is true or not. It isn’t orthodox.

The research appears in the Journal of Evolutionary Biology, where lead author David Fisher shows that the increased evolution of selfless traits — such as sharing food and keeping watch for one another — is mathematically equivalent to the decreased evolution of individually beneficial traits.

“They’re two sides of the same coin,” Fisher explains. “On one side, traits evolve that benefit your kin, but don’t benefit you, because you’re helping your siblings or cousins. On the other side, traits that benefit you but cost your neighbours don’t evolve, because you’re causing damage to related individuals.”

The work is part of the ongoing effort to understand the paradox of altruistic behaviour in the wild, explains Fisher, a research fellow in McMaster’s Department of Psychology, Neuroscience and Behaviour.

Fisher goes on to show that another way evolution can go backwards is through the evolution of an individual’s negative effects on neighbours and group members. For example, a fast-growing tree may take all the sunlight, water and nutrients out of the environment, causing its neighbours to grow slowly. In the next generation, more trees are fast-growing but are also nasty neighbours. As a result, negative social effects are much more prevalent, and so everyone’s growth is reduced.

“That means evolution has gone backwards. Even though growing quickly is beneficial, because of these negative social effects, the population, on average, grows more slowly,” he says. Paper. (paywall) – David N. Fisher, Jonathan N. Pruitt. Opposite responses to selection and where to find them. Journal of Evolutionary Biology, 2019; DOI: 10.1111/jeb.13432 More.

Of course, they must see evolution as a benevolent deity instead of an impersonal one, if it can act to prevent a bad outcome, as described above. Well, if it’s an established religion, it’s an established religion.

See also: How bacteria use harpoons to speed horizontal gene transfer Well, if that’s a way bacteria evolve, what becomes of common descent and speciation? What do we mean by “bacterial species”?

Devolution: Getting back to the simple life

and

Could we all get together and evolve as a group?

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Published on March 21, 2019 05:38

March 20, 2019

What? Oumuamua was just a comet? After all the ET hype?

Could 'Oumuamua be an extra-terrestrial solar sail?

Artist’s impression of interstellar asteroid/comet, Oumuamua /ESO, M. Kornmesser

Well of course it was something like that:

New research flags jets of water vapor—rather than alien technology—as the source of the mysterious object’s anomalous motions…

Against the standard “comet” hypothesis, theorists have devised a host of bizarre possibilities: Perhaps ‘Oumuamua was a fluffy, fractal-like clump of dust, or a threadbare “comet skeleton” stripped of its weighty ices—either of which could be accelerated solely by the subtle pressure of starlight itself. Suffice to say, such low-density objects have never before been seen in the solar system. Most controversially, as postulated by the prominent Harvard University astrophysicist Avi Loeb, perhaps it was an alien artifact—a gossamer-thin sheet-like spacecraft engineered to coast on starlight through the interstellar depths. Such “star sails” are a crucial aspect of the Breakthrough Initiatives, a private effort to develop interstellar missions for which Loeb serves as chief scientific advisor. If we are contemplating building star sails now to visit nearby stars, Loeb reasons, perhaps other galactic civilizations have already constructed them as well to visit us. Lee Billings, “‘Oumuamua, Our First Interstellar Visitor, May Have Been a Comet After All” at Scientific American

Yeah. Sure. But let’s not lose sight of the fact that it was orthodox science media (Scientific American, we are looking at you… ) who were marketing the space alien thing, not some crackpot in a tinfoil hat. And yet the same people have the nerve to sponsor reams of stuff on why “people” believe in pseudoscience.

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See also: Astronomer: We’re too dumb to think space object Oumuamua was an extraterrestrial lightsail.Hmmm. In the real world, when you are an only child so far as you know, it is hard to compare yourself to your siblings. Few readily accept criticism for failure to measure up to the standards of imaginary beings.

and

A study of the causes of science skepticism sails right by the most obvious cause of skepticism: Repeated untrustworthiness

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Published on March 20, 2019 17:07

Survival at a price: Bacteria cut off flagella to stay alive

Starving bacteria can eject their tails to save energy and stay alive

The flagella being ejected/Morgan Beeby

Bacteria have a survival plan for when they are starving:

Some bacteria use tails, or flagella, to swim through liquids—including those in our bodies. However, new research published today in PLOS Biology reveals a surprisingly drastic measure taken by some bacteria when facing starvation: they eject their flagella, leaving themselves paralyzed, but conserving energy so they can stay alive…

First author Josie Ferreira, from the Department of Life Sciences at Imperial, said: “Before we started our experiments, we thought we had caught the bacteria in the process of assembling their motor-flagella complexes. To our surprise, we found the opposite: not only had the bacteria ejected their flagella, they had plugged the hole it left behind. This suggested to us it was a deliberate action.”

Bacterial use their flagella to get around, even swimming through thick gut mucus as in the case of food-poisoning bacterium Campylobacter jejuni. However, flagella are costly to build and power, and constantly grow throughout the bacteria’s life, using up a lot of resources.

The team found that bacteria placed in environments that lacked nutrients ejected their flagella into the growth medium. The discarded flagella were complete, including the adaptor structure that connects flagella to their motors, suggesting that they were ejected whole from their base, and not broken off.

Lead author Dr. Morgan Beeby, from the Department of Life Sciences at Imperial, said: “The bacteria’s actions appear to be deliberate. It’s not like when our fingers or toes drop off from frostbite—it’s more a calculated act like mountaineer Aron Ralston cutting off his arm in the film 127 Hours to free himself from under a rock.”

Bacteria have been observed swimming more slowly when nutrients are low, but this is the first time they have been observed jettisoning their flagella completely in a bid to save energy.
Imperial College London, “Starving bacteria can eject their tails to save energy and stay alive” at Phys.org

But how can bacteria be smart enough to know that they should develop a mechanism to do that safely? That’s like the female birds who supposedly choose the sex of their offspring according to the population of mates and plan for their future. Or the male bees who supposedly know that they can mate with the female offspring of other bees that they help raise. Or the mares who supposedly cause an abortion because they perceive that the stallion will not accept his offspring.

The world of Darwinian evolution features so many exceptionally clever animals that are nothing like the humdrum creatures we must tie down or tranquillize in order to help. And the profs just attribute it all to natural selection, as if that would explain anything in a situation where some prevision seems required.

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Hat tip: Philip Cunningham

See also: Symbiotic bacteria help frogs find mates (but the real story is all the assumptions that got corrected) Contrary to assumption, 1) smell was important in locating mates and 2) males and females had different smells 3) produced by symbiotic bacteria. One wonders how many other life forms would challenge simple evolution tales if they were closely studied.

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Published on March 20, 2019 16:34

Templeton winner: Atheism is inconsistent with the scientific method

Gleiser – Own work//CC BY-SA 4.0

Yesterday, we noted that physicist Marcelo Gleiser won the Templeton Prize. Now we think we have a better idea why Darwinian evolutionary biologist Jerry Coyne is mad (“Templeton Prize awarded to physicist for blending science and woo”). We thought Coyne maybe didn’t have enough to do in his retirement if he even cares so much but then there Gleiser said something that must have yanked his chain real hard:

A physics and astronomy professor whose specializations include cosmology, 60-year-old Gleiser was born in Rio de Janeiro, and has been in the United States since 1986.

An agnostic, he doesn’t believe in God—but refuses to write off the possibility of God’s existence completely.

“Atheism is inconsistent with the scientific method,” Gleiser told AFP Monday from Dartmouth College, the New Hampshire university where he has taught since 1991.

“Atheism is a belief in non-belief. So you categorically deny something you have no evidence against.”

“I’ll keep an open mind because I understand that human knowledge is limited,” he added. AFP, “Physicist Marcelo Gleiser: ‘Science does not kill God’” at Phys.org

That is, of course, a problem. To prove that something cannot exist, one needs a mathematical type of proof. For a look at this kind of question, see Robert J. Marks on Things that exist that are unknowable – though in that case, we are looking at a number that must exist and yet is unknowable.

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See also: 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).

and

Neuroskeptic: Atheists are NOT genetically damaged Of course, the claim is nonsense but then those of us who have listened to rubbish about the God gene and such can’t help hiding a giggle. Hey, given that it’s Hate Your Local Atheist Week anyway, how about “Atheists have mutant genes, don’t live as long ” (This relates to Jerry Coyne being upset at Gleiser’s win. Coffee ready yet?)

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Published on March 20, 2019 07:00

Robert J. Marks: Things Exist That Are Unknowable

The mathematically provable idea that something exists but is unknowable has clear philosophical and theological implications. Here’s a look atChaitin’s number:

Here is why Chaitin’s number is mind-blowing: There are many problems in mathematics that can be disproved by one counterexample. Consider the theorem that all skunks are black and white. Show me a pink skunk and the theorem is disproved. Chaitin’s number—one number—can be used to prove or disprove almost every known math conjecture that can be disproven by a single counterexample…

It is an astonishing fact that, given a lot of computing time and power, any list of problems that can be disproven by a single counterexample could be proved or disproved if we knew Chaitin’s number to finite precision. Think of it. A list of the most perplexing math problems not yet solved by the world’s top mathematicians can be answered with one single number. And not only does Chaitin’s number exist, we know it lies between zero and one. More.

He goes on to explain why we cannot know the number.

Robert J. Marks is one of the authors of Introduction to Evolutionary Informatics

Also by Robert J. Marks: Random Thoughts on Recent AI Headlines: There is usually a story under those layers of hype but not always the one you thought

When Thomas Sowell was writing his syndicated column on economics, I always looked forward to his sporadically appearing “Random Thoughts on the Passing Scene.” Reminding readers that imitation is the sincerest form of flattery, I offer my own “Random Thoughts on Recent AI Headlines.”

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Published on March 20, 2019 05:50

March 19, 2019

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 (on that score, see 2011 Templeton winner Sir Martin Rees).

Researchers: Mammals’ “arms” backdated 100 million years; predate dinosaurs

A variety of bones from early mammal relatives/ (c) Jacqueline Lungmus, Field Museum

From ScienceDaily:

Bats fly, whales swim, gibbons swing from tree to tree, horses gallop, and humans swipe on their phones — the different habitats and lifestyles of mammals rely on our unique forelimbs. No other group of vertebrate animals has evolved so many different kinds of arms: in contrast, all birds have wings, and pretty much all lizards walk on all fours. Our forelimbs are a big part of what makes mammals special, and in a new study in the Proceedings of the National Academy of Sciences, scientists have discovered that our early relatives started evolving diverse forelimbs 270 million years ago — a good 30 million years before the earliest dinosaurs existed.

“Aside from fur, diverse forelimb shape is one of the most iconic characteristics of mammals,” says the paper’s lead author Jacqueline Lungmus, a research assistant at Chicago’s Field Museum and a doctoral candidate at the University of Chicago. “We were trying to understand where that comes from, if it’s a recent trait or if this has been something special about the group of animals that we belong to from the beginning.” …

Lungmus and Angielczyk found that a wide variety of different forelimb shapes evolved within the therapsids 270 million years ago. “The therapsids are the first synapsids to increase the variability of their forelimbs — this study dramatically pushes that trait back in time,” says Lungmus. Prior to this study, the earliest that paleontologists had been able to definitively trace back mammals’ diverse forelimbs was 160 million years ago. With Lungmus and Angielczyk’s work, that’s been pushed back by more than a hundred million years. Paper. (open access) – Jacqueline K. Lungmus, Kenneth D. Angielczyk. Antiquity of forelimb ecomorphological diversity in the mammalian stem lineage (Synapsida). Proceedings of the National Academy of Sciences, 2019; 201802543 DOI: 10.1073/pnas.1802543116
More.

So many good ideas seem to have got started quite early and been around nearly forever. One wonders if flexible forelimbs got started quickly too…

See also: “Super-Ancient Mobile Organisms” Push Mobile Life Back To 2.1 Billion Years Ago

Access Research Network’s new Question of the Month (It’s about stasis) $50 VISA certificate prize

and

Stasis: Life goes on but evolution does not happen

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Published on March 19, 2019 15:40

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