Michael J. Behe's Blog, page 72

May 15, 2022

Studies of co-evolution biased toward “striking and exaggerated phenotypes”, researchers say

The authors seem to suspect that “the widespread impression that coevolution is a rare and quirky sideshow to the day-to-day grind of ecology and evolution” is wrong and that new tools for uncovering it will show it to be more common.

Abstract Studies of coevolution in the wild have largely focused on reciprocally specialized species pairs with striking and exaggerated phenotypes. Textbook examples include interactions between toxic newts and their garter snake predators, long-tongued flies and the flowers they pollinate, and weevils with elongated rostra used to bore through the defensive pericarp of their host plants. Although these studies have laid a foundation for understanding coevolution in the wild, they have also contributed to the widespread impression that coevolution is a rare and quirky sideshow to the day-to-day grind of ecology and evolution. In this perspective, we argue that the focus of coevolution has been biased toward the obvious and ignored the cryptic. We have focused on the obvious—studies of reciprocally specialized species pairs with exaggerated phenotypes—mainly because we have lacked the statistical tools required to study coevolution in more generalized and phenotypically mundane systems. Building from well-established coevolutionary theory, we illustrate how model-based approaches can be used to remove this barrier and begin estimating the strength of coevolutionary selection indirectly using routinely collected data, thus uncovering cryptic coevolution in more typical communities. By allowing the distribution of coevolutionary selection to be estimated across genomes, phylogenies, and communities and over deep timescales, these novel approaches have the potential to revolutionize the way we study coevolution. As we develop a road map to these next-generation approaches, we highlight recent studies making notable progress in this direction.

Scott L. Nuismer, Bob Week, and LukeJ.Harmon, Uncovering Cryptic Coevolution, American Naturalist, vol. 199, no. 6, June 2022

The paper is open access.

Co-evolution must require a fair amount of cooperation between utterly different life forms. If natural selection is the model, one failure would end a multi-stage process.

Hat tip: Pos-darwinista

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Published on May 15, 2022 18:34

Rebranding some junk DNA as spam DNA

Perhaps science is a bit more like business than we think. In business, products get rebranded when vice presidents outnumber customers for the old brand. And now:

“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.
Nelson J.R. Fagundes, Rafael Bisso-Machado, Pedro I.C.C. Figueiredo, Maikel Varal, André L.S. Zani, What We Talk About When We Talk About “Junk DNA”, Genome Biology and Evolution, Volume 14, Issue 5, May 2022, evac055, https://doi.org/10.1093/gbe/evac055

So what happens when we find out that a lot of spam DNA does have a function?

You may also wish to read: Someone out there is actually defending junk DNA Can someone please tell them, the Titanic has sunk — its seaworthiness is no longer an issue?

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Published on May 15, 2022 07:51

May 14, 2022

At Mind Matters News: Among 5000 known exoplanets, there are some really strange ones

Planets so strange that they prompt a rethink of the “planetary rulebook.”:

PBS tells us that Hoth, the frozen planet in Star Wars, is not just imagination. It has a real-life counterpart among the exoplanets. Granted, astronomers call it OGLE-2005-BLG-390Lb but even they think of it as “Hoth.” …

Astronomers had expected to see solar systems like our own but instead they demonstrated that there are other types of solar systems out there. Whether these exoplanets could host what we think of as life is another question.

News, “Among 5000 known exoplanets, there are some really strange ones” at Mind Matters News (May 14, 2022)

Various lists of strange planets are linked and discussed.

Takehome: To sum up, whatever we see or read about planets in science fiction, something out there is likely stranger still.

It will be most interesting to see how many of the more conventional exoplanets have life and if there is in fact a reliable formula for predicting it. Those who claim that Earth is just an ordinary planet are certainly wrong — but is Earth unique? The universe is fine-tuned, as is Earth, and that would be an argument for life on exoplanets.

You may also wish to read: Steve Meyer on why a supposed multiverse is no answer to the extreme fine-tuning of our universe. Meyer on multiverse cosmologists: “The speculative cosmologies (such as inflationary cosmology and string theory) they propose for generating alternative universes invariably invoke mechanisms that themselves require fine-tuning, thus begging the question as to the origin of that prior fine-tuning.”

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Published on May 14, 2022 20:26

Denton’s prior fitness argument: Everything seems to have come together to produce humans

One of the arguments in Michael Denton’s new book, The Miracle of Man (2022), arguing that nature is fine-tuned for human life, is the
prior fitness argument. In a podcast, Denton, who is also an MD, “marvels at the engineering sophistication of the human heart and hands.”

But the remarkable thing is prior fitness:

One or two such examples are interesting. But where the argument gains dramatic force is in the accumulation of many examples, stretching from physics and the characteristics of our sun to chemistry and the ensemble of unique characteristics of planet Earth, water, carbon, and the transition metals.

Evolution News, “Miracle of Man: Denton’s Prior Fitness Argument” at Evolution News (May 12, 2022)

Didn’t Freeman Dyson (1923–2020) say, “The more I examine the universe and the details of its architecture, the more evidence I find that the universe in some sense must have known we were coming.” The idea isn’t new; there’s just much more evidence for it.

You may also wish to read: Michael Denton’s new book: Nature is fine-tuned for human existence – check the stats Publisher: Drawing on discoveries from a myriad of scientific fields, Denton masterfully documents how contemporary science has revived humanity’s special place in nature.

The book is still doing well at Amazon:

#19 in Cosmology (Books)
#36 in Anatomy (Books)
#89 in Earth Sciences (Books)

Best Sellers Rank: #10,335 in Books (See Top 100 in Books)

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Published on May 14, 2022 19:43

“Lost” coral species found “inside” another species

Described as a”cryptic“ species due to its elusiveness:

With about one-third of the world’s corals currently under threat of extinction due to climate change, Curtin researchers have made the encouraging discovery of a ‘lost’ species of coral that had been hidden for more than 50 years…

“The speciesPlesiastrea peroni was described some 200 years ago however as time went on taxonomists clumped it with Plesiastrea versipora but we have now resurrected the former species, which had been hidden for more half a century,” Juszkiewicz said.

“We trawled through 200 years of historical and modern-day literature to firstly understand the larger morphological characteristics of Plesiastrea versipora, which was first described as a single species in 1816.

“By diving on various sites around Australia and the Indo-Pacific, we collected samples, which we used to study the micromorphology and microstructure of the coral skeleton to further identify its unique intricate features.

“After carrying out genetic sequencing, we found this species of coral actually contained a second, cryptic species, which we named Plesiastrea peroni — and this is found north of the Tropic of Capricorn in Australia and across the Indo-Pacific.

“Being able to accurately identify species is paramount to quality ecological research and conservation decision-making, so this study will allow coral ecologists and biologists to know which species of Plesiastrea they are working on.”

Curtin University, “‘Lost’ coral species resurrected” at ScienceDaily (May 5, 2022)

Of course, the story raises the question of just how important saving “species” (see speciation) is. A shift in an ecology can be critical but the disappearance, reappearance, or brand new development of a hard-to-distinguish species may not have much environment impact.

Note: Sometimes species are declared extinct but turn out not to be. They are sometimes called “Lazarus species.” See, for example, Extinction (Or Maybe Not): New Scientist Offers Five “Lazarus Species” (2017).

The paper requires a fee or subscription.

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Published on May 14, 2022 18:34

May 13, 2022

Researchers: Cells organize themselves in our organs by increasing in volume when tissues bend

By bending “sheet” of cells, similar to the one that makes up our skin, the researchers noticed more precisely that the cells swelled to take the shape of small domes/Aurélien Roux

They hope that their “surprising discovery” could enable in vitro culture of organs, which might be a humane alternative to animal experimentation:

How do our cells organize themselves to give their final shape to our organs? The answer lies in morphogenesis, the set of mechanisms that regulate their distribution in space during embryonic development. A team from the University of Geneva (UNIGE) has just made a surprising discovery in this field: when a tissue curves, the volume of the cells that compose it increases instead of decreasing. This discovery opens new avenues for in vitro organ culture, a partial alternative to animal experimentation.

Université De Genève, “Our cells take their ease in the curves” at Eurekalert (May 13, 2022)

Remarkably,

In a recent study, Professor Roux’s team investigated how the cells that make up a tissue react and adapt when it is bent. By rolling a monolayer of cells in vitro, which is a compact, flat assembly of cells arranged next to each other, the UNIGE scientists made a counterintuitive discovery. “We found that the volume of cells located in the curvature increased by about 50% after five minutes instead of decreasing, and then returned to normal within 30 minutes,” explains Aurélien Roux, the last author of this study. This is the opposite of what can be observed when bending an elastic material.

By bending this “sheet” of cells, similar to the one that makes up our skin, the researchers noticed more precisely that the latter swelled to take the shape of small domes. “The fact that this increase in volume is staggered in time and transient also shows that it is an active and living system,” adds Caterina Tomba, first author of the study and former researcher in the Department of Biochemistry at the UNIGE.

Université De Genève, “Our cells take their ease in the curves” at Eurekalert (May 13, 2022)

“The fact that this increase in volume is staggered in time and transient also shows that it is an active and living system,” adds a researcher.

Once again, we are expected to believe that such a system can just develop in a gradual Darwinian fashion.

The paper is open access.

You may also wish to read: In embryos, we are told, “nothing is left to chance in the ‘seating plan’ for the first few cells.” “Nothing is left to chance” even in cell spacing in worm eggs but we are told there is no design behind the universe?

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Published on May 13, 2022 20:27

Casey Luskin: ID as fruitful approach to science

Rather than a science stopper:

In his Kitzmiller v. Dover testimony, biologist Kenneth Miller referred to intelligent design as a “science stopper.” Similarly, in his book Only a Theory, Miller stated, “The hypothesis of design is compatible with any conceivable data, makes no testable predictions, and suggests no new avenues for research. As such, it’s a literal dead end…”

Casey Luskin, “Science Stopper? Intelligent Design as a Fruitful Scientific Paradigm” at Evolution News (May 9, 2022)

Luskin offers a number of examples of areas where ID is a fruitful approach, including

Evolutionary computation: ID produces theoretical research into the information-generative powers of Darwinian searches, leading to the discovery that the search abilities of Darwinian processes are limited, which has practical implications for the viability of using genetic algorithms to solve problems.

Anatomy and physiology: ID predicts function for allegedly “vestigial” organs, structures, or systems whereas evolution has made many faulty predictions of nonfunction.

Bioinformatics: ID has helped scientists develop proper measures of biological information, leading to concepts like complex and specified information or functional sequence complexity. This allows us to better quantify complexity and understand what features are, or are not, within the reach of Darwinian evolution.

Casey Luskin, “Science Stopper? Intelligent Design as a Fruitful Scientific Paradigm” at Evolution News (May 9, 2022)

The trouble is, many people would just as soon that research into evolutionary computation anatomy and physiology, and bioinformatics, however fruitful, not be done if it undermines a comfortable Darwinism.

This is the 12th and final entry in Casey Luskin’s series, which is a modified excerpt from The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos (2021).

Incidentally, here are two hilarious vids about fake COVID news from Shanghai. Couldn’t think where to put it but wouldn’t want you to miss out.

Note: The content is available. The warning is part of the joke.

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Published on May 13, 2022 19:57

Researchers see one particle on two paths, say it shows quantum physics is right

One particle on two paths: Quantum physics is right

The lab at the ILL in Grenoble Laurent Thion, ILL. Credit: Vienna University of Technology

Quantum physics killed off straightforward materialism, just when it appeared to triumph. Albert Einstein would not like this:

The double-slit experiment is the most famous and probably the most important experiment in quantum physics: individual particles are shot at a wall with two openings, behind which a detector measures where the particles arrive. This shows that the particles do not move along a very specific path, as is known from classical objects, but along several paths simultaneously: Each individual particle passes through both the left and the right opening.

Normally, however, this can only be proven by carrying out the experiment repeatedly and evaluating the results of many particle detections at the end. At TU Wien, researchers developed a new variant of such a two-way interference experiment that can correct this flaw: A single neutron is measured at a specific position—and due to the sophisticated measurement setup, this single measurement proofs already that the particle moved along two different paths at the same time. It is even possible to determine the ratio in which the neutron was distributed between the two paths. Thus, the phenomenon of quantum superposition can be proven without having to resort to statistical arguments.

Vienna University of Technology, “One particle on two paths: Quantum physics is right” at Phys.org (May 11, 2022)

So it’s definitely the same neutron moving along two different paths at the same time. That’s somewhat like bilocation, the ability to be in two places at the same time, which is credited to beings with supernatural powers. (But, of course, macro beings can’t actually do it. )

Albert, check your mail.

The paper is open access.

Note: A British philosopher, looking for a way to redefine free will, dismisses quantum mechanics: Julian Baggini’s proposed new approach assumes the existence of the very qualities that only a traditional view of the mind offers. Baggini discounts the importance of quantum mechanics and believes that neuroscience disproves free will; he is wrong on both counts.

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Published on May 13, 2022 19:00

Researchers: A key cell division protein is still a puzzle

Structure of key protein for cell division puzzles researchers

Left: Scheme of the kinetochore organization with the CCAN subcomplexes binding to the centromere protein A (CENP-A). Right: Model of the surface of the CCAN’s 16 components organized in different subcomplexes. Credit: MPI of Molecular Physiology

They’ve made some progress with mapping the 3D structure of hundreds of proteins at the core of cell division but unanswered questions remain:

The groups of Andrea Musacchio and Stefan Raunser at the Max Planck Institute of Molecular Physiology in Dortmund are now able to reveal the first detailed structure of a key protein complex for human cell division known as CCAN. By using cryo-electron microscopy, the researchers show important features of the complex’s 16 components and challenge previous assumptions about how the complex is able to recognize the centromere, a crucial region of chromosomes in cell division.

The centromere is a constriction in the chromosome, made of DNA and proteins. Most importantly, the centromere is the dock for the kinetochore, a machinery of about 100 proteins that drives the separation of two identical chromosomes during cell division and their delivery to the daughter cells. Previous research has shown that the kinetochore docks onto the centromere through the CCAN complex: The CCAN interacts with the centromere protein A, the landmark protein of the centromere. CCAN is also responsible for replenishing the centromere protein A once the cell division has taken place. Yet, the details of the interaction between CCAN and the centromere protein A remain elusive…

“Contrary to what was expected, this structure does not directly recognize the centromere protein A in the standard configuration,” says Musacchio.

The centromere protein A is most commonly packed with DNA and other proteins as a nucleosome, the standard unit of the genetic material. The authors are now suggesting that the centromere protein A may be embedded in the centromere with a different configuration that may facilitate the crucial interaction with CCAN. They plan to identify conditions that could lead to this new configuration and prove their hypothesis.

Max Planck Institute of Molecular Physiology, “Structure of key protein for cell division puzzles researchers” at Phys.org (May 13, 2022)

In other words, contrary to expectation, the system is even more complex than supposed. At this point, unguided evolution becomes overwhelmingly implausible because it would take only one misstep to end the process. But people believe what they believe.

The paper is open access.

You may also wish to read: In embryos, we are told, “nothing is left to chance in the ‘seating plan’ for the first few cells.” So: “Nothing is left to chance” even in cell spacing in worm eggs but we are told there is no design behind the universe?

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Published on May 13, 2022 18:39