Michael J. Behe's Blog, page 504
March 28, 2019
Researchers: Microbes can make evolution work faster for their hosts
They argue that, considering the host organism and its microbes together (a holobiont), evolution can work faster because the microbes evolve more quickly:
A famous example of this concept is the relationship between corals and their symbionts, the zooxanthellae. Researchers have demonstrated that some corals can evolve to tolerate higher water temperatures by changing the makeup of their symbiont communities. Because microbes have much shorter generation times than coral polyps, the genetic composition of the symbiont populations can evolve much more rapidly than that of their hosts, and these changes can confer higher tolerance on the holobiont unit.Izhak Mizrahi, Fotini Kokou, “Opinion: Individuals Are Greater Than the Sum of Their Parts” at The Scientist
Okay, but then aren’t the microorganisms the unit of selection rather than the host’s genes? This might work for adaptations to change in habitats (they describe one), but it won’t be Darwinism.
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See also: How much evolution can symbiosis account for?
and
ID Predictions On Orphan Genes And Symbiosis
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Do some particles defy the universe’s push for disorder?
rubidium/Dnn87 (CC BY 3.0)That’s an apparent implication of a recent experiment. Generally, left to itself, “a system strives toward equilibrium with its environment” or, in plain terms, “things always go downhill.” They spoil, they crumble, they disintegrate. Sandcastles become sand. Except:
It’s common and intuitive, and precisely what a team of physicists expected to see when they lined up 51 rubidium atoms in a row, holding them in place with lasers. The atoms started in an orderly pattern, alternating between the lowest-energy “ground” state and an excited energy state. The researchers assumed the system would quickly thermalize: The pattern of ground and excited states would settle almost immediately into a jumbled sequence.
And at first, the pattern did jumble. But then, shockingly, it reverted to the original alternating sequence. After some more mixing, it returned yet again to that initial configuration. Back and forth it went, oscillating a few times in under a microsecond — long after it should have thermalized.
It was as if you dropped an ice cube in hot water and it didn’t just melt away, said Mikhail Lukin, a physicist at Harvard University and a leader of the group. “What you see is the ice melts and crystallizes, melts and crystallizes,” he said. “It’s something really unusual.” Marcus Woo, “Quantum Machine Appears to Defy Universe’s Push for Disorder” at Quanta
As Woo goes on to explain, physicists call this “quantum many-body scarring,” with one idea being that the atoms “remember” a past state and return to it, though just how they remember is unclear The work was being done as part of a push for quantum computing.
“There is some beautiful structure that somehow coexists with a totally random environment,” Papić said. “What kind of physics allows this to happen? This is a kind of deep and profound question that runs through many areas of physics, and I think this is another incarnation.” Marcus Woo, “Quantum Machine Appears to Defy Universe’s Push for Disorder” at Quanta
Won’t argue.
Note: rubidium
Paper. (paywall)
See also: Whether Or Not Man Has Free Will, Quantum Mechanics Means That Nature Does
If quantum mechanics were a researcher, she’d be fired
Quantum Mechanics: Pushing The “Free-Will Loophole” Back To 7.8 Billion Years Ago
At Nature: For Now, “Uncertainty Seems The Wisest Position” On The Implications Of Quantum Mechanics
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Quantum physicist David Bohm on why there cannot be a Theory of Everything
Researchers clearly observe quantum effects in photosynthesis
Inspiring Philosophy on quantum mechanics and the death of materialism
and
Is the search for meaning in quantum physics a form of religion?
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March 27, 2019
Researcher: Origin of photosynthesis founded on “incorrect assumptions”
In an open access paper:
Thinking twice about the evolution of photosynthesis
Tanai Cardona
Published:20 March 2019 https://doi.org/10.1098/rsob.180246
Abstract
Sam Granick opened his seminal 1957 paper titled ‘Speculations on the origins and evolution of photosynthesis’ with the assertion that there is a constant urge in human beings to seek beginnings (I concur). This urge has led to an incessant stream of speculative ideas and debates on the evolution of photosynthesis that started in the first half of the twentieth century and shows no signs of abating. Some of these speculative ideas have become commonplace, are taken as fact, but find little support. Here, I review and scrutinize three widely accepted ideas that underpin the current study of the evolution of photosynthesis: first, that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those in oxygenic photosynthesis; second, that the probability of acquiring photosynthesis via horizontal gene transfer is greater than the probability of losing photosynthesis; and third, and most important, that the origin of anoxygenic photosynthesis pre-dates the origin of oxygenic photosynthesis. I shall attempt to demonstrate that these three ideas are often grounded in incorrect assumptions built on more assumptions with no experimental or observational support. I hope that this brief review will not only serve as a cautionary tale but also that it will open new avenues of research aimed at disentangling the complex evolution of photosynthesis and its impact on the early history of life and the planet. More.
“I shall attempt to demonstrate that these three ideas are often grounded in incorrect assumptions built on more assumptions with no experimental or observational support.”? The trouble with evidence is that it can go either way. Assumptions built on assumptions with the imprimatur of central dogma are much safer even if the outcome is crud.
See also: Researchers help build “public library” to understand photosynthesis.
Will A New Type Of Photosynthesis, Just Discovered, Change The Hunt For Alien Life?
Researchers clearly observe quantum effects in photosynthesis
and
Photosynthesis pushed back even further. Time to revisit the “Boring Billion” claim
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Researchers: Dickinsonia (571–541 mya) could have had mouth and guts
Ilya Bobrovskiy, The Australian National University (ANU)
From ScienceDaily:
“These soft-bodied creatures that lived 558 million years ago on the seafloor could, in principle, have had mouths and guts — organs that many palaeontologists argue emerged during the Cambrian period tens of millions of years later,” said Mr Bobrovskiy from the ANU Research School of Earth Sciences.
“Our discovery about Dickinsonia — and many other Ediacaran fossils — opens up new possibilities as to what they actually looked like.”
P1
Ediacara biota were strange creatures that lived on the seafloor 571 to 541 million years ago. They grew up to two metres long and include the earliest known animals as well as colonies of bacteria…
Mr Bobrovskiy said Dickinsonia had different types of tissues and must have been a true animal, a Eumetazoa, the lineages eventually leading to humans. Paper. (paywall) – Ilya Bobrovskiy, Anna Krasnova, Andrey Ivantsov, Ekaterina Luzhnaya, Jochen J. Brocks. Simple sediment rheology explains the Ediacara biota preservation. Nature Ecology & Evolution, 2019; DOI: 10.1038/s41559-019-0820-7 More.
The researchers found that the way the body was preserved does not rule out it having features associated with a true animal: “Now we know that what we are looking at is an impression of a soft organic skeleton that may have been anywhere within Dickinsonia’s body. What we’re seeing could be a part of Dickinsonia’s bottom, the inside of its body or part of its back.”
Associate Professor Jochen Brocks commented, “These fossils comprise our best window into earliest animal evolution and are the key to understanding our own deep origins.”
Yes, in the sense that sudden emergence rather than a long, slow Darwinian process seems more likely all the time. If his team is right, they just pushed the emergence of another true animal further back before the Cambrian explosion.
See also: Gunter Bechly: Dickinsonia Is NOT Likely An Animal (September 2018)
Rob Sheldon: How We Know The 558 Mya Animal Dickinsonia Remains Really Contained Fats
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Unique giant virus messes with current theories of viral evolution
mythical monster Medusa/shakko Own work, CC BY-SA 3.0 )
The newly identified Medusavirus infects amoebas, causing them to grow a hard shell. (The mythological Medusa turned her victims into stone.) Among other things, it was “ the first giant virus to have been isolated from a heated environment.” From ScienceDaily:
Along with the location of its discovery, Medusavirus holds a number of distinguishing features compared with other giant viruses. Its DNA codes for all five types of histones, the key proteins that help compact DNA within the nucleus. In fact, no other known virus has all five types. Further, Medusavirus encoded neither RNA polymerase nor DNA topoimerase II, whereas all other giant viruses encode at least one.
These features could explain why the replication of Medusavirus DNA begins and completes in the host nucleus to eventually fill the amoeba nucleus with viral DNA, which again is unlike other giant viruses.
Moreover, the morphology of the capsid surface was unique, in that it was covered with an extraordinary number of spherical-headed spikes. In addition, the amoeba genome encoded several capsid surface proteins.
The existence of histone genes in Medusavirus and capsid protein genes in amoeba suggest lateral gene transfer going both directions — host-to-virus and virus-to-host.
Overall, the findings suggest that Medusavirus offers a new model for host-virus co-evolution and that the Medusavirus is a new family of large DNA viruses. Paper. open access) – Genki Yoshikawa, Romain Blanc-Mathieu, Chihong Song, Yoko Kayama, Tomohiro Mochizuki, Kazuyoshi Murata, Hiroyuki Ogata, Masaharu Takemura. Medusavirus, a novel large DNA virus discovered from hot spring water. Journal of Virology, 2019; DOI: 10.1128/JVI.02130-18 More.
Giant viruses have only been known from the past few decades. There is still debate about whether viruses are actually life forms. Surely, there will be many game changers to come. Anyone attempting to compile an evolutionary history of giant viruses would be like the person who writes the history of a major league playoff series after the first game. Without the crystal ball.
See also: One way viruses get spread “never should have evolved”
and
Reset! Different segs of virus genome can exist in different cells but work together
Before you go: Viruses devolve. (PaV)
Virus expert highlights the conflict over whether viruses are alive In short, it is an open question. The question relates to the role viruses can play in evolution, among other things. Are they precursors of life, detritus of life, or something in between? Or all three? Keep the file open.
Viruses invent their own genes? Then what is left of Darwinism?
Why viruses are not considered to be alive
Another stab at whether viruses are alive
Phil Sci journal: Special section on understanding viruses
Should NASA look for viruses in space? Actually, it’s not clear that RNA came first. Nor is it clear that viruses precede life. A good case can doubtless be made for viruses being part of the scrap heap of existing life. But no matter. If you think you can find viruses in space, boldly go.
Why “evolution” is changing? Consider viruses
The Scientist asks, Should giant viruses be the fourth domain of life? Eukaryotes, prokaryotes, archaea… and viruses?
and
Are viruses nature’s perfect machine? Or alive?
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March 26, 2019
Why a senior scientist doesn’t “believe” in “science”
She left her position after she got fed up with the climate science wars. She quotes Robert Tracinski, who says,
Some people may use “I believe in science” as vague shorthand for confidence in the ability of the scientific method to achieve valid results, or maybe for the view that the universe is governed by natural laws which are discoverable through observation and reasoning.
But the way most people use it today—especially in a political context—is pretty much the opposite. They use it as a way of declaring belief in a proposition which is outside their knowledge and which they do not understand. Robert Tracinski, “Why I don’t ‘believe’ in ‘science’” at The Bulwark
Curry goes on to cite experiences that make clear that “I believe in science” often functions as a polite version of “Shut up or else.”
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See also: A study of the causes of science skepticism sails right by the most obvious cause of skepticism: Repeated untrustworthiness
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Pushback against abandoning “statistical significance” in science
What’s hot? What’s not?/Niklas Bildhauer, WikimediaRemember the recent call to abandon statistical significance in science research? There’s been some pushback:
Statistical significance sets a convenient obstacle to unfounded claims. In my view, removing the obstacle (V. Amrhein et al. Nature 567, 305–307; 2019) could promote bias. Irrefutable nonsense would rule.John P. A. Ioannidis, “Retiring statistical significance would give bias a free pass” at Nature
Ioannidis is a well-known scourge of bad data. See, for example, Another Well-Earned Jab At “Nutrition Science”
A statistician argues that two separate problems Are being conflated:
By focusing on the term ‘statistical significance’, we ignore the more important issue of what constitutes sufficient evidence of a true association. Let’s have that discussion and redefine what we mean by a statistically significant finding. Valen E. Johnson, “Raise the bar rather than retire significance” at Nature
Without the restraint provided by testing, an estimation-only approach will lead to overfitting of research results, poor predictions and overconfident claims. Julia M. Haaf, Alexander Ly & Eric-Jan Wagenmakers, “Retire significance, but still test hypotheses” at Nature
Of course, as science embraces post-modernism, “irrefutable nonsense” could be the new standard. Along with ever more strenuous demands that we trust science.
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See also: Abandon statistical significance, learn to live with uncertainty, scientists demand Let’s see where this goes. Will it lead to less magic with numbers or more and bigger magic?
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Michael Behe responds to the critics at his university, Parts 2 and 3
Yesterday, we noted Michael Behe’s response to Lehigh colleagues’ criticism of his new book, Darwin Devolves Here is Part 2:
Recently two of my Lehigh University Department of Biological Sciences colleagues published a seven-page critical review of Darwin Devolves in the journal Evolution. As I’ll show below, it pretty much completely misses the mark. Nonetheless, it is a good illustration of how sincere-yet-perplexed professional evolutionary biologists view the data, as well as how they see opposition to their views, and so it is a possible opening to mutual understanding. This is the second of a three-part reply. It continues directly from Part 1…
In their review Lang and Rice write that perhaps the very fact that there were two copies of a particular gene would itself be helpful, because of the extra activity it would add to the cell. I agree that is possible. However, it is special pleading, because most duplicated genes would not be expected to behave that way. For every extra restriction put on the gene that is supposed to duplicate (such as partial duplication, duplication that joins it to another gene, and so on), a careful study of the topic must adjust the mutation rate downward, because fewer genes/events are expected to meet those extra restrictions.
The third and most serious problem Lang and Rice overlook is that they assume without argument that a duplicated gene would be able to integrate into an organism’s biology strictly by Darwinian (or at least unintelligent) processes. Yet not all genes or functions are the same, so critical distinctions must be made.
More.
and
It’s hardly news that a group can share strong views on topics of mutual interest to its members, which many on the outside find less than compelling. Theoretical particle physicists, lawyers, members of the military, union members, business people, clergy, and on and on. It would be hard to find a group that didn’t have such shared views. Of course, that includes evolutionary biologists and scientists in general. I would like to delicately suggest that a large chunk of the disconnect (although certainly not the only factor) between the public and biologists over evolution is that, as a rule, biologists share a commitment to Darwin’s theory that the general public does not. That shared commitment leads biologists (and scientists in general) to require substantially less evidence to persuade them of the theory’s verity and scope than someone outside the tribe.
Contra Lang and Rice, it’s preposterous to say that the data “are more than sufficient to convince any open minded skeptic that unguided evolution is capable of generating complex systems.” Unless one defines a skeptic of Darwin’s theory (the most prominent proposed “unguided” explanation) as closed-minded, a quick visit to the library will disabuse one of that notion. More.
Exactly. Darwinism is magic. No two ways about it. Every time a Darwinian pathway can be thunk up that is even a zillionth plausible, we are expected to assume that that must have been the pathway used because Darwinism is true. It’s just the same as this: You can act like you won the lottery once you have bought a ticket.
No other approach to any history of anything in the world will do that for you. No wonder Darwinism sounds so much like a religion and its adherents are the last to see it.
Amazon Best Sellers Rank: #3,483 in Books (See Top 100 in Books)
#1 in Developmental Biology (Books) #6 in Creationism #8 in Science & Religion
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See also: Michael Behe’s response to Lehigh colleagues’ criticism If Behe’s critics were right, new life forms would be popping into existence all the time. But increasingly, political correctness matters so much more than truth to nature that we will be hearing stranger things yet about the Darwinian magic they espouse.
and
Two views of Ben Shapiro’s interview with Steve Meyer A critic, French-Canadian neuroscientist Jean-Francois Gariépy, who appears to be an alt right figure, has made his own vid, at The Public Space reviewing/attacking Shapiro’s interview with Meyer.
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Two views of Ben Shapiro’s interview with Steve Meyer
Steve Meyer is the author of Signature in the Cell and Darwin’s Doubt. It’s nice to see someone actuallylistening, for once, about what’s wrong with Darwinism:
Why might it be the best? Partly because of the long video format — a full hour (with a provocative final question for Steve that you need to subscribe to The Daily Wire to see), and very well produced. Partly because Shapiro has done his homework. He knows the common challenges to intelligent design and poses them very articulately, and he’s obviously absorbed Meyer’s books, especially Darwin’s Doubt and Signature in the Cell, as well other material on ID. That is more than you can say for some scientists and journalists I’m thinking of right now. David Klinghoffer, “Ben Shapiro May Have Done the Best Interview with Stephen Meyer That I’ve Seen” at Evolution News and Science Today
“Journalists?” In recent years, people have grown a little tired of the elite broadcast swamp stinking up the place with their obsessive refusals to sense reality when it is smacking them in the face.
Earth to Airstrip One Productions, Inc.: Your ratings are plunging. The future belongs to people who wonder about the same things other people do, not about the things you do.
And as for “scientists,” some of us are waiting to see whether they will just genuflect before the war on science and the war on math. The fact that top science types are really concerned about the US federal government tying cash coerced from the taxpayer to intellectual freedom on campus is not a good sign.
Meanwhile, a critic, French-Canadian neuroscientist who is claimed by some to be an alt right figure (but that’s disputed), has made his own vid, at The Public Space reviewing/attacking Shapiro’s interview with Meyer:
“Intelligent Design Continues To Be Wrong | TPS #360″ begins around 15:40.
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See also: Philosopher of science Steve Meyer will be on Ben Shapiro’s show Sunday The Twitterati are enraged as usual, this time about “bunk science.”
and
New US free speech policy miffs boffins at Nature The universities are “spooked by” Trump, are they? Well, they brought him on themselves. They could have listened before, when someone nicer than he is was telling them.
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March 25, 2019
Michael Behe’s response to Lehigh colleagues’ criticism
Some of Michael Behe’s colleagues wrote a critical review of his book Darwin Devolves here:
By reviewing Behe’s latest book, we run the risk of drawing attention—or worse, giving credibility—to his ideas. Books like Darwin Devolves, however, must be openly challenged and refuted, even if it risks giving publicity to misbegotten views. Science benefits from public support. Largely funded by federal grants, scientists have a moral responsibility (if not a financial obligation) to ensure that the core concepts of our respective fields are communicated effectively and accurately to the public and to our trainees. This is particularly important in evolutionary biology, where—over 150 years after On the Origin of Species—less than 20% of Americans accept that humans evolved by natural and unguided processes (Gallup 2014). It is hard to think of any other discipline where mainstream acceptance of its core paradigm is more at odds with the scientific consensus.
Why evolution by natural selection is difficult for so many to accept is beyond the scope of this review; however, it is not for a lack of evidence: the data (only some of which we present here) are more than sufficient to convince any open minded skeptic that unguided evolution is capable of generating complex systems. A combination of social and historical factors creates a welcoming environment for an academic voice that questions the scientific consensus. Darwin Devolves was designed to fit this niche. Gregory I. Lang Amber M. Rice, “Evolution unscathed: Darwin Devolves argues on weak reasoning that unguided evolution is a destructive force, incapable of innovation” at Evolution
and Behe has responded as follows:
They begin with logical error #1 by deriding the First Rule of Adaptive Evolution as a “quality sound bite” that is “simplistic and untruthful to the data.” Recall that the First Rule states, “Break or blunt any functional gene whose loss would increase the number of a species’ offspring.” Also recall that I explained, in both the book and the journal article where it was first published, that it is called a “rule” in the sense of being a rule of thumb, not an unbreakable law, and it is called the “first” rule because that is what we should generally expect to happen first to help a species adapt, simply because there are many more ways to break a gene than to build a new constructive feature.
As you might imagine, I have read the Evolution review closely. Yet nowhere do the authors even try to show why the First Rule isn’t a correct statement. They point to mutations that are not degradative, but fail to show quantitatively that those other types will arise faster than degradative ones. In fact, the other types are expected to be orders of magnitude slower.
The reviewers agree that the First Rule is fine for explaining many results from the experimental evolution of microbes such as bacteria and yeast, but they balk at extending it beyond the lab. In fact, they actively argue that lab results really can’t tell us much about the real world: “No deletion is beneficial in all environments and beneficial loss of function mutations that arise in experimental evolution are unlikely to succeed if, say, cells are required to mate , the static environment is disturbed, or glucose is temporarily depleted.” All of those situations, of course, will be common outside a laboratory.Michael Behe, “A Response to My Lehigh Colleagues, Part 1” at Evolution News and Science Today:
If Behe’s critics were right, new life forms would be popping into existence all the time. But increasingly, political correctness matters so much more than truth to nature that we will be hearing stranger things yet about the Darwinian magic they espouse.
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See also: Michael Behe: How To Tell If Scientists Are Bluffing
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Michael J. Behe's Blog
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