How OOL science continues to be the weak link on design deniers' team.

 Game Over? Nick Lane Wants Another Inning 

David Coppedge 

The score is 36-0, but the Darwin Team isn’t ready to concede. Lehigh University biochemist Michael Behe, writing for World Magazine (see our coverage here), described how he attended a conference of scientists to hear Nobel laureate John E. Walker, the world’s expert on ATP synthase, explain how it might have evolved. To design advocates, this rotary engine is a paragon of intelligent design. Walker, who shared a Nobel Prize for elucidating the motor’s rotary mechanism, spent his whole time describing the intricacies of this molecular machine, and never offered an evolutionary explanation for it until the Q&A session. Then, he was asked directly how a mindless process could produce such a stunning piece of work. Walker stumbled, offering only a fragment of speculation that it must have arisen “Slowly, through some sort of intermediate or other.” That’s when Behe, out of earshot, muttered two simple words, “Game over.”

Game over. The losing team heads for the showers with heads bowed. The Darwin Team’s MVP had just struck out at the bottom of the ninth. Calling the game in such an obvious wipeout would have been superfluous. The crowds file out of the stands. Suddenly, eight players run onto the field! “Wait! Wait!” they cry. “Let us have a time at bat!”

The rescue team, led by Nick Lane of University College London, waves a paper over their heads. It’s hot off the press from PLOS Biology, titled, “A prebiotic basis for ATP as the universal energy currency.” Lane shouts, We have the intermediate! It’s AcP! One of the refs eyeballs the paper for a minute. Will it be worth calling the teams back onto the field for another inning? 

A Plausible Scenario? 

The gist of the hypothesis is that acetyl phosphate (AcP), a simple molecule with the formula C2H5O5P, can phosphorylate ADP into ATP in water, if ferric ion (Fe3+) is present. The team believes their lab work offers a plausible scenario for prebiotic ATP formation without the need for ATP synthase. 

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis.This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ions. We then show that Fe3+ and AcP are surprisingly favoured.  

Sounds Impressive. Can It Work?  

The team tells the referee about additional surprising benefits of their intermediate. Visions of the Miller spark apparatus come to mind: 

Surprisingly, our results demonstrate that maximal ATP synthesis occurred at high water activity and low ion concentrations, indicating that prebiotic ATP synthesis would be most feasible in freshwater systems.Likewise, ferrous iron can be oxidized to ferric iron by photochemical reactions or oxidants such as NO derived from volcanic emissions, meteorite impacts, or lightning strikes, which also points to terrestrial geothermal systems as a plausible environment for aqueous ATP synthesis. 

Questions & Answers 

powers a disequilibrium in the ratio of ADP to ATP, which amounts to 10 orders of magnitude from equilibrium in the cytosol of modern cells. Molecular engines such as the ATP synthase use ratchet-like mechanical mechanisms to convert environmental redox disequilibria into a highly skewed ratio of ADP to ATP.” But we cannot say how that happened.

But how could a simple prebiotic system composed mostly of monomers sustain a disequilibrium in ATP to ADP ratio that powers work? Well, “One possibility is that dynamic environments could sustain critical disequilibria across short distances such as protocell membranes.”

Didn’t you just assume the existence of a protocell with a membrane? Where did those come from? Look, we’re not trying to come up with a complete picture of how life originated. We’re just trying to explain why ATP is the universal energy currency for life as it exists today, and how it might have emerged.

Emerged… by chance, you mean? Isn’t that circular reasoning? How so? What other possibility is there?

There’s intelligence, the only cause ever observed that is capable of assembling complex parts into a functional whole. Sorry; we thought this was a scientific baseball diamond.

It is. So what is your explanation for the functional information in the simplest life? Your paper admits that “ATP links energy metabolism with genetic information.” What is the source of that genetic information? Uh, some sort of intermediate or other.

The referees convene and shout out, “GAME OVER!” 

On reading the fossil record.

 Fossil Friday: Moniopterus — Snake, Beetle, or Mollusk?

Günter BechlyEgg-shaped fossils of about two inch size have been described as Moniopterus japonicus from the Miocene of Japan. It is a perfect showcase for how paleontologists play fast and loose with the over-interpretation of poorly preserved fossils. Moniopterus was initially described as the only known example of fossil sea-snake eggs by Hatai et al. (1974). Wow, that sounds interesting, if we gloss over the little lapse that the authors accidentally placed the fossils in the bony fish family Ophichthyidae instead of the sea-snake subfamily Hydrophiinae, because both animals have the same common name in Japanese. Ooops, that’s an embarrassing mistake for professional scientists writing a technical paper, but anyway, at least they found the first sea-snake eggs, or did they?

About twenty years later, another study recognized the same material as fossilized pupal chambers of a coleopteran insect (Johnston et al. 1996). Hmmm, that’s quite a different take on the same fossils, but it gets even better. A re-examination of the holotype specimen by Haga et al. (2010) provided no evidence in support of these previous interpretations. Instead the fossils turned out to be borings of a rock-boring mytilid bivalve of the genus Lithophaga. So, a trace fossil of a mollusk had been misidentified in different phyla as snake egg and as beetle pup

That this case of blatant misidentifications is not an isolated example is shown by the case of alleged vertebrate eggs from the Cretaceous of the Gobi Desert, which turned out to be fossilized pupal chambers of beetles (Johnston et al. 1996). But on the other hand, should we trust the latter study at all, given the blunder they made with Moniopterus? Scientists are only humans and many of them see what they want to see. Fossils often leave a lot of room for wild imagination and wishful thinking. Of course, they still prove Darwinian evolution beyond a reasonable doubt! Just follow the science and don’t ask silly questions.a. 

References 

1.Hatai K, Masuda K & Noda H 1974. Marine fossils from the Moniwa Formation along the Natori river, Sendai, northeast Honshu, Japan, part 2. Problematica from the Moniwa Formation. Transactions and Proceedings of the Paleontological Society of Japan NS 95, 364–371. DOI: https://doi.org/10.14825/prpsj1951.1974.95_364.

2.Johnston PA, Eberth DA & Anderson PK 1996. Alleged vertebrate eggs from Upper Cretaceous redbeds, Gobi Desert, are fossil insect (Coleoptera) pupal chambers: Fictovichnus new ichnogenus. Canadian Journal of Earth Sciences 33(4), 511–525. DOI: https://doi.org/10.1139/e96-040.

3.Haga T, Kurihara Y, Kase T 2010. Reinterpretation of the Miocene Sea-Snake Egg Moniopterus japonicus as a Boring of Rock-Boring Bivalve Lithophaga (Mytilidae: Mollusca). Journal of Paleontology 84(5), 848–857. DOI: https://doi.org/10.1666/09-126.1.

I rant some more against reductive spiritualism.

 Psalms139:13BSB"For You formed my inmost being;a

You knit me(Objective first person singular) together in my mother’s womb." 

Can a reductive spirit soul be the fruit of sexual reproduction. Note that natural processes occurring in the impregnated womb are not merely responsible for the impersonal tent that the ghost who is the real person(the real me) ,but are JEHOVAH'S instrumentalities in bringing the soul into being. 

John3:6NIV"Flesh gives birth to flesh, but the Spirit gives birth to spirit." 

So the human cannot give birth to the superhuman. 

Matthew22:17,18NIV"17Then what was said through the prophet Jeremiah was fulfilled:

18“A voice is heard in Ramah,

weeping and great mourning,

Rachel weeping for her children

and refusing to be comforted,

because they(objective third person plural) are no more.” d" 

Death for the bible writers resulted in a reversion to one pre life state not a progression to a high post life existence. This is why they can coherently present the resurrection of the dead as a hope and not an incoherent word salad as is the case with Christendom's theologians. Thus it was not merely the impersonal fleshly coverings of these children that was dissolved their personhood came to an end. Until the one who calls things that are not(including things that once we're) as though they are(see romans 4:17) calls them to mind. 

Can we talk about this? II

 Listen: Demonizers and Dehumanizers 

Evolution News @DiscoveryCSC 

A new episode of ID the Future brings the second half of a panel discussion at the 2022 Center for Science & Culture Insider’s Briefing. This portion begins with bioethicist and Discovery Institute Senior Fellow Wesley J. Smith making a surprising argument: His own field, bioethics, is at war with true medical ethics. Specifically, its most prominent figures — hailing from elite universities in the United States and Europe — are dedicated to emptying our medical culture of traditional ethical standards that protect human rights and are guided by a commitment to inherent human dignity.

Some leading bioethicists see human beings as of no more inherent value than yeast. Smith stands athwart this anti-human trend and urges listeners to wake up and resist. Then John West, managing director of Discovery Institute’s CSC, spotlights those who demonize people who have resisted demands to be vaccinated against the COVID-19 virus, with some even calling for such people to be restricted to house arrest, or imprisoned. West also notes that many of those calling for such strong-arm tactics make no distinction between those who have and haven’t already had COVID-19, despite the fact that there is abundant scientific evidence that having had COVID-19 is a more effective form of vaccination than any vaccination shot. West decries the demonizing and bullying tactics he references, calling such behavior anti-science and anti-reason. He urges supporters of vaccinations to meet the other side not with insults but with reasoned discourse and scientific evidence. Download the podcast or listen to it here.

The seas testify against Darwin

 Secrets that Give Sea Lions and Jellyfish Their Edge as Swimmers 

David Coppedge 

The Illustra Media documentary Living Waters focuses on four marine organisms, each worthy of admiration: dolphins, sea turtles, salmon, and humpback whales. But before and after the detailed accounts, scenes of many other swimmers parade across the screen. Can you guess which of them wins the prize for most efficient swimmer? It may not be your first guess. It’s not necessarily the fastest, just the one that gets the most distance per expenditure of energy.

Neelesh Patankar, a mechanical engineer from Northwestern, and John Dabiri, a bioengineer from Caltech, measured the efficiency of a wide variety of organisms. They determined that top prize goes to: the jellyfish. In an article at The Conversation, Akshat Rathi explains why jellyfish “are the most efficient swimmers” in the world. That’s quite a distinction among the many other swimmers that are already at the top of their game: 

The new measure has two implications. First, among those that have typical swimming and flying actions, which includes most fish and all birds, each animal is as energy efficient as it can be. This means that, given their size and shape, each animal is able to spend the least amount of energy to move the most distance. Second, this measure confirms a previous finding that jellyfish are unusually energy efficient, beating all the thousands of fish and birds Patankar studied.

“Put another way, a whale and a tuna are equally energy efficient,” Patankar said. “Except jellyfish, which have an unusual action that makes them more efficient.” 

What’s the Secret? 

Beautiful images of these creatures flash by briefly in the Illustra film. Time did not allow producer Lad Allen to discuss their mechanics, but the subject was considered during the planning stages. We mentioned jellyfish efficiency in an earlier post. What’s the secret that gives jellies the edge? 

While working on the energy-consumption coefficient, he came across recent work done by Dabiri and his colleagues which showed that the unique contract-and-relax action of jellyfish allowed it to recapture some of the energy it spends on motion. This means a jellyfish can travel a lot more distance for the same amount of energy spent by other animals adjusted for its weight and size. 

The Cambrian Explosion 

It’s interesting to note, also, that jellyfish (phylum Cnidaria) are among the phyla that appear abruptly in the Cambrian explosion — see our article where an expert said, “The earliest widely accepted animal fossils are rather modern-looking cnidarians.” Given the high efficiency of these deceptively simple-looking animals, it’s not surprising that engineers are attempting to imitate their secrets. “Dabiri is already working on exploiting jellyfish propulsion,” Rathi says.

There’s another swimmer that might surprise you, this time for its stealth. These graceful animals make cameo appearances at the beginning and end of Living Waters. Phys.org reports: 

At a maximum speed of 25 miles per hour, sea lions may not be the fastest-swimming mammal in the sea. But they are unrivaled when it comes to stealth — their signature clap-and-glide flipper motion propels them through water and leaves virtually no wake. 

The benefits of turbulence-free motion underwater are obvious. Imagine submarines that glide stealthily beneath sensitive detectors. At George Washington University, mechanical engineers and students are attempting to “build a machine to mimic what sea lions naturally do.”  

It wouldn’t be easy to design a system from scratch that could match the sea lion’s specifications — they produce high levels of thrust while leaving little traceable wake structure. So it makes sense to learn as much as we can about how they do it — with the thought that someday we might be able to engineer something that mimics our biological model. 

The secret of wake-free swimming appears to be related to the sea lion’s use of its fore-flippers, rather than a tail (as with dolphins and fish). At The Conservation, Megan Leftwich describes in more detail how this mode of locomotion produces more thrust. A video shows how researchers at George Washington University are measuring carefully the flipper motions of California sea lions, mapping them into computer models that can inform the design of artificial flippers. This is an exercise in “Studying Nature’s Solutions,” the title says.

If the world’s best human designers are attempting to build machines to mimic what these animals “naturally do,” it’s a reasonable inference that sea lions and jellyfish originated from an intelligent cause — one with superior knowledge of propulsion, fluid mechanics, and optimization. 

The old God's Of the classics v. The new Gods of modernism v. The even newer God's of postmodernism?

Darwin and the Loss of the Enlightenment Paradigm .

Neil Thomas

In two articles so far (here and here), I have been exploring how justified the new atheists’ appropriation of Darwinian ideas is. This is the third and final post. As we’ve seen, Erasmus Darwin was a quintessential legatee of Enlightenment prepossessions. As its somewhat virtue-signaling name implies, the thinkers of the Enlightenment wished to distance themselves from anything that smacked of religious “superstition.” This led to the determination to declare a unilateral declaration of independence from the metaphysical sphere in favor of purely “scientific” modes of explanation. Yet in the face of the last century of scientific discoveries we have come to realize that hubristic expectations stemming from the Enlightenment dream of encompassing the whole of reality in some grand material theory of everything have been forced into a reluctant retreat.1

Almost Complete Ignorance

As a plethora of popular books, articles, and TV programs have recently intoned, our almost complete ignorance of the nature of ultimate reality has been laid bare by the work of Planck, Einstein, Heisenberg, Carlo Rovelli, and a host of microbiology specialists. Taken together, these scientific advances have united to challenge the Newtonian/Enlightenment paradigm. Scientists can no longer deliver certainty and predictability in the aftermath of such disconcerting advances in physics or in microbiology, which represent an unsuspected level of ultra-diminutive reality that has only revealed its bare existence in the last seven decades or so thanks to the invention of the electron microscope in 1944. Indeterminacy and probabalism have emerged to subvert the Enlightenment conception of a predictable clockwork universe. We have been forced to acknowledge that the dimension of reality we know of is merely the observable, superficial part and that this rests on and is sustained by invisible trestles of substrate reality of which we have little inkling and to which our Cartesian notions of predictability and comprehensibility do not, alas, apply. 

Whose Reality?  

In short, the bright new dawn of Erasmus Darwin’s Enlightenment world has been replaced by the hauntingly surreal specter of what is now routinely referred to as “quantum weirdness.” Like it or not, Erasmus’s simple and predictable world is no more, and we now find ourselves confronted by the truly vertigo-inducing predicament of being subject to an unpredictable cosmos we simply do not understand. It appears to me that the only intellectually defensible position to adopt in the light of such unanticipated scientific advances is to keep an open mind. The new atheists on the other hand continue to cling anachronistically to the same would-be omniscient paradigm of reality as that in which Erasmus Darwin reposed his faith. But whereas Erasmus had the extenuation of knowing nothing of the profounder reaches of reality into which modern scientific advances have given us at least some fleeting glimpses, the same excuse cannot be pleaded for the new atheists whose stance, either tacitly or wittingly, turns a blind eye to those hidden dimensions of existence. 

Under the illusion of being the “bright” (their term) or enlightened ones, they appear, on the contrary, to have become the doctrinaire victims of a peculiarly modern form of obscurantism. It is as if they are doggedly clinging to an obsolete worldview which denies the relevance of much cutting-edge science. Their outlook has little in common with that of Charles Darwin whose later years were marked by what Peter Vorzimmer once termed “frustrated confusion.”2 In that respect Darwin might be posthumously welcomed as an avatar of postmodern man in that he anticipated the decidedly non-omniscient spirit of our modern age. Such, needless to say, is not the mental universe inhabited by the new atheists whose philosophic stance seems more akin to that of Charles’s grandfather than to that of the grandson. 

Notes 

2)See on this point Marcus de Sautoy, What We Cannot Know: From Consciousness to the Cosmos (London: Fourth Estate, 2017) and Carlo Rovelli, Reality Is Not What It Seems: The Journey to Quantum Gravity (London: Penguin, 2016).

2)Darwin: The Years of Controversy, p. 254.      

Atheism makes it possible to be an intellectually fulfilled Darwinist?

 Erasmus Darwin and Credible Denial. 

Neil Thomas 

In a post yesterday I began exploring how justified the new atheists’ appropriation of Darwinian ideas is. Consideration of Erasmus Darwin’s writings suggests that his unbelief could well have been father to the thought in the matter of his evolutionary speculations. He was certainly more prone to gratuitous displays of atheistical dissent than was his grandson Charles. This was clearly shown in what turned out to be an amusing “own goal” he scored against himself arising from the provocative inscription he once chose to have embossed on the exterior of his coach. The offending words, “E Conchis Omnia” (everything comes from seashells), suggested rather too unambiguously to many orthodox believers that humans had originally developed from creatures crawling along the seabed. One is here reminded irresistibly of Richard Dawkins paying to have atheistic messages emblazoned on the sides of London buses. 

Unsurprisingly, Erasmus’s all-too transparent subtext was not lost on a Lichfield neighbor of his, a Church dignitary by the name of Canon Seward. Seward, offended by the idea that sea shells could be thought to be the ancestors of humans, attacked the exhibitionistic show of (philosophical) materialism in a satirical poem, comparing Erasmus with Epicurus and Lucretius, the arch-materialists of the Classical past: 

He [=Erasmus] too renounces the Creator,

And forms all sense from senseless matter

Makes man start up from dead fish bones,

As old Deucalion did from stones.1 

Predictably, Erasmus was before long obliged to remove the inscription from his coach, fearing loss of revenue from his medical practice were he not to do so.

We have recently been made aware of the power of “cancel culture” even in our own day. Against the backdrop of a decidedly more persecuting age,2 Erasmus was thenceforth obliged to make the outward claim that he was a theist, but his abiogenetic conception of the beginning of the world and the subsequent wholly natural processes of evolution he postulated were advanced in suspiciously ambiguous terms which might (tactically) be termed “two-faced,” as the following words indicate: 

Would it be too bold to imagine, that in the great length of time, since the earth began to exist, perhaps millions of ages before the commencement of the history of mankind, would it be too bold to imagine, that all warm-blooded animals have arisen from one living filament, which THE GREAT FIRST CAUSE endued with animality, with the power of acquiring new parts, attended with new propensities, directed by irritations, sensations, volitions, and associations; and thus possessing the faculty of continuing to improve by its own inherent activity, and of delivering down those improvements by generation to its posterity, world without end!3 

The passage advances an awkward, logically contradictory hybrid of spontaneous generation and divine creation. Erasmus wishes to assure readers that this process was initiated under God’s superintendence, yet the phrase “which THE FIRST GREAT CAUSE endued with animality” seems to be something of a parenthesis which might be omitted without injuring the flow of his sentence. This in turn indicates that it might have been an interpolation tacked on pro forma to avert clerical ire. The truthfulness of his theistic claims must then remain highly moot, all the more so since his philosophical conjectures were unorthodox and very often, in 18th-century terms, sacrilegious.

Erasmus Darwin thought a jaunty form of Augustan verse traditionally associated with lighter themes4 was the best cover for his rather outré poetical effusions on evolution. It became especially imperative for people holding views like those of Erasmus to dissemble after the French Revolution of 1789 and the Terror which followed it. From that time onward there grew up a genuine fear of any emulation of French science whose practitioners, rightly or wrongly, were suspected of instrumentalizing their science to further insurrectionary political goals. Understandably then, against the background of the climate of fear, we must often read between the lines in order to get to Erasmus’s true meaning. 

Atheism, Political Emancipation, Revolution 

age in which Erasmus Darwin grew to maturity and which became the crucible of so many revolutionary impulses. By dint of an “assimilation of Biblical and theological elements to secular frames of reference”6 progress was, in Enlightenment thinking, imagined as being achievable in historical time (as opposed to the distant chiliastic, on-the-stroke-of-Doomsday hope offered by Christian apocalyptic). The ultimate effect of this large change of perspective from divine to secular was to translate Scriptural prophecy rather freely into preemptive revolutionary action — people “doing it for themselves” to improve their condition by the form of direct action which could do away with the need for apocalyptic hopes. As the contemporary examples of the American and French revolutions showed, this could involve bloodshed, yet the pious hope was that the violence would have a cleansing effect which would ultimately lead to the greater good.

As the late Roy Porter observed, it was Erasmus whose “man-centred view of man making himself” resulted in his “Promethean vision of infinite possibilities. God had become a distant cause of causes; what counted was man acting in Nature. The theodicy, the master narrative, had become secularized.”7 His was a very new form of secular cosmogony in explicit opposition to the older European master narrative enshrined in the Bible and the 12 books of John Milton’s Paradise Lost. It is perhaps otiose to remark that the ancient Greeks might have called this hubris. 

Notes 

1)In Greek mythology Deucalion was the son of Prometheus. With his wife Pyrrha he survived a flood sent by Zeus to punish human wickedness; they were then instructed to throw stones over their shoulders, and these turned into humans to repopulate the world. By this reference Seward doubtless meant to arraign Erasmus for adhering to what Wordsworth would later refer as a ‘creed outworn’ (as opposed to Christianity). See Desmond King-Hele, Erasmus Darwin and Evolution (Sheffield: Stuart Harris, 2014), p. 153.

2)Erasmus had misgivings about publishing his poem Zoonomia or the Laws of Organic Life because he feared accusations of heresy, and, indeed, when it was published, it occasioned much ecclesiastical opprobrium. In 1817 the Italian translation was even placed on the Papal Index of proscribed books.

3)Zoonomia or the Laws of Organic Life, two volumes (London: J. Johnson, 1794-6), volume 1, p. 505.

4)Such as Alexander Pope’s mock-heroic “Rape of the Lock” (1712/14).

5)Jennifer Hecht, Doubt: A History (New York: HarperOne, 2003), p. 402.

6)M. H. Abrams, Natural Supernaturalism. Tradition and Revolution in Romantic Literature (New York: Norton, 1971), p.64.

7)Roy Porter, Enlightenment. Britain and the Creation of the Modern World (London: Penguin, 2001), p. 445.

The difference between artificial intelligence and actual intelligence is qualitative not quantitative.

 Jay Richards: Myths, Metaphysics, and Artificial Intelligence.

David Klinghoffer 

The myths of artificial intelligence are the theme of the latest Science Uprising episode. Philosopher Jay Richards is one of the scholars featured, discussing what he calls the metaphysics behind those myths. It isn’t a superior grasp of the technology involved that drives some (Stephen Hawking, Elon Musk, and others) to warn that AI will achieve superiority over human beings, drive us out of work, and finally out of existence. It’s the hidden premise that humans are just “meat machines” rather than spiritual beings in a creator’s image. If that were true, of course it would follow that other, faster machines would likely overtake and replace us.

Richards is the author of The Human Advantage: The Future of American Work in an Age of Smart Machines, among other books. If you missed the new Science Uprising episode, find it Here.

Darwinism schooled again by primeval tech.

Armed Forces in the Cell Keep DNA Healthy 

David Coppedge .

Science reporters struggle for metaphors to describe the complex operations they see going on in the cell. For example: 

The Orchestra 

News from the University of Geneva likens the human genome to a “complex orchestra.” Their research led to “unexpected” and “surprising” findings showing “harmonized and synergistic behavior” in the regulation of genes. The metaphor of a conductor keeping all the various players in harmony came to mind: 

A team of Swiss geneticists from the University of Geneva (UNIGE), the École Polytechnique Fédérale de Lausanne (EPFL), and the University of Lausanne (UNIL) discovered that genetic variation has the potential to affect the state of the genome at many, seemingly separated, positions and thus modulate gene activity, much like a conductor directing the performers of a musical ensemble to play in harmony. These unexpected results, published in Cell, reveal the versatility of genome regulation and offer insights into the way it is orchestrated 

The Armed Forces 

Another metaphor popular among reporters is “armed forces.” This metaphor will prove instructive as we read about DNA protection and damage repair. Let’s look at some of the stages in this process where we will find soldiers, emergency medical technicians, ambulances and military hospitals in action, each well trained and equipped for defense. 

Surveillance and Inspection 

Any disciplined military operation requires high standards. Soldiers at boot camp know that drill sergeants can be ruthless when inspecting rifles, shoe shines, and barrack beds. Similarly, machines in the genome inspect DNA for errors and won’t tolerate less than perfection. A news item from North Carolina State University describes MutS, a machine that inspects unzipped DNA strands looking for errors. Any mismatch makes this drill sergeant stop and stare the recruit in the face, even if he is one in a million. 

Fortunately, our bodies have a system for detecting and repairing these mismatches — a pair of proteins known as MutS and MutL. MutS slides along the newly created side of the DNA strand after it’s replicated, proofreading it. When it finds a mismatch, it locks into place at the site of the error and recruits MutL to come and join it. MutL puts a nick in the newly synthesized DNA strand to mark it as defective and signals a different protein to gobble up the portion of the DNA containing the error. Then the nucleotide matching starts over, filling the gap again. The entire process reduces replication errors around a thousand fold, serving as our body’s best defense against genetic mutations and the problems that can arise from them, like cancer. 

First Response 

If casualties occur, they have to be detected. A protein named ATF3 is captain of a squad that acts as “first responder” to DNA damage, as this from Georgia Regents University explains. Let’s say a DNA strand breaks because of sunlight, chemotherapy or a cosmic ray. If not corrected quickly, the cell could become cancerous or die. What happens first? 

In the rapid, complex scenario that enables a cell to repair DNA damage or die, ATF3, or activating transcription factor 3, appears to be a true first responder, increasing its levels then finding and binding to another protein, Tip60, which will ultimately help attract a swarm of other proteins to the damage site. 

Combat Operations 

Viruses have invaded! The armed forces go into high alert. The Salk Institute for Biological Studies describes the flurry of activities that result, because every organism “must protect its DNA at all costs.” 

Before panicking, the cell’s commanding officers need intelligence. If a DNA break puts the cell in stress, was it a natural break, let’s say from a cosmic ray, or from a virus, like an insurgent tossing a grenade? A false move could lead to friendly-fire casualties. 

The researchers explain how the cell figures out if the DNA damage was internal or external. First, the MRN complex gives the “all hands on deck” signal. It stops replication and other cell operations until the break is mended.  

What’s interesting is that even a single break transmits a global signal through the cell, halting cell division and growth,” says O’Shea. “This response prevents replication so the cell doesn’t pass on a break.” 

The viral response begins the same way, but doesn’t give the global alarm. Instead, the alarm is localized, and sentries in the area dispatch the invaders. There’s a reason for this. “If every incoming virus spurred a similarly strong response, points out O’Shea, our cells would be frequently paused, hampering our growth.” But when the cell becomes preoccupied with DNA damage repair, the viruses can infiltrate.

A video in the article applies the armed forces metaphor: 

Govind Shah: “DNA repair proteins serve as security guards inside the nucleus. They catch virus DNA and escort them out of the cell. If a cell experiences a huge amount of DNA damage, then these security guards will be pulled away from the viral DNA and allow the viral DNA to replicate to high levels.”

Clodagh O’Shea: “We discovered that if you have DNA damage in your own genome, and the alarm goes off, actually that recruits in all of the forces: all of the police, national guard–everyone’s there. All the forces are dealing with your own DNA damage, and there’s nothing left to actually even see or actually turn off the virus.” 

This gave them an idea. Shah says, “So why not use this to kill cancer cells” with viruses engineered to enter tumor cells? The programmed response they discovered will cause the cell to let the viruses in while it’s preoccupied with fixing DNA breaks. “If the cell can’t fix the DNA break, it will induce cell death-a self-destruct mechanism that helps to prevent mutated cells from replicating (and thus prevents tumor growth).”  

Medics 

We’re all familiar with the images of battlefield helicopters delivering medics to give first aid to the wounded, or airlifting them to the nearest triage station or hospital. The cell nucleus has hospitals, an article at Biotechniques says, and “A molecular ambulance for DNA” knows how to get the casualties to the emergency room. 

Double-strand breaks in DNA are a source of stress and sometimes death for cells. But the breaks can be fixed if they find their way to repair sites within the cell. In yeast, one of the main repair sites resides on the nuclear envelope where a set of proteins, including nuclear pore subcomplex Nup84, serves as a molecular hospital of sorts. The kinesin-14 motor protein complex, a “DNA ambulance,” moves the breaks to repair sites, according to a new study in Nature Communications. 

Researchers at the University of Toronto found it “very surprising” that the ambulance driver is the well-known motor protein kinesin-14 

Hospital Staff 

News from the University of Texas MD Anderson Cancer Center introduces some of the specialists in the DNA repair hospital: fumarase, a metabolic enzyme; DNA-PK, a protein kinase; and histone methylation enzymes that regulate the repair process. These skilled doctors perform restorative surgery for “DNA double-strand breaks (DSBs),” which “are the worst possible form of genetic malfunction that can cause cancer and resistance to therapy.” 

Clean-Up Crew 

Cells invest a lot of energy in their ribosomes, the organelles that translate DNA. Ribosomes are assembled from protein and RNA domains. What happens with the leftovers? An item from the University of Heidelberg describes molecular machines that barcode the fragments for delivery to a barrel-shaped shredder called the exosome. Though not described in military terms, the agents are under strict orders and required to pass through checkpoints. 

According to Prof. Hurt, the production of ribosomes is an extremely complex processthat follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be “trimmed” at specific points during the manufacturing process, and the superfluous pieces are discarded. “Because these processes are irreversible, a special check is needed,” explains Ed Hurt. 

The number of “armed forces” personnel involved in DNA defense and cell quality control is astonishing. It’s beyond a well-conducted orchestra. It’s like a military operation, with strict protocols, hierarchical command structure and trained specialists. These systems are goal-oriented: they exist to protect the genome. They are on duty inspecting components even when nothing is wrong. And when things do go wrong, they know just what to do, as if well-trained in following orders.

We aren’t surprised to notice that these articles say nothing about evolution. Why? Because we all know from our experience that phenomena characterized by hierarchical command and control systems with documented procedures and skilled agents are always intelligently designed. 

The new atheists: More Darwinian than Darwin?

 Darwin and the “New Atheists”  

Neil Thomas 

The somewhat superannuated 19th-century “conflict model” once used to define embattled evolutionary and religious claims to truth status has in our own time made an unheralded comeback in the writings of a diverse group of social commentators widely referred to as the “new atheists.”1 For much of the 20th century that older, conflict model, represented by the writings of the late Victorian era Andrew Dixon White2 and others, was modified in light of intellectual developments which came preponderantly to view science and religion as separate domains, each with its own sharply defined epistemological boundary.3 In the last few decades, however, some ideologically engaged scientific activists and commentators with erstwhile Oxford biologist Richard Dawkins at their head have seized the opportunity to weaponize Darwinism to push an atheist agenda against the backdrop of what they see as a dangerous uptick in global religious sentiment. In this and two subsequent posts I wish to explore how justified the group’s appropriation of Darwinian ideas is. 

Darwin’s Doubts 

ground zero as that advanced by Anaximander and his follower Anaximenes.5 And like the Greeks, Erasmus advanced no empirical evidence that would allow his claims to be tested. Not surprisingly then, evolution was widely regarded before 1859 as the minority preoccupation of a group of eccentrics rather than as a key to unlocking the mysteries of human existence.

Fast forward to a century later and we find that Charles Darwin was acutely aware of the checks and balances set up by modern science in order to establish any given theory as a demonstrable fact. Realizing that his grandfather’s ideas did not meet modern standards of proof, he looked for a sounder causal foundation for the Erasmian contribution to evolution. This he was to find in the theory of natural selection which he derived and developed from the writings of Thomas Malthus. It was via Malthus that Darwin thought to have discovered a mechanism or vera causa to underpin his grandfather’s ideas. In time, however, he began to harbor doubts about what he had first confidently hoped would be his game-changer with the capacity to bring evolutionary thought into a new era of acceptance and public prestige.

In later decades of his life, however, Charles began to doubt whether his postulated theory of natural selection would have been enough on its own to effect all the extraordinary transmutations evidenced by the world’s profusion of widely different species. This thought even led him to flirt with Lamarckian ideas of evolution which he had previously scorned.6

The upshot of the author’s second thoughts was that the sixth edition of the Origin was very different from the 1859 version and in some cases quite inconsistent with the first iteration of his ideas.7 Most strikingly, there arose within him a growing tension concerning his public postulation of an evolutionary theory dependent on natural selection and his claim in older age to be a “Theist” (Darwin’s own capitalization).8 It therefore appears that the more valid historical parallel for the new atheists is not Charles himself but Charles’s grandfather. The preoccupation of the Darwin family with evolutionary speculation was something which grew by stages9 and it is at a much earlier stage that a less ambiguous correlation emerges between evolutionary thought and atheism. 

Atheists Old and New 

What links Erasmus Darwin with the modern proponents of atheism is that the grandfather grew up against the background of that crypto-atheistical doctrine of deism according to which God had shrunk to the status of a deus absconditus or — to use the deprecatory contemporary cognomen — “absentee landlord.” Given such a backdrop of non-belief the question arises: Which came first in Erasmus’s thinking: the chicken or the egg? By which I mean: Was his desire to ponder possibilities of a purely material and naturalistic process of creation and evolution triggered by a deist conviction that, even if God had ever existed, he had now long since disappeared from human ken and was in that sense functionally irrelevant to human affairs? In other words, was his whole theory of evolution triggered by what is now called materialist confirmation bias (as one strongly suspects is the case of the new atheists)? For it is clear that if one has been convinced (or has convinced oneself) that there neither is nor can ever be evidence of divine direction in human affairs, then one is forced to speculate on some wholly material alternative, however illogical, impracticable, and physiologically improbable it might appear. 

Notes 

1)See The Four Horsemen: Dawkins, Dennet, Harris, Hitchens with a Foreword by Stephen Fry (London: Transworld/Penguin, 2019).

2)A History of the Warfare of Science with Theology in Christendom (New York: Appleton, 1896).

3)James Moore, The Post-Darwinian Controversies: A Study of the Protestant Struggle to Come to Terms with Darwin in Great Britain and America 1870-1900 (Cambridge: CUP, 1979). 

4)See renowned quantum mechanics specialist Carlo Rovelli’s The First Scientist: Anaximander and his Legacy (Yardley PA: Westholme, 2011).

5)See Erasmus Darwin, The Temple of Nature, facsimile of 1803 edition (Aldershot: Scolar Press, 1973), canto 1, ll. 295-315. 

6)Erasmus Darwin may have been first to put forward the suggestion of life having emerged from the depths of the oceans and evolving into different species in response to a striving for perfection in different environments. This was the somewhat simplistic (and erroneous) conception of physiological adaptation by sheer will-power he shared with Denis Diderot and the French biologist, Lamarck. 

7)See Peter J. Vorzimmer, Charles Darwin: The Years of Controversy: The Origin of Species and Its Critics 1859-1882 (London: London UP, 1972).

8)As Neal C. Gillespie once pointed out, Darwin was successful in banishing God from his science but not from his worldview. See his Charles Darwin and the Problem of Creation (Chicago: Chicago UP, 1979). 

9)The absolute origin of the Darwin family’s abiding preoccupation can be traced as far back as the year 1719 when Erasmus Darwin’s father, Robert, discovered the fossilized skeleton of a large part of a plesiosaur, described in the Philosophical Transactions of the Royal Society of that same year and now on display in the Natural History Museum in London. For Erasmus the finding of an extinct organism was taken as proof that species over long ages must undergo quite radical morphological change, and this inference was to lead him to develop his theory of common descent for the world’s animal types. See Charles Darwin’s The Life of Erasmus Darwin, edited by Desmond King-Hele (Cambridge: CUP, 2003), Introduction, p. xiii.  

Yet more on Darwinism place in the alt-wrong's master race delusions.

 Darwinian Racism, Past and Present 

Evolution News @DiscoveryCSC 

 

A new episode of ID the Future spotlights Darwinian racism, past and present. In this first half of a panel discussion at the 2022 Center for Science & Culture Insider’s Briefing, Darwin Day in America author John West introduces the other panel members, notes an upcoming book, Darwin Comes to Africa, and discusses his experience visiting the Museum of Criminal Anthropology (pictured above) in Turin, Italy, where the work of infamous Darwinian criminologist Cesare Lombroso’s racist ideas about evolution and race are on dramatic display. Then historian Richard Weikart, author of Darwinian Racism, debunks the popular media claim that white nationalist racism in America is a Southern evangelical phenomenon. Weikart shows that the most prominent white nationalists demonstrate little if any interest in promoting Christianity, but they very consistently anchor their racist ideas of white superiority and the racial struggle for supremacy in Darwinism, with straightforward links to Charles Darwin’s own ideas and arguments in The Descent of Man.

Weikart emphasizes that Darwinism does not necessarily lead its adherents to racism and, in fact, most Darwinists today are not racists. But racist ideas were woven into modern evolutionary thinking from the beginning and do serve as a major inspiration for white nationalist writers and even for some recent mass shooters. Weikart ends his lecture with a twist. He says there is one strongly anti-racist component in Darwinian materialism: such materialism, if true, means that all humans are equally without value — just so many DNA survival machines in a world without higher purpose or meaning. A grim takeaway, but only for those who feel compelled to embrace modern Darwinism. If you are open to questioning it, there are a wealth of resources here and at intelligentdesign.org showing that the evidence points strongly in another direction. Download the podcast or listen to it here. 

Re: Human origins, the science is anything but.settled.

 New Nobel Laureate, Svante Pääbo, on the “Politics” of Paleontology and Humans Origins 

David Klinghoffer 

Congratulations to Swedish paleogeneticist Svante Pääbo, awarded a Nobel Prize today: 

…for his discoveries concerning the genomes of extinct hominins and human evolution

Humanity has always been intrigued by its origins. Where do we come from, and how are we related to those who came before us? What makes us, Homo sapiens, different from other hominins?

Through his pioneering research, Svante Pääbo accomplished something seemingly impossible: sequencing the genome of the Neanderthal, an extinct relative of present-day humans. 

In the past, Ann Gauger and Denyse O’Leary have cited him for his acute remarks on the political aspects of human origins studies.  

“The Myth of 1 Percent” 

He commented on human-chimp genetic similarity, often said to be 99 percent identical, an idea that even Science magazine has conceded is a “myth.” From, “Relative Differences: The Myth of 1%”: 

Could researchers combine all of what’s known and come up with a precise percentage difference between humans and chimpanzees? “I don’t think there’s any way to calculate a number,” says geneticist Svante Pääbo, a chimp consortium member based at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “In the end, it’s a political and social and cultural thing about how we see our differences.”  

The Myth of Objectivity  

In an interview with Edge, “Mapping the Neanderthal Genome,” he explained why paleontology can seem to be such a bitter field. It’s the sparsity of the data, and the politics. 

As an outsider to paleontologists, I’m often rather surprised about how much scientists fight in paleontology. And I am thinking about why that is the case. Why do we have less vicious fights in molecular biology, for example? I suppose the reason is that paleontology is a rather data-poor science. There are probably more paleontologists than there are important fossils in the world. To make a name for yourself is to find a new interpretation for those fossils that are extant. This always goes against some earlier person’s interpretation, who will not like it very much.

There are many other areas of science where we can agree to disagree, but at least we often generally agree on what data we need to go out and collect to resolve the issue and no one wants to come out too strongly on one side or the other because the data could, in a year or two, prove you are wrong.

But in paleontology you can’t decide what you will find. You cannot in most cases go out and test your hypothesis in a directed way. It’s almost like social anthropology or politics — you can only win by somehow yelling louder than the other person or sounding more convincing. 

These are welcome and candid observations, refuting notions that human origins is a fully objective area of research. They also echo things that our colleagues Günter Bechly and Casey Luskin have said here. 

Hope for the dead.

 Romans4:17KJV"(As it is written, I have made thee a father of many nations,) before him whom he believed, even God, who quickeneth the dead, and calleth those things which be not as though they were." 

No syncretism of the biblical concept of the resurrection of the dead with Greco Roman philosophical speculation about a purported afterlife of a reductive spirit soul is possible.  

Acts17:32KJV"32And when they heard of the resurrection of the dead, some mocked: and others said, We will hear thee again of this matter." 

So Paul's audience was sensible enough to understand that the concept of an afterlife and that of a resurrection of the dead were mutually exclusive. Thus while  there was a division between those willing to pursue truth no matter where that pursuit led and those dogmatically clinging to the old modes of thought,all understood that they were being presented with a new concept that was irreconcilable with their previous notions about death and what followed. 

As romans4:17 quoted above suggest the resurrection involves the bringing into being of what was not or to be more specific the restoring of what used to be. 

So rather than look to those denounced by scripture as being in darkness mentally for hope re: the state of the dead we chose to share brother Paul's hope 

Acts24:15KJV"And have hope toward God, which they themselves also allow, that there shall be a resurrection of the dead, both of the just and unjust."

On the multiverse as nontheist mythology.

 The Multiverse: From Epicurus to Comic Books and Beyond 

Evolution News @DiscoveryCSC 

On a new episode of ID the Future, Discovery Institute Senior Fellow Andrew McDiarmid explores the roots of the idea that our universe is just one of many universes, an idea stretching back to the ancient atomists and given new life in the modern era, first by physicist Hugh Everett. McDiarmid looks at how the idea percolated into comic books and from there into other areas of popular culture. He caps off the episode with a reading of a recent article about the multiverse hypothesis by Stephen Meyer, author of the bestseller, Return of the God Hypothesis: Three Scientific Discoveries That Reveal the Mind Behind the Universe.

Meyer shows why some atheist scientists are attracted to the multiverse. As he explains, there is little if any good evidence for the idea, but atheists need it to explain away the fact that the laws and constants of the universe are exquisitely fined-tuned to allow for life. The fine-tuning smacks of intelligent design, and physicist Leonard Susskind has frankly remarked that the multiverse is needed to answer the arguments of design proponents. But as Meyer explains, not only does the multiverse hypothesis lack evidence, it doesn’t even remove the need for a fine-tuner, a point that the makers of recent comic book movies from Marvel and DC seem to grasp. Download the podcast or listen to it here. 

Seeking straight answers from reductive spiritualists.

 I (i.e my soul) can see(and see better at that) without eyes, why eyes? If I can think(and think better at that) without a brain ,why a brain? If I can live(and live better too) without a body,why a body. If the physical form is worse than useless to me why is separation from it to be counted as a loss? 

John7:35NIV"Whoever eats my flesh and drinks my blood has eternal life, and I will raise them up at the last day." 

If the flesh and blood of Christ was not necessary to the sustenance of his soul how could it possess any sacrificial value? If our flesh and blood is unnecessary for the sustenance of our souls, how could an offering of worse than useless flesh and blood be regarded as a substitute for our spirit souls?

Why "a simple beginning" remains Darwinism's unicorn.

 Michael Behe in World Magazine — “Game Over” for Darwinism 

David Klinghoffer 

Our biologist colleague Michael Behe has written a wonderful cover story for World Magazine. His theme is how science has vindicated the words of the Psalmist: “I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well.”

That inference to intelligent design — recognizing a “purposeful arrangement of parts” in biological systems, large and small — doesn’t require a scientist to draw it. It was available to the thoughtful observer of life thousands of years. But the closer and deeper that technology has permitted us to peer into such systems, the more evident it has become that they reflect a deliberate design.

Behe traces science’s progress from Aristotle to Galen to William Harvey, Marcello Malpighi, Antonie van Leeuwenhoek, and finally “John Walker, a British scientist who has studied ATP synthase for over 40 years — fully one-quarter of the time since his countryman, the naturalist Charles Darwin, first proposed his theory of evolution in 1859.” 

Walker Had the Floor 

Professor Behe was present at a “semi-secret” scientific gathering “whose theme was a specific controversial question: Did Darwinian evolution have any limitations?” ATP synthase (pictured above) is a fearfully and wonderfully made molecular machine, the “power plant of the cell.” John Walker had the floor and was discussing his area of expertise. Behe explains: 

ATP synthase is not simple. Comprising thousands of amino acid building blocks in about 10 kinds of protein chains, its intricate structure carefully directs a flow of acid particles, beginning from outside the cell, through deep channels in the machine’s organization, into the cell’s interior. Somehow, like the cascade of water over a hydroelectric dam that turns a turbine, the flow of acid through the channels rotates a central camshaft. The cams push against multiple discrete areas of a stationary region of the synthase, distorting their shapes. The distortion forces together two bound feed-chemicals, ADP and phosphate, provoking them to react to yield the energy-rich-yet-stable molecule ATP. As the camshaft completes a turn, the ATP is released into the cell, and the machine begins another cycle. Incredibly, the many copies of the machine in each person produce about 150 pounds of ATP molecules every day, but each is used rapidly as energy — in effect, recharging each cell like a reusable battery.

And Walker’s more recent studies — using the ­newest, most powerful iteration of microscopy, called “cryo-electron” microscopy — would reveal its mechanism in unprecedented detail. 

A Snipe Hunt 

But there was an obvious problem: 

By now, the scientists assembled before Dr. John Walker had run out of patience. The man had just held forth for nearly an hour on this miracle of biological architecture. Elegant and complex, precision-engineered, multiplied daily in the billions across the biosphere and on which the entirety of life depends. Finally, during the Q&A period, a questioner asked him directly: How could a mindless Darwinian process produce such a stunning piece of work?

Walker’s entire reply (paraphrasing): “Slowly, through some sort of intermediate or other.”

Far out of earshot I muttered two simple words: “Game over.”

If a Nobel laureate who has worked on one of life’s most fundamental systems for four decades can’t give an account of how it supposedly arose through a series of lucky mutations and natural selection — despite knowing its innermost workings in spectacular detail — then it’s reasonable to conclude no such account exists, and the effort to find one is a snipe hunt 

A snipe hunt is a “fool’s errand” because the so-called snipe in the metaphor is an imaginary animal. And indeed the game is over for Darwinian evolutionary theory: an unguided evolutionary explanation for what Behe calls irreducibly complex structures, including ATP synthase, will not be found. It remains for Darwin’s apologists, some of them rather vicious, to recognize this and permit the public to hear it, too. Read the rest of Behe’s essay for World here. 

Why time is no friend of Darwin.

 Fossil Friday: Walking Whales and Why All Critiques of the Waiting Time Problem Fail 

Günter Bechly 

This Fossil Friday features the reconstructed skeletons of Pakicetus (below) and Ambulocetus (above), which are so-called “walking whales” from the Eocene of Pakistan. These fossils are often celebrated as missing links and a success story for Darwinism. However, they indeed create a fatal problem for neo-Darwinism, which is known as the waiting time problem. The general problem is that the window of time established by the fossil record for the transition from “walking whales” to fully marine whales is orders of magnitude too short to accommodate the waiting times for the origin and spread of the required genetic changes, based on the standard mathematical framework of population genetics. This problem has been elaborated in a popular way in several publications of the ID community (Meyer 2013, Evolution News 2016, LeMaster 2018), and in the Illustra Media documentary Living Waters.

An Ongoing Multidisciplinary Research Project

The waiting time problem is the subject of an ongoing multidisciplinary research project funded by Discovery Institute. We have already published the theoretical ground work in two peer-reviewed papers in mainstream science outlets (Hössjer et al. 2018, 2021). An application on the example of whale origins is forthcoming by Bechly et al. (in prep.).

The waiting time problem has been the target of scornful critique by anti-ID spokesmen (e.g., Moran 2016, Rasmussen 2021, Stern-Cardinale 2022, Farina 2022), who claimed that it is fallacious and fails to challenge Darwinism. We will address this critique in great detail in our forthcoming technical paper, but let me here briefly refute the main points for a lay audience so that you are equipped for eventual debates. 

Reviewing the Main Points 

1.) Critics often explicitly or implicitly suggest that the waiting time problem is a pseudo-problem invented by evil and stupid creationists. This is a silly and embarrassingly incompetent argument, which only shows that these critics have not only failed to grasp the problem, but also seem to be totally unaware that the waiting time problem has a long history and has been much discussed in mainstream science (especially population genetics). It even plays an important role in cancer research. They should talk to Harvard professor Martin Nowak, who is an evolutionary biologist and expert on the waiting time problem. Here are just a few references of renowned scientists publishing about this “crazy stuff” as Farina (2022) calls it: Bodmer (1970), Karlin (1973), Christiansen et al. (1998), Schweinsberg (2008), Durrett et al. (2009), Behrens et al. (2012), and Chatterjee et al. (2014). It was not before Behe & Snoke (2004, 2005) and Behe (2007, 2009) that the waiting time problem was recognized as an argument for intelligent design. Durrett & Schmidt (2008) attempted to refute Behe but arrived at a prohibitive waiting time of 216 million years for a single coordinated mutation in human evolution, while only about 6 million years are available since the origin of the human lineage from a common ancestor with chimps. Behe arrived at 1015 years by using empirical data about an actual waiting time for a coordinated mutation that conveyed chloroquine drug resistance in malaria. He simply transposed these empirical findings on humans, considering their much lower population size and much longer generation time. Durrett & Schmidt’s result was based on a mathematical model, which of course must make certain simplifications that can introduce errors. When such model calculations conflict with hard empirical data, we should trust the empirical data as pointing closer to the truth. Anyway, both numbers are prohibitive and refute the feasibility of a Darwinian mechanism of macroevolution. 

2.) Most critics considered the most powerful objection to be the “Texas sharpshooter fallacy.” They claimed that nature does not go for specific mutations as a target but is totally random. This argument fails because it presupposes the existence of many targets, which is contradicted by the rarity of function in the search space for proteins and by the common phenomenon of convergence. The argument also fails to recognize that life cannot allow for periods of maladaptation only to descend a local peak of the fitness landscape to explore other ones. Instead, life has to further adapt to its local fitness peak, which requires specific solutions for specific problems. It’s not like any beneficial mutation could do. A stem whale would have no use for a mutation that would be beneficial for a stem bird, such as improving skeletal pneumaticity. In the computer models applied in our publications on the waiting time problem we also allowed for alternative targets and fuzzy targets, so not just one pre-specified binding site, which prevents another possible critique. 

3.) Some critics failed to grasp the concept of coordinated mutations and even called it meaningless. They suggested that every individual mutation can be selected for. This shows that they did not get the simple point that in coordinated mutations each individual mutation is neutral and thus in principle cannot be selected for. Only the combination of coordinated mutations has a selection value, which is the whole point, and the reason why they were called “coordinated mutations” in the first place. 

4.) Some critics claim that the waiting time problem implies that mutations have to occur in a specific sequence. This is simply false and maybe based on a misunderstanding of the technical term “coordinate gene.” The fact is that no ID proponent ever claimed that the waiting time problem only applies for particular sequences of mutations. For any set of reasonable parameters, the waiting times for coordinated mutations (i.e., mutations that have to occur together to have a selection value) will be prohibitive, irrespective of the order of these mutations. What is true is that the waiting time problem gets even worse when such mutations also have to occur in a specific sequence. 

5.) Critics also claimed that the waiting time problem ignores recombination, which according to Farina (2022) “baselessly discounts the profound evolutionary benefit” and is “dramatically accelerating the accumulation of beneficial mutations.” This shows how ignorant the critics are of the actual technical literature, because the influence of recombination of the waiting time problem has been studied by Christiansen et al. (1998), who have shown that: “Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small [my emphasis] compared to that of the mutation rate and population size.” In our papers (Hössjer et al. 2018, 2021, Bechly et al. in prep.) we show that recombination does not affect the waiting time under realistic assumptions for parameters like mutation rates and population sizes. 

6.) Critics also claim that the problem is merely theoretical but not realistic in biological terms, e.g., because it does not apply to concrete examples or because coordinated mutations are not necessary. We will address the latter claim very thoroughly in our forthcoming paper, where we do apply the theoretical framework to the concrete example of whale origins. We will also show, based on mainstream evo-devo data, that coordinated mutations indeed are required. This is also suggested by the fact that even simple characters like skin color turned out to be highly polygenic, thus controlled by many different genes. By the way: The waiting time problem has also been applied to the concrete example of human origins by Durrett & Schmidt (2008) and Sanford et al. (2015) with prohibitive results for Darwinian evolution. 

And Finally 

Last but not least, some critics were puzzled by how papers by ID proponents on the waiting time problem could somehow make it into peer-reviewed journals like the prestigious Journal of Theoretical Biology. Well, that’s easy: because it is good peer-reviewed science and the usual censorship of the Darwinist mafia sometimes fails to sabotage the publication of inconvenient research, even though they always try very hard. It is the height of hypocrisy when the very same people turn around and claim that ID proponents don’t publish their stuff in the peer reviewed literature. Darwinists, as is well known, love to play the game of “Heads I win, tail you lose.” 

References 

Behrens S, Nicaud C & Nicodéme P 2012. An automaton approach for waiting times in DNA evolution. Journal of Computational Biology 19(5), 550–562. DOI: https://doi.org/10.1089/cmb.2011.0218

Behe MJ 2007. The Edge of Evolution. Free Press, New York (NY), 336 pp.

Behe M 2009. Waiting Longer for Two Mutations. Genetics 181(2), 819–820. DOI: https://doi.org/10.1534/genetics.108.098905

Behe MJ & Snoke DW 2004. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Science 13(10), 2651–2664. DOI: https://doi.org/10.1110/ps.04802904

Behe MJ & Snoke DW 2005. A response to Michael Lynch. Protein Science 14(9), 2226–2227. DOI: https://doi.org/10.1110/ps.051674105

Bodmer WF 1970. The evolutionary significance of recombination in prokaryotes. Symposium of the Society for General Microbiology 20, 279–294.

Chatterjee K, Pavlogiannis A, Adlam B & Nowak MA 2014. The time scale of evolutionary innovation. PLoS Computional Biology 10(9):d1003818, 1–7. DOI: https://doi.org/10.1371/journal.pcbi.1003818

Christiansen FB, Otto SP, Bergman A & Feldman MW 1998. Waiting with and without Recombination: The Time to Production of a Double Mutant. Theoretical Population Biology53(3), 199–215. DOI: https://doi.org/10.1006/tpbi.1997.1358

Durrett R & Schmidt D 2008. Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. Genetics 180(3), 1501–1509. DOI: https://doi.org/10.1534/genetics.107.082610

Durrett R, Schmidt D & Schweinsberg J 2009. A waiting time problem arising from the study of multi-stage carcinogenesis. Annals of Applied Probability 19(2), 676–718. DOI: https://doi.org/10.1214/08-AAP559

Farina D 2022. Exposing the Discovery Institute Part 2: Stephen Meyer. Professor Dave Explains May 13, 2022. https://youtu.be/Akv0TZI985U

Hössjer O, Bechly G & Gauger A 2018. Phase-type distribution approximations of the waiting time until coordinated mutations get fixed in a population. Chapter 12, pp. 245–313 in: Silvestrov S, Malyarenko A & Rancic M (eds). Stochastic Processes and Algebraic Structures – From Theory Towards Applications. Volume 1: Stochastic Processes and Applications. Springer Proceedings in Mathematics and Statistics 271. DOI: 10.1007/978-3-030-02825-1_12

Hössjer O, Bechly G & Gauger A 2021. On the waiting time until coordinated mutations get fixed in regulatory sequences. Journal of Theoretical Biology 524:110657, 1–37. DOI: https://doi.org/10.1016/j.jtbi.2021.110657

Karlin S 1973. Sex and infinity: A mathematical analysis of the advantages and disadvantages of genetic recombination. pp. 155–194 in: Bartlett MS & Hiorns RW (eds). The Mathematical Theory of the Dynamics of Biological Populations. Academic Press, New York (NY), xii+347 pp.

LeMaster JC 2018. Evolution’s waiting-time problem and suggested ways to overcome it—A critical survey. BIO-Complexity 2018(2), 1–9. DOI: https://doi.org/10.5048/BIO-C.2018.2

Meyer SC 2013a. Darwin’s Doubt. HarperOne, New York (NY), viii+498 pp.

Moran L 2016. Targets, arrows, and the lottery fallacy. Sandwalk Jan. 14, 2016. https://sandwalk.blogspot.com/2016/01/targets-arrows-and-lottery-fallacy.html

Rasmussen MN 2021. Waiting Time Problem” and imaginary hurdles for evolution. Pandas Thumb June 12, 2021. https://pandasthumb.org/archives/2021/06/ID-and-imaginary-hurdles.html

Sanford J, Brewer W, Smith F & Baumgardner J 2015. The waiting time problem in a model hominin population. Theoretical Biology and Medical Modelling 12:18, 1–18. DOI: https://doi.org/10.1186/s12976-015-0016-z

Schweinsberg J 2008. The waiting time for m mutations. Electronic Journal of Probability13, 1442–1478. DOI: https://doi.org/10.1214/EJP.v13-540

Stern-Cardinale D 2022. Creation Myth: The “Waiting Time Problem” Creation MythsFebruary 15, 2022. https://youtu.be/F748itCI_es 

Primeval tech vs. modern tech.

 Why AlphaFold Has Not Solved the Protein-Folding Problem.

Paul Nelson 

The online database AlphaFold represents an amazing breakthrough by any measure of the word “breakthrough.” Biology is a much stronger science today for having AlphaFold in its analytical armamentarium.

But the algorithm, powerful as it is, has NOT solved the protein-folding problem, if we take that problem to mean this:

predicting the three-dimensional conformation of a protein strictly from its primary DNA sequence, ab initio.

An analogy to natural language may help. Suppose I give you a character string in English which you’ve never seen before, with no surrounding semantic context, and no corresponding lexicon or dictionary referents, even approximate. Here are two such words — these are words used weekly in Nelson family conversations for over 25 years:

googlimasha

mecky

My wife and daughters know EXACTLY what these words mean. Do you? Unless we’ve told you, almost certainly not. (Scroll down to the end for their meanings.) As far as the reader is concerned, these words are singletons, and you can only guess at their meanings (functional roles in English).

AlphaFold uses existing sequences and their known conformations / structures to predict unknown structures. Under the natural language analogy, AlphaFold levers itself off the existing genetic and proteomic dictionaries. But if a sequence exists as a singleton, in an isolated region of sequence space, AlphaFold performs poorly. Which means the protein folding problem, in its original form, remains unsolved. 

Yours to Discover 

A new unpublished MS by Yves-Henri Sanejouand of the French National Centre for Scientific Research is worth your attention, in relation to the protein folding problem, but also the high frequency of unique (singleton) proteins in eukaryotic species. See, “On the unknown proteins of eukaryotic proteomes.” The fascinating implications of Sanejouand’s preliminary analysis are yours to discover.

But if one extends one’s scope to include ALL nucleic acid sequences on Earth (not just eukaryotes), things get really wild. In a new paper, in press at Environmental Microbiology, Eugene Koonin and colleagues argue that — given their sequence diversity — viruses on Earth must have many independent origins. See, “The global virome: how much diversity and how many independent origins?” 

No Current Viable Theory  

After you read Koonin et al.’s paper, reflect for a moment on its implications. The vast majority of nucleic acid diversity on this planet is unique, represented by singletons (emphasis added): 

…we can also roughly estimate the size of the virus pangenome, in other words, the total number of genes in the virosphere. Large viruses encompass many poorly conserved, species-specific genes that obviously represent the bulk of the virus pangenome. Assuming 10 such unique genes per virus species, there would be 108 to 1010 unique virus genes altogether, a vast gene repertoire, to put it modestly. 

All these sequences must have been processed through a ribosome, borrowed from a free-living cell. There is currently no viable theory for the replication of viral genomes without the simultaneous presence of organismal systems (basically, ribosomes) to be hijacked. Thus the evolutionary clock for the origin of 108 to 1010 viral genes cannot start ticking until the origin of ribosomes. 

This appears to be the Mother of All Waiting Times Problems.

Oh, and those words I mentioned earlier? “Googlimasha” is a noun. It means “what Paul made that afternoon for dinner, but doesn’t want to tell his daughters when he picks them up at the end of their school day, because they will complain that they’re not in the mood for pork chops, or whatever, and Paul — having just slaved over dinner prep — simply isn’t interested in their spoiled suburban bellyaching.”

As for “mecky,” it can be a noun but most often is an adjective. It describes the hybrid state of “heck” and “messy,” in other words, an awful situation getting steadily worse. In its noun form, it is a term of endearment for Paul himself, frequently used by his daughter who is now a high school science teacher in Yonkers, NY. 

Primeval tech continues to be the bane of Darwinism.

 Grand Central Station and Beyond: Molecular Machines Visualized in 3D 

David Coppedge 

Cryo-electron microscopy is allowing cell biologists to see irreducibly complex molecular machines in all their three-dimensional glory. We are privileged in our day to see things that earlier microscopists could not have dreamt were possible thanks to super-resolution imaging technologies. 

Cilia Update 

Molecular biologists at the University of Basel boasted this month about discovering a “miniature train station” at the base of the cilium. Evolution News readers may know that biologist Michael Behe spoke of these trains years ago in his first two books, based on what was then known about how cilia are constructed. A few attempts to animate cilia with earlier cryo-EM views, such as this one at XVIVO, reveal the parts of cilia and flagella and how they operate once constructed. But there’s nothing like imaging them with real microscopes at near-atomic resolution to see how they are built. The imagery of train stations seems appropriate. 

Cilia are firmly anchored to the cell at their base. “Here is the start station for cilia transport,” explains Hugo van den Hoek, first author of the study. “Trains are assembled here, loaded with cargo and placed on the rails.”There are a total of nine different rails inside cilia, called microtubules. Each of them consists of two tracks, one for outbound trains and one for inbound. The trains transport proteins such as signaling molecules and building materials to the tip of the cilia. At their destination station, the train is unloaded and disassembled. 

A combination of cryo-EM tomography and fluorescence microscopy allowed the research team to observe grand central station.  

“This powerful combination of technologies has allowed us to reconstruct the first molecular model of the ciliary base and observe how it regulates the assembly and entry of these large protein trains,” explains Paul Guichard.  

Anyone sense foresight here? Functional information?

The paper in Science by Van den Hoek et al., “In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains,” continues with the train metaphor over 90“Their findings elucidate how intraflagellar transport trains assemble before they enter cilia and demonstrate the possibility of visualizing dynamic events with molecular resolution inside native cells.” times

Illustrating Behe’s claim back in 1996 that scientific papers never explain how these machines could be made by a Darwinian process, this paper is again silent about evolution. It only notes that cilia and flagella are “evolutionarily conserved eukaryotic organelles” which implies that they appeared already working and have not evolved significantly since. They also mention serious diseases that result from faulty assembly of these exquisite ATP-powered moving machines. This also speaks to the impossibility of chance formatio

Readers can feast their eyes on the detailed images coming from these powerful new imaging technologies 

“Their findings elucidate how intraflagellar transport trains assemble before they enter cilia and demonstrate the possibility of visualizing dynamic events with molecular resolution inside native cells.” 

Cilia were also highlighted recently in news from Washington University. Engineers there would like to understand how cilia initiate their well-known beat motions to get ideas for treating ciliopathies and, perhaps, mimicking cilia in engineered machines for drug delivery or chemical sensing. 

Cilia are tiny, hair-like structures on cells throughout our bodies that beat rhythmically to serve a variety of functions when they are working properly, including circulating cerebrospinal fluid in brains and transporting eggs in fallopian tubes.

Defective cilia can lead to disorders including situs inversus — a condition where a person’s organs develop on the side opposite of where they usually are. 

Their work was published in the Journal of the Royal Society Interface. 

Kir2.1: An Elegant Ion Channel 

Cryo-electron microscopy unveiled another marvelous molecular machine to the eyes of researchers at the Sorbonne. It’s called Kir2.1, part of a family of potassium channels that create the voltage used by neurons. Here’s what Kir2.1 does for us: 

Inward-rectifier potassium (Kir) channels are a group of integral membrane proteins that selectively control the permeation of K+ (potassium) ions across cell membranes. They are particular in that the channels conduct K+ions easier in the inward direction (into the cell) than in the outward direction (out of the cell). The small outward K+ current through Kir channels controls the resting membrane potential and membrane excitability, regulates cardiac and neuronal electrical activities, couples insulin secretion to blood glucose levels, and maintains electrolyte balance. 

The source paper by Fernandes et al. was published open access in Science Advances allowing readers to see the beautiful images of this channel with its four-part structure and selectivity filter. They claim it is the “first structure” published of Kir2.1. The average resolution is at 4.3 Angstroms, with some parts at 3.7 Angstroms. Considering that the width of a hydrogen atom is about 1 Angstrom, that’s amazing.  

This is the first time that the entire human Kir2.1 channel has been resolved at high resolution; it is also the first cryo-EM structure of a Kir2 channel. 

How does the channel work as a rectifier, creating a voltage between inner and outer membranes? And how do they know when to act? 

The inward-rectification mechanism results from a block on the cytoplasmic side of the channels by endogenous polyamines and Mg2+ that plug the channel pore at depolarized potentials, resulting in decreased outward currents. The blockers are then removed from the pore when the K+ ions flow into the cell at hyperpolarized potentials. This voltage-dependent block results in efficient conduction of current only in the inward direction. In addition to being inwardly rectifying, Kir channels respond to a variety of intracellular messengers that directly control the channel gating, including phosphoinositides (PIPs), G proteins (Kir3 channels), adenosine 5′-triphosphate (Kir6 channels), and changes in pH (Kir1 channels). The Kir family is encoded by 16 genes (KCNJ1 to KCNJ18) and classified in seven subfamilies (Kir1 to Kir7). 

The Kir2.1 channel doesn’t just sit there in the membrane selecting potassium ions; it moves! It flexes and bends during operation. Readers can download six movies of the machine undergoing its precise conformational changes. 

As the channel flexes, specific contacts between amino acids are made and broken to permit the accurate passage of potassium ions through the selectivity filter and three other constriction points, one called the G-loop where final potassium gating is thought to occur. The constrictions, as narrow as 1/5 of an Angstrom, act like gates that block everything until the right potassium ion has been authenticated. Here’s a taste of the precision: 

In conclusion, our human Kir2.1 channel cryo-EM structure describes a well-connected interaction networkbetween the PIP2-binding site residues, R218 and K219, and the G-loop region (E303) via residues R312 and H221. Our data suggest that the conformational changes required for the G-loop opening are most likely controlled by PIP2 binding. The replacement of R312 with histidine leads to a complete loss of the interaction network described above. Therefore, the interaction network integrity between subunits seems necessary for the proper allosteric transmission of the signal between R312 and the G-loop of the adjacent subunit upon PIP2 binding, which possibly allows the release of the constriction point on the G-loop. We can then hypothesize a PIP2-dependent G-loop gating mechanism that consists of the following: PIP2 binding triggers local conformational changes in the position of the side and main chains of R218 and K219, which, because of the structural proximity, lead to significant changes in the position of H221, displacing it laterally toward the intracellular medium. This movement would, in turn, cause E303 and R312 of the adjacent chain to move in the same direction, causing the G-loop to open. 

Without meaning to overdo the technical jargon, the design only becomes evident in the details. Once again, readers will look in vain for any mention of how this channel emerged or evolved. 

Zechariah ch.l the Bible in living English.

  

Zechariah ch.1 BibLE.

On the eighth new moon in the year two of Darius, Jehovah’s word came to the prophet Zecariah the son of Berekiah the son of ʽIddo, 2 “Jehovah was provoked at your fathers. 3 And say to them ‘Says Jehovah of Armies, Come back to me, quoth Jehovah of Armies, and I will come back to you, says Jehovah of Armies. 4 Do not be like your fathers, to whom the former prophets called out “Says Jehovah of Armies, Come back from your bad courses and practices” and they did not hear nor listen to me, quoth Jehovah. 5 Your fathers, where are they? and the prophets, do they live forever? 6 But my words and my decrees with which I charged my servants the prophets, did they not overtake your fathers? and they turned back and said “As Jehovah of Armies designed to do to us, in accordance with our courses and practices, so he has done with us.”’”

7* On the twenty-fourth day of the eleventh month (the month of Shebat) in the year two of Darius, Jehovah’s word came to the prophet Zecariah the son of Berekiah the son of ʽIddo, 8** “I saw last night, and there was a man riding on a brown pony standing between the myrtles in the bog, and behind him ponies brown, sorrel, and white. 9 And I said ‘What are these, sir?’ and the angel that was speaking with me said to me ‘I will let you see what these are.’ 10 And the man standing between the myrtles answered ‘These are what Jehovah has sent to patrol the earth.’ 11 And they answered Jehovah’s angel that stood between the myrtles ‘We have patrolled the earth and find all the earth settled and quiet.’ 12 And Jehovah’s angel answered ‘Jehovah of Armies, how long before you will have any tenderness for Jerusalem and the cities of Judah, to which you have been hostile these seventy years?’ 13 And Jehovah answered the angel that was speaking with me with kindly words, comforting words; 14 and the angel that was speaking with me said to me ‘Call out “Says Jehovah of Armies, I am greatly jealous for Jerusalem and Sion, 15 and I am greatly incensed with the nations that are at ease, because I had been a little incensed and they helped on to disaster. 16 So Jehovah says, I have come back to Jerusalem in tenderness; my house shall be built in it, quoth Jehovah of Armies, and a measuring-line shall be stretched over Jerusalem.” 17 Call out again “Says Jehovah of Armies, My cities shall again overflow with good things, and Jehovah will again comfort Sion and again choose Jerusalem.”’”

18 And I raised my eyes and saw, and there were four horns; 19* and I said to the angel that was speaking with me “What are these?” and he said to me “These are the horns that have scattered Judah, Israel and Jerusalem.” 20 And Jehovah showed me four smiths; 21** and I said “What are these coming to do?” and he said “These are the horns that have scattered Judah so that not a man raised his head; and these have come to sharpen blades to knock off the horns of the nations that raised horns against the country of Judah to scatter it.”