Yet another dead end in the quest for a plausible human origins Narrative?

 What Are They Teaching at Washington University? S. Joshua Swamidass and the Chimp-Human Divergence

Cornelius G Hunter 

I once had a rare and valuable baseball card I wanted to sell. I placed an ad and was shortly contacted by a collector. But to my dismay he wasn’t interested. He had probably looked at hundreds of baseball cards and it only required one look for him to know that my treasured card held no value for him. He did not attempt any negotiating tricks, just a polite “thank you” and off he went. I would have felt better about the encounter if he had tried to haggle down the price. For I would have had the comfort of knowing my card held at least some value. Instead, there was no price discovery—apparently the card was worthless.

I too am a collector of sorts. And like that baseball card collector I have looked at hundreds of specimens. No matter how unlikely the source or the venue, I will go there and have a look. And in short order, I will know exactly what I am looking at, and if there is any value there. But unlike the baseball card collector, my subject is not something you can touch. What I am interested in are the arguments and evidences for evolution. Ever since Darwin, evolutionists have insisted that their idea is undeniable—beyond all reasonable doubt. I find that complete certainty to be fascinating. So I search, find, analyze and categorize every justification and explanation for that conclusion that I can find.

My goal is to find the strongest, most powerful, such arguments and evidences, and to understand how we can have such certainty. This brings us to S. Joshua Swamidass’s recent article, Evidence and Evolution where Swamidass explains, in typical fashion, that the evidence for evolution is powerful and compelling. Swamidass describes the evidence as stunning. As a professor in the Genomic Medicine Division at Washington University, Swamidass deserves to be listened to. This is definitely a specimen I want to have a look at.

In his article, Swamidass’ focus is human evolution. Evolutionists believe that we humans evolved from a small ape-like creature and that our closest relative on the evolutionary tree is the chimpanzee. The chimpanzee must be our closest relative, they reason, because the chimp’s genome is closest to ours, and according to evolution, genetic mutations are the fuel behind evolutionary change.

The problem with this reasoning is that the chimpanzee is not very similar to humans according to many other measures. There are enormous differences between the two species. Simply put, from an evolutionary perspective the genetic data are not congruent with the other data. Swamidass’ evidence will need to overcome this obvious problem.

But that’s not all.

The basic idea of humans arising via a long series of genetic mutations is, itself, not indicated by the science and unlikely to say the least. Remember, the mutations have to be random. According to evolution, you can’t have mutations occurring for some purpose, such as creating a design. And natural selection doesn’t help—it cannot induce or coax the right mutations to occur. This makes the evolution of even a single protein, let alone humans, statistically impossible. So this is another enormous problem Swamidass’ evidence will need to overcome.

But that’s not all.

The incredible designs in the human body are not the only thing those random mutations have to create—they will also have to create human consciousness. Evolutionists may try to explain consciousness as an “emergent” property that just luckily arose when our brain somehow evolved. Or they may try to explain that consciousness is really no more than an illusion. But these are just more demonstrations of anti realism in evolutionary thought. Evolutionary theory constructs mechanisms and explanations that do not correspond to the real world. So this is another problem Swamidass will need to overcome.

But that’s not all.

In recent decades the genomes of humans and chimps have been determined, and they make no sense on evolution. One of the main problems is that the genes of the two species are almost identical. They are only about 1-2% different and, if you’re an evolutionist, this means you have to believe that the evolution of humans from a small, primitive, ape-like creature was caused by only a tiny modification of the genome.

This goes against everything we have learned about genetics. You can insert far greater genetic changes with far less change arising as a consequence. It makes little sense that tiny genetic changes could cause such enormous design changes to occur. This is yet another problem for Swamidass to overcome.

But that’s not all.

Not only is evolution limited to tiny genetic modifications to create the human, but the majority of those modifications would have had to be of little or no consequence. Here is how a 2005 paper on the chimpanzee-human genome comparisons put it:

In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.

The paper is written from an evolutionary perspective, assuming that humans and chimpanzees share a common ancestor. Given that a priori assumption, they were forced to conclude that most of the mutations affecting protein-coding genes led to “neutral and slightly deleterious alleles.” So not only are evolution’s random mutation resources meager, in terms of both quality and quantity as explained above, but even worse, those mutations mostly led to “neutral and slightly deleterious alleles.” This is no way to evolve the most complex designs in the world and it is yet another problem for Swamidass to overcome.

But that’s not all.

The supposed divergence rate between chimps and humans also has an unexplainable variation towards the ends of most chromosomes. This is another problem that seems to make no sense on evolution, which Swamidass must explain.

But that’s not all.

This supposed divergence rate between chimps and humans also has an unexplainable variation that correlates with chromosomal banding. Again, this makes no sense on evolution. Why should the chimp-human divergence vary with the banding pattern? Evolutionists have only just-so stories to imagine why this would have happened, and it is another problem for Swamidass to address.

But that’s not all.

This supposed divergence rate between chimps and humans is not consistent with the supposed divergence rate between the mouse and rat. The mouse-rat divergence is about an order of magnitude greater than the chimp-human divergence. And yet the mouse and rat are much more similar than the chimp and human. It makes no sense on evolution. In fact, before the rat genome was determined, evolutionists predicted it would be highly similar to the mouse genome. As one paper explained:

Before the launch of the Rat Genome Sequencing Project (RGSP), there was much debate about the overall value of the rat genome sequence and its contribution to the utility of the rat as a model organism. The debate was fuelled by the naive belief that the rat and mouse were so similar morphologically and evolutionarily that the rat sequence would be redundant.

The prediction that the mouse and rat genomes would be highly similar made sense according to evolution. But it was dramatically wrong.

Another approach is to ignore the morphological similarities and reason from the number of generations available to produce the genomic differences between the mouse and rat. The mouse-rat divergence date is estimated by evolutionists to be older than the chimp-human divergence date. Furthermore, the lifespan and generation time for mice and rats are much shorter than for chimps and humans. From this perspective, and given these two effects, one would conclude that the mouse-rat genetic divergence should be much greater—at least two orders of magnitude greater—than the chimp-human genetic divergence. But it isn’t. It is only about one order of magnitude greater.

So either way the mouse-rat comparison does not help to explain things and is another problem for Swamidass to explain.

Swamidass arguments and evidences

The science makes no sense on evolution. If we begin by assuming chimps and humans share a common ancestor, we end up with all kinds of contradictions and failures. So what exactly are Swamidass’ arguments and evidences? How is it that he is so certain? What is it in the data that he finds to be so stunning? And most importantly, how does he resolve the above problems?

Well, he doesn’t.

Astonishingly, Swamidass doesn’t even mention the above problems. It is as though they don’t exist. After some stories and high claims of certainty, here is what Swamidass says:

As predicted by common ancestry, human and chimpanzee genomes are extremely similar (greater than 98% similarity in coding regions), much more similar than we would expect without common descent. Remarkably, just as predicted by the fossil record, humans are about 10 times more genetically similar to chimpanzees than mice are to rats.

First, the high chimp-human genomic similarity was not predicted by common ancestry. No such prediction was made and no such prediction is required by common ancestry. Common ancestry would be just fine with very different levels of similarity than 98-99%. In fact, this high similarity makes no sense on evolution, for several of the reasons given above.

Swamidass’ claim that this evidence is a stunning confirmation of common ancestry is utterly at odds with the science. It is in stark contrast to the scientific facts.

Second, Swamidass’ claim that mouse-rat divergence, compared with the chimp-human divergence, is “just as predicted by the fossil record” is also blatantly false. While evolutionists can always combine various explanatory mechanisms to rationalize just about any comparison, that does not make for stunning evidence that is “just as predicted.”

Finally, the real strength of Swamidass’ argument lies in its metaphysics. The professor states that the chimp-human genome comparison is “much more similar than we would expect without common descent.”

Without common descent?

The evolutionist has just made an unbeatable (and unfalsifiable) argument.

This is not science. Swamidass’ claim about what is and isn’t likely “without common descent” is not open to scientific scrutiny.

Scientists, qua scientists, do not have knowledge of all possible explanations for the origin of life. This is why scientists, qua scientists, make statements about theories, not about the complement of a theory. A scientist cannot know that something is unlikely “without” his theory. That implies knowledge of all other possible theories. And that knowledge does not come from science.

This is the strength of Swamidass’ argument. Notice that with this metaphysical knowledge, all of the scientific problems melt away. No wonder he does not address them. They are inconsequential. At worst, they are simply interesting puzzles. The truth of the matter is already known.

If Swamidass is correct then, yes, of course, the genomic data must be strong evidence for common ancestry. But it all hinges on his metaphysics. This is not about science. It never was.

Cosmic fine-tuning necessary but not sufficient for the Origin of Life?

 Theistic Cosmology and Theistic Evolution — Understanding the Difference

Eric Hedin 

Astronomers have convincingly shown that the laws of nature are sufficient to account for the formation of stars and planetary systems throughout the universe. Given the initial conditions of our universe, as determined from big bang cosmology, and given the values of the fundamental physical parameters and the strengths of the four fundamental forces of nature, scientists can make predictions of the subsequent state of the cosmos that match the essential macroscopic structure found in our universe today. This predictive ability based on nature’s laws lends credence to the validity of our understanding of those laws and the initial conditions that manifested in the beginning. This achievement attests to the remarkable comprehensibility of the universe — how the discoverability of its laws and properties is commensurate with our mental ability to comprehend them.1

Many scientists have written about the remarkable fine-tuning of the laws and initial conditions of our universe that must exist within narrowly defined limits to allow life‘s existence.2,3 Additional research into the particular properties of our galaxy, star, solar system, Earth, and its moon have revealed a comprehensive suite of specific conditions that must have come together for Earth to be able to support life in its various forms over the long course of its history.4

In my book Canceled Science, after discussing many of the finely tuned conditions for life, I ask whether the culmination of fine-tuning that resulted in the existence of Earth could have come about naturally, or would some behind-the-scenes purposeful intervention be necessary? I suggest that the skill and foresight necessary to orchestrate the cosmic beginning so that the Earth eventually formed as part of our solar system seems “compatible with the traditional understanding of God’s attributes of great wisdom and power. Beyond that, we cannot say.”5

Far from Common

The uniqueness of planet Earth is becoming more apparent (see here) as the inventory of extrasolar planets continues to grow without revealing any other planets that could substitute for our home. Estimates of the low probability of obtaining all the features of the Earth-moon-Sun system required for maintaining livable conditions over the years do not necessarily point to any violations of the laws of physics in its formation, but all we are learning suggests that our congenial environment is far from common. 

The concept of theistic cosmology does not seem necessary to explain Earth and its solar environment, since the outcome in view is not physically impossible, albeit unlikely. How is this different from the concept of theistic evolution? The difference is that the outcome needed to be explained by evolution — life with all its millions of species culminating in humans — is not known to be compatible with the established laws of physics.6

One argument in support of this contention deals with predictability. Starting with the initial conditions of our universe and the specific values of the forces of nature, the laws of physics would not lead to a prediction of the origin of life as we know it.7 This argument grows even stronger when we consider that our uniform and repeated experience with the laws of nature demands that on the whole, entropy will increase and specified complexity will decrease with the passage of time. Neither of these universal principles of nature is consistent with a natural origin of life.

Theistic evolution or evolutionary creationism8 maintains that evolution is a done deal but that God’s behind the scenes influence was necessary to bring about the full panoply of life, including humans, that we have today. If, however, God’s guiding hand worked throughout history in the development of every species of life, as scientific observers, we would perceive not the hand of God, but a law of nature at work. The concept of the evolution of all life from a common ancestor, if attributed either to a law of nature or a natural process guided by God, is at odds with our most fundamental understanding of how nature works.9 In our study of science, we have found that the laws of nature do not contradict one another. We don’t have laws of nature that only apply piecemeal. 

Deep Levels of Design

What alternative view could explain the deep levels of design that appear in all life on Earth? If God didn’t redirect a law of nature to act contrary to nature, how should we explain the historically increasing complexity and diversity of life on Earth? My respect as a physicist for the laws of nature doesn’t preclude my acceptance of intelligent beings like us manipulating matter and energy to bring about outcomes that would never occur naturally. In like manner, extrapolating this everyday experience, neither science nor theology precludes us from accepting that God manipulated nature as often as desired to introduce various species of life and to maintain Earth’s habitability.

Neither does the frequency of intervention disparage the source of the agency. We admire an architectural and construction firm that designs and builds a beautiful home for us to live in. Would it be reasonable for someone to criticize the firm because the house didn’t also prepare dinner for its occupants every night? I suppose a house could be built that did so, but would it be desirable? Choosing a menu, selecting ingredients, and working to prepare dinner is something my wife and I enjoy doing together (although sometimes, when we’re tired after a long day of work, a “home-cooked” meal might be nice!). 

Perhaps in a similar manner, the laws of physics that limit what outcomes can occur naturally in our universe provide us with the pleasure and discipline of creative work. As I mentioned in an earlier article, “Is Life an Information Ratchet?,” gravity may cause a landslide to build up a pile of rocks at the bottom of a hill, but it will never make a castle. The laws that limit natural outcomes not only provide opportunities for us to manipulate material for our purposes, but their limitations also required God’s interventions to produce life by manipulating atoms into living organisms (however exactly that may have been accomplished).

Science and Experience

A reason for advocating this view is that it fully comports with our science and experience. It’s a juggler’s nightmare to assert that a law of nature is only valid except when it’s not valid. Rearrangements of physical matter into forms that would never occur naturally (such as the arrangement of the atoms that form my car) don’t constitute a violation of any law of nature if we acknowledge the immaterial intelligence and will of the human agent. The same principle applies when acknowledging God as the intelligent, non-contingent being who intervenes in nature to bring about the unnatural outcome of life in all its myriad forms.

NOTES

Benjamin Wiker and Jonathan Witt, A Meaningful World (Downers Grove, IL: InterVarsity Press, 2006).

Stephen C. Meyer, Return of the God Hypothesis: Three Scientific Discoveries That Reveal the Mind Behind the Universe (New York: HarperCollins, 2021).

Geraint F. Lewis and Luke A. Barnes, A Fortunate Universe: Life in a Finely Tuned Cosmos (Cambridge: Cambridge University Press, 2016).

Hugh Ross, Improbable Planet: How Earth Became Humanity’s Home (Grand Rapids, MI: Baker Books, 2016).

Eric Hedin, Canceled Science: What Some Atheists Don’t Want You to See (Seattle: Discovery Institute Press, 2021), 139.

The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos, William A. Dembski, Casey Luskin, Joseph M. Holden, Editors (Eugene, OR: Harvest House Publishers, 2021).

Gerald L. Schroeder, The Hidden Face of God: Science Reveals the Ultimate Truth (New York: Touchstone, 2001), 58.

https://biologos.org/common-questions/what-is-evolutionary-creation .

Jay Richards, “Is Theistic Evolution a Viable Option for Christians?”, Ch. 39 in The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos, William A. Dembski, Casey Luskin, Joseph M. Holden, Editors (Eugene, OR: Harvest House Publishers, 2021).

Putting the ghost in the machine?

 All We Need to Do to Give a Robot a Soul Is… (Error 404)

Denyse O'Leary 

Academic publisher Taylor & Francis asks in TechXplore, “Should robots be given a conscience?” I give away no spoilers by revealing that we are meant to think that that is both doable and desirable.

T & F is publishing Eve Poole’s Robot Souls later this year. Poole is a British writer and academic, and author of Capitalism’s Toxic Assumptions, Buying God, and Leadersmithing.

Her Thesis is that, in our quest for the most functional software, we left out the “junk,” which includes our “emotions, free will and a sense of purpose”:

Our junk code consists of human emotions, our propensity for mistakes, our inclination to tell stories, our uncanny sixth sense, our capacity to cope with uncertainty, an unshakeable sense of our own free will, and our ability to see meaning in the world around us.

She proposes “Giving them to all intents and purposes a soul.”

Very well. But how? T & F tells us:

In the new book, Poole suggests a series of next steps to make this a reality, including agreeing [on] a rigorous regulation process, and an immediate ban on autonomous weapons along with a licensing regime with rules that reserve any final decision over the life and death of a human to a fellow human.

She argues we should also agree [on] the criteria for legal personhood and a road map for Al towards it.

Insert Here…But How?

Okay. Setting aside the fact that we live in a world where Russia, China, and North Korea would not likely heed any such demands, bans, or criteria, how exactly does all this get us toward a soul? In reality, programmers don’t leave souls out of robots because they don’t find them useful; they simply and obviously have no idea how to insert them.

Actually, we have only one way of producing new human souls (ahem) and those souls animate only humans. But then does Poole even believe in a “soul” in any meaningful traditional sense?

The traditional model of the soul is that it is the (immortal) rational and moral part of a human being. Yet the publisher’s comments make clear that we are talking about inserting irrational elements into machines: “But on considering why all these irrational properties are there, it seems that they emerge from the source code of soul. Because it is actually this ‘junk’ code that makes us human and promotes the kind of reciprocal altruism that keeps humanity alive and thriving.”

Reviewer David J. Gunkel of Northern Illinois University assesses Poole’s project as “an innovative conceptualization of soul as the messy but necessary ‘junk code’ of consciousness.”

Blue-Sky Talk About Robots

So this proposal is part theory of consciousness and part blue-sky talk about what robots will be able to do one day. If there are specific formulas for making a robotic soul, we are given no hint so far.

There is already a large literature on the topic of conscious AI, bound by one common thread: We don’t have any idea what consciousness is but we are pretty sure we can endow robots with it anyway. 

To take but one example of thousands, neuroscientist Ryota Kanai, founder and CEO of Tokyo-based startup Araya, has said, “If we consider introspection and imagination as two of the ingredients of consciousness, perhaps even the main ones, it is inevitable that we [will] eventually conjure up a conscious AI, because those functions are so clearly useful to any machine.”

Yes, and it would be “clearly useful” for a dog to learn the pass codes by which humans operate his kennel doors. But it hardly follows that he can. He doesn’t and can’t know what he would need to learn. Perhaps we could say the same for the project of inserting human consciousness (a soul?) into a machine.

An article in The Economist back in 2017 meandered around in this Hard Problem of Consciousness for a while, eventually concluding that “The nub of the hard problem, then, is to make this ineffability effable.”

Um, okay… That’s as clear a prescription for giving a machine a soul as we are likely to get.

A convening of the Gods old and new

Evaluating fitness.

 Why Knockouts and Deletions Are Insufficient for Inferring Function — The Mystery of Cell “Vaults” 

Paul Nelson 

The other day, UPS brought me a copy of Larry Moran’s new book, What’s in Your Genome: 90% of Your Genome Is Junk (University of Toronto Press). Moran, an emeritus professor of biochemistry at the U. of Toronto, is a well-known opponent of intelligent design (but also a friendly acquaintance of some ID proponents, including me; Moran and I met in person at the 2016 Royal Society meeting on the extended evolutionary synthesis). In his new book, much of which has appeared previously in slightly different form on his blog Sandwalk, Moran argues that “functional DNA is any stretch of DNA whose deletion from the genome would reduce the fitness of the individual” (p. 98).

Moran puts this definition in bold font, so the reader can’t miss it. I appreciate that, as it makes his argument easier to follow. But I wonder how Moran would respond to the long-standing mystery of cell “vaults.” This is a vault:

Striking structure, right? And widely conserved in eukaryotic cells. Vaults are big; according to the Wikipedia entry, three times the size of ribosomes.

Not Well Understood

The Wiki entry also reports that the function of vaults is not well understood. Most importantly, as a direct challenge to Moran’s definition of “function,” knockouts of the major vault proteins in mice showed no phenotype.

Does that mean vaults have no functional role? Of course not. Fitness is always determined relative to some background. Not showing a phenotype (for instance, when a gene is deleted) does not equal “no function.” Likewise, our analytical difficulties about finding the right fitness background to assess possible vault functions says nothing about whether vault functions exist.

My favorite non-biological example of the trickiness of assessing function against a fitness measure or system background comes from Jules Verne’s novel Around the World in Eighty Days. Phileas Fogg has purchased the steamship Henrietta from its captain, as Fogg is crossing the Atlantic, so that he can burn all the non-essential materials on the ship to feed its steam boiler and engine. The 1956 movie version shows the Henrietta with much of its decking and cladding, etc., removed to serve as fuel.

Now an observer whose fitness background for steamships is limited to “transport from point A to point B” might mistakenly infer that the removed materials served no function. But that would be nonsense. 

Darwin had male chauvinism down to a science?

 Darwin: Why Women Are Inferior

Nancy Pearcy 

Editor’s note: We are delighted to present a preview adapted from Nancy Pearcey’s forthcoming book The Toxic War on Masculinity. The book will be published on June 27, but you can pre-order now!

Any list of toxic male behavior includes disrespect for women, and Darwin bears some responsibility for that as well. He was convinced that males are superior to females — that man attains “a higher eminence, in whatever he takes up, than can woman.” He concluded that “the average of mental power in man must be above that of woman.” 

Darwin explained male superiority by proposing that among social animals, young males have to pass through many contests to win a female — and many additional battles to retain their females. Over time, he said, natural selection will favor the stronger, more courageous males. Although modern men do not literally fight for a mate, he wrote,

yet they generally have to undergo, during manhood, a severe struggle in order to maintain themselves and their families; and this will tend to keep up or even increase their mental powers, and, as a consequence, the present inequality between the sexes. 

By contrast, Darwin wrote, women at home nurturing the young are out of reach of natural selection; thus they have evolved more slowly and their mental powers are lower. (It was assumed in his day that males pass on more of their traits to their sons, and females, to their daughters.) 

Darwin did acknowledge that women have “greater tenderness and less selfishness” than men, and even greater “powers of intuition, and rapid perception.” But he dismissed these traits as “characteristic of the lower races, and therefore of a past and lower state of civilization.” Even women’s positive traits were devalued as evidence of their inferiority. 

Darwin’s theory thus gave supposedly scientific authority to the idea that women are intellectually inferior to men — that women have no ideas or insights that warrant male respect. Women were pushed off their Victorian pedestal and relegated to a lower rung on the evolutionary ladder. 

In reality, of course, the survival of the human species depends just as much on characteristically female activities like giving birth and nurturing the young. Nevertheless, evolutionary thinkers preferred to exalt the more typically male activities like hunting and fighting as most important for the progress of the species. 

Beasts at Heart

Other evolutionary thinkers likewise promoted theories of male supremacy. The most influential popularizer of Darwinism in America was the sociologist Herbert Spencer, who argued that survival of the fittest weeds out all but the most aggressive men: 

In the course of the struggles for existence among wild tribes, those tribes survived in which the men were not only powerful and courageous, but aggressive, unscrupulous, intensely egoistic. Necessarily, then, the men of the conquering races which gave origin to the civilized races were men in whom the brutal characteristics were dominant. 

How could women survive in relationships with such brutal men? Spencer’s answer was that women needed to develop the “ability to please.” It would help if they also acquired “the powers of disguising their feelings” in order to hide the sense of “antagonism produced in them by ill treatment.”

The lesson of evolution, apparently, was that men are brutal beasts and that women must appease and placate them, while learning to hide their resentment of “ill treatment.” 

Many leading scientists of the day agreed with Darwin that women were less evolved than men. Anthropologist James McGrigor Allan held that “physically, mentally and morally, woman is a kind of adult child.” Thomas H. Huxley, whose fierce defense of Darwinism earned him the moniker Darwin’s Bulldog, said even education could not lift women to intellectual equality with men. Since women’s inferior abilities were a product of natural selection, he argued, they were not “likely to be removed by even the most skillfully conducted educational selection.” There was no hope, apparently, for women to escape their inferior position. 

The new York library a brief architectural history.

David Berlinski unsettles science.

 Iterations of Immortality

David Berlinski

Editor’s note: We are delighted to welcome Science After Babel, the latest book from mathematician and philosopher David Berlinski. This article is adapted from Chapter 7. 

The calculus and the rich body of mathematical analysis to which it gave rise made modern science possible, but it was the algorithm that made possible the modern world. They are utterly different, these ideas. The calculus serves the imperial vision of mathematical physics. It is a vision in which the real elements of the world are revealed to be its elementary constituents: particles, forces, fields, or even a strange fused combination of space and time. Written in the language of mathematics, a single set of fearfully compressed laws describes their secret nature. The universe that emerges from this description is alien, indifferent to human desires.

The great era of mathematical physics is now over. The three-hundred-year effort to represent the material world in mathematical terms has exhausted itself. The understanding that it was to provide is infinitely closer than it was when Isaac Newton wrote in the late 17th century, but it is still infinitely far away. 

One man ages as another is born, and if time drives one idea from the field, it does so by welcoming another. The algorithm has come to occupy a central place in our imagination. It is the second great scientific idea of the West. There is no third.

An algorithm is an effective procedure — a recipe, a computer program — a way of getting something done in a finite number of discrete steps. Classical mathematics contains algorithms for virtually every elementary operation. Over the course of centuries, the complex (and counterintuitive) operations of addition, multiplication, subtraction, and division have been subordinated to fixed routines. Arithmetic algorithms now exist in mechanical form; what was once an intellectual artifice has become an instrumental artifact.

Old as the Hills, and Cunning

The world the algorithm makes possible is retrograde in its nature to the world of mathematical physics. Its fundamental theoretical objects are symbols, and not muons, gluons, quarks, or space and time fused into a pliant knot. Algorithms are human artifacts. They belong to the world of memory and meaning, desire and design. The idea of an algorithm is as old as the dry humped hills, but it is also cunning, disguising itself in a thousand protean forms. It was only in this century that the concept of an algorithm was coaxed completely into consciousness. The work was undertaken more than sixty years ago by a quartet of brilliant mathematical logicians: Kurt Gödel, Alonzo Church, Emil Post, and A. M. Turing, whose lost eyes seem to roam anxiously over the second half of the 20th century.

If it is beauty that governs the mathematician’s soul, it is truth and certainty that remind him of his duty. At the end of the 19th century, mathematicians anxious about the foundations of their subject asked themselves why mathematics was true and whether it was certain, and to their alarm discovered that they could not say and did not know. Caught between mathematical crises and their various correctives, logicians were forced to organize a new world to rival the abstract, cunning, and continuous world of the physical sciences, their work transforming the familiar and intuitive but hopelessly unclear concept of the algorithm into one both formal and precise.

Unlike Andrew Wiles, who spent years searching for a proof of Fermat’s last theorem, the logicians did not set out to find the concept that they found. They were simply sensitive enough to see what they spotted. We still do not know why mathematics is true and whether it is certain. But we know what we do not know in an immeasurably richer way than we did. And learning this has been a remarkable achievement, among the greatest and least known of the modern era. 

Serene in the Cloudless Sky

Dawn kisses the continents one after the other, and as it does a series of coded communications hustles itself along the surface of the earth, relayed from point to point by fiber-optic cables, or bouncing in a triangle from the earth to synchronous satellites, serene in the cloudless sky, and back to earth again, the great global network of computers moving chunks of data at the speed of light: stock-market indices, currency prices, gold and silver futures, news of cotton crops, rumors of war, strange tales of sexual scandal, images of men in starched white shirts stabbing at keyboards with stubby fingers or looking upward at luminescent monitors, beads of perspiration on their tensed lips. E-mail flashes from server to server, the circle of affection or adultery closing in an electronic braid; there is good news in Lisbon and bad news in Saigon. There is data everywhere and information on every conceivable topic: the way raisins are made in the Sudan, the history of the late Sung dynasty, telephone numbers of dominatrices in Los Angeles, and pictures too. A man may be whipped, scourged, and scoured without ever leaving cyberspace; he may satisfy his curiosity or his appetites, read widely in French literature, decline verbs in Sanskrit, or scan an interlinear translation of the Iliad, discovering the Greek for “greave” or “grieve”; he may search out remedies for obscure diseases, make contact with covens in South Carolina, or exchange messages with people in chat groups who believe that Princess Diana was murdered on instructions tendered by the House of Windsor, the dark demented devious old Queen herself sending the order that sealed her fate.

All of this is very interesting and very new — indeed, interesting because new — but however much we may feel that our senses are brimming with the debris of data, the causal nexus that has made the modern world extends in a simple line from the idea of an algorithm, as logicians conceived it in the 1930s, directly to the ever-present always-moving now; and not since the framers of the American Constitution took seriously the idea that all men are created equal has an idea so transformed the material conditions of life, the expectations of the race. 

It is the algorithm that rules the world itself, insinuating itself into every device and every discussion or diagnosis, offering advice and making decisions, maintaining its presence in every transaction, carrying out dizzying computations, arming and then aiming cruise missiles, bringing the dinosaurs back to life on film, and, like blind Tiresias, foretelling the extinction of the universe either in a cosmic crunch or in one of those flaccid affairs in which after a long time things just peter out.

Our Fantastic and Artificial World

The algorithm has made the fantastic and artificial world that many of us now inhabit. It also seems to have made much of the natural world, at least that part of it that is alive. The fundamental act of biological creation, the most meaningful of moist mysteries among the great manifold of moist mysteries, is the construction of an organism from a single cell. Look at it backward so that things appear in reverse (I am giving you my own perspective): Viagra discarded, hair returned, skin tightened, that unfortunate marriage zipping backward, teeth uncapped, memories of a radiant young woman running through a field of lilacs, a bicycle with fat tires, skinned knees, Kool-Aid, and New Hampshire afternoons. But where memory fades in a glimpse of the noonday sun seen from a crib in winter, the biological drama only begins, for the rosy fat and cooing creature loitering at the beginning of the journey, whose existence I’m now inferring, the one improbably responding to kitchy kitchy coo, has come into the world as the result of a spectacular nine-month adventure, one beginning with a spot no larger than a pinhead and passing by means of repeated but controlled cellular divisions into an organism of rarified and intricately coordinated structures, these held together in systems, the systems in turn animated and controlled by a rich biochemical apparatus, the process of biological creation like no other seen anywhere in the universe, strange but disarmingly familiar, for when the details are stripped away, the revealed miracle seems cognate to miracles of a more familiar kind, as when something is read and understood.

Meaning in Molecules

Much of the schedule by which this spectacular nine-month construction is orchestrated lies resident in DNA — and “schedule” is the appropriate word, for while the outcome of the drama is a surprise, the offspring proving to resemble his maternal uncle and his great-aunt (red hair, prominent ears), the process itself proceeds inexorably from one state to the next, and processes of this sort, which are combinatorial (cells divide), finite (it comes to an end in the noble and lovely creature answering to my name), and discrete (cells are cells), would seem to be essentially algorithmic in nature, the algorithm now making and marking its advent within the very bowels of life itself.

DNA is a double helix — this everyone now knows, the image as familiar as Marilyn Monroe — two separate strands linked to one another by a succession of steps so that the molecule itself looks like an ordinary ladder seen under water, the strands themselves curved and waving. Information is stored on each strand by means of four bases — A, T, G, and C; these are by nature chemicals, but they function as symbols, the instruments by which a genetic message is conveyed.

A library is in place, one that stores information, and far away, where the organism itself carries on, one sees the purposes to which the information is put, an inaccessible algorithm ostensibly orchestrating the entire affair. Meaning is inscribed in molecules, and so there is something that reads and something that is read; but they are, those strings, richer by far than the richest of novels, for while Tolstoy’s Anna Karenina can only suggest the woman, her black hair swept into a chignon, the same message carrying the same meaning, when read by the right biochemical agencies, can bring the woman to vibrant and complaining life, reading now restored to its rightful place as a supreme act of creation.

The mechanism is simple, lucid, compelling, extraordinary. In transcription, the molecule faces outward to control the proteins. In replication, it is the internal structure of DNA that conveys secrets, not from one molecule to another but from the past into the future. At some point in the life of a cell, double-stranded DNA is cleaved, so that instead of a single ladder, two separate strands may be found waving gently, like seaweed, the bond between base pairs broken. As in the ancient stories in which human beings originally were hermaphroditic, each strand finds itself longingly incomplete, its bases unsatisfied because unbound. In time, bases attract chemical complements from the ambient broth in which they are floating, so that if a single strand of DNA contains first A and then C, chemical activity prompts a vagrant T to migrate to A, and ditto for G, which moves to C, so that ultimately the single strand acquires its full complementary base pairs. Where there was only one strand of DNA, there are now two. Naked but alive, the molecule carries on the work of humping and slithering its way into the future.

There, That Is What Intelligence Is

A general biological property, intelligence is exhibited in varying degrees by everything that lives, and it is intelligence that immerses living creatures in time, allowing the cat and the cockroach alike to peep into the future and remember the past. The lowly paramecium is intelligent, learning gradually to respond to electrical shocks, this quite without a brain let alone a nervous system. But like so many other psychological properties, intelligence remains elusive without an objective correlative, some public set of circumstances to which one can point with the intention of saying, There, that is what intelligence is or what intelligence is like.

The stony soil between mental and mathematical concepts is not usually thought efflorescent, but in the idea of an algorithm modern mathematics does offer an obliging witness to the very idea of intelligence. Like almost everything in mathematics, algorithms arise from an old wrinkled class of human artifacts, things so familiar in collective memory as to pass unnoticed. By now, the ideas elaborated by Gödel, Church, Turing, and Post have passed entirely into the body of mathematics, where themes and dreams and definitions are all immured, but the essential idea of an algorithm blazes forth from any digital computer, the unfolding of genius having passed inexorably from Gödel’s incompleteness theorem to Space Invaders VII rattling on an arcade Atari, a progression suggesting something both melancholy and exuberant about our culture.

The computer is a machine, and so belongs to the class of things in nature that do something; but the computer is also a device dividing itself into aspects, symbols set into software to the left, the hardware needed to read, store, and manipulate the software to the right. This division of labor is unique among man-made artifacts: it suggests the mind immersed within the brain, the soul within the body, the presence anywhere of spirit in matter. An algorithm is thus an ambidextrous artifact, residing at the heart of both artificial and human intelligence. Computer science and the computational theory of mind appeal to precisely the same garden of branching forks to explain what computers do or what men can do or what in the tide of time they have done.

A Combinatorial System

Molecular biology has revealed that whatever else it may be, a living creature is also a combinatorial system, its organization controlled by a strange, hidden, and obscure text, one written in a biochemical code. It is an algorithm that lies at the humming heart of life, ferrying information from one set of symbols (the nucleic acids) to another (the proteins).

The complexity of human artifacts, the things that human beings make, finds its explanation in human intelligence. The intelligence responsible for the construction of complex artifacts — watches, computers, military campaigns, federal budgets, this very essay — finds its explanation in biology. Yet however invigorating it is to see the algorithmic pattern appear and reappear, especially on the molecular biological level, it is important to remember, if only because it is so often forgotten, that in very large measure we have no idea how the pattern is amplified. Yet the explanation of complexity that biology affords is largely ceremonial. At the very heart of molecular biology, a great mystery is vividly in evidence, as those symbolic forms bring an organism into existence, control its morphology and development, and slip a copy of themselves into the future.

The transaction hides a process never seen among purely physical objects, one that is characteristic of the world where computers hum and human beings attend to one another. In that world intelligence is always relative to intelligence itself, systems of symbols gaining their point from having their point gained. This is not a paradox. It is simply the way things are. Two hundred years ago the French biologist Charles Bonnet asked for an account of the “mechanics which will preside over the formation of a brain, a heart, a lung, and so many other organs.” No account in terms of mechanics is yet available. Information passes from the genome to the organism. Something is given and something read; something ordered and something done. But just who is doing the reading and who is executing the orders, this remains unclear.

There is always another side to the story

What the science says about the case for Darwinism.

The tab has to be paid some at some point.

Fall of the three brains theory?

 Reptilian Brain Myth Is Still Alive and Kicking

Denyse o' Leary 

Do we have a three-part brain — reptilian, mammalian, and human? Curiously, psychology textbooks teach us that we do and neuroscience studies teach us that we don’t. Who to believe? And how did that happen anyway?

In the 1960s, Yale University physiologist and psychiatrist Paul D. MacLean (1913–2007) offered the triune brain theory. On that view, the reptilian brain (brain stem) controls things like movement and breathing; the mammalian brain controls emotion (limbic system); and the human cerebral cortex controls language and reasoning (neocortex). That might have been just another theory except that it was widely promoted by celebrity astronomer Carl Sagan (1934–1996) in his book The Dragons of Eden (Random House, 1977). Praised in The Atlantic as “a rational, elegant, and witty book,” Dragons won a Pulitzer Prize in 1978, for “a distinguished book of non-fiction by an American author that is not eligible for consideration in any other category.”

Chiming Beautifully

The theory chimed beautifully with materialist thought of the day. The cool people already assumed a long slow process of evolution from mud to mind, with stops along the way for reptile, mammal, and ape. And, as we were constantly reminded, many of us may have got stuck along the way.

But, as neuroscience advanced over the years, unwelcome facts began to surface. The human brain is just not organized as if the story happened in that way. As University of Oslo psychology professor Christian Krog Tamnes puts the matter in an interview at Science Norway, “Those of us who research brain development and brain evolution have known for quite some time that this isn’t true”:

Instead, the cells that are similar to each other were found scattered throughout the brains of both species.

Emotions, such as fear and sadness, are not made in one specific place in the brain. In fact, several parts of the brain are always involved.

Which parts of the brain are active vary from time to time, and from person to person.

For example, Tamnes points to a paper on the topic last year: Despite 320 million years of separate evolution, lizards and mice share a core set of neuron types that are found all over the brain, “including in the cerebral cortex, challenging the notion that certain brain regions are more ancient than others.”

Northeastern University neuroscientist Lisa Feldman Barrett offers, “So if we absolutely need to have a metaphor, it’s much better to think of the brain as an orchestra. Even playing a simple song requires a lot of pieces to talk together effectively and in a coordinated way.”

So we can still have lots of problems but our Inner Lizard is not one of them.

What Psychology Students Are Learning

Psychology lecture rooms and textbooks have been curiously slow to let go of the reptilian brain myth, however. Is that perhaps because it is socially reassuring to think that everyone who questions our sincerely held beliefs is, neurologically maybe, a rat or reptile throwback? In 2020, Joseph Cesario and colleagues reported on a study of what psychology students are told about such matters:

This belief, although widely shared and stated as fact in psychology textbooks, lacks any foundation in evolutionary biology.

“Our experience suggests that it may surprise many readers to learn that these ideas have long been discredited among people studying nervous-system evolution. Indeed, some variant of the above story is seen throughout introductory discussions of psychology and some subareas within the discipline… 

“To investigate the scope of the problem, we sampled 20 introductory psychology textbooks published between 2009 and 2017. Of the 14 that mention brain evolution, 86% contained at least one inaccuracy along the lines described above. Said differently, only 2 of the field’s current introductory textbooks describe brain evolution in a way that represents the consensus shared among comparative neurobiologists.”

CESARIO, J., JOHNSON, D. J., & EISTHEN, H. L. (2020). YOUR BRAIN IS NOT AN ONION WITH A TINY REPTILE INSIDE. CURRENT DIRECTIONS IN PSYCHOLOGICAL SCIENCE, 29(3), 255–260.

More information on the textbooks is offered here.

Puzzled by Sagan’s Role

Science writer and editor Ross Pomeroy seems genuinely puzzled by the role Sagan played in helping to popularize triune brain theory: “Carl Sagan was, and to this day is, generally regarded as an honest and skeptical broker of scientific information. That he presented such a disputed theory essentially as fact to the lay public is a bit surprising. What’s more, Carl Sagan continued to push the theory three years later in his far more widely read book, Cosmos.”

It’s not really so surprising if we look at the big picture. First, Sagan was a one-way skeptic. There were many things he was not skeptical about at all because they suited the popular worldview he shared and helped shape. 

For example, as Justin Gregg recounted in 2013, in 1961, he joined a semi-secret society called the Order of the Dolphin, which sought a way to communicate with intelligent extraterrestrials. He bought into the idea that dolphins had a sort of super-intelligence and a language like ours. The theory was that if we could decipher that language, we could decipher any extraterrestrial one. The Order was certainly dedicated. Gregg recounts, “As the Princeton historian D. Graham Burnett has noted, members wore insignia shaped like bottlenose dolphins and sent each other coded messages to hone their dolphinese and alien-language-decoding skills.”

Were They Nuts?

It might seem so at this distance. But club members back then included evolutionary biologist J. B. S. Haldane (1892–1964) and chemistry Nobelist Melvin Calvin — alongside SETI founder Frank Drake (1930–2022).

The lesson here is that science functions better when we follow the evidence, as the neuroscientists are doing, than when we form fan clubs for cozy ideas championed by science celebs, as the psychologists appear to be doing — at least in this area.

The extraterrestrials at home?

The porn/sex-trafficking axis.

Accurate timekeeping is always by design?

 Compasses, Clocks — Intelligent Design in Time

David Coppedge 

One can look at a piece of art or engineering and use the design filter to rule out chance or natural law. How much more is the design inference valid when seeing a sequence of events that work together for a purpose? If a sculpture appears designed, how much more a pendulum clock, or a symphony? Life is filled with dynamically changing, yet carefully regulated processes.

Hippos and Hedgehogs

Take the protein Sonic Hedgehog (SHH), whimsically named after a Japanese videogame character able to run at supersonic speeds, curl into a ball and attack enemies. Well known for its role in regulating embryonic development, SHH doesn’t just sit in the cell; it signals other proteins with the precision of a conductor. Patterns in the embryo, such as left-right symmetry and dorsal-ventral axis, are regulated by this important protein, coded for by the sonic hedgehog gene. Kim and Blackshaw, writing in Science, tell about a new function for this dynamic regulator that carries on throughout life.

Virtually all mammalian physiological functions fall under the control of an internal circadian rhythm, or body clock. This circadian rhythm is governed by master neural networks in the hypothalamus that synchronize the activity of peripheral clocks in cells throughout the body. Environmental perturbations that are a regular part of modern life, such as artificial light and international travel, can disrupt circadian rhythms, leading to adverse consequences for mental and physical health. On page 972 of this issue, Tu et al. report that primary cilia–mediated Sonic Hedgehog (SHH) signaling allows cells in the master circadian clock to maintain synchronization and control circadian rhythmicity in mice, identifying an unexpected functional role for this developmental regulator.

How can a tiny protein within a cell have dramatic effects on the hypothalamus, and by extension on the entire body? 

The master circadian pacemaker responsible for regulating our daily rhythms is located in the suprachiasmatic nucleus (SCN) in the anterior hypothalamus. The cells that make up this pacemaker maintain intercellular coupling of molecular circadian rhythms, ensuring synchrony of SCN neurons. Robust clocks keep time using redundant mechanisms, and the SCN is no exception. Signals that promote cellular synchrony include paracrine signaling by fast neurotransmitters and multiple neuropeptides as well as gap junction–dependent electrical coupling. This cellular synchrony ensures the robust output of the central clock and renders it resistant to signals that reset peripheral clocks.

At this point in the story, one of the superheroes of irreducible complexity enters: the cilium, described by Michael Behe in his books. Neurons in the SCN synchronize their clocks via SHH signals sent and received through their primary cilia. Those non-motile cilia then transmit the timing signals inside via the molecular trucks inside the cilia: the intraflagellar transport (IFT) trains. 

The master circadian pacemaker in the suprachiasmatic nucleus (SCN) contains neuromedin S–expressing (NMS+) neurons that have primary cilia. The number and length of these cilia change throughout the day, which alters Sonic Hedgehog (SHH) signaling through Smoothened (SMO) co-receptors expressed on the cilia. When this signaling is disrupted, the cellular oscillators in the SCN become uncoupled, which affects circadian rhythmicity in mice. 

Kim and Blackshaw call the discovery “surprising” for a protein that had been almost exclusively studied for its role in development. The new study by Tu et al. shows that adult organisms rely on SHH every day to keep the body clock running on time. That’s why they call it a “Super sonic circadian synchronizer.” 

SHH is essential for the development and specification of many brain structures during embryogenesis, including the SCN, and it also regulates axonal targeting, dendrite formation, and synaptogenesis. An ongoing role for SHH signaling in the adult SCN raises several important questions. It is unclear what cells are the relevant source of SHH or how its synthesis and release are regulated. Primary cilia regulate many other classes of extracellular signaling—such as Notch, Wnt, Hippo, and mammalian target of rapamycin (mTOR) pathways—often through receptor-independent mechanisms. Thus, it is unclear whether other extrinsic factors might contribute to controlling SCN function. 

The Hippo pathway, which regulates body size, also transmits its signals about body size through the cilium. Look at this diagram to get a taste of the dynamic signals going on in the cell for that symphony of signals. The cilium looks more irreducibly complex than ever!

Encompassing a Body Compass

Understanding how SHH interacts with day-night cycles can help solve the problem of jet lag. It takes a while to resynchronize our body clock to the time of day in another location when we zoom off to another time zone and find the sun angle at odds with expectations. Time for a reset!

Just as the body clock can be reset by external cues, our internal compass can be reset by an external cue: namely, head direction. Results of experiments at McGill University, also done on mice, shows how whole-body actions interact with signals inside of cells.

This ability to accurately decode the animal’s internal head direction allowed the researchers to explore how the Head-Direction cells, which make up the brain’s internal compass, support the brain’s ability to re-orient itself in changing surroundings. Specifically, the research team identified a phenomenon they term ‘network gain’ that allowed the brain’s internal compass to reorient after the mice were disoriented. “It’s as if the brain has a mechanism to implement a ‘reset button’ allowing for rapid reorientation of its internal compass in confusing situations,” says Ajabi.

Fast Clocks, Slow Clocks

Speaking of development, we know that different animals have different gestation times: humans take nine months, mice around 20 days. Yet all of us live under the same day-night cycle. How do these “heterochronies” regulate themselves? It comes down to the dynamic activities going on inside cells as well, says a Focus article in Science Advances. The author’s one mention of evolution contributes nothing to the science:

In evolutionary developmental biology, differences in genetically controlled temporal programs are well recognized and referred to as heterochronies. These include differences in the time of initiation, duration, or rate of a process in comparison with an organisms’ ancestors or other species. Whereas shifts in the time of initiation or duration have been linked to genetic variation of regulatory sequences or differential expression dynamics, other heterochronies that emerge from changes in the rate of a process are distinct and usually involve the same genetic program operating at different speeds. This has been termed allochrony and does not seem to be explained by variations in regulatory sequences (Fig. 1, A to C). However, less is known about the mechanisms driving allochronies.

Nothing in Figure 1 owes anything to Darwinian evolution. Audiences know intuitively that any delicate dance is the work of a choreographer.

Developmental processes need to operate in harmony to synchronize cells, tissues, organs, and the whole organism. It is increasingly clear that a central element of this delicate dance is achieved by each cell using its own clock…. Cells offer the most basic model to expose timing control processes and to investigate the intrinsic genetic mechanisms that control timing.

Teresa Rayon’s article goes on to discuss the harmony between biochemical reactions, motor neurons, mitochondrial activity, metabolic rate and epigenetic mechanisms. The differences in scale between these players working toward a common goal—homeostasis—is astonishing.

Clocks that Must Not Reset

The body adjusts for day and night cycles, but some body clocks dare not change outside of tight limits: heart rate and breathing. We have a “resting heart rate” during sleep that was thought to be under the sole control of the parasympathetic nervous system, the nerve network that relaxes us. Scientists at Manchester University found, however, that the “fight-or-flight” sympathetic nervous system (SNS) works in concert with it to keep the heart ticking within its acceptable range. Listen to this orchestra play:

Importantly, transcription factors in the sinus node lost rhythmicity following the sustained β-adrenergic blockade. Thus, the team proposed that day-night rhythms in the sinus node are orchestrated by rhythmic β-adrenergic input from the SNS to regulate ion channel gene expression. “It’s a way of thinking about the involvement of the autonomic nervous system, not as commonly accepted, which is these very short range, immediate acute modulations of ion channel function, but through long range modulation by affecting gene expression in the heart or in the sinus node,” said D’Souza.

Here again is a case of tight coordination between cell signals and a body composed of trillions of cells. Talk about the tail wagging the dog: the goings on in specific ion channels in a cell membrane can influence the brain and the heart that are orders of magnitude larger. Sleep tight; your body knows what parts have to slow down and what parts must keep going.

No Real Hope for Evolution

One study on biological clocks attempted to “Darwinize” them, but only for the very simplest case: the KaiA/B/C oscillator in cyanobacteria (see this video for a quick presentation of this clock). “The central role of circadian rhythms in many biological processes, controlled by the day and night cycle on Earth, makes their evolution a fascinating topic,” say eight evolutionists in an open-access paper in Nature. They attempt to show a stepwise evolution “From primordial clocks to circadian oscillators.” Good luck.

Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additionsof KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that only possess KaiBC…. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

The authors build phylogenetic trees to argue that KaiC is more ancient than KaiA and KaiB. While admittedly rigorous, their work does not explain the origin of KaiBC itself, the gene that codes it, or its functional connection to diurnal cycle. KaiC, as shown in the video, is the largest and most complex protein in the clock with 518 amino acids arranged in a geometrically-elegant pair of hexamers that can undergo conformational changes essential for its operation. Its function is intimately tied to specific serine and threonine residues at precise locations.

At best, their evolutionary hypothesis shows a division of labor when KaiA is present. Oddly, the authors say that the KaiBC clock in R. sphaeroides “can perform both autophosphorylation and nucleotide exchange on its own and does so faster than its more recently evolved counterparts.” The paper leaves many unasked and unanswered questions. They offer no stepwise evolution from the simple prokaryotic clock to the “complex and highly sophisticated” circadian clocks in eukaryotes. There is no mention of mutations or natural selection. And a chicken-and-egg conundrum arises when asking which came first: the gene or the protein. Why would a gene sequence 518 aa long emerge by mistake without a function being known for it? That’s too improbable. If the protein came first and ticked like a clock, how did the code for it become embedded in the genome, which has a different alphabet? In the concluding discussion, the authors give an essentially magical explanation, calling the simplest of clocks “an example of convergent evolution.” If one did not already believe in the creative power of natural selection, this paper would prove little and make less sense.

In the arts, design is evident in both static and dynamic works. If paintings and sculptures evince design, much more do finely crafted instruments performing in harmony in real time. That’s ID in the 4th dimension.

The fall of the selfish gene?

 Cognitive Cells? A Newer Challenge to Neo-Darwinism

Denyse O Leary

In September 1957, Nobel Prize-winning biophysicist Francis Crick (1916–2004) announced the “Central Dogma” in biology, at a symposium at Oxford University. The dogma is currently given in the Biology Dictionary thus: “genetic information flows primarily from nucleic acids in the form of DNA and RNA to functional proteins during the process of gene expression.” This view that genes rule underpins mainstream assumptions about how traits are inherited; from there, it governs accepted assumptions about evolution. So the ground on which Darwin’s modern defenders stand, propounding the only true history of life, is narrow but it is firm.

Sir Francis Crick is perhaps better known to laypeople for his 1994 book, The Astonishing Hypothesis: The Scientific Search for Soul, which he opened by announcing

The Astonishing Hypothesis is that “You”, your joys and your sorrows, your memories and your ambitions, your sense of identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased it: “You’re nothing but a pack of neurons.”

And the pack of mindless neurons that you think is you was created by those genes.

An Interesting New Paper

But what about the evidence that neurons self-organize? An interesting new paper in Progress in Biophysics and Molecular Biology calls for a different Central Dogma, recognizing forces other than genes:

Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology’s still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing.

The word “cognitive” is worth examining. According to Merriam–Webster, it means

of, relating to, being, or involving conscious intellectual activity (such as thinking, reasoning, or remembering)

or

based on or capable of being reduced to empirical factual knowledge.

Which definition do the authors, William B. Miller Jr. (UCLA), František Baluška (University of Bonn), and Arthur S. Reber (University of British Columbia), mean when they tell us that “As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.” Do they mean that cells, in some sense, think?

Thoughtful Cells

They don’t quite say but the hints are intriguing. Darwin-shaped biology lags behind the times, they say, despite the accumulating contrary evidence that “non-random genetic mutations are common, linked to structural factors, epigenetic impacts, and biased DNA repair mechanisms,” among other things.

More directly, they write: “The crux of that difference separating Crick’s Central Dogma from a modern idiom is the contemporary recognition that cellular cognition governs the flow of biological information.”

So cells are smarter than we thought… ? They offer a brief look at the many bewilderingly complex feedback loops in typical cells. In their view, how should biology change? Here are some snippets from their Conclusion:

When biology is framed as an informational interactome, all forms of biological expression interact productively in a continuous, seamless feedback loop. In that reciprocating living cycle, there is no privileged level of causation since all aspects of the cell as an organized whole participate in cellular problem-solving

So the cell acts on itself (self-organization) instead of merely being acted upon by the neo-Darwinian genes. But also, they write,

The origin of self-referential cognition is unknown. Indeed, it can now be declared biology’s most profound enigma. Yet, that instantiation can be properly accredited as equating with the origin of life.

“Self-Referential Cognition”

In short, we have no idea how cells, which have been around for billions of years, could become so complex that they can be compared to intelligent beings (“self-referential cognition”) without any design in nature at all. Well, maybe they couldn’t have. Maybe the main thing to take away here, whether the authors intend it or not, is this: If biologists don’t want intelligent design, they will surely need to come up with something more convincing than Crick’s materialism.

Two other things are worth noting: Dogmas in science often do not age well because challenges are mounted by brilliant investigators but the dogma is defended by tenured mediocrities and — in the case of any type of Darwinism — pop science writers and education pressure groups. Even when the dogma is mouldy and rotten, it can be hard to overturn once it is embedded in the institutional culture on which their careers all depend.

Second, conundrums like this help us understand why panpsychism (all life forms/cells are conscious) is beginning to replace materialism in science.

Here’s the Problem

In a nutshell: The only really satisfactory form of materialism is eliminative materialism, meaning that minds are merely what brains do and human consciousness is simply an evolved illusion. You are indeed nothing but a pack of neurons. But if so, that very theory is an illusion like all the others.

In a world of awe-inspiringly complex life forms, it probably makes more sense for the materialist to adopt panpsychism. Thus words like “cognitive” and “self-referential” can be attached to cells without risk. I am not claiming that the authors are panpsychists, of course. My point is that their approach should be welcome to panpsychists.

Anyway, there is a definite nudge in that direction. University of Chicago biochemist James Shapiro titled a 2021 journal paper “All living cells are cognitive.” The same year, prominent neuroscientist Antonio Damasio, said in a book excerpt at The Scientist, that we cannot deny viruses “some fraction” of intelligence, based on the way their strategies resemble those of insects. Scientific American has run a number of pieces sympathetic to panpsychism over the years. New Scientist also offered a sympathetic long form discussion last year.

From a panpsychist perspective, human consciousness is not a mere illusion generated by a pack of neurons. It is the most highly developed known form of consciousness among life forms, all of which are conscious to some extent. That is, it is real in the same way that cell cognition and self-organization are real. So humans can learn about cells and propound theories about them that are not necessarily illusions but rather a meta level of consciousness.

Of course, panpsychism doesn’t do much to resolve the “profound enigma” of how such a world of life could come to exist without any intelligent intention or design. But that’s not what the materialist most needs right now anyway. He most needs to believe that his own findings are not just a user illusion. He can admit the profound enigma and leave the matter there.