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Showing posts with label Darwin skeptic. Show all posts
Showing posts with label Darwin skeptic. Show all posts

Friday, 28 March 2025

Junk DNA =Junk science?

 Nobelist Thomas Cech on “Junk RNA” 


We can add Nobel Prize-winning biochemist Thomas Cech to the ever-growing list of scientists who reject the “junk DNA” paradigm. Or, more pertinently, the junk RNA paradigm. RNA tends to get left as sidenote in most discussions of genetics, much to Cech’s annoyance — Dr. Cech has always been more in interested in RNA than most of his colleagues, which led him to co-win the Nobel Prize in 1989 for discovering RNA’s catalytic powers.

Adventures with RNA

Now Cech as written a book, The Catalyst: RNA and the Quest to Unlock Life’s Deepest Secrets (W. W. Norton), on his adventures in RNA research. Towards the end he discusses his perspective on the idea of genetic junk. Cech writes

The coding regions of all the human genes that specify proteins make up only about 2 percent of our genome. When we add the introns that interrupt those coding regions — the sequences that are spliced out after the DNA is transcribed into the precursors to mRNA — we account for another 24 percent. That leaves about three-quarters of the genome that is “dark matter.” For decades this 75 percent was dismissed as “junk DNA” because whatever function it had, if any, was invisible to us. 

But as technologies for sequencing RNA have improved, scientists have discovered that most of this dark-matter DNA is in fact transcribed into RNA. Some portion of this DNA is copied into RNA in the brain, other portions in muscle, or in the heart, or in the sex organs. It’s only when we add up the RNAs made in all the tissues of the body that we see the true diversity of human RNAs. The total number of RNAs made from DNA’s “dark matter” has been estimated to be several hundred thousand. These are not messenger RNAs, but rather noncoding RNAs — the same general category as ribosomal RNA, transfer RNA, telomerase RNA, and microRNAs. But what they’re doing is still, for the most part, a mystery. 

The RNAs that emerge from this dark matter are called long noncoding RNAs (lncRNAs). While they are particularly numerous in humans, they are also abundant in other mammals, including the laboratory mouse. In a few cases, they clearly have a biological function. For example, a lncRNA called Firre contributes to the normal development of blood cells in mice; an overabundance of Firre prevents mice from fending off bacterial infections, as their innate immune response fails. Another lncRNA, called Tug1, is essential for male mice to be fertile. But such verified functions are few and far between. The function of most lncRNAs remains unknown. 

As a result, many scientists do not share my enthusiasm for these RNAs. They think that RNA polymerase, the enzyme that synthesizes RNA from DNA, makes mistakes and sometimes copies junk DNA into junk RNA. A more scholarly description of such RNAs might explain them away as “transcriptional noise” — the idea being, again, that RNA polymerase isn’t perfect. It sometimes sits down on the wrong piece of DNA and copies it into RNA, and that RNA may have no function. I readily admit that some of the lncRNAs may in fact be noise, bereft of function, signifying nothing. 

However, I’ll point out that there was a time in the not-too-distant past when telomerase RNA and microRNAs and catalytic RNAs weren’t understood. They hadn’t been assigned any function. They, too, could have been dismissed as “noise” or “junk.” But now hundreds of research scientists go to annual conferences to talk about these RNAs, and biotech companies are trying to use them to develop the next generation of pharmaceuticals. Certainly one lesson we’ve learned from the story of RNA is never to underestimate its power. Thus, these lncRNAs are likely to provide abundant material for future chapters in the book of RNA

Retarding Progress

Notice that the problem for Cech is not merely that he thinks the “junk RNA” hypothesis is false. The problem is that it is a presupposition that could be holding back scientific progress. After all, the scientists who (in Cech’s words) “do not share my enthusiasm for these RNAs” will not likely make discoveries about RNA that they think is junk. It’s scientists like Cech, who come to biology expecting plan and purpose, who will. 

The implication of that is pretty significant: Darwinism is not turning out to be a fruitful heuristic for understanding genetics. (Since the lack of function in so-called “genetic dark-matter” is, of course, a prediction of the Darwinian model.) The trouble is, there isn’t another framework to take its place — well, not an acceptable one, anyway. 

As far as I can tell, Cech assumes RNA will have function simply from experience, not from any underlying model or paradigm. RNA keeps turning out to have purpose, so he has learned to expect to find purpose. In contrast, other scientists don’t share his assumption because they (like Cech) are working in a paradigm that predicts junk, and (unlike Cech) they form their expectations based on that paradigm, not on the emerging pattern of evidence. Which is fair enough — it’s just a matter of how seriously you take your paradigm. 

A New Paradigm

But if not taking a paradigm seriously turns out to be a path to scientific discovery, eventually you should start looking for a new paradigm. I would be interesting in hearing Dr. Cech’s answer to a question… Deep down, why do you really expect that genetic dark-matter has hidden functions? The neo-Darwinian paradigm didn’t predict that — what paradigm does?

Whatever his answer might be, it’s increasingly clear that the junk DNA narrative is over. Of course, some scientists still cling to it, but as they age out of the field it’s unlikely that many new researchers will inherit their assumption. The Darwinian prediction is being falsified. The older generation of scientists may not be ready to confront the implications of that. But the next generation will.  

Darwinism designs Darwinism?

 The Convoluted Concept of Evolving Evolvability


Try to wrap your mind around the concept that evolvability evolves by natural selection. On second thought, don’t. It’s not conducive to mental health.

Valuing charity, I try to approach new evolutionary papers with dispassionate tolerance, seeking understanding before forming an opinion about them one way or another. This one was a particular challenge. It’s like trying to imagine a Mobius strip wrapping a Klein bottle in hyperspace. What on earth is meant by natural selection favoring the evolution of evolvability? Is this even a potentially useful notion for understanding how the world works?

Mentions of “evolvability” here at Evolution News can be found scattered through articles by several contributing authors, but none I searched for have treated it in detail. Now that two papers on evolvability have appeared in separate journals in February 2025, it’s a good time to examine the concept. 

The first paper, in PNAS, led by Luis Zaman from the University of Michigan, will not require much analysis, for two reasons: (1) The authors are consumed with Darwinism to the point of absurdity, and (2) Their justification is entirely built on a computer model running Avida. Even the title of the press release mentions evolution five times! “Evolution, evolution, evolution: How evolution got so good at evolving.” 


Now, a University of Michigan study shows that perhaps why evolution is so effective is that evolution is itself something that can evolve. The research is published in the Proceedings of the National Academy of Sciences.

“Life is really, really good at solving problems. If you look around, there’s so much diversity in life, and that all these things come from a common ancestor seems really surprising to me,” said Luis Zaman, an evolutionary biologist at U-M and lead author of the study. “Why is evolution so seemingly creative? It seems like maybe that ability is something that evolved itself.” 

Forms of the word “evolution” appear 38 times in this short press release, and 214 times in the paper. Such overuse of a word appears pathological, like an addiction. Worse, it contains no biological field work at all. Its conclusions are rationalized entirely by a computer model with imaginary organisms in silico that were designed to evolve or fail by natural selection. Live Science liked the paper, but because the Avida platform that supported this computer game has been debunked extensively by others at Evolution News (here, here, and here), it deserves no further serious consideration other than for the possible entertainment value, like watching clowns in a curved maze looking for a penny in the nonexistent corner.

Much Empiricism About Nothing

The second paper, published in Science, gets more into the weeds. Barnett, Meister, and Rainey titled their work “Experimental evolution of evolvability.” For a synopsis of the paper, see the Perspective by Edo Kussell (“Enabling evolvability to evolve”) in the same issue of Science, or see the press release from the Max Planck Institute for Evolutionary Biology featuring two of the authors, Michael Barnett and Paul Rainey.

A new study by researchers at the Max Planck Institute for Evolutionary Biology (MPI-EB) sheds fresh light on one of the most debated concepts in biology: evolvability. The work provides the first experimental evidence showing how natural selection can shape genetic systems to enhance future capacity for evolution, challenging traditional perspectives on evolutionary processes.

Right at the outset, we see them “challenging traditional perspectives on evolutionary processes,” leading one to proceed with caution as if handed a bottle of New Coke. Arguing that mutation and selection interact, they propose a concept called “lineage-level selection.” Here we go; just what the world needs now: not love, sweet love, but another type of natural selection. 

A caption to the opening diagram explains:

Central to this is lineage-level selection: bacterial lineages (connected nodes) were required to repeatedly evolve between two phenotypic states. Mutational transitions were initially unreliable, leading to lineage deathand replacement by more successful competitors. Final surviving lineages evolved mutation-prone sequencesin a key gene underpinning the phenotypes, enabling rapid transitions between states.

According to their concept, “natural selection optimises genetic systems for future adaptations.” Lineage selection locates the target of selection in the lineage rather than in the individual or population. In this view, your genealogy determines how natural selection will let you evolve.

Imaginary Foresight by Natural Selection

Dr. Marcos Eberlin wrote about Foresight as a sign of intelligence. In the theory of Barnett et al., however, foresight evolves (believe it or not). It’s not real foresight. It’s just imaginary foresight. They call it “evolutionary foresight.” Selection looks down through the halls of time and muses, “Which of my future lineages might win the competition for fitness?” It decides that the winner will be the most evolvable one. This is where the authors start playing mind games with your sanity. “This is not the selection you are looking for,” they say with a hypnotic gesture of the hands.

Evolution by natural selection is a blind process, but living systems can appear to possess evolutionary foresight. Mechanistically, this is conceivable. Certain configurations of gene regulatory networks, developmental systems, chromosomal architectures, and mutational processes have apparent adaptive utility in future environments. Taking advantage of such future adaptive potential requires not only memory of evolutionary history but often an ability to regenerate previously achieved phenotypic states. In this work, we show how selection on lineages can incorporate prior evolutionary history into the genetic architecture of a single cell, such that mutation appears to anticipate future environmental change.

They lost me on the assertion that “evolutionary foresight” is mechanistically conceivable. That is certainly not your grandpa’s Darwinism. At that point, I looked into their Materials and Methods to see what scientific experiments they did to support this notion. Sure enough, they ran actual lab experiments for three years on real organisms, not just computer models. 

Madness in the Methodology

They carefully studied populations of the bacterium Pseudomonas fluorescens (pictured at the top) kept in “glass microcosms” (presumably flasks or test tubes) each with billions of cells. Some of the populations were able to manufacture cellulose (CEL+) and some were not (CEL–). When starved for oxygen, bacteria with the genes to make cellulose created cellulose mats on which individuals could get close to the air/liquid interface for access to oxygen. The presence of cellulose made by CEL+members, therefore, provided a fitness advantage (meaning, the ability to avoid dying). 

The team identified “hypermutable” loci with 10,000 times the mutation rate that they describe as similar to “contingency loci” in pathogenic bacteria. Having a contingency plan sounds like design, but they believe the ability for rapid mutation gives the bacterium “foresight” in the form of “evolutionary potential.” The press release explains,

“Our findings show that selection at the level of lineages can drive the evolution of traits that enhance evolutionary potential, offering a fascinating glimpse into how evolution can gain what appears to be ‘foresight’.” Michael Barnett, the study’s first author, added: “By demonstrating the evolution of a hyper-mutable locus, we show that adaptation is not just about surviving in the present but also about refining the ability to adapt in the future.”

The results challenge the long-held view that evolution operates without foresight. Instead, they reveal how natural selection can embed evolutionary history into genetic architecture, enabling organisms to “anticipate” environmental changes and accelerate their adaptation.

Several design words can be seen there: architecture, anticipation, embedding. Are these things that blind selectors do? In a response to the paper, David G. King, emeritus professor from Southern Illinois University, saw something different going on: neither random mutation nor directed mutagenesis:

For example, the insertions and deletions that characterize short tandem repeats (and also enable phenotypic switching in bacterial contingency genes) confer “tuning knob” or “rheostat” functionality on many, perhaps most eukaryotic genes. Without being biased in the direction of adaptation, repeat number mutability helps assure a relatively advantageous distribution [of] mutation effects.

If so, this would indicate a function for such hypermutable loci. They act like “mutational sponges” that diffuse the harmful effects of random mutations. King explains,

This is the domain of “mutation protocols” whereby an abundant supply of unbiased mutations entails a minimal probability of harm. Put simply, mutations produced “according to protocol” are constrained to avoid vast domains of DNA sequence space where deleterious results would be practically guaranteed.

Design is evident in concepts like a “tuning knob” or “rheostat” functionality. Another idea not discussed in the paper is the possibility that the populations of bacteria form “quasispecies” in which members of a population retain functional loci that can be shared by horizontal gene transfer. In both cases, genetic changes would not be random.

Conceptual Flaws

But since the authors wish to argue that natural selection (NS), which they admit is “a blind process,” somehow had foresight to “enhance evolutionary potential” (i.e., evolvability), their convoluted concept is subject to the critical scrutiny of NS by illustrious writers including John West (“a corrosive impact on society”), Neil Thomas (“a conceptually incoherent term”), Jonathan Wells (“cannot explain the arrival of the fittest”), and others. Have Barnett et al. twisted NS into a creative force beyond its means by its very nature as an unguided process? Here are a few considerations to keep in mind:

No origin of species: They started with one species and ended with the same species. 
Artificial selection: They acted like breeders, which is intelligent design, the opposite of NS.
Investigator interference: They forced the organisms to “evolve or perish” according to criteria they had set up in advance.
Unnatural assistance: When a population went “extinct” they transferred cells from a living population to keep it going (see the diagram in Kussell’s Perspective article).
Limited options: They forced the organisms to exhibit only one of two phenotypic states.
Personification: They applied terms like foresight, anticipation, and future adaptive potential to blind, mindless processes.
Magical thinking: Only in Darwin’s Fantasyland can NS be deemed capable of “refining the ability to adapt in the future.”
Obfuscation: Inventing concepts like “the evolution of evolvability” is no more conducive to understanding than speaking of “the phlogistification of phlogiston"

Conclusion: Keep Your Investment on Design

Try as they might to resurrect NS from the dead, Barnett et al. and Zaman et al. are stuck with blind, unguided processes with no foresight or desire to adapt. Scientists in Darwin’s day saw through his flawed attempt to present natural selection as analogous to artificial selection, as Robert Shedinger has exposed in Darwin’s Bluff.

Design scientists, by contrast, have the tools in their toolkit to explain adaptation. It takes foresight (real foresight by a designing intelligence, not imaginary “evolutionary” foresight) to engineer a machine for robustness against potential risks. More and more, scientists are finding that life comes equipped with built-in capabilities for adapting to environmental changes. This has been the focus of lively conferences on biological engineering over the past few years. The next Conference on Engineering in Living Systems (CELS), sponsored by Discovery Institute, is coming this summer in Seattle and promises to be a fertile occasion for enlightening discussions in Adventureland and Tomorrowland instead of Fantasyland.

Thursday, 20 March 2025

More memories of an iconoclast.

 Humor, Humility, and a Treasured Friend and Colleague: Sternberg Remembers Jonathan Wells


On a new episode of ID the Future, I continue a series of interviews celebrating the life and legacy of Dr. Jonathan Wells, our close colleague and friend who passed away in 2024 at the age of 82 years old. Dr. Wells was one of the first Fellows of Discovery Institute’s Center for Science and Culture and made significant contributions to science and to arguments for intelligent design. Today, evolutionary biologist Dr. Richard Sternberg shares personal anecdotes and insights into Dr. Wells’s character, his contributions to biology and epigenetics, and the profound impact he had on those around him.

One of the character traits Sternberg most admired in Wells was his humility, which formed a backdrop for their many conversations. Wells would occasionally bring up lessons he had learned about hubris from Faust, the famous tragic play by German polymath Johann Wolfgang von Goethe. “The more you know, the more you realize that you know too little and there’s always some other horizon,” says Sternberg, encapsulating his friend’s view. Wells’s commitment to intellectual honesty served him well in his career as a biologist and in the debate over evolution.

Dr. Sternberg also highlights Dr. Wells’s deep concern for the truth. “He saw how ideology could be used to not only bend the truth, but also to just subvert it,” explains Sternberg. Wells committed himself early in his career to following the evidence wherever it led, a decision that led to a brave and relentless search for scientific truth. And the perfect compliment to that bravery and humility? Wells’s sense of humor. Sternberg gives examples. The episode concludes with reflections on Dr. Wells’s lasting influence on the future of intelligent design. Download the podcast or listen to it here.

Wednesday, 19 March 2025

Marcel-Paul Schützenberger: Darwin skeptic.

 

Marcel-Paul Schützenberger


 

Until his death, the mathematician and doctor of medicine Marcel-Paul Schützenberger (1920-1996) was Professor of the Faculty of Sciences at the University of Paris and a member of the Academy of Sciences. [See "From the Editors" for additional biographical information.] In 1966, Schützenberger participated in the Wistar Symposium on mathematical objections to neo-Darwinism. His arguments were subtle and often misunderstood by biologists. Darwin's theory, he observed, and the interpretation of biological systems as formal objects, were at odds insofar as randomness is known to degrade meaning in formal contexts. But Schützenberger also argued that Darwin's theory logically required some active principle of coordination between the typographic space of the informational macromolecules (DNA and RNA) and the organic space of living creatures themselves -- which Darwin's theory does not provide. In this January 1996 interview with the French science monthly La Recherche, here published in English for the first time, he pursued these themes anew, finding inspiration for his ideas both in the mathematical ideas that he had pioneered and in the speculative tradition of French biological thought that stretched from Georges Cuvier to Lucien Cuenot. M.P. Schützenberger was a man of universal curiosity and great wit; throughout his life, he was both joyful and unafraid. The culture that he so brilliantly represented disappears with him, of course. It was his finest invention and it now belongs to the inventory of remembered things.



Q: What is your definition of Darwinism?



S: The most current, of course, a position generically embodied, for example, by Richard Dawkins. The essential idea is well-known. Evolution, Darwinists argue, is explained by the double action of chance mutations and natural selection. The general doctrine embodies two mutually contradictory schools -- gradualists, on the one hand, saltationists, on the other. Gradualists insist that evolution proceeds by means of small successive changes; saltationists that it proceeds by jumps. Richard Dawkins has come to champion radical gradualism; Stephen Jay Gould, a no less radical version of saltationism.



Q: You are known as a mathematician rather than a specialist in evolutionary biology...



S: Biology is, of course, not my specialty. The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines. And finally, it is worth observing that the great turbid wave of cybernetics has carried mathematicians from their normal mid-ocean haunts to the far shores of evolutionary biology. There up ahead, Rene Thom and Ilya Prigogine may be observed paddling sedately toward dry land, members of the Santa Fe Institute thrashing in their wake. Stuart Kauffman is among them. An interesting case, a physician half in love with mathematical logic, burdened now and forever by having received a Papal Kiss from Murray Gell-Mann. This ecumenical movement has endeavored to apply the concepts of mathematics to the fundamental problems of evolution -- the interpretation of functional complexity, for example.



Q: What do you mean by functional complexity?



S: It is impossible to grasp the phenomenon of life without that concept, the two words each expressing a crucial and essential idea. The laboratory biologists' normal and unforced vernacular is almost always couched in functional terms: the function of an eye, the function of an enzyme, or a ribosome, or the fruit fly's antennae -- their function; the concept by which such language is animated is one perfectly adapted to reality. Physiologists see this better than anyone else. Within their world, everything is a matter of function, the various systems that they study -- circulatory, digestive, excretory, and the like -- all characterized in simple, ineliminable functional terms. At the level of molecular biology, functionality may seem to pose certain conceptual problems, perhaps because the very notion of an organ has disappeared when biological relationships are specified in biochemical terms; but appearances are misleading, certain functions remaining even in the absence of an organ or organ systems. Complexity is also a crucial concept. Even among unicellular organisms, the mechanisms involved in the separation and fusion of chromosomes during mitosis and meiosis are processes of unbelieveable complexity and subtlety. Organisms present themselves to us as a complex ensemble of functional interrelationships. If one is going to explain their evolution, one must at the same time explain their functionality and their complexity.



Q: What is it that makes functional complexity so difficult to comprehend?



S: The evolution of living creatures appears to require an essential ingredient, a specific form of organization. Whatever it is, it lies beyond anything that our present knowledge of physics or chemistry might suggest; it is a property upon which formal logic sheds absolutely no light. Whether gradualists or saltationists, Darwinians have too simple a conception of biology, rather like a locksmith improbably convinced that his handful of keys will open any lock. Darwinians, for example, tend to think of the gene rather as if it were the expression of a simple command: do this, get that done, drop that side chain. Walter Gehring's work on the regulatory genes controlling the development of the insect eye reflects this conception. The relevant genes may well function this way, but the story on this level is surely incomplete, and Darwinian theory is not apt to fill in the pieces.



Q: You claim that biologists think of a gene as a command. Could you be more specific?



S: Schematically, a gene is like a unit of information. It has simple binary properties. When active, it is an elementary information-theoretic unit, the cascade of gene instructions resembling the cascade involved in specifying a recipe. Now let us return to the example of the eye. Darwinists imagine that it requires what? A thousand or two thousand genes to assemble an eye, the specification of the organ thus requiring one or two thousand units of information? This is absurd! Suppose that a European firm proposes to manufacture an entirely new household appliance in a Southeast Asian factory. And suppose that for commercial reasons, the firm does not wish to communicate to the factory any details of the appliance's function -- how it works, what purposes it will serve. With only a few thousand bits of information, the factory is not going to proceed very far or very fast. A few thousand bits of information, after all, yields only a single paragraph of text. The appliance in question is bound to be vastly simpler than the eye; charged with its manufacture, the factory will yet need to know the significance of the operations to which they have committed themselves in engaging their machinery. This can be achieved only if they already have some sense of the object's nature before they undertake to manufacture it. A considerable body of knowledge, held in common between the European firm and its Asian factory, is necessary before manufacturing instructions may be executed.



Q: Would you argue that the genome does not contain the requisite information for explaining organisms?



S:Not according to the understanding of the genome we now possess. The biological properties invoked by biologists are in this respect quite insufficient; while biologists may understand that a gene triggers the production of a particular protein, that knowledge -- that kind of knowledge -- does not allow them to comprehend how one or two thousand genes suffice to direct the course of embryonic development.



Q: You are going to be accused of preformationism...



S: And of many other crimes. My position is nevertheless strictly a rational one. I've formulated a problem that appears significant to me: how is it that with so few elementary instructions, the materials of life can fabricate objects that are so marvelously complicated and efficient? This property with which they are endowed -- just what is its nature? Nothing within our actual knowledge of physics and chemistry allows us intellectually to grasp it. If one starts from an evolutionary point of view, it must be acknowledged that in one manner or another, the earliest fish contained the capacity, and the appropriate neural wiring, to bring into existence organs which they did not possess or even need, but which would be the common property of their successors when they left the water for the firm ground, or for the air.



Q: You assert that, in fact, Darwinism doesn't explain much.



S: It seems to me that the union of chance mutation and selection has a certain descriptive value; in no case does the description count as an explanation. Darwinism relates ecological data to the relative abundance of species and environments. In any case, the descriptive value of Darwinian models is pretty limited. Besides, as saltationists have indicated, the gradualist thesis seems completely demented in light of the growth of paleontological knowledge. The miracles of saltationism, on the other hand, cannot discharge the mystery I have described.



Q: Let's return to natural selection. Isn't it the case that despite everything the idea has a certain explanatory value?



S: No one could possibly deny the general thesis that stability is a necessary condition for existence -- the real content of the doctrine of natural selection. The outstanding application of this general principle is Berthollet's laws in elementary chemistry. In a desert, the species that die rapidly are those that require water the most; yet that does not explain the appearance among the survivors of those structures whose particular features permits them to resist aridity. The thesis of natural selection is not very powerful. Except for certain artificial cases, we are yet unable to predict whether this or that species or this or that variety will be favored or not as the result of changes in the environment. What we can do is establish after the fact the effects of natural selection -- to show, for, example that certain birds are disposed to eat this species of snails less often than other species, perhaps because their shell is not as visible. That's ecology: very interesting. To put it another way, natural selection is a weak instrument of proof because the phenomena subsumed by natural selection are obvious and yet they establish nothing from the point of view of the theory.



Q: Isn't the significant explanatory feature of Darwinian theory the connection established between chance mutations and natural selection?



S:With the discovery of coding, we have come to understand that a gene is like a word composed in the DNA alphabet; such words form the genomic text. It is that word that tells the cell to make this or that protein. Either a given protein is structural, or a protein itself works in combination with other signals given by the genome to fabricate yet another protein. All the experimental results we know fall within this scheme. The following scenario then becomes standard. A gene undergoes a mutation, one that may facilitate the reproduction of those individuals carrying it; over time, and with respect to a specific environment, mutants come to be statistically favored, replacing individuals lacking the requisite mutation. Evolution could not be an accumulation of such typographical errors. Population geneticists can study the speed with which a favorable mutation propagates itself under these circumstances. They do this with a lot of skill, but these are academic exercises if only because none of the parameters that they use can be empirically determined. In addition, there are the obstacles I have already mentioned. We know the number of genes in an organism. There are about one hundred thousand for a higher vertebrate. This we know fairly well. But this seems grossly insufficient to explain the incredible quantity of information needed to accomplish evolution within a given line of species.



Q: A concrete example?



S: Darwinists say that horses, which were once mammals as large as rabbits, increased their size to escape more quickly from predators. Within the gradualist model, one might isolate a specific trait -- increase in body size -- and consider it to be the result of a series of typographic changes. The explanatory effect achieved is rhetorical, imposed entirely by trick of insisting that what counts for a herbivore is the speed of its flight when faced by a predator. Now this may even be partially true, but there are no biological grounds that permit us to determine that this is in fact the decisive consideration. After all, increase in body size may well have a negative effect. Darwinists seem to me to have preserved a mechanic vision of evolution, one that prompts them to observe merely a linear succession of causes and effects. The idea that causes may interact with one another is now standard in mathematical physics; it is a point that has had difficulty in penetrating the carapace of biological thought. In fact, within the quasi-totality of observable phenomena, local changes interact in a dramatic fashion; after all, there is hardly an issue of La Recherche that does not contain an allusion to the Butterfly Effect. Information theory is precisely the domain that sharpens our intuitions about these phenomena. A typographical change in a computer program does not change it just a little. It wipes the program out, purely and simply. It is the same with a telephone number. If I intend to call a correspondent by telephone, it doesn't much matter if I am fooled by one, two, three or eight figures in his number.



Q: You accept the idea that biological mutations genuinely have the character of typographical errors?



S: Yes, in the sense that one base is a template for another, one codon for another, but at the level of biochemical activity, one is no longer able properly to speak of typography. There is an entire grammar for the formation of proteins in three dimensions, one that we understand poorly. We do not have at our disposal physical or chemical rules permitting us to construct a mapping from typographical mutations or modifications to biologically effective structures. To return to the example of the eye: a few thousand genes are needed for its fabrication, but each in isolation signifies nothing. What is significant is the combination of their interactions. These cascading interactions, with their feedback loops, express an organization whose complexity we do not know how to analyze (See Figure 1). It is possible we may be able to do so in the future, but there is no doubt that we are unable to do so now. Gehring has recently discovered a segment of DNA which is both involved in the development of the vertebrate eye and which can induce the development of an eye in the wing of a butterfly. His work comprises a demonstration of something utterly astonishing, but not an explanation.



Q:But Dawkins, for example, believes in the possibility of a cumulative process.



S: Dawkins believes in an effect that he calls "the cumulative selection of beneficial mutations." To support his thesis, he resorts to a metaphor introduced by the mathematician Emile Borel -- that of a monkey typing by chance and in the end producing a work of literature. It is a metaphor, I regret to say, embraced by Francis Crick, the co-discoverer of the double helix. Dawkins has his computer write a series of thirty letters, these corresponding to the number of letters in a verse by Shakespeare. He then proceeds to simulate the Darwinian mechanism of chance mutations and selection. His imaginary monkey types and retypes the same letters, the computer successively choosing the phrase that most resembles the target verse. By means of cumulative selection, the monkey reaches its target in forty or sixty generations.



Q: But you don't believe that a monkey typing on a typewriter, even aided by a computer...



S:This demonstration is a trompe-l'oeil, and what is more, Dawkins doesn't describe precisely how it proceeds. At the beginning of the exercise, randomly generated phrases appear rapidly to approach the target; the closer the approach, the more the process begins to slow. It is the action of mutations in the wrong direction that pulls things backward. In fact, a simple argument shows that unless the numerical parameters are chosen deliberately, the progression begins to bog down completely.



Q:You would say that the model of cumulative selection, imagined by Dawkins, is out of touch with palpable biological realities?



S: Exactly. Dawkins's model lays entirely to the side the triple problems of complexity, functionality, and their interaction.



Q: You are a mathematician. Suppose that you try, despite your reservations, to formalize the concept of functional complexity...



S: I would appeal to a notion banned by the scientific community, but one understood perfectly by everyone else -- that of a goal. As a computer scientist, I could express this in the following way. One constructs a space within which one of the coordinates serves in effect as the thread of Ariane, guiding the trajectory toward the goal. Once the space is constructed, the system evolves in a mechanical way toward its goal. But look, the construction of the relevant space cannot proceed until a preliminary analysis has been carried out, one in which the set of all possible trajectories is assessed, this together with an estimation of their average distance from the specified goal. The preliminary analysis is beyond the reach of empirical study. It presupposes -- the same word that seems to recur in theoretical biology -- that the biologist (or computer scientist) know the totality of the situation, the properties of the ensemble of trajectories. In terms of mathematical logic, the nature of this space is entirely enigmatic. Nonetheless, it is important to remember that the conceptual problems we face, life has entirely solved; the systems embodied in living creatures are entirely successful in reaching their goals. The trick involved in Dawkin's somewhat sheepish example proceeds via the surreptitious introduction of a relevant space. His computer program calculates from a random phrase to a target, a calculation corresponding to nothing in biological reality. The function that he employs flatters the imagination, however, because it has that property of apparent simplicity that elicits naïve approval. In biological reality, the space of even the simplest function has a complexity that defies understanding, and indeed, defies any and all calculations.



Q: Even when they dissent from Darwin, the saltationists are more moderate: they don't pretend to hold the key that would permit them to explain evolution...



S: Before we discuss the saltationists, however, I must say a word about the Japanese biologist Mooto Kimura. He has shown that the majority of mutations are neutral, without any selective effect. For Darwinians upholding the central Darwinian thesis, this is embarrassing... The saltationist view, revived by Stephen Jay Gould, in the end represents an idea due to Richard Goldschmidt. In 1940 or so, he postulated the existence of very intense mutations, no doubt involving hundreds of genes, and taking place rapidly, in less than one thousand generations, thus below the threshold of resolution of paleontology. Curiously enough, Gould does not seem concerned to preserve the union of chance mutations and selection. The saltationists run afoul of two types of criticism. On the one hand, the functionality of their supposed macromutations is inexplicable within the framework of molecular biology. On the other hand, Gould ignores in silence the great trends in biology, such as the increasing complexity of the nervous system. He imagines that the success of new, more sophisticated species, such as the mammals, is a contingent phenomenon. He is not in a position to offer an account of the essential movement of evolution, or at the least, an account of its main trajectories. The saltationists are thus reduced to invoking two types of miracles: macromutations, and the great trajectories of evolution.



Q: In what sense are you employing the word 'miracle'?



S:A miracle is an event that should appear impossible to a Darwinian in view of its ultra-cosmological improbability within the framework of his own theory. Now speaking of macromutations, let me observe that to generate a proper elephant, it will not suffice suddenly to endow it with a full-grown trunk. As the trunk is being organized, a different but complementary system -- the cerebellum -- must be modified in order to establish a place for the ensemble of wiring that the elephant will require to use his trunk. These macromutations must be coordinated by a system of genes in embryogenesis. If one considers the history of evolution, we must postulate thousands of miracles; miracles, in fact, without end. No more than the gradualists, the saltationists are unable to provide an account of those miracles. The second category of miracles are directional, offering instruction to the great evolutionary progressions and trends -- the elaboration of the nervous system, of course, but the internalization of the reproductive process as well, and the appearance of bone, the emergence of ears, the enrichment of various functional relationships, and so on. Each is a series of miracles, whose accumulation has the effect of increasing the complexity and efficiency of various organisms. From this point of view, the notion of bricolage [tinkering], introduced by Francois Jacob, involves a fine turn of phrase, but one concealing an utter absence of explanation.



Q: The appearance of human beings -- is that a miracle, in the sense you mean?



S: Naturally. And here it does seem that there are voices among contemporary biologists -- I mean voices other than mine -- who might cast doubt on the Darwinian paradigm that has dominated discussion for the past twenty years. Gradualists and saltationists alike are completely incapable of giving a convincing explanation of the quasi-simultaneous emergence of a number of biological systems that distinguish human beings from the higher primates: bipedalism, with the concomitant modification of the pelvis, and, without a doubt, the cerebellum, a much more dexterous hand, with fingerprints conferring an especially fine tactile sense; the modifications of the pharynx which permits phonation; the modification of the central nervous system, notably at the level of the temporal lobes, permitting the specific recognition of speech. From the point of view of embryogenesis, these anatomical systems are completely different from one another. Each modification constitutes a gift, a bequest from a primate family to its descendants. It is astonishing that these gifts should have developed simultaneously. Some biologists speak of a predisposition of the genome. Can anyone actually recover the predisposition, supposing that it actually existed? Was it present in the first of the fish? The reality is that we are confronted with total conceptual bankruptcy.



Q:You mentioned the Santa Fe school earlier in our discussion. Do appeals to such notions as chaos...



S:I should have alluded to a succession of highly competent people who have discovered a number of poetic but essentially hollow forms of expression. I am referring here to the noisy crowd collected under the rubric of cybernetics; and beyond, there lie the dissipative structures of Prigogine, or the systems of Varela, or, moving to the present, Stuart Kauffman's edge of chaos -- an organized form of inanity that is certain soon to make its way to France. The Santa Fe school takes complexity to apply to absolutely everything. They draw their representative examples from certain chemical reactions, the pattern of the sea coast, atmosphere turbulence, or the structure of a chain of mountains. The complexity of these structures is certainly considerable, but in comparison with the living world, they exhibit in every case an impoverished form of organization, one that is strictly non-functional. No algorithm allows us to understand the complexity of living creatures, this despite these examples, which owe their initial plausibility to the assumption that the physico-chemical world exhibits functional properties that in reality it does not possess.



Q: Should one take your position as a statement of resignation, an appeal to have greater modesty, or something else altogether?



S: Speaking ironically, I might say that all we can hear at the present time is the great anthropic hymnal, with even a number of mathematically sophisticated scholars keeping time as the great hymn is intoned by tapping their feet. The rest of us should, of course, practice a certain suspension of judgment.



Sunday, 16 March 2025

More on our privileged homeworld.

 The Growing Evidence of Earth’s Privilege


On a classic episode of ID the Future, astrobiologist Guillermo Gonzalez, co-author of The Privileged Planet, begins a two-part conversation with host Casey Luskin by providing a rapid survey of some of the growing evidence that Earth is finely tuned in numerous ways to allow for life. He draws a helpful distinction between local fine-tuning and universal fine-tuning. And he tells us about the many extra-solar planets astronomers have discovered in recent years and how all that new data continues to undermine the misguided assumption (encouraged by the misnamed “Copernican principle”) that Earth is just a humdrum planet. Far from it, Gonzalez argues.

The conversation highlights Gonzalez’s essay in the open-access anthology Science and Faith in Dialogue. The book presents a cogent, compelling case for concordance between science and theism. In addition to chapters from Dr. Gonzalez and Dr. Luskin, the book also contains entries from other scientists and scholars in the intelligent design research community, including philosopher of science Stephen Meyer, Brazilian chemist Marcos Eberlin, historian of science Michael Keas, and physicist Brian Miller. The book is available as a free PDF download.

Download the podcast or listen to it here. This is Part 1 of a two-part conversation. 

Friday, 14 March 2025

There are no simple beginnings anywhere in biology.

 Directed Evolution”: The Tiniest Brain Is Not Simple


The nematode worm Caenorhabditis elegans has the smallest brain in a free-living animal. There are two forms of C. elegans, male and hermaphrodite. The hermaphrodite brain contains only 302 neurons and the male 385 neurons. The physical characteristics and brain design are different, but there is much in common. The entire body contains approximately 900 cells and is only one millimeter long. Because of its small size, scientists have conducted a significant amount of research on the brain, in the hope of discovering how brains in general function. A few years ago, researchers were able to determine the entire map of the brain, called a connectome, and published the results in the journal Nature.1 C. elegans is the first animal where this was accomplished.

Even a cursory examination of the connectome shows the complexity of the brain, despite its tiny size. Additional complexity is exhibited by the diversity of the types of neurons and the variety of connections. There are three basic types of neurons — sensory neurons, motor neurons, and interneurons. Sensory neurons respond to various stimuli (chemical, physical, etc.). Motor neurons connect to muscles to control movement. Interneurons are generally intermediate between sensory and motor neurons. 

C. elegans Behaviors

C.elegans exhibits a number of behaviors, some that are complex. That is surprising considering it is a simple organism with such a small brain. The basic behaviors include feeding, fasting, mating, egg laying, and several forms of movement. These include swimming when in liquid media and “crawling” on solid surfaces. They also exhibit a non-movement behavior called quiescence. Research has found that the behaviors are controlled by various neural networks as well as being regulated by neurotransmitters such as serotonin and dopamine and neuropeptide signaling.2 These forms of neural signaling exist in all animal brains. The conclusion of the same research regarding these behaviors is that, “Episodic regulation of C. elegans behavior is complex because episode incidence and timing are regulated by the interplay between multiple circuit systems.”

In addition to basic behaviors, C. elegans is also capable of learning, including associative and non-associative learning. A paper published in the Journal of Neurochemistry documented the learning behaviors, including attraction and aversion to salt, temperature, and other substances.3 What might be surprising to many is that this learning involves both short-term and long-term memory mechanisms, which include regulation of neurotransmitters. The conclusion of the same paper was the expectation that the findings “Will provide critical insights in the context of learning and memory disorders in higher organisms, including humans.”

General Characteristics of the Brain
                    elegans exhibits a number of behaviors, some that are complex. That is surprising considering it is a simple organism with such a small brain. The basic behaviors include feeding, fasting, mating, egg laying, and several forms of movement. These include swimming when in liquid media and “crawling” on solid surfaces. They also exhibit a non-movement behavior called quiescence. Research has found that the behaviors are controlled by various neural networks as well as being regulated by neurotransmitters such as serotonin and dopamine and neuropeptide signaling.2 These forms of neural signaling exist in all animal brains. The conclusion of the same research regarding these behaviors is that, “Episodic regulation of C. elegans behavior is complex because episode incidence and timing are regulated by the interplay between multiple circuit systems.”

In addition to basic behaviors, C. elegans is also capable of learning, including associative and non-associative learning. A paper published in the Journal of Neurochemistry documented the learning behaviors, including attraction and aversion to salt, temperature, and other substances.3 What might be surprising to many is that this learning involves both short-term and long-term memory mechanisms, which include regulation of neurotransmitters. The conclusion of the same paper was the expectation that the findings “Will provide critical insights in the context of learning and memory disorders in higher organisms, including humans.”

General Characteristics of the Brain
             Arecent study led by scientists at Hebrew University analyzed the structure of neural networks in C. elegans. One of the findings is that, “The positions of the chemical synapses along the neurites are not randomly distributed nor can they be explained by anatomical constraints. Instead, synapses tend to form clusters, an organization that supports local compartmentalized computations.”4 On the other hand the study shows that, “The vast majority of the 302 neurons in C. elegans nematodes lack elaborate tree-like structures. In fact, many of these neurons consist of a single (unipolar) neurite extension, on which input and output synaptic sites are intermittently positioned.” That contrasts with larger brains of advanced animals which do have complex neuron structures. There is a total of 83 sensory neurons and 108 motor neurons. There are approximately 100 classes of neurons that have been identified. There are approximately 5,000 chemical synapses and 1,500-1,700 electrical synapses (gap) junctions.

In the paper that describes the connectome, some of the complexity is summarized as follows, “The major motor neurons as well as their primary pre-motor interneurons are highly interconnected and receive some input from most of the remaining neurons, defying simple interpretation of motor output. The complex circuitry must underlie both the many known behaviours in C. elegans, and the underpinnings for less well understood or novel behaviours, such as learning and memory, inter-animal communication, social behaviour and the complexities of mating.”5 Another important finding concerning the connectome is, “The notable similarity in the placement of the nodes to the neuroanatomy of the worm reflects economical wiring, a property commonly found for nervous systems, including in C. elegans.” 

Examination of Neuron Triplets
                 One notable aspect of the neural networks is that there are a number of triplets, meaning a cluster of three neurons. The paper by the Hebrew University scientists observes, “The clustered organization of synapses is found predominantly in specific types of tri-neuron circuits, further underscoring the high prevalence for evolved, rather than for random, synaptic organization that may fulfill functional role.” One simple instance of a three-neuron cluster is a “feed forward” loop. For example, neuron A is a sensory neuron, neuron B is an interneuron, and neuron C is a motor neuron. Feed forward networks are common in both biological and artificial neural networks. The significance of this is likely that, “The ubiquitous appearance of these circuits in biological networks suggests that they may carry key computational roles, including noise filtering and coincidence detection.” Other research has found that the number of feed forward connections increases as the worm matures.6

Additional detailed examination of three neuron clusters found that, “For three different layouts, where each of the three neurons can be either sensory, inter, or motor neuron, there are 63 possible circuit combinations. Of these 63 combinations, few circuits emerged as forming clustered synaptic connections, significantly more than randomly expected.”7 The two combinations that are the most common are: (1) two sensory neurons form a postsynaptic contact with an interneuron; and, (2) an interneuron that is presynaptic with two motor neurons. The researchers theorize that combination (1) may function as a signal integrator, and combination (2) may function by synchronizing activation. It seems logical that these would be common circuits as these two functions are likely common in controlling animal behavior.

The Touch Response Neural Network
                   An interesting example of one neural network in C. elegans that has been elucidated is the “tap withdrawal circuit,” also called the touch response, which controls how the worm responds to being physically touched. The behavior is interesting for a number of reasons, one being that the response exhibits habituation. The neural network is illustrated in Figure 2 here. The network consists of four sensory neurons (red triangles), five interneurons (circles), and two motor neurons (blue triangles). There is a total of seven excitatory chemical synapses (green lines with arrows) and 15 inhibitory chemical synapses (red lines with circles). There are also six electrical (gap junction) synapses (blue lines with squares). The response is activated when the sensory neurons detect a tap. The stimulus is then transferred via the interneurons (PVC and AVD), which then pass it to the command neurons (AVA and AVB). The two output states are either “move forward” (FWD motor neuron) or “move in reverse” (REV motor neuron). The response is modulated through competition between the two command neurons. The competition between commands for moving forward or reverse is evident based on the number of inhibitory synapses. It is obvious that even for such a simple behavior the neural circuit is relatively complex.

Tiny But Not Simple

There are several observations that can be drawn from research into the brain of C. elegans. One is that even though the brain is tiny, it does not have a simple structure. One might expect the smallest known brain to have a structure that is either relatively uniform or random. An example of a uniform structure is that found in crystals, which form a symmetrical lattice. A random structure would be expected if the positions of the neurons were not specified, but rather develop through a random process. Contrary to being either uniform or random, the brain does have a complex structure that is specified and repeatable.

A second observation is that the brain contains a large number (approximately 100) of different types of neurons, both in terms of design and function. They are not all identical. That also would not be expected for the smallest brain. A third observation is that small neural networks within the brain control various behaviors, such as the touch response network. It is possible that some of these neural networks are irreducibly complex.

The fourth observation concerns the origin of the C. elegans brain. The usual Darwinian evolution explanation is given in the paper that documented the organization of the synapses, “The mere existence of such structures may actually further underscore the directed evolution to form such clusters, which presumably carry fine functional roles along the neurites. Taken together, local compartmentalized activities, facilitated by the clustered synaptic organizations revealed herein, can enhance computational and memory capacities of a neural network. Such enhancement may be particularly relevant for animals with a compact neural network and with limited computational powers, thereby explaining the evolutionary forces for the emergence of these synaptic organizations.”8 The key phrases are “evolutionary forces” and “directed evolution.” Such terms have never been generally accepted as valid scientific explanations, particularly regarding the origin of novel biological structures. 

In contrast, the design of the brain of C. elegans exhibits a number of characteristics associated with intelligent design. They include the specified complexity of the overall design and small neural networks. It also includes engineering design, including the efficient wiring. Also apparent is that a significant amount of information is needed to specify the design and function of the brain.

Notes

1.Cook, et al., “Whole-animal connectomes of both Caenorhabditis elegans sexes,” Nature, Vol. 571, 4 July 2019.
2.McCloskey, et al., “Food responsiveness regulates episodic behavioral states in Caenorhabditis elegans,” J Neurophysiol117: 1911-1934, 2017.
3.Aelon Rahmani and Yee Lian Chew, “Investigating the molecular mechanisms of learning and memory using Caenorhabditis elegans,” Journal of Neurochemistry, 2021; 159.
3.Ruach, et al., “The synaptic organization in the Caenorhabditis elegans neural network suggests significant local compartmentalized computations,” PNAS, 2023, Vol. 120, No. 3.
4.Cook, et al.
Witvliet, et al., “Connectomes across development reveal principles of brain maturation,” Nature, Vol. 596, 12 August 2021.
5.Ruach, et al.
6.Ruach, et 


Total structural collapse.

 Non-Adaptive Order: An Existential Challenge to Darwinian Evolution

Michael Denton February 15, 2016 12:07 AM 

Editor's note: In his new book Evolution: Still a Theory in Crisis, Michael Denton not only updates the argument from his groundbreaking Evolution: A Theory in Crisis (1985) but also presents a powerful new critique of Darwinian evolution. This article is one in a series in which Dr. Denton summarizes some of the most important points of the new book. For the full story,get your copy of Evolution: Still a Theory in Crisis. For a limited time, you'll enjoy a 30 percent discount at  CreateSpace by using the discount code QBDHMYJH.

At London's famous Natural History Museum in South Kensington, a statue of Richard Owen had been prominently placed for many decades at the head of the main staircase. But in a curiously symbolic event on May 23, 2008, the statue was moved to one of the adjacent balconies to make room for a statue of Charles Darwin, which now sits in pride of place.


The reason for this gesture? The Natural History Museum is a grand temple to Darwinian evolution, and Owen was a staunch defender of the alternative structuralist conception of nature -- a conception that, if true, would relegate Darwinian selectionism to a very trivial role in the evolution of life.Owen founded the museum and served as its first curator and director. He made huge contributions to comparative anatomy and paleontology in the 19th century, including coining the term "dinosaur" and defining the term "homology." Owen believed that there was a substantial degree of order inherent in living systems, manifest in what he termed "primal patterns," the grand taxa-defining homologs or ground plans that underlie the adaptive diversity of life.

Because of his vigorous opposition to the functional conception of nature, Owen was vilified by Huxley and other supporters of Darwin. After the publication of the Origin, Owen's contribution to biology was increasingly downplayed by the Darwin camp, and his rejection of the conception that all biological order was to "serve some utilitarian end" was dismissed as archaic and treated as based on failed metaphysical assumptions. Little wonder they moved his statue!

While many of the taxa-defining homologs -- including, among others, the feather, the poison claw of the centipede, the retractable claw of cats, the mammalian diaphragm, and mammary glands -- are clearly adaptive, a great many others, such as the odd number of segments in centipedes, the concentric whorls of the flower, the insect body plan, and the pentadactyl limb, convey the powerful impression of being basically non-adaptive Bauplans. The fact that many exhibit curious geometric and numeric features reinforces the impression that they are indeed abstract non-adaptive patterns, quite beyond the explanatory reach of any adaptationist or selectionist narrative.

In all those cases Darwinian explanations are simply ruled out of court. The difficulty of accounting for arbitrary geometric and numerical patterns in terms of bit-by-bit selection was one of the basic thrusts of William Bateson's vigorous attack on Darwinian orthodoxy, where he argued that such stories descend into "endless absurdity."1

If indeed a significant proportion of the taxa-defining primal patterns serve no specific adaptive function and never did, as common sense dictates and as Owen thought to be true of the Bauplan of the tetrapod limb, then I think a fair assessment has to bethatDarwinism(more specifically, cumulative selection) cannot supply an explanation for the origin of a significant fraction of the defining homologs of the Types and hence for the natural system itself.

References:

(1) Bateson, Materials for the Study of Variation, 410.

Thursday, 13 March 2025

The fifth element?

 Life as a Habitability Requirement


Astrobiologists often speak of a planet’s requirements for life, but can we turn that around? Is life a requirement for a planet’s habitability? A team of geographers from the UK, with help from an ecologist at Montana State University, decided to calculate the energy output of animals. The resulting calculation is astonishing.
                                                  Animals, considered as a dynamic factor of the biosphere, contribute a huge amount of energy to landscape changes on the earth — more than some geological processes. The research paper in PNAS by Harvey et al. explains the significance of their results, with some surprising numbers. This paragraph needs a “wow” emoticon next to it:
       Animals profoundly influence Earth surface processes and landforms, but their collective significance has not been quantified. Integrating data across freshwater and terrestrial ecosystems, we uncovered over 600 animals with reported geomorphic effects, including five livestock taxa. Many more are doubtless overlooked due to inherent geographical and taxonomic biases in published research. We conservatively estimate that wild animal species collectively contribute ≈76,000 GJ energy or more to geomorphic processes annually, equivalent to the energy expended by hundreds of thousands of extreme floods. Livestock acting as geomorphic agents are estimated to exceed this contribution by three orders of magnitude. Our results reveal that the energy of animal geomorphic agents is a significant and overlooked driver of landscape change at the global level.
            Their results are most likely underestimated by orders of magnitude. The title, “Global diversity and energy of animals shaping the Earth’s surface,” leads us to think of the many ways that “ecosystem engineers” large and small are at work in this essential role.
                                      Animals cause landform change both directly, by mixing soils and sediments (bioturbation) and via the displacement of Earth materials (bioerosion and bioconstruction), and indirectly, by conditioning rock, soil, and sediment particles to be more or less susceptible to erosion and transport by geophysical processes. For example, riverbed gravels can become less mobile when bound by caddisfly silk or more mobile when disturbed by benthivorous feeding fish.
                                                     Even a lowly ant mound, termite pillar, gopher hole, or tortoise burrow contribute to the sum total of gigajoules of energy expended by animals in shaping the world. Here are some of the “zoogeomorphic species” of animals mentioned: salmon, burrowing scorpions, crayfish, beaver, worms, spiders, reptiles, frogs, fish, crustaceans, nesting birds, bivalves, gastropods, shrimp, kangaroos, boar, aardvarks… In short, almost every living thing is at work shaping the globe: “It has been suggested that all ecosystems on Earth are engineered by organisms to some degree,” they say. Watching elephants transform African landscapes makes us wonder what ecosystem roles were played by the mighty sauropods in times past.
                                                                         We humans, of course, play a dominant role in altering the environment. But even in pre-industrial times, the vast herds of livestock managed by people groups around the world have contributed a thousand times the energy of undomesticated species. And consider that the UK scientists did not even attempt to calculate all the ecosystem engineering that occurs in the oceans. (Read here about the roles of salps and plankton in their diel migration activities that transfer carbon to the ocean floor, and read here about the cable bacteria that transfer protons from the seafloor.) These authors only focused on land animals and freshwater creatures. So yes, their calculation of 76,000 gigajoules is likely very low.

Life as a Requirement for Habitability

As the authors of this fascinating paper say in their conclusion, “Our analysis has revealed that the energy of zoogeomorphic species represents a significant and overlooked driver of geomorphic change at the global level.” 
                                But now let’s ask if a planet needs living things to function as a habitat for life. That’s a different question. It could extend the long list of requirements adduced by scientists such as Michael Denton who argue that a planet suitable for complex life requires the fine-tuning of multiple physical factors. What if a planet also needs an active, energy-expending biosphere to be habitable?
                                That question was put forth by four scientists from Colombia on the arXiv preprint server, led by Jorge I. Zuluaga. They submitted their paper for publication to the journal Biogeosciences in 2014, but I could not find out whether it was ever published. We should only consider it, therefore, an interesting speculation. Nevertheless, it was seriously considered by The Planetary Society, and Zuluaga et al. did offer several empirical evidences in support of constraining “The Habitable Zone of Inhabited Planets.” 
                                   In the Planetary Society article, Jaime Green thinks that Zuluaga et al. are only answering the question, “Does inhabitation affect habitability” rather than “Is inhabitation a requirement for habitability?” He can accept that life might enhance a planet’s habitability but leaves it open whether the presence of life is a requirement. Recognizing that we have no data for an answer till we “touch down on alien soil” and make observations on another planet, he states in his conclusion, 
                                                          In looking for Earth-like planets that might be home to life, we should be careful to keep our minds open to all possibilities, including that a planet might be habitable because life is there.
                                          
A Bolder Claim

The argument of Zuluaga et al. seems bolder than a mere claim that life affects habitability. In a PDF from the Universidad Nacional de Colombia, they asked, “Is it possible to neglect the effects of life when calculating the boundaries of habitability?” Interested readers may find their arguments and diagrams worth considering. If a sterile planet has all the abiotic factors in place, will it be habitable, or at least less habitable than an inhabited planet in the habitable zone? For example, “an inhabited planet maintains habitable temperatures under a wider range of insolation conditions” than a lifeless planet, even if it orbits within the continuously habitable zone where water can exist in liquid form. Would Mars sprout organisms if it were moved into our sun’s CHZ, the ice melted, and water became abundant? 
                     In a statement that might be of interest to design advocates, Zuluaga et al. point out that 
                           Orderliness in life (which is incomparably higher than that of the surrounding environment) is supported in a way unprecedented in the inanimate world: via competitive interaction.
                                            Here are three “bottom line” considerations from their presentation:
                          Biota-environment feedbacks are likely to (substantially) alter the environment of an inhabited planet.
The equilibrium state of a complex system cannot be predicted while neglecting one of its (major) components.
Living phenomena have (unique) properties able to drive the environment to (otherwise) unstable physical states.
                    
A Bridge Too Far for Materialists
                        
          To a materialist or a naturalist, such talk can bleed over into the Gaia hypothesis, which many scientists find bordering on vitalism. Hungarian scientist Eörs Szathmáry commented on this borderland in PNAS, worrying about the hypothesis that the “biosphere has a decisive role in keeping the Earth habitable — in other words, the biosphere looks after itself, somewhat similarly to organisms that also look after themselves.” This sounds mystical to a materialist. Pointing to a recent paper by Boyle et al. in PNAS, Szathmáry offered hope that natural selection can be incorporated as a mechanism that maintains biogeochemical cycles in a non-vitalistic way.
                                               Yet materialists are often surprised, if not shocked, by the early appearance of life on the Earth. Michael Marshall wrote in New Scientist,
                   When did life begin on Earth? New evidence reveals a shocking story. Fossils and genetics are starting to point to life emerging surprisingly soon after Earth formed, when the planet was hellishly hot and seemingly uninhabitable.
                                                          “The Song, Not the Singer
                                         Is it shocking because the Earth needed life to be habitable? Szathmáry and Boyle each considered the views of W. Ford Doolittle who extends natural selection to everything, even the biosphere. “It’s the song, not the singer,” Doolittle famously proposes; any replicator, biotic or not, can be acted on by natural selection. This may be a bridge too far for materialists. Szathmáry says,
                             But then, what is the status of biogeochemical cycles if we think in terms of replicators, vehicles/interactors, and the levels of selection? In other words, do biogeochemical cycles evolve by natural selection after all? This issue is hotly debated. Doolittle offers the solution that biogeochemical cycles are interactors: “This works as long as there are replicators…that cause the differential formation of the interactors that favor their differential replication, reproduction, or persistence.” (ref. 4, p. 173). According to this view, multispecies communities, ecosystems, and even Gaia can undergo evolution by natural selection for persistence. Effects of genes can percolate upward to a Gaian level, as kind of extended phenotype sensu Dawkins. Gaia can be seen as the most inclusive clade, and clade selection for persistence could contribute to the survival of the biota. Time will tellwhat such an extended concept of evolution by natural selection is worth.
           To ID advocates, though, neither Gaia nor vitalism are necessary to argue for a biosphere as a requirement for habitability. An intelligent and wise designer would have the foresight to understand all the requirements and supply them simultaneously. We can debate the hypothesis of biology as a prerequisite for habitability, while agreeing on the wisdom of a designer engineering a world that can sustain and extend habitability through the presence of a dynamic biosphere. As Zuluaga et al. argue, “Life alters the environment by taking and excreting energy and waste products giving rise to (powerful) feedbacks on the environment.” These feedbacks, in turn, work to optimize the habitability of an inhabited planet, they argue. And think about that; optimization is a key concept in intelligent design.