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Wednesday, 10 May 2023

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.




A "simple" lifeform.


Fall of the new Rome.


Tuesday, 9 May 2023

Darwinism's ministry of truth maintains control of the origins' narrative?

 The Darwin Wall Still Stands; but for How Long?


Picture a city in which the city council has a super-majority in one political party. Those in the majority control the media outlets as well. Suppose they decide to flex their muscles and forbid any statements from the other party to be heard without having the right to filter them first. In this way, they keep the minority party in a virtual sound-proof room behind one-way glass. The majority leaders can hear the minority speaking, sometimes shouting to be heard, but nobody in the city can hear them because they are censored. Once in a while, the majority mentions something that the minority has complained about, but translates it for the media, and only responds with their own counterarguments. The minority can’t do anything about it because they lack the power, the communication channels, and the votes to change anything. Would this not be a case of totalitarian dictatorship?

Darwinians are like that. They control the narrative on origins in almost all the mainstream journals, the schools, the state universities, the national parks, and the natural history Museums . The mainstream media join in and take their side. A few exceptions can be noted, but the influential, powerful forces in academia all toe the Darwinian line. Science reporters accept their pronouncements as gospel and regurgitate them to the public, masticating them first into easily digested tidbits with sugar and spice. Professors open to ID know to keep quiet unless they have tenure, and even that is not a guaranteed protection from harassment or censorship.

A Forbidden Phrase

In a paper in Nature Communications, the forbidden phrase “irreducible complexity” appeared in scare quotes. It was mentioned not for the purpose of considering it fairly, but for shooting it down immediately with a preemptive strike. It was mentioned in an essay about the Type III Secretion System (T3SS) and its alleged evolutionary relationship to the bacterial flagellum. Here’s the quote:

The bacterial type III secretion system (T3SS) is an impressive biological machine known not only for its importance in bacterial virulence (1,2) but also, due to its evolutionary relationship to the bacterial flagellum, for its role in the negation of the ‘irreducible complexity’ of flagella (3). In their recent publication (4), Kaval et al. present new data on the process of expression, production, and assembly of a T3SS (termed T3SS2) in the bacterium Vibrio parahaemolyticus….

Did authors Itzhak Fishov and Sharanya Namboodiri cite Michael Behe’s work? No; they didn’t even mention his name. Reference 3 points to another Darwinist paper that presumably negates Behe’s argument. With a quick flick of the wrist, they eliminated what could have been a lively discussion about the said “evolutionary relationship” between the T3SS and the flagellum. Like the dictatorial city council, it wouldn’t matter how loudly Dr. Behe might shout his objections to the statement from the sound-proof room behind the one-way glass, he could not be heard in this leading journal, because he is a well-known “enemy of the regime” in Darwin Party circles. This insult against a tenured professor was peer-reviewed and published by Nature. I didn’t find any popular science article about this paper, but one can assume a reporter would obediently take the dictation and regurgitate it like, “the T3SS is a molecular machine whose evolutionary relationship to the bacterial flagellum squashes the unscientific notion of ‘irreducible complexity’ promoted by some religious fanatics.”

Let’s Dig into This a Little

Does Reference 3 negate Behe’s argument for irreducible complexity? I read the paper in Molecular Microbiology by Bailey Milne-Davies, Stephan Wimmi, and Andreas Diepold from November 2020. If one screens out the arguments by assertion, the answer is clearly no. By assertion, I mean statements like this:

Bacteria do not live in isolation. They constantly interact with and often actively move through their environment. Interestingly, in many cases, a single evolutionary ancestor evolved to meet both requirements, protein export and locomotion….

The T3SS is at the core of both the bacterial flagellum, a rotary motor that is the most widely distributed means of bacterial locomotion (Miyata et al., 2020), and the injectisome, a molecular injection device used by many Gram-negative bacteria to manipulate the eukaryotic host cells. Both systems harness ion gradients across the membrane to export the subunits of their extracellular appendages. While the flagellum then rotates this appendage in order to propel the bacterium through the surrounding medium, the injectisome evolved to specialize in protein export, specifically the translocation of effector proteins into eukaryotic host cells.

Talk about begging the question. From there, the three authors list proteins common to the T3SS and flagellum (as if this demonstrates common ancestry), but they also point out many unique proteins in the flagellum. 

Although the proteins that form the cytosolic complex in the flagellum and injectisome display clear sequence homology, the function and quaternary structure of the cytosolic complex strongly differ between the two machineries. On the distal side, flagella assemble a hook and the long flagellar filament, while injectisomes form a hollow needle. Beyond this core of proteins, the flagellum has additional components that form a bushing for rotation in the periplasm (L-/P-ring), and stator proteins that serve as an anchor in the rigid peptidoglycan, against which the rotor can rotate, powered by the influx of ions

Where did those come from? They evolved. Enough said. They share components, don’t they? What more proof do you need? 

Here’s where they mention irreducible complexity without attribution.

The T3SS is one of the most complex bacterial molecular machines, incorporating one to over a hundred copies of more than 15 different proteins into a multi-MDa transmembrane complex (Table 1). The system, especially the flagellum, has, therefore often been quoted as an example for “irreducible complexity,” based on the argument that the evolution of such a complex system with no beneficial intermediates would be exceedingly unlikely. However, it is now clear that, far from having evolved as independent entities, many secretion systems share components between each other and with other cellular machineries (Egelman, 2010; Pallen and Gophna, 2007).

So if a Porsche and a Chevy both have door handles and steering wheels, the former clearly evolved from the latter. Is that the depth of reasoning here?

Most of the paper involves similarities between protein machines. These protagonists on the one-sided debate stage smother the reader with similarities. They knock down their straw-man interlocutor by misconstruing his argument. As usual, they mis-define IC and ID with the boilerplate definitions that these machines are so complex, their evolution is “unlikely.” The true ID definition
 is that irreducibly complex systems are “best explained by an intelligent cause, not an undirected process such as natural selection.” IC systems are composed of a number of independent parts, each necessary for the function of the system.

Even with their media advantage, the authors in Reference 3 admit, “the exact evolutionary relation between injectisomes and flagella is debated.” Species with supposed intermediate forms are proposed, but they look to me like broken T3SS or flagella, not machines evolving into each other. They wave the co-option argument and engage in possibility thinking, with 14 instances of the word “possible” to suggest what might be evolving.

Evolutionary Magic

Finally, they land on their trusty magic wand, convergent evolution: “Besides the general diversification of both systems, a case of convergent evolution of flagella and injectisomes was recently discovered.” Their final summary turns evolution into a magician, and personifies bacteria and molecular machines as if they take conscious charge of their own evolution:

Evolution allows adaptation of a functional concept to many different needs. In this review, we highlighted the amazing capability of the T3SS to vary its components, structure, and function to the specific requirements of bacteria in different ecological niches and under changing external conditions. Flagella not only ensure motility in a variety of environments, but also play an essential role in pathogenicity. By modifying their flagella, bacteria can find suitable colonization sites and enhance attachment to surfaces, which can increase infection success. In the same light, the injectisome permits the bacterium to exploit host cells for promoting infection, whether by controlling immune responses or establishing suitable sites for dissemination. Together these systems work to promote bacterial survival in constantly changing environments. Beyond these adaptations, it has become clear that the T3SS is a dynamic structure, with subunits exchanging in working complexes. Given the limited number of studies on protein exchange in the T3SS, it is possible that more cases of dynamic components will be discovered and that the benefits for the bacteria will become clearer. Research on how bacteria can adapt and evolve virulence mechanisms such as the T3SS will not only allow to better understand how bacteria and their environment interact, but also uncover potential ways to combat pathogenic bacteria by targeting their T3SS.

This is known as cheating. The whole point of Darwinian evolution was to rid biology of teleology. Irreducible complexity is ignored other than the one swipe at the straw man. Only once do they demonstrate loss of function from an essential part: “Although most flagellins are partially functionally redundant, deletions of additional flagellins negatively affects flagellar formation and function.” Nowhere do they point to random mutations able to innovate essential proteins to build a flagellum or T3SS in the first place.

Behind the one-way soundproof glass, Casey Luskin is waving his article (also here) on why these machines could not have evolved from one another, and Michael Behe is giving his debate rebuttal unheard by the audience. 

Censorship Is a Doomed Strategy

In my experience as a science writer, I have never in 22 years seen a Darwin-orthodox journal or science news site take ID arguments seriously. If mentioned at all, they are mis-defined and immediately dismissed. The science establishment, consisting of academic deans, lobbyists, and journal editors, pretty much treats the thriving ID community like it doesn’t exist. 

On the bright side, one can always tell who is on the wrong side of history. It’s the totalitarians — the ones who try to stifle debate and censor those not friendly to the regime. We can take heart that experience shows that Berlin walls are erected to fall. They have finite lifetimes. Not everyone in East Germany agreed with the regime, but they were powerless, and many were scared. If we stay the course, and continue to influence individuals, we will undoubtedly find many behind the Darwin Wall welcoming a path to freedom of thought.


Carbon :the Divine element?


Curiousity + Industry< IQ?


Future AI overlord vs. Titan.


The biggest and blackest hole yet?


Yet more on why no simple beginning


Monday, 8 May 2023

What is the biblical orthodoxy re: the only true God?


Darwinism vs. the history of life.

 A Question For Larry Moran


Recently Larry Moran, Professor in the Department of Biochemistry at the University of Toronto, asked for assistance. Professor Moran will be attending the upcoming “New trends in evolutionary biology” Scientific meeting at The Royal Society, and he has asked for help in deciding what question to pose to the speakers. For Douglas Futuyma, who will be defending the status quo against the scientific evidence, Moran already has a couple of ideas, such as:

As you explain in your textbook, describing the pathways to modern species contributes to the FACT of evolution and the FACT of descent with modification but how those genetic changes actually occur and become fixed is part of evolutionary theory. Do you distinguish between evolutionary theory and the actual history of life?

Moran, like Futuyma, defends the belief that the species arose by chance. As the all-caps help to illustrate, he is a modern-day Epicurean. And I’m sure Professor Moran would not disagree that this is a softball question—a setup for Futuyma to rail on those who think the scientific evidence is actually a problem for evolution. But Moran is mistaken here, as this is not a debate against creationists.

This line of defense—that scientific failures are relevant to the theory of evolution, but not to the fact of evolution—is standard theory protectionism, routinely used by evolutionists when they are presented with any of the many empirical problems with their Epicurean theory.

Not only is this argument a revealing own-goal (it provides a live demonstration that evolution is not exposed to the empirical evidence and is not falsifiable), but it is not relevant in The Royal Society meeting since the bad guys, in this case, are fellow evolutionists who simply are beginning to reckon with the science.

They completely agree that evolution is a fact. So Moran can set aside the silly canards about “the FACT of evolution and the FACT of descent with modification.”

On the other hand, Darwin’s God suggests a slightly different approach. If Moran wants to ask a meaningful question of Futuyma, why not query his fellow Epicurean where and how he discovered that “the Creator” would not likely have bestowed “two horns on the African rhinoceroses and only one on the Indian species.” That was, after all, one of Futuyma’s points in his book, Science on Trial.

And if there is time for a follow-up Moran might, as diplomatically as possible, ask the ardent evolutionist why anyone should take him seriously?

Nationalism, and evangelicalism's divided house..

 



Ps. John ch.18:36LSB"Jesus answered, “My kingdom is not of this world. If My kingdom were of this world, then My servants would be fighting so that I would not be delivered over to the Jews; but as it is, My kingdom is not from here.”

1Corinthians ch.2:6ESV"Yet among the mature we do impart wisdom, although it is not a wisdom of this age or of the rulers of this age, who are doomed to pass away. "

On the DEI Gordian knot.


Face to face with a monster.


A priest who honours his God.

 1Samuel ch.2:30ASV"Therefore JEHOVAH, the God of Israel, saith, I said indeed that thy house, and the house of thy father, should walk before me for ever: but now JEHOVAH saith, Be it far from me; for them that honor me I will honor, and they that despise me shall be lightly esteemed."  

The Christ being preached by Christendom seems to me to more closely resemble the Satan of the bible (see 2Corinthians11:14) than that loyal and submissive servant of JEHOVAH portrayed in Scripture. A "priest" who honors himself above his God like high priest Eli whom is rebuked by JEHOVAH in the above quote for permitting his sons to help themselves to the best part of the offering meant exclusively for the Lord JEHOVAH. The Lord JEHOVAH makes it clear in this quote that it is well beneath his dignity to receive any offering or countenance any mediation from such a "priest".

Only the true Christ(i.e the Christ of scripture) can mediate acceptably for our sins. In him JEHOVAH has provided a priest who honors his God and not himself.

1Samuel ch.2:35ESV"And I will raise up for myself a faithful priest, who shall do according to what is in my heart and in my mind. And I will build him a sure house, and he shall go in and out before my anointed forever."

 John ch.7:18ASV"He that speaketh from himself seeketh his own glory: but he that seeketh the glory of him that sent him, the same is true, and no unrighteousness is in him."

John ch.8:50ASV" But I seek not mine own glory: there is one that seeketh and judgeth."


Sunday, 7 May 2023

Fraternising with the enemy?


Design deniers schooled again?

 Sandgrouse Takes the Royal Society to Design School


A new episode of ID the Future offers a look at how scientists from MIT and Johns Hopkins University are picking up clever engineering tricks by studying the feather design of the Namaqua sandgrouse. Ordinary bird feathers are already a master class in ingenious design, but as Jochen Mueller and Lorna Gibson show in a recent Royal Society Interface paper, the males of this desert-dwelling sandgrouse from southwestern Africa “have specially adapted feathers on their bellies that hold water, even during flight, allowing the birds to transport water back to the chicks at the nest.” Episode guest Brian Miller talks with host Casey Luskin about the details of the ingenious design and tells how these feathers are inspiring human inventions, one of which could help desert communities collect water from the air more efficiently. Dr. Miller takes listeners through a summary of other inventions inspired by designs in biology. He discusses how this invention strategy is proving so fruitful that it’s now treated as an interdisciplinary subdiscipline, known as biomimetics.

Download the podcast or listen to it here. For more from Miller about this exciting field and how it repeatedly highlights evidence of intelligent design in biology, see his chapter in the new book Science and Faith in Dialogue, available as a free digital Download.

Breaking News : Evolution is still a fact.

 The BBC on Evolution: It Just Gets Worse


The previous post reviewed Chris Baraniuk’s Article for the BBC about why evolution is such a great theory (“one of the greatest theories in all of science”), a fact, and so forth. The post showed how terrible the evidence is for evolution. In a sense, evolutionists themselves provide the most powerful critique of their theory. Just listen to their own explanations of why it is a fact. But there is more to the story. It gets worse because, well, that previous post didn’t cover Baraniuk’s complete article. That previous post only looked at part of Baraniuk’s article. It only looked at those parts of Baraniuk’s article that at least made some sense.

After discussing Richard Lenski’s long term experiment (LTEE), Baraniuk steps back to discuss the role of genes in evolution. Here is what he has to say

Over the last century scientists have catalogued the genes from different species. It turns out that all living things store information in their DNA in the same way: they all use the same "genetic code".

What's more, organisms also share many genes. Thousands of genes found in human DNA may also be found in the DNA of other creatures, including plants and even bacteria.

These two facts imply that all modern life has descended from a single common ancestor, the "last universal ancestor", which lived billions of years ago.

So, to paraphrase, we have two premises and a conclusion. The premises are:

P1: All living things store information in their DNA in the same way.
P2: Organisms also share many genes.

And the conclusion is:

C1: All modern life has descended from a single common ancestor.

It would be wrong to say this is a false claim. When we say that someone has made a false claim, the implication is that, while wrong, there was at least some logical reasoning present, some logical thread to follow. A false claim is a claim that starts with some evidence and in the process of getting to the conclusion, fouls up in some sort of an observable way. There was a stumble in an otherwise, at least somewhat, logical train of thought. We can at least see what the fellow was getting at. We can sympathize a bit, and reconstruct his attempt, and fix if for him, at least as best as we can. It may still be a hopeless argument, but at least we can see where he was going.

For the evolutionist there is no train of thought—no logical reasoning present. It is closer to, ironically, what Darwin described as “the convictions of a monkey's mind.”

It is complete gibberish.

To say that the conclusion C1 above does not follow from the premises P1 and P2 would be like saying your pet dog failed to beat you at chess when all he did was barf all over the board. Your dog not only failed to beat you, he didn’t even play the game.

It is not that evolutionists make a few mistakes here and there in an otherwise well thought out attempt. It is that they completely fail to provide anything remotely resembling a scientific argument for their Epicurean conviction that the entire biological world (and everything else for that matter), arose by itself.

Saturday, 6 May 2023

On the cosmogony of the physical and moral universes

 Watch: Brian Keating and Jordan Peterson on All Things Cosmological


Our friend Professor Brian Keating recently joined Jordan Peterson for an intriguing dialogue about all things cosmological and Keating’s book Losing the Nobel Prize: A Story of Cosmology, Ambition, and the Perils of Science’s Highest Honor. Keating is a brilliant astrophysicist, an observant Jew, and a fascinating figure in the dialogue about science and religion. He and Peterson discuss how to fight your personal dragons and find the great adventure of your life, how to distinguish evidence for the multiverse from mere dust, and what we learned in 2015 when scientists found gravitational radiation from the fusion of two massive black holes a billion years ago.  

A couple of years ago on his podcast Into the Impossible, Dr. Keating interviewed our own Dr. Stephen Meyer about his  book Return of the God Hypothesis. Check out both interviews!    

“The Jordan Peterson Podcasts: Black Holes, Time Travel, and the Origin of the Universe with Dr. Brian Keating“
“Into the Impossible with Dr. Brian Keating: Stephen Meyer and the Return of the GOD Hypothesis"

The "hammer of God" saves Christendom.


Darwinism's version of the design inference?

 Meet Intelligent Design’s Naturalistic Cousin: Assembly Theory


From “A New Idea for How to Assemble Life,” by science writer Philip Ball at Quanta Magazine

Assembly theory started when [Lee] Cronin asked why, given the astronomical number of ways to combine different atoms, nature makes some molecules and not others. It’s one thing to say that an object is possible according to the laws of physics; it’s another to say there’s an actual pathway for making it from its component parts. “Assembly theory was developed to capture my intuition that complex molecules can’t just emerge into existence because the combinatorial space is too vast,” Cronin said.

See if you can spot the notion highly similar to Bill Dembski’s “specification” in this section:

for a complex object to be scientifically interesting, there has to be a lot of it. Very complex things can arise from random assembly processes — for example, you can make protein-like molecules by linking any old amino acids into chains. In general, though, these random molecules won’t do anything of interest, such as behaving like an enzyme. And the chances of getting two identical molecules in this way are vanishingly small. Functional enzymes, however, are made reliably again and again in biology, because they are assembled not at random but from genetic instructions that are inherited across generations. So while finding a single, highly complex molecule doesn’t tell you anything about how it was made, finding many identical complex molecules is improbable unless some orchestrated process — perhaps life — is at work.

We should be crystal clear — calling Assembly Theory the “naturalistic cousin” of ID is OUR take on the work of Cronin’s group. Dr. Cronin himself (pictured above), and his collaborators, would disavow any connection to intelligent design reasoning, and they should not be held responsible for our interpretation. 

But, when one notices conceptual similarities and parallels, it would be remiss for us not to highlight them. Assembly Theory is fascinating and potentially fruitful, and so, we’re over here cheering on the effort. 

The fossil record's uprising against gradualism continues apace.

 Fossil Friday: The Stubborn Mystery of the Tully Monster


Tullimonstrum gregarium is an enigmatic but abundant fossil organism from the famous locality of Mazon Creek, which is dated to a Carboniferous age of about 307 million years. The Tully monster, named after its discoverer the amateur fossil collector Francis Tully, has been designated as the official state fossil of Illinois, but it has puzzled scientists for more than 50 years since its first description by Richardson (1966). 

Tullimonstrum is a relatively large (about 13 inch), soft-bodied bilaterian animal with an apparently segmented body, unpaired fins, a pair of long stalked eyes, and a long proboscis terminating in a toothed pincer-mouth. Based on the same evidence of thousands of fossils, different scientists have identified Tullimonstrum in dozens of studies either as a relict from the strange Cambrian phyla, anomalocarid-like or rather Opabinia-like arthropod, annelid worm, mollusk, tunicate, or conodont, but until recently never as a vertebrate. A few years ago, two high-profile studies, published in the prestigious journal Nature and involving 22 scientists, surprisingly claimed to finally have solved the mystery. They identified Tullimonstrum not only as a vertebrate (Clements et al. 2016) but more precisely as a relative of modern lampreys (McCoy et al. 2016).

A Very Comprehensive Analysis

These experts based their results on a very comprehensive analysis of more than 1,200 museum specimens. But just a year later a team of seven eminent paleontologists published a new study (Sallan et al. 2017), based on the very same fossil evidence, which strongly disputed this identification as vertebrate and lamprey, as well as the detailed interpretations of the different body structures as trilobed brain, gill pouches, chorda, myomeres, and fin rays. These authors boldly stated that “the ‘Tully Monster’ is not a vertebrate,” and suggested that alternative identifications as mollusk, anomalocarid, or non-vertebrate deuterostome (e.g., tunicate larva) are more congruent with the data. While Clements et al. (2016) found the melanosome structure of the eyes of Tullimonstrum to prove a vertebrate affinity, a synchrotron spectroscopic analysis of the eye pigments by Rogers et al. (2019) found them more similar to those of cephalopod mollusks.

Now, a new paper by a team of five Japanese scientists has published a micro-CT analysis of 153 fossils of the Tully monster (Mikami et al. 2023). These authors also came to the conclusion that it is definitely not related to vertebrates, but represents an invertebrate of unknown affinity.

How Much Confidence?

This is yet another case where groups of renowned scientists, who all look at the very same evidence of numerous well-preserved fossils, can neither agree upon the identification of the preserved body structures nor even the phylum to which the animal should be attributed. How much confidence should we really place in such dubious fossil evidence when it is boldly claimed to prove Darwinian evolution as a fact or to represent long-sought “missing links”?

Notes

Clements T, Dolocan A, Martin P, Purnell MA, Vinther J & Gabbott SE 2016. The eyes of Tullimonstrum reveal a vertebrate affinity. Nature 532(7600), 500–503. DOI: https://doi.org/10.1038/nature17647
McCoy VE, Saupe EE, Lamsdell JC, Tarhan LG, McMahon S, Lidgard S, Mayer P, Whalen CD, Soriano C, Finney L, Vogt S, Clark EG, Anderson RP, Peterman H, Locatelli ER & Briggs DEG 2016. The ‘Tully monster’ is a vertebrate. Nature 532(7600), 496–499. DOI: https://doi.org/10.1038/nature16992
Mikami T, Ikeda T, Muramiya Y, Hirasawa T & Iwasaki W 2023. Three-dimensional anatomy of the Tully monster casts doubt on its presumed vertebrate affinities. Palaeontology 66(2):e12646. DOI: https://doi.org/10.1111/pala.12646
Richardson ES Jr 1966. Wormlike Fossil from the Pennsylvanian of Illinois. Science 151(3706), 75–76. DOI: https://doi.org/10.1126/science.151.3706.75-a
Rogers CS, Astrop TI, Webb SM, Ito S, Wakamatsu K & McNamara ME 2019. Synchrotron X-ray absorption spectroscopy of melanosomes in vertebrates and cephalopods: implications for the affinity of Tullimonstrum. Proceedings of the Royal Society B 286(1913):20191649, 1–8. DOI: https://doi.org/10.1098/rspb.2019.1649
Sallan L, Giles S, Sansom RS, Clarke JT, Johanson Z, Sansom IJ & Janvier P 2017. The ‘Tully Monster’ is not a vertebrate: characters, convergence and taphonomy in Palaeozoic problematic animals. Palaeontology 60(2), 149–157. DOI: https://doi.org/10.1111/pala

OOL Science looks to the heavens for a boost?

 Uracil Discovered on Asteroid Ryugu — What Does It Mean for the Origin of Life?

Carl Linnaeus 

Recently, chemical composition data were obtained from samples retrieved by the Japanese spacecraft Hayabusa2 that was landed in two locations on the asteroid (162173) Ryugu. In December 2020 Hayabusa2 successfully returned to Earth with its precious pristine samples, uncontaminated by residues from Earth (except maybe some metallic material originating from the collection device). Published in Science, early analysis of organic compounds extracted from the collected samples included significantly racemic mixtures of several amino acids, indicating that these samples were relatively free of Earthly contamination from biopolymers.1 (All proteins in life are made of racemically pure L-amino acids.) Prior analysis of meteorites could not boast of such purity uncontaminated by Earth’s biological products. 

Therefore, these Ryugu samples appear to be our first chance to examine which organic compounds may be produced in a prebiotic setting in our solar system. In addition, we don’t have to rely on uncertain estimates of the conditions on Earth when the solar system was forming. Asteroids containing significant amounts of carbon, never visited by extraterrestrials like us, may provide a reasonable idea of what abiotic chemistry can produce.

It Came from Outer Space?

A recent article in Nature Communications reported that uracil, one of the nucleobases found in RNA, was identified in these pristine Ryugu samples.2 For those who place their bets on the RNA world hypothesis, this is a significant finding, at least in their opinion. They finally have evidence that at least one of the nucleobases of RNA has been discovered outside of Earth, thus, they say, upholding the notion that our biochemistry could have been seeded from outer space! As Live Science summarizes, “After becoming trapped on asteroids like Ryugu, these molecules may have eventually hitched a ride to Earth via meteorite impacts, where they sparked the first stirrings of life in primordial oceans.”

This may be our earliest chance to remark on valid data of prebiotic chemicals free of Earthly contamination. So it would be logical to consider first the initial chemical analysis described in Science to broadly classify all organic compounds, identified using two sensitive analytical methods. Concerning the building blocks of life, they found several amino acids, but all in racemic mixtures. This is precisely what chemists predict. It is extremely difficult to produce optically pure compounds from smaller compounds. The chemistry of mirror-imaged compounds is exactly the same, differing only in the spatial orientation of covalently bonded atoms (analogous to your right and left hands being equivalent). Life only uses one of these chemical forms to make proteins, RNA, DNA, complex carbohydrates and many lipids. 

Only the Simplest Amino Acids

On Ryugu just some of the simplest amino acids were detected, including glycine, D/L-alanine, D/L-serine, and D/L-valine, along with other amino acids not used to build proteins (Fig. 1). These results agree well with the earlier experiments by Stanley Miller and others where simple organic structures were readily produced in prebiotic simulations. However, over eight amino acids with more complex critical functional groups have still not resulted among the various permutations of prebiotic reactions tested. It’s not just dealing with racemic mixtures that confounds the supporters of abiogenesis, but how to form those more elaborate amino acids whose side chains play critical roles in the activity and structure of all proteins.


Fig. 1. Chemical structures of the four amino acids identified from Ryugu that match those found in proteins plus examples of three amino acids (among 11) that are not found in proteins.

The chemical analysis also reported thousands of organic compounds, classified in multiple groups, that may or may not be found in the context of living organisms. If a primordial soup were to originate from this mixture, any biomolecules would have to contend with a myriad of possible side reactions with a variety of reactive compounds competing for the rights to produce a biopolymer. Would the situation be different if the asteroid material were to simply seed the Earth with these needed building blocks? The competing contaminants still far outnumber the biologically relevant molecules. 

The RNA Route

Let’s consider whether the prospects are better if we take the RNA route. Uracil was clearly identified from Ryugu. The engineering threshold to form nucleotides, the building blocks for RNA, is much higher than that for proteins. The core unit to which nucleobases and phosphate are bound is the 5-carbon sugar D-ribose. Several mechanisms have been proposed to explain how carbohydrates may have originated in an abiotic environment.3 The challenges to integrate D-ribose into nucleotides abiotically can be summarized as three major chemical barriers. 1) Abiotic production of five-carbon sugars will yield four chemically equivalent stereoisomers in both the D and L forms, thus resulting in eight stereoisomers at approximately equal levels (Fig. 2A). How does D-ribose get selected through random chemistry without even considering that longer chain sugars will also be present? 2) Ribose can interconvert from an open-chain form to a six-membered ring structure (pyranose form) or to a five-membered ring (furanose), both of which present as alpha and beta configurations at carbon 1 (Fig. 2B). At equilibrium the pyranose form comprises 80 percent while the furanose form is 20 percent of the ribose. RNA uses the furanose form, so how does this minor component win out in any abiotic reactions? 3) Nitrogen at position 1 of uracil needs to be bonded with carbon 1 of D-ribose in a beta configuration through a thermodynamically unfavored reaction. How can this reaction occur abiotically?



Fig. 2 Chemistry of 5-carbon sugars. A. Structures of the four D-pentoses are shown with stereochemical projections (bold bars are bonds extending towards the viewer while hatched bars extend away). Note the differences in spatial orientations of all hydroxyl (OH) groups. L-sugars are simply the mirror images of these structures accounting for a total of eight stereoisomers. B. Interconversion of D-ribose between pyranose and furanose ring structures. Arrangements of alpha and beta configurations are indicated by hatched lines at carbon 1. RNA uses only the furanose form with the nucleobase bonded in the beta configuration. C. Enzymatic coupling of uracil to ribose 5-phosphate. The enzyme positions both substrates appropriately to catalyze this stereospecific displacement forming a new chemical linkage.

Ignoring Conundrums

While the first two conundrums are most often sidestepped by those upholding the RNA-world philosophy, the latter reaction is not an impossible task so we will consider how life manages this feat. Most cells can salvage RNA or DNA building blocks normally obtained nutritionally following digestion. The liberated nucleobases can be coupled using D-ribose charged with a pyrophosphate group at carbon 1 in the alpha configuration. Notice the specificity life uses where neither the beta configuration nor the pyranose ring form will work for this reaction. This substrate permits a specifically oriented approach by the appropriate nitrogen of the nucleobase, directed completely by the respective enzyme, to effect displacement of pyrophosphate. This results in the nucleobase bonding to carbon 1 in the beta configuration (Fig. 2C). The release of pyrophosphate fulfills the thermodynamic requirements of this elaborate reaction. 

Attempts have been made to carry out this reaction under purportedly abiotic conditions. These efforts led to some ingenious planning to devise new chemical synthetic schemes involving electrospray of microdroplets containing D-ribose, phosphate, and nucleobases.4 Researchers provide evidence proposing how the microdroplets might make this reaction more thermodynamically favored. It’s feasible for all four nucleotides to be made via this route. 

Other Serious Concerns

But this report did not address the other serious concerns already discussed. They used pure D-ribose, not a mixture of sugars as would be expected prebiotically, and minimally not D/L-ribose. The alpha/beta configuration of the products, or their ring structures, were not indicated (most likely resulting in mixtures of all possible products). It thus becomes difficult to evaluate the relevance of this reaction to producing biologically viable RNA building blocks. Finally, the yields of desired products by this mechanism were low, at 2.5 percent or less. While the attempt to produce RNA building blocks via an abiotic mechanism is to be applauded, this still falls far short of what life needs to get started from the complex mixture of organic compounds present in a prebiotic world. 

Readers are encouraged to investigate further to more fully understand the difficult issues involved in forming life using undirected organic chemistry alone. Chemist Dr. James Tour at Rice University, for one, has addressed abiogenesis including in discussions on his YouTube Channel . See also his chapter in the freely downloadable book Science and Faith in Dialogue.

Thursday, 4 May 2023

Darwinism : Pros and Cons

 New DiscoveryU Course: Jonathan Wells Takes an Objective Look at the Evidence for Evolution


The word “science,” as molecular and cell biologist Jonathan Wells notes, comes from the Latin scientia, or knowledge. There’s nothing about the idea that remotely suggests that knowledge about life, the universe, or their origins must be strictly materialist in nature. The notion that such knowledge must reject mind as a casual factor is a materialist presumption — not science.

In a new course from Discovery U , Dr. Wells asks what happens when we discard the ideology and ask candidly about biological origins without recourse to presumptions. This is what’s called empirical science, and it is open to natural explanations of phenomena, or explanations that include intelligent design. It all depends on the evidence! “Darwin,” says Jonathan Wells, “redefined science to exclude design,” but we needn’t accept that redefinition.

In 40 lectures, including quizzes, Dr. Wells leads students through the evidence that supports, or fails to support, chemical evolution at the origin of life, natural selection as a creative force in nature, Darwin’s tree of life, and more. At the DiscoveryU page, you can watch free previews of Lecture 1 and Lecture 2. It’s a fine resource for homeschool students, and public school and university students looking for a supplement to their biology coursework, and for anyone else curious to know what an objective consideration reveals about life, how it arose and attained the complexity we see today.

There couldn’t be a more qualified instructor to cover this material. Dr. Wells holds two PhDs, from UC Berkeley in molecular and cell biology, and from Yale in religious studies. He is a Senior Fellow with Discovery Institute’s Center for Science and Culture and the author of Icons of Evolutions, The Design of Life, The Myth of Junk DNA, and other books.

Wednesday, 3 May 2023

Yet more scientific confirmation of the thumb print of JEHOVAH.


Nothing simple about this beginning.

 The Marvel of a Seed


Imagine offering a large cash prize to any research group that can achieve the goal of making a flower grow out of a bucket of dirt. If you wonder what’s the challenge in that — “We grow flowers out of dirt all the time!” — you’d better read the fine print. For this challenge allows you to start with nothing more than the bucket of dirt, along with all the water and air you want.

Sometimes, we can take for granted the most commonplace things, when in reality these may be exhibitions of the highest wonder. After a hard winter in the Midwest, the ground is frozen, the trees are bare, the grass is brown, and not a flower can be found. But then something wonderful unfolds as the season cycles towards spring — warmth from the sun thaws the ground and the landscape begins to transform from the shadow of death to life. In the woods near our house, springtime brings forth thousands of bluebells, carpeting the ground that has appeared dead for months. Soon, daffodils blossom around the house, followed by tulips and phlox, and the yard quickly fills with yellow dandelions, alas. (Dandelions are mostly considered a nuisance weed where I live.)

A Challenge for the Researchers

So, what’s so hard about producing a flower from a bucket of well-watered dirt? Naturally, it seems to happen prolifically, but of course it all starts with a seed. So, the challenge for the researchers is to produce a seed that grows into a flower, using the available ingredients of dirt, water, and air. Game on!

From a cursory examination, a seed may seem like a fairly simple little thing, but more analysis reveals layers of functional complexity. The following highlights this:
                    Seed development is a complex process that requires coordinated integration of many genetic, metabolic, and physiological pathways and environmental cues. Different cell cycle types, such as asymmetric cell division, acytokinetic mitosis, mitotic cell division, and endoreduplication, frequently occur in sequential yet overlapping manner during the development of the embryo and the endosperm, seed structures that are both products of double fertilization.

RICARDO A. DANTE, BRIAN A. LARKINS AND PAOLO A. SABELLI, “CELL CYCLE CONTROL AND SEED DEVELOPMENT,” FRONTIERS IN PLANT SCIENCE, VOLUME 5 (2014) 
               To claim that researchers in synthetic biochemistry have no idea how to form even a single cell out of prebiotic materials, let alone the complex interactions of many cells within a seed, is no exaggeration. If a well-equipped research facility, staffed by the world’s best scientists, couldn’t produce a seed or even a single living cell from raw materials, what basis is there for assuming unguided natural processes could do it?
 
As Time Goes By

Time is not the golden ticket for nature to succeed at producing a complex, functional arrangement of atoms resulting in a living cell. Our observations of natural processes demonstrate that over time, natural processes degrade all complex, functional systems. New cars gradually turn into rusty wrecks; a newspaper left outside turns to pulp with no legible information; an unfortunate opossum killed on a country road isn’t regenerated by sunlight and rain but suffers decomposition. The more time passes, the more such systems dissolve, until they blend with the surrounding environment to become unrecognizable. Nature relentlessly degrades information-rich systems, inexorably moving them towards an equilibrium characterized by homogeneous mixtures, nearly devoid of information.

If nature has shown itself time and time again to be an agent of decay, what has science discovered concerning the development of cells? Just this, that every cell comes from a preexisting cell. The supposition of materialism, that at some point in the early history of Earth a cell arose from “dirt,” is utterly without observational support. To suppose that the unguided effects of some combination of gravity and the electromagnetic force brought together millions of atoms of dirt, water, and air into the phenomenally complex, interdependent, functional structures and mechanisms of a living cell, is not supported by science. Such a belief ignores and defies centuries of scientific observations and study. It is a fantasy requiring an a priori commitment to an idea, akin to believing the Earth is flat. 

Far Beyond Human Limits

The marvel of the seed extends beyond its ability to grow into a flower or other type of plant. The design of the seed includes producing myriads of other seeds via successive generations of growth. 

Given our observations of nature, and realizing that the intelligence required to produce a seed from the raw materials of Earth far exceeds human limitations, what shall we conclude produced such marvels as the welcome sight of springtime flowers? Ascribing their origin to intelligent design is a rational conclusion consistent with the facts. 

The science of identifying the thumb print of JEHOVAH?

 God’s Grandeur: Ann Gauger on the Scientific Case for Intelligent Design


On a new episode of ID the Future, host Jay Richards begins a two-part conversation with biologist Ann Gauger about her newly edited volume, God’s Grandeur: The Catholic Case for Intelligent Design. Part 1 of their discussion focuses on the scientific case presented in the book. Dr. Gauger gives an engaging overview of some of the most compelling biological evidence for design, including the genetic code that governs storage and transmission of information and the origin and purpose of molecular machines. Gauger also clarifies what science shows about human uniqueness, revealing how different we are from animals and arguing that it is indeed possible that the entire human race came from two original parents. Learn more about the book and get a free chapter at GodsGrandeur.org. Download the podcast or listen to it here

Tuesday, 2 May 2023

Why chance and necessity can't be trusted with the puzzles of the origin of life.

People Can Do Puzzles — And Why That matters


Occasionally, during the winter months, my family enjoys doing a jigsaw puzzle. We recently completed two 1,000-piece puzzles. If you’ve ever worked on one of these puzzles, when you first dump the pieces in a jumble onto the table, it can seem like a daunting task. With persistence, however, the thing begins to come together. 

Our ability to complete a puzzle hinges upon clues that are unavailable to nature, were natural processes given the task of assembling the puzzle. Assembling proteins, DNA, and other molecular components of a living cell are the puzzles of nature. Why do I say this?

Clue #1: We are given a clear picture of how the completed puzzle should look. The picture on the puzzle box gives the overarching meaning or purpose for the many interlocking pieces. Nature has no teleological picture of how things should turn out. Whatever nature attempts to assemble is done blindfolded, without foresight. What difference would this make? Just imagine trying to put together a jigsaw puzzle without having a clue about how the completed picture should look. I suppose some intrepid puzzle enthusiasts might attempt this, but without the end goal in view, progress would at best be painstaking, tentative, and slow.

Clue #2: We can constantly visually examine each piece to observe its relationship to other pieces. These visual clues include information about the shape and orientation of the puzzle piece cutouts that allow it to uniquely connect with its neighboring pieces. We also have available to us the visual clues of the image fragments on each piece, helping us to quickly discern if a given piece matches others.

Very Picky About Relationships

What does nature have available to it, when attempting to assemble a system such as a complex biomolecule? The nature of chemical bonding will allow some “pieces” to be selected, while excluding others. But nature has no clues concerning which atom or molecule, among those that could bond, is the appropriate one to bring the project closer to a particular end result. End results, such as functional proteins, are known to be very picky when it comes to getting the right relationships among the component pieces.

To better understand the handicap nature plays with, imagine trying to complete a puzzle blindfolded! Undaunted, someone might maintain that it could still be done, however tediously, by trying one piece after another, until your sense of touch informed you that you had found the piece that uniquely fit with its neighbor. Some puzzles are designed this way, where only one piece has the appropriate cutouts to fit in a particular location. However, what if multiple different pieces had the same shape, but only one piece had the correct image to match the pattern building up to form the predetermined completed picture? Your sense of touch would be insufficient. The tactile clues for which piece to insert next couldn’t supply you with the necessary information. Getting the right pieces assembled in the right arrangement to produce the right final picture would be reduced to luck

What’s the Chance of That?

Let’s start with a simple puzzle with a child’s level of difficulty, having only 60 pieces. Trying to assemble it blindfolded, not knowing what the final image is, and wearing mittens so that you can’t feel the cutout shapes makes this “simple” task impossible. Let’s see why. 

The first piece is “free.” Then you have 59 choices for the second piece. If, by luck you got it right, you would then have 58 choices for the third piece, and so on. So, the probability of getting all the pieces assembled correctly is 1:59! That is, 59 factorial, which works out to about 1 chance in 1080. This is equivalent to finding one unique proton out of all the protons in the entire universe! These impossibly small odds are for something that is merely “child’s play” for a normally intelligent human.

Humans Can Do Puzzles

The point here is not really to ponder how improbable it would be for natural processes to correctly assemble a jigsaw puzzle (and admittedly, the real odds would be much smaller than calculated in the paragraph above, since each piece has two sides and each piece has a continuous degree of orientations it could be rotated through in order to properly fit it into place). The point is that humans can do puzzles. This has consequences for our picture of reality. Under a materialistic view, holding that nothing exists except the matter and energy and spacetime of our universe, the inescapable, but absurd, conclusion is that natural processes can correctly assemble jigsaw puzzles.

Under the materialistic view, natural processes gave rise to humans (as a sort of intermediate step to the completed puzzle), and humans then put together puzzles (as well as cars and computers and cities). So, from beginning to end, the materialist must believe that the primordial hydrogen plasma of the universe, governed by nothing other than the laws of physics, will in just a few billion years turn into humans who do jigsaw puzzles!

The power of intelligence is remarkable. What could never happen by the unguided operation of the forces of nature acting on matter, is done as a relaxing pastime by intelligent humans. If this unnatural accomplishment seems a puzzle to the materialist, then perhaps a different perspective is in order. Since our intelligence instantiates outcomes (cars, computers, cities, and puzzles) that cannot arise by unguided nature, then our humanness cannot be naturally derived either. A view of reality that embraces an intelligent mind behind the universe corresponds most reasonably to the big picture that emerges when we properly fit together all the puzzling pieces of our existence.

File under "well said." XCVI

 "Whenever you find yourself on the side of the majority, it is time to reform (or pause and reflect)."

Mark Twain.

On using stats for illumination rather than support?

 Ross Pomeroy Reminds us of P-Value Problems


Ross Pomeroy’s Article in yesterday’s Real Clear Science was a much needed reminder about the dangers of statistical hypothesis testing. But while Pomeroy rightly points out important problems, particularly with the so-called P-value, out here on the ground, the problem is much worse.

One of Pomeroy’s several legitimate concerns is the use of what is essentially a default value of 0.05 for P. Too often scientists don’t realize that, as David Colquhoun has pointed out, this will lead to false conclusions at least 30 percent of the time. Pomeroy also points out the common fallacy of interpreting the P value as the probability that the null hypothesis is true.

The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.” 
                     The result of such mishandling of hypothesis testing is that, “Quite simply, a large amount of published research is false.”

Would that it would end there. Unfortunately, when it comes to evolutionary studies, fixing these problems is like rearranging the deck chairs on the Titanic. These concerns about selecting a good alpha value and understanding the nuances of what P actually means, while important, pale in comparison to a much larger infraction: using the P-value to mask what is, in fact, a strawman argument.

One of the key, underlying, assumptions in using the P-value is that there are only two alternatives, the null and alternative hypotheses. These two hypotheses must be complementary—they must be distinct, mutually exclusive, and exhaustive. In other words, one of them must be true, and the other must be false. They cannot both be true, or both be false. They cannot overlap, and there can be no other possibilities.

And while such a perfect pair of hypotheses is possible in simple academic problems such as colored marbles in an urn, real world problems often are more complicated. Take something as seemingly simple as the question of whether or not it will rain today. Is it not binary? Either it will rain, or it will not rain. Right?

Well no. The weather has a multitude of complexities. It is spatially and temporally varying, with an infinite degree of variation. What if it sprinkles? What if the rain evaporates before it reaches the ground? How do you define the time and location? What if it rains in one location but not another?

What the P-value, and its null hypothesis, allows is for trivial null hypotheses to be erected and easily knocked down like strawmen, thus “proving” ones favored explanation. 

Curtains for the selfish gene?

 New Book Puts Richard Dawkins’s “Selfish Genes” in the ICU


Biologist Richard Dawkins came to prominence in 1976 with his Book The Selfish Gene. Nearly half a century later, we’re entitled to wonder how the work has held up. In his recent book, Selfish Genes in ICU?, Dr. Michael Jarvis considers that question, asking whether recent findings in biology match the predictions of Dawkins’s selfish gene concept.

Jarvis, who holds a PhD in biology from the University of Cape Town (where he focused on zoology), takes his reader on a historical journey. He first describes the origin of the universe and the history of Earth, and moves on to Darwin’s theory of evolution. Here, he outlines four key points in The Origin of Species, while paying special attention to one challenge Darwin faced: the Cambrian explosion. From there, Jarvis describes Dawkins’s selfish gene concept — the idea that a gene can be seen as a “selfish unit” that exploits an organism to carry out its own process of replication. Stated another way, the selfish gene concept holds that natural selection takes place at the gene level.

In subsequent chapters Jarvis dives into some discoveries that (spoiler alert!) don’t really match with the selfish gene idea. Jarvis does a nice job of laying out the evidence so that the reader can decide what to think.
                          

Teaser on the Human Eye

One of my favorite parts of the book is the sections on biological function and complexity. I won’t give it all away, but here’s a teaser from the section on the human eye:
                      In the past some scientists suggested that the human eye retina was actually a poor design. Richard Dawkins proposed this argument. In his 1986 book The Blind Watchmaker he concluded that the vertebrate eye is functionally sub-optimal because the retina photoreceptors are oriented away from incoming light.
                        Jarvis addresses head-on this frequently repeated claim of poor design. He goes on to cite recent discoveries and explains how this new research affects our understanding of the purported “sub-optimal” design. He notes that our retinas contain special Müller cells which funnel light through the optic nerve onto the retina, compensating for any loss of vision related to the “backwards wiring” of the vertebrate retina:
                      Research by Amichai Labin and Erez Riba from Israel’s internationally recognized Technion – Israel Institute of Technology in Haifa has shown that the surface of the retina also has so-called Müller cells. These cells not only compensate for the light sensitive receptors being “back to front.” Their function actually results in vision being better than it would have been if the light sensitive cells had been the so-called “right-way round.”
                               To learn more about the complexity of the eye you can read my article here or Casey Luskin’s article here.
                        
An Update on Two Decades

In the final chapters of the book, Dr. Jarvis updates his reader on what the last twenty years have revealed about evolution. His focus here is on the study of epigenetics, orphan genes, Hox genes, mitochondrial DNA, and directed mutagenesis, all shedding light on how genes evolve and whether or not they are units of selection. Throughout, he argues that these recently discovered genetic features don’t fit the selfish gene concept. 

Here’s one example from the field of epigenetics. Epigenetics is the study of mechanisms that change gene expression but that are not heritable. Epigenetic mechanisms allow for both behavior and the environment to affect how a gene works. Here’s the problem epigenetics poses for selfish genes: if a gene is the unit of selection, what benefit does a non-heritable change that is only evidenced in the organism have for the unit of selection? Why would such a mechanism ever be selected in the first place? Hence, epigenetics only makes sense in a system-wide context.

Let’s look at one more of Jarvis’s examples: master regulatory genes, aka Hox genes. These genes have the purpose of being master regulators within a system context. Their activation and function depend upon upstream and downstream genes respectively. A master regulatory gene is helpless without its system context. How then could such a gene be a unit of selection? Do master regulatory genes really desire to reproduce more than they do to serve the organism? Is there evidence for that? Definitely not.

Into the Melting Pot

In gentle fashion, Jarvis lays out numerous pieces of evidence that jeopardize Dawkins’s view that genes are selfish and act as the units of selection. That makes this book the perfect gift for an inquisitive friend who might not be familiar with some of the recent challenges to Dawkins’s ideas. 

Jarvis concludes that “selfish genes are in the ICU” and he encourages the reader to place recent discoveries into what he calls a melting pot — a place where many different people and ideas exist and often produce something new. He concludes with a question to the reader: “Are you and I ready for a new theory of evolution that may be as difficult to accept as were the revelations of Albert Einstein?”