At Evolution News: For Darwinism, Pregnancy Is the “Mother of all Chicken-and-Egg Problems”

_{Eric Hedin

November 30, 2022

Intelligent Design}

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Here’s a really devilish problem to pose to your favorite friend, teacher, or relative who’s a Darwinist true believer. As Your Designed Body co-author Steve Laufmann observes, the relationship between an embryo and its mother is a relationship between unequals. The embryo’s systems are not yet complete so it depends on its mother for its life. This entails communication between the entities.
But as Laufmann asks, how could such a thing as pregnancy evolve gradually, without guidance or foresight, “when you have to have it in order to have a next generation. Nobody has ever addressed a problem like that.” No, they haven’t, at least not persuasively, which is why Laufmann calls it the “mother of all chicken-and-egg problems.” Darwinian evolution has many of those, as it takes an engineer like Steve Laufmann, or a physician like his co-author Howard Glicksman, to fully recognize. Evolutionary biologists tend to silently glide over such issues, which clearly point to intelligent design. Either that, or they are satisfied by vague speculations. Watch:

Evolution News

I’ve just ordered a copy of Your Designed Body and I look forward to reading it. Perceiving that the human body (or an animal’s body) is a designed system helps keep the wonder of life front and center. The reductionism approach, while useful for gaining knowledge of the biological details, carries the risk of losing sight of the big picture. Gandalf alludes to this in an argument against Saruman, “And he that breaks a thing to find out what it is has left the path of wisdom.” [J. R. R. Tolkien, The Fellowship of the Ring, (Houghton Mifflin Co., Boston: 1994), p. 252).

Comments

Per Alan Fox's paper,
"Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid.",,, Modern examples of punctuated equilibria in enzyme evolution have been characterized in bacteria that are adapting to the impact of humans on their environment. The phosphotriesterase enzyme from Pseudomonas diminuta catalyses the hydrolysis of a range of synthetic insecticides and chemical warfare agents, none of which were synthesized until the 1940s [19]. Remarkably, phosphotriesterase hydrolyses the insecticide parathion with an efficiency that approaches catalytic perfection (kcat/KM = 4 × 107 s?1 M?1) [20]. The enzyme appears to have evolved from a lactonase ancestor with a very weak promiscuous phosphotriesterase activity (kcat/KM < 10 s?1 M?1), to near perfection, in approximately 50 years [21]. Similarly, Pseudomonas sp. strain ADP has evolved to use the herbicide atrazine, introduced into the environment in vast quantities beginning in 1958, as a novel carbon source [22–24]. An entire catabolic pathway has evolved to metabolize atrazine [25], co-opting three enzymes from the amidohydrolase family. The first enzyme in the pathway, atrazine chlorohydrolase [26], diverged from melamine deaminase, though it retains none of the original activity [27]. While it shares 98% sequence identity with the extant melamine dehydrogenase, it has adapted to the novel substrate and hydrolytically dechlorinates atrazine with a catalytic efficiency that is within the range of ‘average’ enzymes [28] at 1.5 × 104 s?1 M?1 [25]. These examples demonstrate that enzyme evolution can be extraordinarily rapid, as shown in figure 2b. Similarly rapid bursts of enzyme evolution can be observed in laboratory studies. A canonical example involved experimental evolution of a Salmonella enterica strain that was incapable of synthesizing the amino acid tryptophan, because the trpF gene (encoding the enzyme phosphoribosylanthranilate isomerase, PRAI) had been deleted. This strain was forced to evolve a compensatory function in an homologous enzyme from the histidine biosynthetic pathway—the N-(5?-phospho-l-ribosyl-formimino)-5-amino-1-(5?-phosphoribosyl)-4-imidazolecarboxamide (ProFAR) isomerase, encoded by hisA—in just 500 generations of laboratory evolution [29]. When suitably strong selection conditions arise, these examples indicate that enzymes can evolve to near catalytic perfection in periods of time that are remarkably short, in the context of the history of life.
AF, you do realize that none of those examples are examples of proteins of one fold of one function evolving into a brand new protein of a new fold with an entirely new function, but are examples of preexistent proteins, with specific folds, making minor tweaks to peripheral loops to deal with environmental pressures? All of which underscores Tawfik's point, "Changes were not to central structures, but to peripheral loops",,, “In fact, to our knowledge no macromutations … that gave birth to novel proteins have yet been identified.”
Dan S. Tawfik Group – The New View of Proteins – Tyler Hampton – 2016 Excerpt: Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, To the extent that Tawfik’s selection experiments were successful, it is because mutations were localized and contextualized. Mutation had a key but confined role. If evolution proceeded, the prevailing architecture of the active sites and protein shapes nonetheless remains intact. Changes were not to central structures, but to peripheral loops. A great deal of flexibility was discovered. Still, it is hard to see how any of this could build proteins—that is, in the sense of building their fundamental shapes, or scaffolds; and build proteins in terms of explaining the key catalytic strategies of each active site. Even in the impressive demonstration of a transition through nine orders of magnitude, in which a full exchange of a promiscuous activity for the primary activity was seen, the overall geometry of the protein was unchanged, and, although substrates had changed, the fundamental active site strategy stayed the same. ,,, “Modern neo-Darwinism and neutral evolutionary treatments,” remark Leonard Bogarad and Michael Deem, “fail to explain satisfactorily the generation of the diversity of life found on our planet.” It is not that they did not evolve, they say, but that “… most theoretical treatments of evolution consider only the limited point-mutation events that form the basis of these theories.” Their sober conclusion is that “point mutation alone is incapable of evolving systems with substantially new protein folds.”60,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations … that gave birth to novel proteins have yet been identified.”69 http://inference-review.com/article/the-new-view-of-proteins
And the examples cited in your paper, (as well as the discussion on ancestral enzymes in the paper), also underscore Dr. Gauger's point, "some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve! That is precisely the point we are making."
“Enzyme Families — Shared Evolutionary History or Shared Design?” – Ann Gauger – December 4, 2014 Excerpt: If enzymes can’t be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. We have now addressed two objections raised by our critics: that we didn’t test the right mutation(s), and that we didn’t use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF’s entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine. Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It’s because modern enzymes can’t be coopted to anything except trivial changes in function. In other words, they don’t evolve! That is precisely the point we are making. http://www.evolutionnews.org/2014/12/a_new_paper_fro091701.html
In short AF, you receive an F on your homework assignment. Try again, and don't tell me the dog ate your homework. P.S. Also from AF's cited paper,
“The non-falsifiable nature of ancestral reconstructions places them in the realm of just-so stories, rather than hypotheses, and doubts have been raised about the ability of ASR studies to reach justifiable conclusions ”
Thanks for pointing their honest admission out Asauber, Their honest admission that their 'just-so stories' for ancestral proteins are unscientific 'just-so stories', put a huge smile on my face. :)bornagain77_{November 30, 2022
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Warts and all, Andrew.Alan Fox_{November 30, 2022
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AF, "The non-falsifiable nature of ancestral reconstructions places them in the realm of just-so stories, rather than hypotheses, and doubts have been raised about the ability of ASR studies to reach justifiable conclusions " Andrewasauber_{November 30, 2022
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Blimey, more homework. Phil, have a look at this paper. https://royalsocietypublishing.org/doi/10.1098/rsif.2015.0036Alan Fox_{November 30, 2022
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Since Alan Fox at 16, like PMI at 5, finds it beneath his intellectual dignity to lay out the, (apparently simple for him), stepwise evolution of pregnancy, perhaps he can, at the very least, show us the very first, teeny-tiny, step of an evolutionary scenario? Perhaps he can show us the first 'teeny-tiny' step of a single protein of one type of function evolving into another protein of a different, but similar, type of function? Is that too much to ask of AF and PMI? Especially since they, obviously, consider themselves to be so much more wise than those of us who are foolish enough to believe in intelligent design?
"Enzyme Families -- Shared Evolutionary History or Shared Design?" - Ann Gauger - December 4, 2014 Excerpt: If enzymes can't be recruited to genuinely new functions by unguided means, no matter how similar they are, the evolutionary story is false.,,, Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 10^15 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. We have now addressed two objections raised by our critics: that we didn't test the right mutation(s), and that we didn't use the right starting point. We tested all possible single base changes in nine different enzymes, Those nine enzymes are the most structurally similar of BioF's entire family We also tested 70 percent of double mutations in the two closest enzymes of those nine. Finally, some have said we should have used the ancestral enzyme as our starting point, because they believe modern enzymes are somehow different from ancient ones. Why do they think that? It's because modern enzymes can't be coopted to anything except trivial changes in function. In other words, they don't evolve! That is precisely the point we are making. http://www.evolutionnews.org/2014/12/a_new_paper_fro091701.html Dan S. Tawfik Group - The New View of Proteins - Tyler Hampton - 2016 Excerpt: Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is “something like close to a miracle.”45,,, To the extent that Tawfik’s selection experiments were successful, it is because mutations were localized and contextualized. Mutation had a key but confined role. If evolution proceeded, the prevailing architecture of the active sites and protein shapes nonetheless remains intact. Changes were not to central structures, but to peripheral loops. A great deal of flexibility was discovered. Still, it is hard to see how any of this could build proteins—that is, in the sense of building their fundamental shapes, or scaffolds; and build proteins in terms of explaining the key catalytic strategies of each active site. Even in the impressive demonstration of a transition through nine orders of magnitude, in which a full exchange of a promiscuous activity for the primary activity was seen, the overall geometry of the protein was unchanged, and, although substrates had changed, the fundamental active site strategy stayed the same. ,,, “Modern neo-Darwinism and neutral evolutionary treatments,” remark Leonard Bogarad and Michael Deem, “fail to explain satisfactorily the generation of the diversity of life found on our planet.” It is not that they did not evolve, they say, but that “... most theoretical treatments of evolution consider only the limited point-mutation events that form the basis of these theories.” Their sober conclusion is that “point mutation alone is incapable of evolving systems with substantially new protein folds.”60,,, “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations ... that gave birth to novel proteins have yet been identified.”69 http://inference-review.com/article/the-new-view-of-proteins A Dentist in the Sahara: Doug Axe on the Rarity of Proteins Is Decisively Confirmed - Brian Miller - February 18, 2019 Excerpt: evolutionists argue that each protein comprising a flagellum resulted from the duplication of an existing gene which then continuously mutated until it stumbled upon a new flagellar function. However, research over the past several years has shown this claim to be implausible.,,, Overly Optimistic Estimate Actually, the previous analysis is overly optimistic since, as demonstrated, most proteins become entirely nonfunctional after less than 10 percent of their sequences randomly change. The probability of a trial finding such a target (c=.10) would often be over 10^300 times less likely than finding the protein family (c=.50 ) target. That number is a 1 with 300 zeros behind it, which is greater than the ratio of the volume of the entire universe to that of a single proton. As a result, the protein targets represent remote islands of functionality very diffusely scattered throughout the larger target region which dramatically decreases the probability for success. https://evolutionnews.org/2019/02/a-dentist-in-the-sahara-doug-axe-on-the-rarity-of-proteins-is-decisively-confirmed/ Right of Reply: Our Response to Jerry Coyne - September 29, 2019 by Günter Bechly, Brian Miller and David Berlinski Excerpt: David Gelernter observed that amino acid sequences that correspond to functional proteins are remarkably rare among the “space” of all possible combinations of amino acid sequences of a given length. Protein scientists call this set of all possible amino acid sequences or combinations “amino acid sequence space” or “combinatorial sequence space.” Gelernter made reference to this concept in his review of Meyer and Berlinski’s books. He also referenced the careful experimental work by Douglas Axe who used a technique known as site-directed mutagenesis to assess the rarity of protein folds in sequence space while he was working at Cambridge University from 1990-2003. Axe showed that the ratio of sequences in sequence space that will produce protein folds to sequences that won’t is prohibitively and vanishingly small. Indeed, in an authoritative paper published in the Journal of Molecular Biology Axe estimated that ratio at 1 in 10^74. From that information about the rarity of protein folds in sequence space, Gelernter—like Axe, Meyer and Berlinski—has drawn the rational conclusion: finding a novel protein fold by a random search is implausible in the extreme. Not so, Coyne argued. Proteins do not evolve from random sequences. They evolve by means of gene duplication. By starting from an established protein structure, protein evolution had a head start. This is not an irrational position, but it is anachronistic. Indeed, Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold. Why? Because such novel folds are so extraordinarily rare in sequence space. Moreover, as Meyer explained in Darwin’s Doubt, as mutations accumulate in functional sequences, they will inevitably destroy function long before they stumble across a new protein fold. Again, this follows from the extreme rarity (as well as the isolation) of protein folds in sequence space. Recent work by Weizmann Institute protein scientist Dan Tawfik has reinforced this conclusion. Tawfik’s work shows that as mutations to functional protein sequences accumulate, the folds of those proteins become progressively more thermodynamically and structurally unstable. Typically, 15 or fewer mutations will completely destroy the stability of known protein folds of average size. Yet, generating (or finding) a new protein fold requires far more amino acid sequence changes than that. Finally, calculations based on Tawfik’s work confirm and extend the applicability of Axe’s original measure of the rarity of protein folds. These calculations confirm that the measure of rarity that Axe determined for the protein he studied is actually representative of the rarity for large classes of other globular proteins. Not surprisingly, Dan Tawfik has described the origination of a truly novel protein or fold as “something like close to a miracle.” Tawfik is on Coyne’s side: He is mainstream. https://quillette.com/2019/09/29/right-of-reply-our-response-to-jerry-coyne/ Watch: Videos Now Available from the Recent ID Conference In Austria Günter Bechly - October 24, 2019 Excerpt: Dr. Brian MILLER, “A Thermodynamic Analysis of the Rarity of Protein Folds” (May 30, 2019). Abstract: “Research by Douglas Axe demonstrated that amino acid sequences that correspond to a functional beta-lactamase protein fold are extremely rare. In response, critics have raised questions related to the accuracy of his analysis. This presentation describes how more recent research on the effects of mutations on the thermodynamic stability of protein folds has confirmed Axe’s result and its general relevance to most proteins. The presentation also applies the results of an evolutionary time-scale study by Chatterjee, Pavlogiannis, Adlam, and Nowak, and discusses the implications for the argument that co-option can explain the appearance of irreducibly complex molecular machines.” https://evolutionnews.org/2019/10/videos-available-from-the-id-conference-in-austria/
bornagain77_{November 30, 2022
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On reflection, I'm quite interested in the evolution of "pregnancy" so I'll do a bit of reading and report anything that I find that might interest others. It may take a while. Of course pregnancy, wombs, placentas, long gestation, and giving birth to well-developed young is a shared trait of a whole clade of mammals, Placentalia and it is in the lineage of the common ancestor of this clade that is the place to start.Alan Fox_{November 30, 2022
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Pleased to see you making an effort, Martin_r.Alan Fox_{November 30, 2022
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Sorry to disappoint you, Barry. Whilst there's a mountain of information on all aspects of biology, nothing is going to convince you that evolution is an explanation for the variety of life that has existed on Earth and what remains today. You can lead a horse to water... Though as, as far as I am aware, this is the only place left where I can interact with proponents of "Intelligent Design" who all seem remarkably reticent about alternative explanations for observed biology. Questions are easy to ask but hard to answer.Alan Fox_{November 30, 2022
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Darwinian fantasy world:
Sex chromosomes are derived from autosomes and have evolved independently many times in different lineages . For example, the human X and Y chromosomes originated about 200-300 million years ago in eutherian mammals1,2 after the split of monotremes, and sex chromosomes evolved independently in birds, snakes, and multiple times in other reptiles, amphibians and fish; they also formed repeatedly in many invertebrate taxa and plants ... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120474/
martin_r_{November 30, 2022
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I’ve just ordered a copy of Your Designed Body and I look forward to reading it
I ordered a copy too. I was wondering what a fellow engineer has to say. I really hope, that I will learn something new, and not what I have heard 1000 times before.martin_r_{November 30, 2022
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Alan Fox, If you can point to me to any article that lays out the stepwise evolution of pregnancy, that would be sufficient. Everyone get ready for Alan's literature bluff.Barry Arrington_{November 30, 2022
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just pointing out that you are a coward and a fraud.
Oh, classy!Alan Fox_{November 30, 2022
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Does Mr Arrington require a stepwise explanation from the evolution of sex, evolution of gametes, differentiation into sperm and eggs, wind-borne pollination, motile gametes in ferns, egg-laying in dinosaurs and monotremes, marsupials (the genitalia in kangaroos is interesting) transitional placental mammals, human biology?Alan Fox_{November 30, 2022
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PyrrhoManiac1
you’re trying to bait me into saying something intemperate
No, just pointing out that you are a coward and a fraud.Barry Arrington_{November 30, 2022
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"Nobody has ever addressed a problem like that." And they still haven't. Andrewasauber_{November 30, 2022
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@7 Nice try, but if you're trying to bait me into saying something intemperate that would justify banning me, you'll have to be far more clever. This "translation" schtick is just quaint.PyrrhoManiac1_{November 30, 2022
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PyrrhoManiac1 writes
No, [the OP is] far too stupid to merit a response. And no, I won’t explain why. If you don’t know enough biology to understand why the OP is inane, I don’t have the time or inclination to hold your hand.
For the uninitiated, I will translate from Internet troll speak into plain English:
No, I have not the foggiest idea how pregnancy could evolve in a stepwise basis. But I am a coward and will not admit that.
You're welcome.Barry Arrington_{November 30, 2022
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"No, it’s far too stupid to merit a response." lol Oooh. You are quite the intellectual. Andrewasauber_{November 30, 2022
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@3
Do you really believe the nonsense you type out? Examine your verb again: reverse engineering. How does reductionism accomplish any of that? It wouldn’t even be an assemblage of Disconnected parts. Even an “assemblage of disconnected parts” requires an assembler, and a designer of those parts.
My point was that intelligent design should have no objections to reductionism as scientific method, since the intelligent design advocate can happily regard reductionism as reverse-engineering design. I was not endorsing this view -- I think I've made my criticisms about reductionism perfectly evident in the past few weeks. @4
How about addressing the issue in the OP?
No, it's far too stupid to merit a response. And no, I won't explain why. If you don't know enough biology to understand why the OP is inane, I don't have the time or inclination to hold your hand.PyrrhoManiac1_{November 30, 2022
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PM1, How about addressing the issue in the OP? Andrewasauber_{November 30, 2022
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PM @1. Do you really believe the nonsense you type out? Examine your verb again: reverse engineering. How does reductionism accomplish any of that? It wouldn't even be an assemblage of disconnected parts. Even an "assemblage of disconnected parts" requires an assembler, and a designer of those parts. Your designer is chance and the laws of nature. Not possible. That's why being an atheist requires so much more faith. We are faithful because of the evidence. Your faith requires you to suppress the evidence. The evidence surrounds you.AnimatedDust_{November 30, 2022
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PM1 at 1, Forget the ism's. Useless. Intelligent Design shows that the complexity of living things exceeds man's current level of technology. That it exceeds blind, unguided chance. So, EVOLUTION is incapable of the planning and engineering involved in creating living things.relatd_{November 30, 2022
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It's weird to see a criticism of reductionism in a post defending intelligent design. Intelligent design requires the idea that organized complexity cannot be "bottom-up" (spontaneous and emergent), but always "top-down" (some intelligent control). This entails that in the absence of design, a mere assemblage of disconnected parts is all that could exist. So reductionism is just revere-engineering intelligent design: the reductionist breaks things down into their constituent parts in order to disclose what the designer had to do in order to construct the organized whole. In other words, any advocate of intelligent design ought to champion reductionism.PyrrhoManiac1_{November 30, 2022
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