The crisis continues says Michael Denton.

 

Biologist Michael Denton Revisits His Argument that Evolution Is a "Theory in Crisis"

Casey Luskin 

A new quarterly journal, Inference: International Review of Science, turns a skeptical eye on the culture and practice of science.

Of particular interest in the first issue is an essay by our colleague, biologist Dr. Michael Denton, on "Evolution: A Theory in Crisis Revisited," first of a promised three-part series. Denton renews and expands his critique of Darwinian theory. This bears some discussion.

Many Darwin defenders are troubled that credible scientists doubt their viewpoint. As a result, we occasionally hear rumors promulgated by ID critics claiming that Michael Denton is no longer skeptical of Darwinian evolution, or even that he has abandoned the argument in his influential 1985 book, Evolution: A Theory in Crisis. Such rumors are quashed by Denton's article in Inference, where he observes:

In Evolution: A Theory in Crisis (Evolution), published in 1985, I argued that the biological realm is fundamentally discontinuous. The major taxa-defining innovations in the history of life have not been derived from ancestral forms by functional intermediates. ... The contrary view remained predominant among evolutionary biologists until, at least, the 1980s, and remains predominant as the view offered the public today.

There have been massive advances and discoveries in many areas of biology sinceEvolution was first published. These developments have transformed biology and evolutionary thought. Yet orthodox evolutionary theory is unable to explain the origins of various taxa-defining innovations.

This was my position in Evolution.

It remains my position today

Clear enough? Denton kicks off the article by taking on one of the most famous icons of evolution, the Galápagos finches, showing that they represent microevolutionary changes but do not demonstrate significant evolution:

From the emerging developmental genetic picture, it is now relatively easy to envisage how gradual adaptive fine-tuning of the expression patterns of a handful of genes could result in the different beak forms of the Galápagos finches we see today.

The evolution of finch beaks requires no causal agency beyond natural selection. Some finch beaks proved advantageous; others, not. The lesson of the Galápagos, and all such cases of microevolution, is that cumulative selection will work its magic just so long as there is an empirically known or plausible functional continuum, at the morphological or genetic level, leading from an ancestral species or structure to a descendent species or structure.

So the evolution of the Galápagos finches is a plausible evolutionary but one entailing only very minor evolutionary change. Well, are there plausible accounts of evolutionary change on a larger scale? Denton examines one case -- the origins of the complex reproductive behavior of the European eel.

These eels begin their lives just off the East Coast of the United States, and undergo many morphological changes, which cause sexual differentiation as they migrate to the shores of Europe. They then migrate back across the Atlantic, undergoing more morphological changes, and return to their spawning grounds in the Sargasso Sea. The story is a lot more complicated than that, and Denton discusses these processes and behaviors in detail. He finds that they are very difficult to explain in evolutionary terms:

The evolutionary factors responsible for such an extraordinarily roundabout way of reproducing are mystifying. What tiny adaptive steps led from the reproductive habits of a normal fish to such a grotesque life cycle? What adaptive significance do such sexual metamorphoses serve? What selective pressures led the adult eels to dissolve their guts and stop feeding to make the journey back to the Sargasso Sea? Why does the anus migrate from the tail to mid-abdomen during the final stages of larval maturation? Why do males stay in Europe for six years and females for nine before returning to the ocean? What selective advantage did eels achieve by making the transition from salt to fresh water? What conceivable "long series of gradations ... each good for its possessor" could possibly have orchestrated the whole performance? I think it would be hard to invent a story more difficult to comprehend in terms of cumulative selection.

He notes that examples like this support his conclusions in Evolution: A Theory in Crisis:

Today, thirty years later, despite the discovery of a huge number of new fossil forms, it is still true, as Darwin confessed, that "the distinctness of specific forms ... not ... blended together by innumerable transitional links is a very obvious difficulty."

But Denton now adds another critique of Darwinian evolution. There are some beneficial features that cannot be built in a step-by-step process. But there are other features that are prevalent throughout biology and that seem to provide no particular adaptive benefit. Denton explains:

Evolutionary novelties pose one obvious challenge to Darwinian theories. The fact that, in most cases, their adaptive status is clearly in doubt poses another. ... The number of segments making up the various parts of the body of different groups of fossil arthropods, including shrimps, lobsters, trilobites, and spiders, is fantastically variable, yet each group almost always has the same number of segments in each body part despite the bizarre and complex variation in its lifestyle and adaptations. On even a cursory consideration of the vast inventory of invertebrate type-defining novelties described in this major work, it would appear that the great majority serve no adaptive purpose. ... If a significant proportion of the taxa-defining patterns serve no specific function, as Owen argued in the case of the tetrapod limb, then cumulative selection cannot provide an explanation for the origin of a significant fraction of the defining homologs, and hence for the natural system itself.

This resembles the arguments Denton made in a 2013 BIO-Complexity paper, "The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism," where he challenges the view that biological organisms are accidents of random mutation and natural selection, instead adopting a structuralist view that body plans are like Platonic "types," woven into the fabric of nature.

Of course there are some conserved features that evolutionary biologists laud as the key to understanding how body plans arose. Denton observes how proponents of "evo devo" think that conserved developmental genes can be redeployed in different organism to control the development of different parts, explaining evolutionary transitions from one form to another:

A remarkable experiment, described in Neil Shubin's Your Inner Fish, demonstrated how one conserved toolkit component, a signaling molecule known as "sonic hedgehog protein," had the same effect on the development of shark fins as on mammalian and chicken digits. Shubin was suitably impressed by this remarkable result. "It means," he observed, "that this great evolutionary transformation [from fish fins into limbs] did not involve the origin of new DNA." Old wine had, instead, been poured into new bottles. "Much of the shift likely involved using ancient genes, such as those involved in shark fin development, in new ways to make limbs with fingers and toes." This view is today widespread among researchers in evolutionary developmental biology, known as evo-devo.

Michael Behe has often made the point that genetic similarity between two proteins may indicate common descent (and I would add that functional genetic similarity could indicate common design rather than common descent), but that doesn't necessarily mean there's a stepwise evolutionary pathway connecting the two to their putative ancestor. Denton offers a similar response to Shubin, noting that genetic similarity in developmental toolkits may suggest a common origin, but that doesn't mean that the differences we observe can be explained in adaptive terms:

The fact that the same toolkit is used universally supports descent with modification, but it does not explain how relevant novelties came about during decent with modification, or whether they were adaptive. That sugar and carbonic acid are composed of the same atoms does not imply that sugar can be converted into carbonic acid by means of a series of individual atomic steps; and that the same atoms, proteins, cell types, gene circuits, gradients, and Turing mechanisms are used to make fins, hands, reptile scales, feathers, fir cones, and flowers does not imply anything beyond the obvious fact that these structures were made using a common toolkit.

Indeed, Denton finds that some differences between homologous structures are very difficult to explain via Darwinian evolution. He tackles the example of "enucleated" red blood cells, blood cells that lack a nucleus, in the major groups of mammals (monotremes, marsupials, and placentals). Denton describes the complex biological processes that cause a blood cell to expel its nucleus. He finds:

There is no known intermediate type of cell midway between the enucleate cell and the nucleated red cells of any other vertebrate species. As I argued in Evolution, where there is an empirical absence of transitional forms, envisaging plausible hypothetical intermediates invariably proves impossible. And so it is here.

Vertebrate erythrocytes are either nucleated or enucleated. But without intermediates or partially enucleated cells, there would be no way of approaching the enucleate state gradually. If there are no intermediates, then the utility of the enucleate red cell could only have been tested when the enucleate cell enters the bloodstream and is forced through the smallest capillaries. The very first test of the utility of the enucleate red cell could only have been carried out after the complex and unique machinery for pushing out the nucleus was already in place.

He closes by noting that many "puzzles" plague evolutionary biology -- puzzles that he will explore in parts two and three of this paper. I will look forward to those.

Get ready to greet your AI overlords?

 

Physics Vs. Determinism.

 

Yet more folowing the science re: theism.

 

The rise of the west.

 

The elephants' elephant.

 

Hosea Chapter 1 American Standard Version

 1.The word of JEHOVAH that came unto Hosea the son of Beeri, in the days of Uzziah, Jotham, Ahaz, and Hezekiah, kings of Judah, and in the days of Jeroboam the son of Joash, king of Israel.

2 When JEHOVAH spake at the first by Hosea, Jehovah said unto Hosea, Go, take unto thee a wife of whoredom and children of whoredom; for the land doth commit great whoredom, departing from JEHOVAH.

3 So he went and took Gomer the daughter of Diblaim; and she conceived, and bare him a son.

4 And JEHOVAH said unto him, Call his name Jezreel; for yet a little while, and I will avenge the blood of Jezreel upon the house of Jehu, and will cause the kingdom of the house of Israel to cease.

5 And it shall come to pass at that day, that I will break the bow of Israel in the valley of Jezreel.

6 And she conceived again, and bare a daughter. And JEHOVAH said unto him, Call her name Lo-ruhamah; for I will no more have mercy upon the house of Israel, that I should in any wise pardon them.

7 But I will have mercy upon the house of Judah, and will save them by JEHOVAH their God, and will not save them by bow, nor by sword, nor by battle, by horses, nor by horsemen.

8 Now when she had weaned Lo-ruhamah, she conceived, and bare a son.

9 And JEHOVAH said, Call his name Lo-ammi; for ye are not my people, and I will not be your God .

10 Yet the number of the children of Israel shall be as the sand of the sea, which cannot be measured nor numbered; and it shall come to pass that, in the place where it was said unto them, Ye are not my people, it shall be said unto them, Ye are the sons of the living God.

11 And the children of Judah and the children of Israel shall be gathered together, and they shall appoint themselves one head, and shall go up from the land; for great shall be the day of Jezreel.

On the right to conscientious objection

 OHCHR and conscientious objection to military service

While the Covenant does not explicitly refer to a right to conscientious objection, in its general general comment no.22 (1993) the Human Rights Committee stated that such a right could be derived from article 18, inasmuch as the obligation to use lethal force might seriously conflict with the freedom of conscience and the right to manifest one’s religion or belief.

The Human Rights Council, and previously the Commission on Human Rights, have also recognized the right of everyone to have conscientious objection to military service as a legitimate exercise of the right to freedom of thought, conscience and religion, as laid down in article 18 of the Universal Declaration of Human Rights and article 18 of the International Covenant on Civil and Political Rights 

On the rise of the multiverse: latest of the new gods

 

Why the irrational atheist would be an atheistic society's only hope.

 Every single time atheists have had the floor to themselves re:governance the result has been a mass murdering thugocracy. While the premise of atheism is irrational the social darwinism that the atheistic regimes of the 20th century have espoused is a perfectly rational conclusion given that premise as starting point.

In the atheistic universe there would be no reason to hope for anything else but the pitiless struggle between bloodlines for supremacy . Even among social animals suppression/culling of bloodlines that were a demonstrable liability to the herd would be rational. The preservation/promotion of bloodlines that were a proven asset to the herd would also be rational. Casting the matter in moral or ethical terms would be nothing but uninformed sentimentality.

Rather than looking to the sky and taking the altruistic generosity of a benevolent Father as an example . We should look to the Brute beast, after all their pitiless struggle for supremacy is the true source of our bounty. 

We see no hang ups re: morality there. If a stronger herd must violently displace a weaker one to advance its aims so be it and neither the displacer nor the displaced thinks of the matter in moral terms, it is simply the way things are and there is no particular way things ought to be.

Even this arbitrary assignment of some special status to life itself would be an atavism from religion/superstition. There is only physics life/consciousness is an illusion, a very flattering illusion, hence its persistence, but really when one thinks of it there is no meaningful difference between living and nonliving matter and neither exists for any objective purpose.

All perfectly rational conclusions given atheism as a premise. Hence the irrational atheist would be an atheistic society's only hope.

On the prisoner's dilemma.

 

Another Friday another missing link (or not).

 Fossil Friday: Is the Four-Legged Snake Tetrapodophis a Missing Link or Not?

Gunter Bechly

The origin of snakes is a hotly debated topic in evolutionary biology. There are controversies about their phylogenetic position, their origin from aquatic vs burrowing (fossorial) ancestors, and of course transitional fossils (Caldwell & Lee 1997, Rieppel et al. 2003, Brandley et al. 2008, Apesteguía & Zaher 2006, Lee et al. 2007, Caldwell 2007, 2008, Zaher et al. 2009, 2023, Longrich et al. 2012, Zaher & Scanferla 2012, Palci et al. 2013a, 2013b, Palci 2014, Caldwell et al. 2015, Hsiang et al. 2015, Yi & Norell 2015, Da Silva et al. 2018, Xing et al. 2018, Garbergoglio 2019a, 2019b, 2019c). While some scientists are convinced that “snakes and mosasauroids/coniasaurs share a limbed common ancestor that was likely aquatic, not fossorial” (Caldwell 2008), other scientists strictly claim that “lizards could not have transitioned to snakes by any other evolutionary path than through fossoriality” (Da Silva et al. 2018). Either way, there should have existed transitional forms, which exhibit at least some typical features of basal snake anatomy combined with four fully developed fore and hind limbs to document the transition of limbless snakes from still quadrupedal walking ancestors.

Assumed Mesozoic stem snakes like the Madtsoiidae and Simoliophiidae as well as the very primitive Cretaceous genera Coniophis, Dinilysia, and Najash did only possess small external hind limbs (of which vestigial remnants are also retained in some living snakes like boids), but show no evidence of forelimbs (Tchernov et al. 2000, Zaher & Rieppel 2002, Rieppel et al. 2003, Apesteguía & Zaher 2006, Garberoglio et al. 2019c).

In their study of the evolution of the snake body plan Garberoglio et al. (2019c) commented:

This basal position of the limbed terrestrial and marine snakes indicates that snakes retain sizeable external hindlimbs and sacral contacts for a substantial time after their origin—from approximately 170 Ma to the youngest confirmed legged snakes, the simoliophiids, at approximately 100 Ma. This indicates that (i) the reduction and loss of the pectoral girdle and forelimbs probably occurred much earlier, given the definitive absence of these structures in simoliophiids and the lack of evidence for their presence in Najash, Dinilysia, and madtsoiids, and was probably a major event in the early radiation of snakes, and one that occurred well before crown (modern) snake origins; (ii) the “forelimb-absent and hindlimb-reduced” morphology was a stable and successful body plan, rather than a transient phase between limbed and limbless conditions; and (iii) the origin of crown snakes was characterized by a major reduction in the hindlimb and pelvis (including loss of sacral contacts).

This All Sounds Well and Good

That is, until you find that other modern studies (e.g., Tchernov et al. 2000, Rieppel et al. 2002, Zaher & Rieppel 2002, Longrich et al. 2012, Zaher & Scanferia 2012, Palci et al. 2013b in part, Hsiang et al. 2015, Garbergoglio et al. 2019a contra Garbergoglio et al. 2019c) do not even agree that the fossil Madtsoniidae and Simoliophidae or even Dinilysia are stem group snakes at all, but recover them nested among living snakes, which would imply that the hind limb reduction occurred more than once in crown group snake. Probably, mainstream evolutionary biologists would respond that such a reduction is simple and therefore not unlikely, as is proven by the fact that several other groups of amphibians and reptilians have produced legless forms. However, this is exactly the point: convergence is all over the place in the animal kingdom and is nothing but incongruent similarity that contradicts a unique nested hierarchy of similarities predicted by Darwinism. Furthermore, there is experimental evo-devo evidence from transgenic mice that the reduction of limbs is not a simple task at all but requires multiple codependent mutations (compare Kvon et al. 2016). Together with the complex changes in skull kinetics of snakes, this raises a significant waiting time problem, because even the geologically available window of time of several million years is orders of magnitude too short to accommodate the genetic changes for this re-engineering of the body plan, based on the mathematical toolkit of mainstream population genetics.

Anyway, because of the fact that no known fossil stem snakes had retained four functional limbs, the discovery of a putative four-legged snake was a real sensation. Eight years ago my good colleague Prof. David Martill, with whom I co-authored several articles and monograph of the fossils of the Lower Cretaceous Crato Formation in Brazil (Martill et al. 2007), described from this locality the long sought missing link of snake evolution in the prestigious journal Science (Martill et al. 2015; also see this YouTube video): the beautifully and completely preserved fossil shows a very elongate snake-like animal with small fore and hind limbs, both with five well-developed digits. They named the 110-million-year-old fossil Tetrapodophis, which means four-legged snake. Their phylogenetic analysis placed it at the very base of the snake lineage. The scientists also identified burrowing adaptations that arguably would support an origin of snakes from fossorial rather than aquatic ancestors. Of course, the discovery was much celebrated in news reports as “a snake version of Archaeopteryx” (e.g., University of Portsmouth 2015, Christakou 2015a, Evans 2015, Yong 2015)

Yong (2015) commented in National Geographic:

Their analysis produced a family tree in which Tetrapodophis came after the earliest known snakes like Eophis, Parviraptor, and Diablophis, but is still very much a snake. But how could that be? Eophis and the others only have two legs, so how could four-legged Tetrapodophis have come after them? The answer is that evolution doesn’t proceed along simple, straight lines.

This is typical Darwinist doublespeak for the simple fact that the fossil does not fit within a Darwinian scenario without ad hoc hypotheses to explain away conflicting data. But in this case there is another little problem: all known fossils of the Jurassic earliest stem snakes (Portugalophis, Eophis, Parviraptor, and Diablophis) do not even have the body region preserved, which would show if they possessed limbs or not (see Caldwell et al. 2015), so that the above statement is also incorrect. Never believe Darwinist pop science journalists, who are notoriously sloppy with facts. But apart from this glitch, the real blows against Tetrapodophis were yet to come.

A First Blow

The first blow came with a very heated discussion about the legal status of the fossil (Christakou 2015b), even though there was no proof that any laws were broken with the export and sale of the fossil. I personally consider this discussion as very much ridiculous, given the fact that countless fossils from the quarries in Brazil were grinded for cement production or used for pavements, without any local scientist caring for this natural heritage. Now, museums around the world, which invested a lot of money and preparation effort to preserve these fossils for science, are now asked to repatriate the collections to Brazilian museums with a very poor track record of proper conservation and curation, all in the name of protecting alleged national treasures of poor countries from evil Western exploitation. Unfortunately, the pervasive woke agenda has taken hold of paleontology as well, which impairs scientific progress and has made fossil collecting to a very frustrating endeavour.

A Second Blow

The second blow came with another silly dispute about the deposition of the specimen. The specimen was deposited in a public museum in Germany as a loan by a private collector, who temporarily limited access to the specimen because it was damaged during the examination with synchrotron micro-CT scanning. Even though access was later restated and the specimen was also meticulously documented with drawings and photographs in the original publication, some scientists made absurd statements like “if the fossil can’t be studied, it doesn’t exist … I don’t want to mention the name Tetrapodophis ever again” (Gauthier quoted in Gramling 2016). Other researchers said the “original paper should not have been published, because the fossil was not officially deposited in a museum or other repository”. This reflects a common politically correct sentiment among scientists against private collections, even though many private fossil collections are better curated and more easily accessible to scientists than public collections in certain dubious countries with a reputation of sloppiness and corruption. Nevertheless, these bigoted scientists rather would leave sensational finds of high scientific value undescribed forever, than having scientific publications based on material in private collections. I find this bizarre, scientifically reprehensible, and politically highly problematic (anti private property in favor of statist bureaucracy). After all, using the same kind of reasoning we could purge all paleontological knowledge from science that is based on museum specimens that were destroyed during World War II, or lost by the post when they were sent on loan to foreign scientists, or simply cannot be relocated in the museum archives anymore, which happens way more often than many people may think. Many scientists seem to have lost their common sense nowadays.

Last but Not Least

The third and truly fatal blow came with several studies by paleontologist Michael Caldwell and his colleagues, who strongly disputed the fossorial adaptation of Tetrapodophis in favor of an aquatic adaptation, and also disputed the snake-affinity in favor of a determination as dolichosaurid lizard (Lee et al. 2016, Caldwell et al. 2016, 2021, Paparella et al. 2018), which is an extinct group of marine reptiles. The press immediately reported that the big splash was a case of mistaken identity (Geggel 2016), and that the assumed missing link between lizards and snakes has been debunked (Hodžić_2021, Lyle 2021, Strauss 2022).

One might think that this misidentification is a minor issue because dolichosaurids are often considered as close relatives of snakes within a clade Pythonomorpha. However, this opens a whole new can of worms, as the status of Pythonomorpha is subject of considerable scientific controversy itself. The Wikipedia article on Pythonomorpha has a good summary of this mess, of which the long story short is as follows: Pythonomorpha was proposed by the famous 19th century paleontologist Edward Drinker Cope (1869) to include mosasaurs and snakes as assumed close relatives, while snakes were believed to have evolved from burrowing lizards. This was rejected by most 20th century experts, who instead suggested that the closest relatives of mosasaurs are monitor lizards (e.g., Russell 1967). Then, Pythonomorpha was resurrected by Michael Caldwell and Michael Lee in the late 1990s (Caldwell & Lee 1997, Lee 1997, 1998, Caldwell 1999, Lee & Caldwell 2000) to include the aquatic extinct reptile groups aigialosaurs, mosasaurs, dolichosaurs, coniasaurs, as well as snakes, which were postulated as derived from aquatic ancestors (also see Pierce & Caldwell 2004, Palci & Caldwell 2007, Caldwell 2008, Paparella et al. 2018). This was again questioned by anatomical evidence (Zaher & Rieppel 1999) and more recent phylogenetic studies, which again placed mosasaurs with monitor lizards and snakes with skinks (Conrad 2008) or with anguinids and iguanas (Simões et al. 2020), or placed mosasaurs more basal than monitor lizards and snakes (Gauthier et al. 2012). On the other hand, more recent analyses (Palci et al. 2013a, Palci 2014, Martill et al. 2015, Reeder et al. 2015) recovered snakes and mosasaurs as sister groups and thus supported a monophyly of Pythonomorpha. The latter would also be congruent with the growing for a monophyletic group called Toxicofera, which would include all squamates with poison glands such as iguanas, monitor lizards, gila monsters, and snakes, under exclusion of skinks, gekkos, and true lizards. However, as always in phylogenetics there is also strong conflicting evidence presented by opponents of the Toxicofera hypothesis (Hargreaves et al. 2015, Mongiardino Koch & Gauthier 2018, Joffroy 2022). If we would draw a least common denominator of all published trees of the past decades, the result would be an unresolved polytomy (as I described in a recent Fossil Friday article about arachnid phylogeny), which rather agrees with the expectations of creationists than those of evolutionary biologists.

A New Turn of Events

Considering this uncertainty it is hardly a surprise that this year a new study brought a new turn of events and again confirmed the status of Tetrapodophis as most basal snake (Zaher et al. 2023). The authors remarked that “Our scorings of Tetrapodophis were based on first-hand observations of the original specimen, and our interpretations of the anatomy and attendant scoring disagree significantly with those of Caldwell et al. (2021), as do our phylogenetic results.” It does not take too much of a prophetic gift to predict that we will not have to wait very long for a rebuttal by Caldwell and his team.

Whoever may ultimately win this dispute, there is no doubt that the true reason for all this uncertainty is the simple fact that the pattern of similarities between different animal groups does not fall into a neatly ordered set of nested hierarchies as often pretended by hardcore Darwinists. In reality, incongruent patterns are all over the place. A snake-like body plan is a good example: Among tetrapod vertebrates a snake-like body only originated in caecilians (Gymnophiona) among lissamphibians and in squamates among amniotes. However, within amniotes this body plan originated not less than 26 times independently (Brandley et al. 2008, Evans 2015). Tetrapodophis could be a missing link to at least two of them respectively, or just might be number 27, who knows. What is also interesting is that scientists found “statistically significant support for at least six examples of the re-evolution of lost digits in the forelimb and hind limb” ((Brandley et al. 2008), which shows the level of absurdity that is readily accepted only to preserve the evolutionary paradigm.

References

Apesteguía S & Zaher H 2006. A Cretaceous terrestrial snake with robust hindlimbs and a sacrum. Nature 440(7087), 1037–1040. DOI: https://doi.org/10.1038/nature04413

Brandley MC, Huelsenbeck JP, Wiens JJ 2008. Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms. Evolution 62(8), 2042–2064. DOI: https://doi.org/10.1111/j.1558-5646.2008.00430.x

Caldwell MW 1999. Squamate phylogeny and the relationships of snakes and mosasauroids. Zoological Journal of the Linnean Society 125(1), 115–147. DOI: https://doi.org/10.1111/j.1096-3642.1999.tb00587.x

Caldwell MW 2007. Snake phylogeny, origins, and evolution: the role, impact, and importance of fossils (1869–2006). pp. 253–302 in: Anderson JS & Sues H-D (eds). Major Transitions in Vertebrate Evolution. Indiana University Press: Indiana, 417 pp.

Caldwell MW 2008. Squamate phylogeny and the relationships of snakes and mosasauroids. Zoological Journal of the Linnean Society 125(1), 115–147. DOI: https://doi.org/10.1111/j.1096-3642.1999.tb00587.x

Caldwell MW & Lee MSY 1997. A snake with legs from the marine Cretaceous of the Middle East. Nature 386, 705–709. DOI: https://doi.org/10.1038/386705a0

Caldwell MW, Nydam RL, Palci A & Apesteguía S 2015. The oldest known snakes from the Middle Jurassic-Lower Cretaceous provide insights on snake evolution. Nature Communications 6: 5996, 1–11. DOI: https://doi.org/10.1038/ncomms6996

Caldwell MW, Reisz RR, Nydam RL, Palci A & Simões TR 2016. Tetrapodophis amplectus (Crato Formation, Lower Cretaceous, Brazil) is not a snake. Society of Vertebrate Paleontology 76th Annual Meeting Program & Abstracts, 108. https://vertpaleo.org/wp-content/uploads/2021/03/SVP-2016-Program-Book-v10-with-covers.pdf

Caldwell MW, Simões TR, Palci A, Garberoglio FF, Reisz RR, Lee MSY & Nydam RL 2021. Tetrapodophis amplectus is not a snake: re-assessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard. Journal of Systematic Palaeontology 19(13), 893–952. DOI: https://doi.org/10.1080/14772019.2021.1983044

Christakou A 2015a. Four-legged fossil snake is a world first. Nature July 23, 2015. https://doi.org/10.1038/nature.2015.18050

Christakou A 2015b. Four-legged snake fossil sparks legal investigation. Nature August 4, 2015. DOI: https://doi.org/10.1038/nature.2015.18116

Conrad JL 2008. Phylogeny And Systematics Of Squamata (Reptilia) Based On Morphology. Bulletin of the American Museum of Natural History 310, 1–182. DOI: https://doi.org/10.1206/310.1Cope ED 1869. On the reptilian orders Pythonomorpha and Streptosauria. Proceedings of the Boston Society of Natural History 12, 250–266. https://www.biodiversitylibrary.org/partpdf/243473

Da Silva FO, Fabre A-C, Savriama Y, Ollonen J, Mahlow K, Herrel A, Müller J & Di-Poï N 2018. The ecological origins of snakes as revealed by skull evolution. Nature Communications 9: 376, 1–11. DOI: https://doi.org/10.1038/s41467-017-02788-3

Evans S 2015. Four legs too many? Science 349(6246), 374–375. DOI: https://doi.org/10.1126/science.aac5672

Garberoglio FF, Gómez RO, Apesteguía S, Caldwell MW, Sánchez ML & Veiga G 2019a. A new specimen with skull and vertebrae of Najash rionegrina (Lepidosauria: Ophidia) from the early Late Cretaceous of Patagonia. Journal of Systematic Palaeontology 17(18), 1313–1330. DOI: https://doi.org/10.1080/14772019.2018.1534288

Garberoglio FF, Gómez RO, Simões TR, Caldwell MW & Apesteguía S 2019b. The evolution of the axial skeleton intercentrum system in snakes revealed by new data from the Cretaceous snakes Dinilysia and Najash. Scientific Reports 9(1): 1276, 1–10. DOI: https://doi.org/10.1038/s41598-018-36979-9

Garberoglio FF, Apesteguía S, Simões TR, Palci A, Gómez RO, Nydam RL, Larsson HCE, Lee MSY & Caldwell Michael W 2019c. New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan. Science Advances 5(11): eaax5833, 1–8. DOI: https://doi.org/10.1126/sciadv.aax5833

Gauthier JA, Kearney M, Maisano JA, Rieppel O & Behkke ADB 2012: Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. Bulletin of the Peabody Museum of Natural History 53(1), 3–308. DOI: https://doi.org/10.3374/014.053.0101

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No Justice for the watchmen? II

 

Exaptation cannot reduce irreducible complexity

 Co-Option and Protein Homology Don’t Explain the Evolution of the Flagellum

Casey Luskin

Critics of intelligent design have not taken arguments for irreducible complexity (IC) sitting down. In a recent post I described how our new peer-reviewed paper, “On the Relationship between Design and Evolution,” in the open-access journal Religions, details the elegant design of the bacterial flagellum. My co-authors (Brian Miller, Stephen Dilley, and Emily Reeves) and I explain why its irreducible complexity poses a challenge to Darwinian evolution. Critics have replied that IC systems can evolve via indirect evolutionary pathways (often called exaptation). That’s where a system might start with one function but then evolve to acquire a new function along the course of its history. Vital to indirect evolutionary pathways is the concept of co-option, which holds that proteins can be borrowed from other systems in the cell, and then modified and retooled to perform entirely new functions in some new system. 

Our article is a response to Rope Kojonen’s book The Compatibility of Evolution and Design. We start by reviewing just what needs to be explained — and ask what is needed to show that such models are plausible.

More generally, a plausible evolutionary explanation of the bacterial flagellum must explain not just the flagellum-chemotaxis propulsion/navigation system but its array of other characteristics, including its delivery system of individual parts, maintenance cycle, feedback loops, and performance efficiencies. In particular, indirect evolutionary accounts (such as co-option or exaptation) must explain how the 35–40 protein parts of the flagellum evolved from parts that originally served different functions in the cell. It must also account for their assembly instructions. The insurmountable barrier to any scenario is the numerous tight constraints identified by Schulz (2021a, 2021b, 2021c) that must be met before the system could function at all. Recall H. Allen Orr’s assessment of co-option (cited by Kojonen above):

“We might think that some of the parts of an irreducibly complex system evolved step by step for some other purpose and were then recruited wholesale to a new function. But this is also unlikely. You may as well hope that half your car’s transmission will suddenly help out in the airbag department. Such things might happen very, very rarely, but they surely do not offer a general solution to irreducible complexity.” (Orr 1996)

So, just how does co-option plausibly explain the origin of the most efficient machine in the universe?

We then note that Kojonen — a very thoughtful critic of ID, who takes ID arguments seriously — endorses such indirect / exaptation / co-option models of flagellar evolution. We explain why this is a question that must be addressed via the scientific evidence:

Kojonen takes the challenge of irreducible complexity head-on. He frames the problem as follows:

“Draper (2002) homes in on the crucial question: Are the requirements for each individual part really as strict as Behe claims? If biological parts are more malleable than Behe assumes, so that less specificity is required for fulfilling their roles, then Behe’s argument against co-option fails. Debunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form. Then, a continuous series of functional forms, leading from no flagellum to a flagellum, must exist so that no change is too large for natural selection to cross, and all modifications can be made. As with Dembski’s argument, it does seem plausible that evolving such complex systems is difficult, and the existence of such an evolutionary pathway has stringent conditions. But difficult or not, it is possible that nature does allow it. Behe thinks that the existence of such pathways is unlikely, but the existence of such pathways is fundamentally an empirical question.24” (Kojonen 2021, p. 118)

Notice two key elements of this passage. First, Kojonen states that the matter is “an empirical question”. Indeed, it is. Once again, the scientific details are paramount. Is there evidence of smooth evolutionary pathways between viable forms or not? This is a fundamentally scientific question. Kojonen’s model hinges in part on empirical evidence.

Protein Rarity Challenges Co-Option

Second, Kojonen also states that “[d]ebunking Behe’s argument, then, depends on the details of how proteins work and how difficult it is to transition from one form to another, somewhat similar, form”. So, Kojonen believes that successfully countering Behe’s argument depends on how proteins work and the prospects for a protein-to-protein transformation. This makes sense. The flagellum, for example, is made of protein parts. The function of each part, as well as the likelihood of a given part evolving into its present form from an ancestral form, is highly relevant. In short, Kojonen believes that his counter to Behe — an attempt to show that the flagellum’s ‘design’ is compatible with mainstream ‘evolution’ — rests upon the plausibility (or implausibility) of protein evolution.

This is significant. We have already examined strong evidence against fine-tuned preconditions and fitness landscapes that are ‘designed’ to enable proteins to evolve. This means that the calculations above (Section 4) directly impact the viability of Kojonen’s response to Behe. If these calculations are correct, then it is safe to say — by Kojonen’s own lights — that he has not met the challenge of irreducible complexity. The flagellum, thus, appears to display a type of design that conflicts with evolution. Thus, to the extent that Kojonen accepts the bacterial flagellum as evidence of ‘design’, he faces an internal coherence problem for his conjunction of ‘design and evolution’.

What Co-Option Must Explain

So what exactly is needed to yield a viable model of indirect evolution / co-option? Some excellent work has been done on this question by folks within the ID community, as we recount: 

Having raised this crucial challenge to Kojonen’s reply to Behe, we will now take co-option on its own terms for the sake of argument. Yet even on these terms, it still fails to be plausible. Kojonen cites authorities that invoke exaptation (also called “co-option” or “indirect evolution”) to explain the evolutionary origin of the bacterial flagellum. Under this model, evolution proceeds by borrowing parts from different systems, retooling them to change their functions, and then combining them into a new system to perform a new function. Philosopher Angus Menuge lists five elements that any co-option account must provide to explain an irreducibly complex system:

Availability of parts.

Synchronization, in which parts are available at the same time.

Localization, in which parts are available at the same location.

Coordination, in which part production is coordinated for assembly.

Interface compatibility, in which parts are “mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’”. (Menuge 2004, pp. 104–5)

Typically, exaptation or co-option accounts do not explain anything beyond part of element (1). In this vein, Kojonen claims that 90% of flagellar parts have homologues that perform functional roles outside the flagellum. As we will see, this is an inaccurate claim — and co-option/exaptation accounts of the evolution of the flagellum face this and additional obstacles.

Kojonen thus follows in the footsteps of many co-option advocates in only assessing the first element of any successful co-option-based model of evolution, and we thus focus our critique there asking the question of whether sequence similarity between flagellar proteins and other proteins helps us solve the problem of its origin. We recount three main problems with such co-option-based evolutionary model of the flagellum.

Problem 1: Mere Sequence Similarity Is Not Evidence of an Evolutionary Pathway

The first main point we make is that merely establishing that two proteins have similar sequences is not sufficient to show that there is an evolutionary pathway to go from one sequence to the other:

In the context of biochemical evolution, the primary evidence for homology between two proteins is typically said to be similarity between amino acid sequences. An initial mistake made by proponents of co-option is therefore to confuse sequence similarity between two proteins with evidence for an evolutionary pathway. Even if other systems have proteins similar to each component of an irreducibly complex system, at most, this suggests homology, which might reflect common ancestry. Mere sequence similarity does not constitute a stepwise evolutionary explanation. Kojonen seems to miss this important nuance. He states that “parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution” (Kojonen 2021, p. 117). He also writes, “The existence of similar parts in other systems, for example, does provide supporting evidence for evolvability” (Kojonen 2021, p. 118). But similarity does not itself indicate a viable evolutionary pathway. As Behe explains:

“Although useful for determining lines of descent… comparing sequences cannot show how a complex biochemical system achieved its function — the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter… Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?25” (Behe 1996, pp. 175–76)

Behe points out that a single author (or mental agent) could be the cause of two different manuals. Accordingly, mere similarity is not evidence that mindless processes can bring about the system in question.

Problem 2: Useful Flagellar Protein Homology Is Not as Widespread as You’d Think

What we often find when evaluating protein similarity is that not all proteins are similar to other proteins — especially in a manner that is useful for constructing evolutionary explanations. We go through the literature and find what it really shows about flagellar protein homology to non-flagellar systems:

But the problem runs deeper than incorrect reasoning about sequence similarity: many parts of the bacterial flagellum are dissimilar to parts of other biological systems. Thus, a second problem facing the co-option model of evolution is that biological parts are often unique and unavailable to be borrowed from other systems (Khalturin et al. 2009; Beiko 2011). But Kojonen claims this is not a problem for the flagellum:

“Though a complete evolutionary explanation for the bacterial flagellum is still missing, critics of Behe have argued that approximately 90% of the parts of the flagellum are similar (or homologous) to parts that have other uses, and this gives grounds for constructing a plausible evolutionary explanation for its evolution. The type III secretion system, for example, has been argued to represent a viable precursor system to the flagellum. (Musgrave 2004; Pallen and Matzke 2006).” (Kojonen 2021, p. 117)

Kojonen cites two sources for his claim that 90% of flagellar parts are homologous to “parts that have other uses”. (Presumably, he is referring to parts that exist elsewhere besides the flagellum itself.) But this claim is highly problematic. One of his sources, Musgrave (2004, p. 81), provides no comprehensive analysis of flagellar homologues but simply asserts, via citations to other sources, that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems, including the sigma factors and the flagellins” — but those sources (discussed below) do not substantiate this claim. Kojonen’s other source, Pallen and Matzke (2006), does provide a comprehensive study of flagellar proteins that are homologous to other proteins, but they too do not substantiate a claim that “90%” of flagellar proteins are homologous to proteins outside of the flagellum.

According to Table 1 of Pallen and Matzke (2006), 15 of the 42 flagellar proteins they studied did not have known homologues.26 So, at best, they only identified homologues for only about 64% of the flagellar proteins they studied (27 out of 42) — significantly less than 90%. Moreover, the vast majority of the remaining 27 proteins for which they reported homology are highly suspect and/or do not support an evolutionary pathway leading to a flagellum:

Two of the claimed flagellar proteins with detected similarities to other proteins are regulatory proteins with unsurprising similarity to other regulators, yet they are not structural components of the flagellum that contribute to its motility function.27

Three of the allegedly homologous proteins had only slight sequence similarity; they were claimed to be homologous based on “structural or functional considerations”.28 Yet because evolution proceeds by modifying sequences of DNA and proteins, a lack of sequence similarity suggests these other proteins are not a viable source that could have been utilized via an evolutionary pathway.Seven of claimed homologous proteins are strictly homologous to other flagellar proteins,29 what might be called “intraflagellar homology”. One cannot explain the initial evolution of the flagellum by claiming it evolved from itself, so these examples are entirely unhelpful towards explaining the how the flagellum first arose from “parts that have other uses” (Kojonen 2021, p. 117) or from “similar parts in other systems” (Kojonen 2021, p. 118), as Kojonen puts it. This tenuous argument may have been derived from Musgrave (2004, p. 81), who argues that flagellar proteins find homologues in “other systems” including “flagellins”—but flagellin is a strictly flagellar protein that only forms a subunit of the flagellum’s propellor.

Eleven of the claimed homologous proteins were similar to proteins in the Type Three Secretory System (T3SS),30 three of which were also claimed to show intraflagellar homology.31 As quoted above, Kojonen cites the T3SS as a potential “viable precursor system to the flagellum”, but this argument has been long-criticized by intelligent design proponents (Illustra Media 2003) as well as by other scientists. More on this below.

Kojonen’s other source for his 90 percent statistic, Musgrave (2004), provides two citations for his claim that “between 80 and 88 percent of the eubacterial flagellar proteins have homologs with other systems” — Aizawa (2001) and Ussery (2004). Ussery (2004) does not discuss homology for flagellar proteins outside of the flagellum; he merely compares sequence diversity across other flagellar proteins that fulfill the same flagellar function in different species of bacteria. Aizawa (2001) does identify some non-flagellar homologues for flagellar proteins, but only finds homologues for four flagellar proteins that were not also identified by Pallen and Matzke (2006).32 All four of these homologues are proteins used in the T3SS. Although there is clear homology between various flagellar proteins and the T3SS, we will explain below that such data are of limited value to account for the evolution of the flagellum.

Adding the four additional flagellar homologues identified by Aizawa (2001) to those identified by Pallen and Matzke (2006) brings the total to 31 out of 42 flagellar proteins that show sequence similarity to other proteins — 74% — which is again moderately less than 90%. But as noted above, the vast majority of these homologues are unhelpful in constructing some kind of an evolutionary pathway. In the end, Kojonen’s citations (and the sources of his citations) reveal at best only 4 out of 42 flagellar proteins (9.5%) are homologous to “similar parts in other systems” which could have potentially served as “precursors” to the flagellum, as Kojonen says. Nine-and-a-half percent is strikingly less than his claimed statistic of 90%.

More on the Type 3 Secretory System (T3SS)

Because the T3SS is so often cited as a potential “precursor” to the flagellum, it’s worth devoting some time to that topic specifically. In our paper we elaborate on various reasons why the T3SS could not have been an evolutionary precursor to the flagellum:

Because quite a few (perhaps up to 15) flagellar proteins appear homologous to proteins in the T3SS, the latter is often cited as a possible evolutionary precursor (or close relative) to the flagellum (Musgrave 2004; Miller 2008, p. 59). It is therefore worth exploring further why the T3SS could not serve as “a viable precursor system to the flagellum”, as Kojonen believes it to be. The T3SS is part of the flagellum itself and is used to pump proteins from inside the cell to outside the cell where they self-assemble into the flagellum. For this function, the T3SS is simply a molecular pump involved in flagellar assembly. Even granting that it could have been co-opted for some function, it is nonetheless unrelated to the flagellum’s motility function and so is unlikely to have been ‘co-opted’ to produce motility, the core function of the flagellum.

Once the flagellum is assembled, the T3SS provides an additional function: a structural component that anchors the flagellum in the cell membrane. Yet even here, it is not part of the motor portion of the assembled flagellum, but could be viewed as something akin to the bracket on an outboard motor. Again, the T3SS is a poor candidate for co-option (and modification) into the proteins that comprise the flagellum’s propulsion function.

Notably, a different molecular machine (called an “injectisome”) uses the T3SS as well (Diepold and Armitage 2015). In the injectisome, the T3SS is involved in both assembling the injectisome and in the injectisome’s function. (The injectisome is used by certain predatory bacteria to inject toxic proteins into eukaryotic cells, which then kill the eukaryotic cells so they can be ingested by the bacterium.) But it is doubtful that the injectisome and its T3SS are useful in explaining the origin of the flagellum. First, there are ecological and phylogenetic considerations that strongly imply the flagellum predates the T3SS and the injectisome and, thus, could not have evolved from these systems (Abby and Rocha 2012a, 2012b; Deng et al. 2017; Coleman et al. 2021).33 As New Scientist reported:”

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later”, says biochemist Howard Ochman at the University of Arizona in Tucson.” (Jones 2008)

Second, even if the T3SS could have served as a precursor to the flagellum, it is not clear that this would provide anything close to a viable evolutionary pathway — a “continuous series of functional forms, leading from no flagellum to a flagellum”, as Kojonen puts it. William Dembski nicely captures the essence of the evolutionary leap required to explain how a flagellum evolved from the T3SS:“[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the T[3]SS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands.” (Dembski 2005, p. 52)

Thus, even if the T3SS were a precursor to the flagellum, it would not necessarily help its evolution. But we further observe that “research indicates that the T3SS and flagellum are so distinct that they may in fact have independent origins (Tan et al. 2021) — a generally unexpected result on an evolutionary view.”

Problem 3: Not Addressing Flagellar Assembly

We further point out in the paper that “even if all the necessary parts were available and co-opted so that they could be constructed in the form of a flagellar motor, co-option does not explain the assembly instructions needed to construct complex systems.” Explaining the assembly of IC systems is something that Behe has called “Irreducible Complexity Squared” — and it is a vital aspect of molecular machines that almost always goes unaddressed by evolutionary models:

It is not just a matter of getting the parts; it’s also putting them together in the right sequence, at the right time, and in the right orientation. Simply having all the ingredients for chocolate cake is not in itself sufficient to produce a cake. Something similar is true for a Corvette engine. So much the more for the most efficient machine in the universe. Microbiologist Scott Minnich and philosopher Stephen Meyer explain this challenge:

“[E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in a factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex.” (Minnich and Meyer 2004)

From beginning to end, the flagellar assembly process is “tightly controlled and regulated in a sequential genetic hierarchy mirroring organelle assembly from the inner membrane to the outer cell surface” (Minnich and Meyer 2004). Indeed, Behe has deemed the origin of flagellar assembly equivalent to “Irreducible Complexity Squared” (Behe 2007, p. 93), because, as he puts it, “not only is the flagellum itself irreducible, but so is its assembly system. The assembly process and the flagellum together constitute irreducible complexity piled on irreducible complexity” (Behe 2019, p. 286).

Yet in his most recent book, Darwin Devolves, Michael Behe observes that when it comes to explaining the evolutionary origin of the flagellum’s assembly, one continues to hear very little from the evolutionary biology community:

“In 1996 [in Darwin’s Black Box] I showed that, despite thousands of papers in journals investigating how that fascinating and medically important molecular machine worked, there were no papers at all that tested how the bacterial flagellum might have arisen by a Darwinian process. The scientific literature was absolutely barren on the topic…. Twenty years on, there has been a grand total of zero serious attempts to show how the elegant molecular motor might have been produced by random processes and natural selection.” (Behe 2019, p. 287; see also Behe 2007, pp. 267–68)

We close this section of our paper by observing that “Like many of his evolutionary colleagues, Kojonen simply elides this problem.” Now this is not necessarily Kojonen’s fault — it’s really just the fact that there is virtually nothing in the mainstream scientific literature trying to explain the evolution of flagellar assembly. 

In the end, we find that the bacterial flagellum contains a form of complexity that challenges not just Darwinian evolution but also co-option-based indirect models of evolution. Rope Kojonen wants us to appreciate the design of the flagellum but also to believe that this form of design can evolve. His project is to harmonize evolution and design (as he envisions them). He wants to count the flagellum as designed, but also wants to ignore the fact that the type of design it displays — irreducible complexity — poses a major problem for evolution. Thus, he wants to join “design and evolution,” but only by setting aside some of the main features of the flagellum. This harms his attempt to reconcile evolution and design in a coherent fashion. As we put it in our article, “Kojonen’s marriage of ‘evolution and design’ has a major problem: the very system that provides strong evidence of design also undercuts evolution. One part of the model saws off the branch upon which the other side sits. Kojonen’s model is internally conflicted.” 

Please read our open-access paper, here, for more details including endnotes and citation information. 

Civil war: Catholic edition.