Junk DNA is junk science? Pros and Cons.

 

Darwinists continue to major in micros?

 Are Guppies Examples of Darwinian Macroevolution?

Emily Reeves

In 1961, in the steep mountain streams of Trinidad where cascading waterfalls create barriers which predatory fish can’t overcome, a biologist named Caryl Haskins noticed and documented the variety and population structure of communities of the small freshwater fish we call guppies. (Haskins et al. 1961)

This launched a series of beautiful experiments led by professor David N. Reznick, who captured guppies from the downstream pools (where predators are prevalent) and moved them upstream (where predators are rare). The experiments were designed to answer the following question: “How, why, and how fast does adaptive evolution happen in the real world?” (Reznick and Travis 2019) What Reznick’s team observed is that the guppies from the downstream pools underwent rapid transformations when placed into the new upstream environment. The transplants took longer to reach sexual maturity and got larger. But the rate at which this happened was surprisingly fast. When the team calculated the rate of evolution for these genetic changes, using a unit called the Darwin, they reported the guppies changed at a rate of 3,700 to 45,000 Darwins while most of the rates found in fossils are only 0.1 to 1.0 Darwins. 

The Darwin is a unit of evolutionary change set by J. B. S. Haldane in 1949. It is mostly used in paleontology to compare macroevolutionary changes in fossils. Since the obvious major difference between the upstream and downstream environments was a lack of predators upstream, the phenotypic observation — that the transplanted guppies had delayed time to sexual maturity and got larger — was interpreted to be the direct effect of no predation by the larger fish. This was initially interpreted as evidence that “evolution in nature could be far more rapid, by several orders of magnitude, than had been inferred from the fossil record.” (Science News Staff 1997) Indeed, Science News reported in 1997:

Because the guppies evolved at rates so much faster than those estimated from the fossil record, Reznick suggests that selection on such short time scales is powerful enough to be behind major evolutionary changes. He argues that the study demonstrates it’s “possible to reconcile large-scale evolutionary phenomena … with what we can see in our lifetimes.” (Science News Staff 1997)

The Humble Guppy

Since this announcement, the humble guppy has been touted not only as an example of evolution happening before our eyes, but also as an example demonstrating that rapid macroevolutionary change is possible. But there were lots of assumptions in these early analyses. For example, everyone (myself included) assumed that predation was directly responsible for the guppy phenotypic differences. This is exemplified in Kenneth Miller’s summary of the experiments in his book Finding Darwin’s God: A Scientist’s Search for Common Ground Between God and Evolution. Miller, who is a critic of intelligent design and a biologist at Brown University, explains that natural selection (specifically predator-based selection) would give a big reward to the upstream transplants for a longer period of growth since larger females mean more eggs.

Once the guppies were transplanted upstream to a predator-free environment, natural selection would give any tendency towards a longer period of growth before sexual maturity a big reward — the chance to produce more offspring, as the number of eggs a female can produce goes up with an increase in body size. (Miller 2007)

But Reznick and his group are careful scientists and they realized that a variety of hypotheses could be responsible for the changes they had observed when high-predation downstream guppies were transplanted to the upstream low-predation environment. Luckily, Reznick and his group were up to the challenge of designing and carrying out experiments to test these hypotheses.

The Risk of Being Eaten

According to the predation-driven selection hypothesis, the guppies grew larger when predation was relaxed. This suggests that in the downstream pools where predation is higher, the larger adults must be more at risk of being eaten than the smaller guppies. They came up with a way to mark individual guppies that would allow them to be recaptured, which facilitated Reznick’s team being able to calculate the death rates for adult and juvenile guppies. However, after collecting this data, they found that death rates were similar for these different sizes of guppies. This discovery showed that the cause of change could not be direct predation. So, what was causing the changes?

Let’s fast forward to when Reznick et al. completed many more experiments and published a review of their results. (Reznick and Travis 2019) They reported:

Instead of direct predation affecting the guppies’ life history, the guppies exhibited density dependent selection which means the population density was affecting life history traits. In the upstream pools where there was lower predation, the populations grew larger which meant population density increased. This might also have a selection effect. To directly quote from their abstract: “We have shown that the agent of selection on the life history, behavior, and physiology in low-predation communities is high population density and the cascade of ecological effects that stems from it.” (Reznick and Travis 2019) In other words the purported mechanism is that when the population of guppies is dense, certain individuals harboring specific alleles have a reproductive advantage, leading to allele frequency changes in the population.

Independent populations of guppies from different streams and pools exhibited parallel allele frequency changes after they were moved from downstream to upstream. From the abstract: “This gradient is repeated in many rivers; in each one, we see the same divergence between guppy populations in life history, behavior, morphology, and physiology.” (Reznick and Travis 2019) This means the same allele frequency changes from one group of guppies from stream A were observed in a different group of guppies from stream B. This is not expected if such changes are due to random mutation (RM). (van der Zee et al. 2022) After all, what are the chances that RM would make the exact same changes over and over again?

No new mutations were observed. Instead, the pre-existing allele frequency in the population shifted and this is hypothesized to be due to natural selection (NS) based on standing genetic variation. They say, “the rapid and repeatable evolution of life histories in six introduced populations means that this evolution was fueled by standing genetic variation rather than by new mutations.” This means the adaptive capacity was built into the population of the organism itself. There was no RM that did something new and helpful,  that was then picked by the “agent” of NS.

What Kind of “Evolution” Is This Then?

Typically, these repeatable, parallel changes are considered an incredible display of natural selection, with many scientists thinking that the standing genetic variation ultimately arose from random mutation as well as the mechanism that is now maintaining it. Thus, RM/NS are identified as the ultimate cause under both the direct and indirect hypotheses for how predators shape guppy evolution. Is this fair? Reznick’s work shows that standing genetic variation was already baked in within the guppy population, leaving no role for random mutation. Because the variation was baked in, this places novelty-generation farther back in history, into a setting where there is less direct access to the environmental pressures that the variation is responding to. But wait, aren’t RM/NS both required for something to be considered evolution and an example of macroevolution?

The Source of Adaptive Information Is Unknown

Identifying the origin of novelty-generation as random mutation is pivotal to providing an authentic instance of Darwinian macroevolution. Instead, what we have here is an example of how populations rapidly adapt using preexisting genetic variation. Thus, these results do not provide favorable evidence for Darwinian macroevolution. Instead, they demonstrate that a previously touted example of “evolution happening before our eyes” is merely an example of population dynamics. This is where preservation of genetic diversity amongst the population means that individuals within the population represent different optimizations for unique environments. The essential question that many people are curious about remains: What is the source of the standing variation or genetic diversity that enables adaptation?

This leaves us at a place where some questions have been resolved, but the most important persist. Random mutation (RM) has been eliminated as the cause for the rapid parallel changes in the guppies. Predatory-driven selection, a form of natural selection, has also been eliminated as a possibility. However, the outstanding question of where the standing genetic variation ultimately came from remains. In my next post I will explore this question further.

The cambrian explosion may be the biggest bang of all?

 Fossil Friday: Kinorhyncha, Yet Another Animal Body Plan from the Cambrian Explosion

Gunther Bechly

This Fossil Friday we will look at an obscure group of animals from a clade of molting invertebrate animals called Ecdysozoa that include the roundworm phyla (Nematoda, Nematomorpha, Priapulida, Loricifera, and Kinorhyncha) as well as tardigrades, velvet worms (Onychophora), extinct lobopods, and arthropods (Telford et al. 2009). Almost all of these ecdysozoan phyla have been recorded from the Lower Cambrian and thus clearly originated with the burst of biological creativity in the Cambrian Explosion, which brought forth all the different animal body plans. As usual the molecular clock estimates would suggest an ancient origin of ecdysozoans deep within the Ediacaran period (Howard 2021, Howard et al. 2020, 2022), which is “highlighting major discrepancy with the known fossil record of the group” (Wang et al. 2024).

Indeed, apart from some dubious trace fossils and microfossils from the terminal Ediacaran (Vannier et al. 2010, Buatois et al. 2014, Moczydłowska et al. 2015, Parry et al. 2017, Chen et al. 2018, 2019, Kesidis et al. 2019, Turk et al. 2021), unequivocal body fossils of the ecdysozoan phyla (i.e., Priapulida and Loricifera) are first appearing in the Early to Middle Cambrian. The extinct Palaeoscolecida (Early Cambrian – Silurian) are considered to be either stem nematomorphs (Hou & Bergström 1994) or rather stem priapulids (Whitaker et al. 2020). Maas et al. (2010) described a possible stem Nematoida (Nematoda+Nematomorpha) from the Middle Cambrian of Australia, but its closer affinities remain unknown. A notable gap in our knowledge of ecdysozoan history was the phylum Kinorhyncha, which until recently had no known fossil record at all. These animals are small marine invertebrates that are also called mud dragons because of their spiny body.

Hardly a decade ago, Chinese scientists described “three dimensionally phosphatized worm-like fossils from the early Cambrian rocks, approximately 535 million years old, in northern Sichuan and southern Shaanxi provinces” of South China (Zhang et al. 2015; also see Fang 2015 and NGIP 2016). They were interpreted as early kinorhynchs and therefore named Eokinorhynchus rarus (featured above). The 2 mm long animals only differed from their living relatives in having more body segments and more distinct spines. In other words: the earliest kinorhynchs were more complex than modern ones. So much for the evolutionary narrative from simple to complex.

Defying Darwinian Explanations

Five years later, Shao et al. (2020) described Zhongpingscolex qinensis from the Early Cambrian (Fortunian Stage) of South China. Their phylogenetic analysis resolved this new taxon as closest relative (sister group) of Eokinorhynchus in the stem group of Kinorhyncha.The authors did not mention three undescribed taxa of fossil kinorynchs with up to 40 mm length from the Middle Cambrian Qingjiang biota in China (Fu et al. 2019; also see Daley 2019).

Based on these findings we can safely count Kinorhyncha among the large number of animal phyla that originated abruptly in the Cambrian Explosion. The more we learn about the fossil record the more the Cambrian Explosion is confirmed as a key event in the history of life, which defies Darwinian explanations

References

Buatois LA, Narbonne GM, Mangano MG, Carmona NB & Myrow P 2014. Ediacaran matground ecology persisted into the earliest Cambrian. Nature Communications 5: 3544, 1–5. DOI: https://doi.org/10.1038/ncomms4544

Chen Z, Chen X, Zhou C, Yuan X & Xiao S 2018. Late Ediacaran trackways produced by bilaterian animals with paired appendages. Science Advances 4(6): eaao6691, 1–8. DOI: https://doi.org/10.1126/sciadv.aao6691

Chen Z, Zhou C, Yuan XL & Xiao SH 2019. Death march of a segmented and trilobate bilaterian elucidates early animal evolution. Nature 573, 412–415. DOI: https://doi.org/10.1038/s41586-019-1522-7

Daley AC 2019. A treasure trove of Cambrian fossils. Science 363(6433), 1284–1285. DOI: https://doi.org/10.1126/science.aaw8644

Fang J 2015. Spiky, Armored Worm Lived Half A Billion Years Ago. IFL Science November 26, 2015. https://www.iflscience.com/spiky-armored-worm-lived-half-billion-years-ago-32315

Fu D, Tong G, Dai T, Liu W, Yang Y, Zhang Y, Cui L, Li L, Yun H, Wu Y, Sun A, Liu C, Pei W, Gaines RR & Zhang X 2019. The Qingjiang biota—A Burgess Shale–type fossil Lagerstätte from the early Cambrian of South China. Science 363(6433), 1338–1342. DOI: https://doi.org/10.1126/science.aau8800

Howard R 2021. The Deep Evolution of Ecdysozoa. Ph.D. thesis, University of Exeter, 459 pp. https://www.proquest.com/openview/257f91384a25d9c55ea9980ed27b561f/&diss=y

Howard RJ, Edgecombe GD, Shi X, Hou X & Ma X 2020. Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan. BMC Evolutionary Biology 20(1): 156, 1–18. DOI: https://doi.org/10.1186/s12862-020-01720-6

Howard RJ, Giacomelli M, Lozano-Fernandez J, Edgecombe GD, Fleming JF, Kristensen RM, Ma X, Olesen J, Sørensen MV, Thomsen PF, Wills MA, Donoghue PCJ & Pisani D 2022. The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. Journal of the Geological Society 179, 1–14. DOI: https://doi.org/10.1144/jgs2021-107

Hou X & Bergström J 1994. Palaeoscolecid worms may be nematomorphs rather than annelids. Lethaia 27(1), 11–17. DOI: https://doi.org/10.1111/j.1502-3931.1994.tb01548.x

Kesidis G, Slater BJ, Jensen S & Budd GE 2019. Caught in the act: priapulid burrowers in early Cambrian substrates. Proceedings of the Royal Society B 286(1894), 20182505, 1–8. DOI: https://doi.org/10.1098/rspb.2018.2505

Maas A, Waloszek D, Haug J & Müller K 2007. A possible larval roundworm from the Cambrian ‘Orsten’ and its bearing on the phylogeny of Cycloneuralia. Memoirs of the Association of Australasian Palaeontologists 34, 499–519. https://www.researchgate.net/publication/238695144

Moczydłowska M, Budd GE & Agić H 2015. Ecdysozoan-like sclerites among Ediacaran microfossils. Geological Magazine 152(06), 1145–1148. DOI: https://doi.org/10.1017/S001675681500045X

NIGP 2016. Scientists Found the First Fossil Record of Kinorhyncha (Scientific Reports, 2015). Nanjing Institute of Geology and Palaeontology Palaeonews No. 2 2015. http://english.nigpas.cas.cn/ns/palaeonews/no2/201602/t20160205_159614.html

Parry LA, Boggiani PC, Condon DJ, Garwood RJ, Leme JDM, McIlroy D, Brasier MD, Trindade R, Campanha GAC, Pacheco MLAF, Diniz CQC & Liu AG 2017. Ichnological evidence for meiofaunal bilaterians from the terminal Ediacaran and earliest Cambrian of Brazil. Nature Ecology & Evolution 1, 1455–1464. DOI: https://doi.org/10.1038/s41559-017-0301-9

Shao TQ, Wang Q, Liu YH, Qin JC, Zhang YN, Liu MJ, Shao Y, Zhao JY & Zhang HQ 2020. A new scalidophoran animal from the Cambrian Fortunian Stage of South China and its implications for the origin and early evolution of Kinorhyncha. Precambrian Research 349: 105616, 1–9. DOI: https://doi.org/10.1016/j.precamres.2020.105616

Telford MJ, Bourlat SJ, Economou A, Papillon D & Rota-Stabelli O 2009. The origins and evolution of the Ecdysozoa. Chapter 8, pp. 71–79 in: Telford MJ & Littlewood DTJ (eds). Animal Evolution: Genomes, Fossils, and Trees. Oxford University Press, Oxford (UK), xvi+245 pp. DOI: https://doi.org/10.1093/acprof:oso/9780199549429.003.0008

Turk KA, Maloney KM, Laflamme M & Darroch SAF 2021. Priapulid Trace Fossils from the Late Ediacaran of Namibia. Conference GSA Connects 2021, Portland (OR). https://gsa.confex.com/gsa/2021AM/webprogram/Paper369978.html

Vannier J, Calandra I, Gaillard C & Żylińska A 2010. Priapulid worms: Pioneer horizontal burrowers at the Precambrian-Cambrian boundary. Geology 38(8), 711–714. DOI: https://doi.org/10.1130/G30829.1

Wang D, Qiang Y, Guo J, Vannier J, Song Z, Peng J, Zhang B, Sun J, Yu Y, Zhang Y, Zhang T, Yang X & Han J 2024. Early evolution of the ecdysozoan body plan. eLife Preprint, 1–22. DOI: https://doi.org/10.7554/eLife.94709.1

Whitaker AF, Jamison PG, Schiffbauer JD & Kimmig J 2020. Re-description of the Spence Shale palaeoscolecids in light of new morphological features with comments on palaeoscolecid taxonomy and taphonomy. PalZ 94(4), 661–674. DOI: https://doi.org/10.1007/s12542-020-00516-9

Zhang H, Xiao S, Liu Y, Yuan X, Wan B, Muscente AD, Shao T, Gong H & Cao, G. 2015. Armored kinorhynch-like scalidophoran animals from the early Cambrian. Scientific Reports 5(1): 16521, 1–10. DOI: https://doi.org/10.1038/srep16521

A look at the search for a third way.

 Another Call for a “New Synthesis”

Daniel Witt

 recently wrote a post critical of biologist Peter Corning’s “synergism hypothesis.” Afterwards Dr. Corning got in touch and advised me to consider his new paper, “Cooperative Genes in Smart Systems: Toward an Inclusive New Synthesis in Evolution,” in Progress in Biophysics and Molecular Biology. 

Of course I was happy to read it. And I’m glad he pointed me to it, because although the paper doesn’t address any of the criticisms from the intelligent design perspective (honestly, I would have been pleasantly surprised if it did) it is quite relevant to the ID/Darwinism debate. 

In the new paper, Corning argues that it’s time to throw out the neo-Darwinian synthesis. He goes farther than the call for an “extended synthesis” that was made by some biologists a few years ago. It’s not that the synthesis needs to be extended, he writes — it needs to be replaced. 

This paper follows closely behind an article in Nature by Oxford’s Denis Noble arguing for much the same thing, which Casey Luskin reviewed here. Luskin wrote: 

Noble’s vision of biology… where dogma is discarded, new ideas are considered, agency and purpose are acknowledged, cells are more complex than computers and machines, proteins are like miniature transformers, and organisms control their genomes, is highly compatible with intelligent design — certainly far more compatible than the biological thinking of the past hundred years. This means biology is moving in the right direction. 

In his paper, Corning adds his voice to Noble’s. He cites Noble to argue that genes “play only a minor role” in evolution. Instead, many factors guide the evolution of life. Evolution is complex and unpredictable, he writes, and “biological evolution is not reducible to physics.” 

“The time has come,” Corning declares, “to abandon the gene-centered Modern Synthesis and The Selfish Gene model of evolution.” The new synthesis should be a “more inclusive, open-ended synthesis, in recognition of the fact that there may still be more influences yet to be discovered.”

Corning identifies several factors in evolution that are neglected by the Modern Synthesis, including: 

Epigenetic guidance of genetic change

Lamarckian evolution (heritable traits introduced by the habits of the parent) 

Horizontal gene transfer 

Symbiosis (or “cooperative effects,” or “synergy”) 

Teleonomy (internal “purposiveness”) 

He even cites the panspermia hypothesis, albeit in one of its more modest forms: the idea that the compounds that eventually formed the first life were seeded on Earth by meteors. 

If Lamarck Can Do It… 

All this points to a truth that is important for the ID position: namely, that “the assured results of modern science” may not be assured forever.

The gene-centered model is a clear example. We were supposed to believe that the “selfish gene” was unassailable and was only doubted by religious fundamentalists and cranks. If ID theorists rejected it, that was because they were at best biased, and at worst, secretly anti-science. 

But now, poof! it’s just another discarded model. 

Or take Lamarckian evolution. According to Corning, old Lamarck is making something of a comeback. Yet when I was first studying biology, Lamarck’s theory was presented to students as nothing but the debunked historical alternative to Darwinian evolution, faintly ridiculous in hindsight. (And to give you an idea of how quickly that means things can change: I don’t remember 9/11.) 

If one theory can return from the dusty, forgotten shelves of the History of Science and spring back to pages of biology journals, then so can another. No theory should be dismissed out of hand simply because the scientific “consensus” is against it. Likewise, no theory is so well-established that it might not someday be discarded. 

There Was No Problem, and Also, We Solved the Problem 

Granted, the fact that biologists such as Corning are calling for a new synthesis does not, in itself, necessarily indicate a flaw in Darwin’s theory. Yes, you could interpret it as a sign that the contemporary formulation of Darwinism is failing and that its devotees are scrambling to repair or replace it. But you could also put a different spin on it — that Darwin’s mechanism works just fine, but so do many other means of evolution. The call for a new synthesis could simply show that life actually has many ways to evolve. 

Corning’s statement in his book Synergistic Selection that “Darwin’s theory does not provide an explanation for the rise of biological complexity” would seem to favor the former view. Yet in this paper, despite the fact that Corning is calling for a new synthesis, he does not seem to want to state that there was ever really any big mystery or explanatory gap in unguided evolution. I suppose to do so would be to admit that ID theorists and critics of Darwin’s theory had a point. That sort of admission would be hard to publish in a peer-reviewed scientific journal (and Corning himself might not like to make it).

This is the sad irony: people will often only admit that an argument against their position has any merit after they think they have come up with a sufficient rebuttal. First, there’s no problem, and you’re ignorant to think that there is — then next thing you know, with no steps in between, you hear that the problem has been solved.

[Editor’s note: Casey Luskin has wryly called this dance move the “retroactive admission of ignorance.” “Years ago,” writes Dr. Luskin, “I began to recognize a repeating phenomenon in the rhetoric of evolutionary literature: Scientists, echoed by science journalists, would only admit a problem with their models or a challenge to their ideas once they thought they had found a solution.” See, for example, here.]

Winning by Not Playing? 

Of course, if you’re going to pull the trigger and move on to Phase 2, “The problem has been solved,” you’d better be darn sure that the problem really has been solved. I suspect a major reason the “new synthesis” has yet to become truly mainstream is that its various hypotheses don’t actually resolve any of the problems posed by ID arguments. 

Actually, it’s worse than that. They don’t even seem to address the arguments at all. 

It’s hard to effectively refute an argument without referencing it. The paper, and the hypotheses it promotes, are presented as being in some sense a rebuttal to the ID position. Yet there are no (even indirect) references to ID arguments in this paper. The mathematical difficulties of getting information for free are not addressed. The fact that only foresight, not natural selection, increases the probability of a system of interworking parts uniting to create a given adaptive feature, is not addressed. The demonstrated improbability of getting even a single truly constructive mutation by chance in the course of Earth’s 4.6-billion-year history is not addressed. The tendency of selective pressures to break things much faster than they build them is not addressed. 

If the architects of the new synthesis show no evidence of knowing more about intelligent design arguments than you can learn from Wikipedia, it’s no wonder defenders of Darwinism might be reluctant to embrace this synthesis as the new authoritative explanation for biological complexity. Although it’s rarely said out loud, the point has never been merely to explain complexity; it’s to explain complexity without design. And to do that, sadly, you sometimes have to actually engage with the design arguments (not all of which, by the way, are obvious enough to think of on your own). 

As tempting as it may be, simply ignoring the dissidents didn’t work for the old synthesis, and it won’t work for the new synthesis either. Eventually — if the new synthesis survives long enough — its proponents will have to come up with their own answers to the challenges facing unguided evolution.  

For OoL research: the pile on continues.

 

Necessary but not sufficient.

 A Closer Look at Natural Law 

Stephen J Iacobini

In my last post on the science of purpose, I pointed out that modern science took its inspiration from a belief that the universe was governed by immutable laws of nature emanating from the mind of God. This idea originated with the ancient Greeks, including Pythagoras, Plato, and Aristotle. Based on these concepts, in the 13th century, St. Thomas Aquinas defined within a Christian framework the specific ways and means of natural causation.

But the history of Western science took a major detour in the 17th century when René Descartes up-ended Thomistic Aristotelianism. The new Cartesian metaphysics provided fertile ground for reductionist science.

“Life Itself”

In his 1991 book Life Itself, theoretical biologist Robert Rosen attempted to reconcile materialist natural law with “life itself.” He explains that science is the endeavor of observing regularities in nature that allow scientists to create a “model” of natural behavior that is in congruence with natural events. For noncomplex natural events such as diffusion, gravitation, refraction, electricity, magnetism etc., it has been possible for scientists to derive mathematical formalisms that quite remarkably comport very well with these phenomena, such that they have great predictive power. And it has been that astonishing success which has led to the mistaken belief that these models of reality are one with nature itself. But Rosen pointed out that one huge shortcoming remains. There are no such formalisms that apply to life. Does that mean that life is at fault? Or does science need to be reimagined?

Resolving the Impasse

The solution, of course, is that scientists have mistakenly reified their formalisms, which is an obvious error. The laws of science are simply models that reflect regularities seen in nature. But they are not nature itself. They are as separate from the objects and events they describe as words on a page are separate from that which the literature attempts to depict.

Recognizing this problem, a number of innovative philosophers have been developing what seems to be an entirely new description of our world, such that it can include not just noncomplex inorganic material events, but truly all of life itself. This new metaphysics is variously termed dispositionalism, or powers ontology. But actually, it is not new. It is a revival of the insights of Aristotle and Aquinas, in a way quite intelligible to present-day philosophy and biology.

The concepts of Aristotle remain with us after almost 2,400 years because he focused directly on the concrete facts of life on display in the world around him. No computers. No calculators. No telescopes, microscopes, or laboratories. Just real life.

His description of reality was accordingly simple. Every thing has a form, i.e., a shape. And for designed objects it is the form which generates or allows the function. Forks are for gripping and spoons are for sipping. Chairs are made for sitting and ladders are made for climbing. And of course, the function of a thing defines its purpose, what Aristotle named telos

Aristotle offered a broad description of reality including inanimate objects. The form and function of stones and water and wood may seem less obvious to modern man than that of a coffee cup or a coat hanger. But the usefulness, i.e., power inherent in the properties of even these primal material objects was quite evident to earlier men.

The idea is simple because it is so fundamental. Every object has an intrinsic power because it has a corresponding inherent property. Stones have the property of solidity which gives them the power of weight and stability. Water has the property of fluidity which gives it the power of free movement. These simple substances can be further designed to acquire additional properties leading, of course, to complexity. Stones can be chiseled to give them the power to cut or penetrate. Water can be channeled to harness kinetic energy. Wood has the property of buoyancy and can be designed to build objects that float, and it also has the property to be shaped or formed into all the innumerable wooden objects one can imagine.

Now Consider Living Creatures

The property of sharp vision gives birds the power to hunt objects at great distances or pluck tiny insects out of the air. The property of echolocation gives bats the power to snatch insects on the wing even in the dark. The property of a keen sense of smell allows a polar bear to smell a seal miles away under the ice. The property of nectar production gives flowers the power to attract pollinating insects. The property of prehensile digits allows many animals the power to clutch objects needed for survival.

All of what I have said so far is immediately obvious. Now here is the payoff. The carbon atom has the property to form covalent bonds in three dimensions, giving it the power to create the scaffolding for complex molecules. Oxygen has the property of a strong electron valence, giving it the power to create an electronic asymmetry with atoms of lesser power. This is why water is a semipolar compound. Nitrogen has properties of chemical bonding intermediate between carbon, hydrogen, and oxygen, giving it the power to combine with these other three elements to create extremely complex organic compounds. And of course, CHNO (carbon, hydrogen, nitrogen, and oxygen) make up 99 percent of the atomic composition of life itself.

One with Reality Itself

As one’s thinking proceeds in this manner, we suddenly find ourselves talking about all of natural reality, from atoms to stones to vibrant living organisms, in the simple terms of properties which confer powers on matter, by virtue of form and function or telos. Nowhere in all of this is there a mathematical formula or need for materialist natural law.

Finally, and most importantly, describing natural kinds in terms of the properties that give them their power of cause and effect is one with reality itself. There is nothing derivative here. This ontology is at the ground of all we can know

This is in fact the divine natural law defined by Thomas Aquinas. His greatest metaphysical insight was to distinguish being from essence. Materialist natural law is an abstract derivative of natural essence, devoid of being. But real properties that bestow real power instantiate being in essence. For that which is in being also is in act. And according to Aquinas, that which is in act does so only as the result of divine intention.

The Jupiter of atheism?

 Compelled by Multiverse Logic

Evolution News

Any “person who is fully knowledgeable about the subjects is compelled by logic to accept the reality of multiverses.”

That emphasis on “compelled” is in the original. From, “The sounds of science — a symphony for many instruments and voices: part II.”

Warning: if one doesn’t accept at least some variant of the multiverse, says co-author and Texas A&M physicist Roland Allen, that refusal “may be potentially harmful to the progress of science, in the same way that not accepting evolutionary biology would be potentially harmful to biology…” He describes six different flavors of the multiverse (1-, 1, 1+, 2, 3 and 4) so if you are still skeptical after stepping away from that cosmological ice cream cart, you’ll have only yourself to blame for being so stubborn and hard to please. 

Well, all right then. You’re a Bad Egg if you doubt the multiverse, whatever the flavor, in the same Basket of Bad Eggs as evolution deniers. And like them, standing in the way of scientific progress.

See   here for more (see pages 23-28) — a comprehensive guide to current controversies and open problems in physics.

By the way, adjectives such as “fully knowledgeable” function as circularity-guaranteeing loops in a decision tree. Do you doubt the existence of a multiverse? Then you’re not fully knowledgeable (and have no right to an opinion).

OoL research has finally found the cheat codes?

 

Neanderthal man:just as sapien as we are?

 Fossil Friday: Suppressed Dissent About Neanderthal DNA in Modern Humans

Günter Bechly

Since the seminal study by Nobel laureate Svante Pääbo almost 15 years ago (Green et al. 2010), there have been numerous publications supporting the idea that non-African modern humans have a few percent of their DNA inherited from Neanderthals through introgression. This has basically become a widely accepted fact and the textbook orthodoxy. However, there is one dissenter. It is not some crank amateur but a professor of evolutionary genetics at the University of Cambridge, William Amos, who has published over 160 peer-reviewed publications including many in the highest-ranked journals such as Nature, Science, Nature Genetics, PLOS, Current Biology, and PNAS. Amos claims that the supposed evidence for introgression has been misinterpreted and is better explained by the hypothesis “that heterozygous sites attract additional mutations at and around them, creating a link between evolutionary rate and population size.“ Testing this hypothesis led him “to the prediction that mutation rate in humans would have dropped as a result of the large loss of variability that occurred during the out of Africa event, and thence to an alternative model to inter-breeding that could explain why non-Africans are closer to Neanderthals than Africans.”

Obscure Forums

So, how did the scientific establishment react to this maverick view? Actually, in spite of his credentials and in spite of his thorough argumentation and analyses, Amos tried in vain to get his dissenting hypothesis published in a peer-reviewed academic journal. Since 2017 his manuscript is still only available as a preprint from bioRxiv (Amos 2017). On his personal webpage Amos writes that “challenging the idea that many humans carry Neanderthal legacies has proved near-impossible!” Therefore, he decided to make a 20-page document freely available as a download on his website. It is titled “Is the idea that many humans carry some Neanderthal DNA correct?” and it summarizes his ideas, analyses, and reasons. The only brief discussions of his alternative hypothesis are found in the obscure forums of BioLogos and Peaceful Science, which is quite telling because these are sites mostly known for bashing intelligent design advocates.

A Parallel with Intelligent Design

Indeed, the case of Professor William Amos represents an interesting parallel with dissenters in the intelligent design community, who challenge the Darwinian orthodoxy and try to get their scientific studies published in peer-reviewed mainstream academic journals. In relatively rare cases it works (see here for a list), but most often the Darwinian thought police make sure that such manuscripts get rejected by the editors without even having been sent to reviewers. You heard right: such dissenting studies are mostly not rejected by peer reviewers because they are considered bad science. They are never seen by peer reviewers but are suppressed by overzealous watchmen of the scientific orthodoxy without further consideration. This is not just hearsay, because I experienced it twice in the past three months myself. So I can very much sympathize with the frustration of William Amos with the scientific community.

The latter community is clearly not driven by an unbiased quest for truth. Indeed, the peer review system has become deeply corrupted. Biologist and Nobel laureate Sydney Brenner said in an interview: “I think peer review is hindering science. In fact, I think it has become a completely corrupt system. It’s corrupt in many ways, in that scientists and academics have handed over to the editors of these journals the ability to make judgment on science and scientists.” Historian Philip Magness agreed and noted in a blog post that “Academic peer review is a highly dysfunctional process, replete with perverse incentives and maddeningly Kafkaesque outcomes.”

References

• Amos W 2017. Testing an alternative explanation for relatively greater base-sharing between Neanderthals and non-African humans. bioRxiv, 25 pp. DOI: https://doi.org/10.1101/133306
• Green RE, Krause J, Briggs AW, … Pääbo, S. 2010. A Draft Sequence of the Neandertal Genome. Science 328(5979), 710–722. DOI: https://doi.org/10.1126/science.1188021

Rabble rouser David berlinski on the deniability of Darwinism

 

AI as Darwinism's loyal opposition?

 Science Paper: Use Artificial Intelligence to Challenge Evolution

Casey Luskin

A new bold paper in the Elsevier journal Progress in Biophysics and Molecular Biology states, “Darwinian evolution has become dogma; AI can rescue what is salvageable.” Authors Olen Brown and David Hullender note, “The publication of scientific disagreements with elements of Darwinian evolution including its modern variants is increasing” and they cite various examples from the literature:

The publication of scientific disagreements with elements of Darwinian evolution including its modern variants are increasing. The view that “Evolution is both a fact and … the most important theory in biology. Evolution explains every situation” (Russo and André, 2019) is being challenged. Wray and Hoekstra in the Comment Does evolutionary theory need a rethink” published in Nature (Wray and Hoekstra, 2014) reported that Kevin Leland and seven colleagues responded “Yes, urgently”, while Gregory Wray and five colleagues responded: “No, all is well”. Typical of balanced questioning is Dennis Noble who wrote “Something has gone deeply wrong in biology” (Noble, 2021).

The paper thus argues that “that the theory of biological evolution, including its modern variants, suffers from several logical deficits, is absurdly improbable mathematically, and also biologically mechanism-deficient.” However, as the title suggests, the authors believe that “Darwinian evolution has become dogma” and some new method is needed to move past non-objective adherence to evolutionary models. They believe this method is artificial intelligence (AI).

Use AI to Challenge Evolution?

The authors propose that “the new approach of AI … is required to move forward scientifically.” They note that AI provides “powerful analytical tools” that can be used for evaluating the merits of scientific theories and ask, “[C]ould a complex computer be programmed to evaluate the theory (many say the fact) of biological evolution? Or perhaps test particular postulates essential to the theory?” They believe AI is well-suited for this task, since it has already been used to “rediscover fundamental equations” in fields such as physics and chemistry, and has been highly successful at playing games and solving puzzles. They believe this makes AI applicable to studying evolution: 

Use AI to Challenge Evolution?

The authors propose that “the new approach of AI … is required to move forward scientifically.” They note that AI provides “powerful analytical tools” that can be used for evaluating the merits of scientific theories and ask, “[C]ould a complex computer be programmed to evaluate the theory (many say the fact) of biological evolution? Or perhaps test particular postulates essential to the theory?” They believe AI is well-suited for this task, since it has already been used to “rediscover fundamental equations” in fields such as physics and chemistry, and has been highly successful at playing games and solving puzzles. They believe this makes AI applicable to studying evolution: 

Evolution, also, is a puzzle. It necessarily involves the absurdly improbable self-assembly of many complex biological machines using simpler parts (Brown and Hullender, 2023). Gartner et al. (2020) stated, “self-assembly of a large biological molecule from small building blocks is like finishing a puzzle of magnetic pieces by shaking the box.” AI works well for chess; we propose that it would work well for assessing ideas about biological evolution, especially the problem of self-assembly. Initially, it should be applied to testing the limits of the usefulness of ‘survival of the fittest’ for microevolution and the highly-improbable self-assembly required for macroevolution.

If AI were used to test and evaluate evolution, would people trust its results? 

Some May Not Like This Approach 

They believe that using AI to test evolution will lead to a problem: evolution will be challenged, and some may not want AI applied in this manner. They write that this should not matter because dogmas should never prevent scientific questions from being asked:

A perceived potential difficulty, which might, however, produce the first positive result of applying AI, is that focused discussion of the tenets, assumptions, and established facts of biological evolution would result. Consensus without criticism is not healthy for science. Biologists can learn from the field of Physics which is open to recognizing new ideas. It has shown itself receptive to change with concepts about gravity evolving from Newton to Einstein and the current interpretations, an example. The consequences of challenging the overall theory and subcomponents of biological evolution are monumentally significant for progress in this field and has ramifications for all of science including the freedom to challenge dogmas. “The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors” —J. Robert Oppenheimer.

[…]

Problems with the Darwinian theory of evolution, including its modern variants, and origin of life theories are significant and require new approaches and a willingness of scientists to look for bold solutions. The application of AI has great promise both for assessing the problems and weaknesses and for providing innovative and significant solutions of great significance for science and humankind. AI can be the pathway to correcting the problems in evolutionary theory, but the human brain must create that pathway. There must be no barriers to freedom of inquiry. There is no place for dogma in science.

Not Turtles All the Way Down?

These are nice statements of the importance of freedom of scientific inquiry. But what would AI find if it were let loose to critically investigate biological evolution? Their main argument is that we need to apply it to such a task. But they predict that if AI were applied to questions of biological origins, it would find serious flaws in evolutionary models: “We conclude that AI has this potential and encourage its application immediately for evaluating theories of biological evolution. It seems remote that AI would conclude that it is ‘turtles all the way down’.”

Surely any conclusion from AI about theories of biological evolution would be highly controversial — people would either accept and tout them or criticize the AI model that was used as flawed and inadequate. But it would be an interesting project to undertake nonetheless.

The origin of life remains the main pressure point re:teleology in nature.

 

The spectre of the cambrian explosion continues to loom over Darwinism

 Fossil Friday: Hemichordate Body Plan and Lifecycle Goes Back to the Cambrian Explosion

Günter Bechly

This Fossil Friday we will discuss the abrupt origin of yet another animal phylum during the famous Cambrian Explosion. It is the marine invertebrate phylum Hemichordata, which is represented by the pterobranchs (including the extinct graptolites) and the acorn worms (enteropneusts) as well as the enigmatic Planctosphaeroidea, which might just be planktic larva of some unknown deep sea acorn worms. Like chordates, hemichordates are deuterostome animals and considered to be the closest relatives (sister group) of echinoderms such as sea urchins and starfish. They have a tripartite body with three body cavities. While pterobranchs are sessile filter feeders, acorn worms are detritivores living in U-shaped burrows in the sea floor. The fossil record of Hemichordata goes back to the Early/Middle Cambrian (Maletz 2014, Nanglu et al. 2020).

The oldest known hemichordate and oldest pterobranch is the zooid fossil Galeaplumosus abilus from the 525-518 million year old Lower Cambrian Chengjiang Konservat-Lagerstätte of southern China (Hou et al. 2011, also see Hou et al. 2017).

Only very few fossil enteropneusts have been described yet in just eight fossil species (Cameron 2018, Yang et al. 2024) from the Cambrian (Walcott 1911, Caron et al. 2013, Nanglu et al. 2016, Yang et al. 2024), the Carboniferous (Bardack 1997, Maletz 2014, Cameron 2016), and the Jurassic periods (Arduini et al. 1984, Alessandrello et al. 2004, Bechly & Frickhinger 1999). Possible trace fossils of acorn worms have been reported from the Lower Triassic of Italy by Twitchett (1996). This rarity is quite remarkable because some other soft-bodied worm-like organisms that burrow in the sea floor are much better represented in the fossil record. Actually, the only enteropneust specimen from the Upper Jurassic Solnhofen limestone of Bavaria in Germany was described by myself as Mesobalanoglossus buergeri (also see Bechly 2015). The featured image shows the holotype specimen (no. SNSB-BSPG 1998-I-15), which is 68.8 cm long and 2.6 cm wide, and deposited at the Natural History Museum in Munich.

Abrupt Appearance, Yet Again

Recently, 39 specimens of the previously unknown acorn worm Cambrobranchus pelagobenthos were described from the Hayiyan Lagerstätte in China (Yang et al. 2024), which belongs to the famous Lower Cambrian Chengjiang biota. The scientists could also describe larvae and juveniles and thereby document the characteristic indirect development with a pelago-benthic lifestyle already for these earliest known representatives of acorn worms.

Thus, both major subgroups of the phylum Hemichordata are known from Lower Cambrian fossils with completely modern morphology and life cycle, which confirms the overall pattern of the abrupt appearance of animal phyla in the Cambrian Explosion. Furthermore, the putative stem-hemichordate Gyaltsenglossus senis was described by Nanglu et al. (2020) from the Cambrian Burgess Shale of Canada. However, with an estimated age of 506 million years, it is 10-20 million years younger than the oldest crown group representatives discussed above and thus requires an ad hoc explanation in terms of ghost lineages to be accommodated within a Darwinian paradigm

References

Alessandrello A, Bracchi G & Riou B 2004. Polychaete, sipunculan and enteropneust worms from the Lower Callovian (Middle Jurassic) of La Voulte-sur-Rhône (Ardèche, France). Memoire della Società Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano (Fascicolo I) 32, 1–16.

Arduini P, Pinna G & Terruzzi G 1981. Megaderaion sinemuriense n.g. n.sp., a new fossil enteropneust of the Sinemurian of Osteno in Lombardy. Atti della Societa Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano 122(1-2), 104–108. https://www.biodiversitylibrary.org/part/325194

Bardack D 1997. Wormlike animals: Enteropeusta. pp. 89–92 in: Shabica CW & Hay AA (eds). Richardson’s Guide to the fossil fauna of Mazon Creek. Northeastern Illinois University, Chicago (IL), 308 pp.

Bechly G 2015. [Chapter] Eichelwürmer (Hemichordata: Enteropneusta). p. 324 in: Arratia G, Schultze HP, Tischlinger H & Viohl G (eds). Solnhofen – Ein Fenster in die Jurazeit. 2 vols. Pfeil Verlag, Munich (Germany), 620 pp. [In German] https://pfeil-verlag.de/publikationen/solnhofen-ein-fenster-in-die-jurazeit/

Bechly G & Frickhinger KA 1999. Acorn worms. pp. 76–79 in: Frickhinger KA (ed.). The Fossils of Solnhofen 2: New specimens, new details, new results. Goldschneck-Verlag, Korb (Germany), 190 pp. [German PDF]

Cameron CB 2016. Saccoglossus testa from the Mazon Creek fauna (Pennsylvanian of Illinois) and the evolution of acorn worms (Enteropneusta: Hemichordata). Palaeontology 59(3), 329–336. DOI: https://doi.org/10.1111/pala.12235

Cameron CB 2018. Class Enteropneusta: Introduction, Morphology, Life Habits, Systematic Descriptions, and Future Research. Treatise Online 109, 1–22. DOI: https://doi.org/10.17161/to.v0i0.7889 (dead link)

Caron J-B, Conway Morris S & Cameron CB 2013. Tubicolous enteropneusts from the Cambrian period. Nature 495, 503–506. DOI: https://doi.org/10.1038/nature12017

Hou X-g, Aldridge RJ, Siveter DJ, Siveter DJ, Williams M, Zalasiewicz J & Ma X-y 2011. An Early Cambrian Hemichordate Zooid. Current Biology 21(7), 612–616. DOI: https://doi.org/10.1016/j.cub.2011.03.005

Hou X-g, Siveter DJ, Siveter DJ, Aldridge RJ, Cong P-y, Gabbott SE, Ma X-y, Purnell MA & Williams M 2017. Hemichordata. Chapter 22, pp. 250–251 in: The Cambrian Fossils of Chengjiang, China: The Flowering of Early Animal Life. 2nd Edition. John Wiley & Sons, Chichester (UK) / Hoboken (NJ), xii+316 pp. DOI: https://doi.org/10.1002/9781118896372.ch22

Maletz J 2014. Hemichordata (Pterobranchia, Enteropneusta) and the fossil record. Palaeogeography, Palaeoclimatology, Palaeoecology 398, 16–27. DOI: https://doi.org/10.1016/j.palaeo.2013.06.010

Nanglu K, Caron J-B, Conway Morris S & Cameron CB 2016. Cambrian suspension-feeding tubicolous hemichordates. BMC Biology 14: 56, 1–9. DOI: https://doi.org/10.1186/s12915-016-0271-4

Nanglu K, Caron J-B & Cameron CB 2020. Cambrian Tentaculate Worms and the Origin of the Hemichordate Body Plan. Current Biology 30(21), 4238–4244.e1. DOI: https://doi.org/10.1016/j.cub.2020.07.078

Twitchett RJ 1996. The Resting Trace of an Acorn-Worm (Class: Enteropneusta) from the Lower Triassic. Journal of Paleontology 70(1), 128–131. https://www.jstor.org/stable/1306375

Walcott CD 1911. Cambrian Geology and Paleontology II: No. 5 – Middle Cambrian annelids. Smithsonian Miscellaneous Collections 57, 109–145. https://repository.si.edu/handle/10088/34820

Yang X, Kimmig J, Cameron CB, Nanglu K, Kimmig SR, de Carle D, Zhang C, Yu M & Peng S 2024. An early Cambrian pelago-benthic acorn worm and the origin of the hemichordate larva. Palaeontologia Electronica 27(1): a17, 1–19. DOI: https://doi.org/10.26879/1356

Darwinism's God?

 Was God a Bacterium? 

Daniel Witt

University of Bonn biologist František Baluška has an explanation for the apparent design in biology. He believes that there was design involved in evolution — yet not from an outside designer, but from the organisms themselves. He maintains that all living organisms are sentient, even down to simplest bacteria, and that they used their minds to evolve.

You read that right. And it’s not a mischaracterization of his views. For example, here’s how Baluška and his collaborators William B. Miller Jr. and Arthur S. Reber summarize the thesis in a recent paper1:

The first eukaryotic cells emerged some 2–1.5 billion years ago, which implies that it took nearly two billion years to get from prokaryotic to eukaryotic cells. Our cellular basis of consciousness (CBC) model states that all living cells utilize cellular sentience to survive and evolve. We argue that the prolonged timeline to evolve eukaryotic cells from prokaryotic cells was necessitated by the complex level of evolutionary novelty required to assemble unitary consciousness from several formerly independent prokaryotic versions of cellular consciousness, as successive orders of cognition…Once an initiating eukaryotic threshold of cognition was attained, eukaryotic evolution (based on its novel eukaryotic version of cellular sentience and cognition) proceeded relatively rapidly alongside an active unicellular sphere, including a huge diversity of protozoa and other protists that has thrived and evolved until our present day. Some 0.8 billion years ago, and on several occasions, colonial protists invented the multicellular forms that evolved into fungi, animals, and plants, emerging first in the sea and later also on land. Cellular cognition enabled multicellularity and permitted its successful continuous evolution toward the higher level of cohesive cellular complexities exhibited in multicellular organisms, with symbiotic fungal–plant/tree roots networks representing one of its most extensively integrated forms.

Notice the use of the word “invented.” For once, this is not a case of sloppy language or the tendency to anthropomorphize natural selection. They are really saying that protists invented complex multicellular life, using their minds. First life evolved the ability to think; then it used that ability to evolve everything else. As they put it later on: “Evolutionary development is creative not only through either mutations or natural selection but also — and mainly — through the linked cognitive activities and preferences of individual organisms.”

Poetic License? 

Peter Corning, an editor of the volume in which the paper appears, seems a little wary of going all-in on the idea of conscious microorganisms. In his introductory essay to the volume, he says that biologists who say primordial organisms exhibit sensation, choosing, and mind are exercising “poetic license.” 

Poetic license is well and good — in poetry. But poetry does not cut it as scientific explanation. If the idea of primordial consciousness is mere poetry, it does not explain. If, on the other hand, it is not mere poetry… well, that is something very astonishing. It speaks either to a non-physical intellect, or else to a level of ordered complexity much harder to account for than the complex systems it is invoked to explain away in the first place. Neither option is quite tolerable, apparently, so Corning seems to be trying to have his cake and eat it too. Primordial “consciousness” can be invoked to get past the nasty difficulties with neo-Darwinism, but if it’s called out as too ridiculous, or demanding explanation, that charge can be brushed away with “poetic license.”

At any rate, I see no evidence that Baluška and his colleagues are being the least bit poetical. They make it very clear that what they are talking about is literally mind, cognition, consciousness, sentience — terms they seem to use interchangeably. They attribute mind to primordial organisms, and attribute evolution to the decisions made by these minds. 

Elsewhere, Baluška and Reber write, “let us be clear about what we mean by sentience or consciousess [sic] as it is manifested in unicellular species. We are referring to feelings, subjective states, a primitive awareness of events, including an awareness of internal states.”

But How Does It Work? 

We should acknowledge that this theory is, unlike some similar attempts, at least an actual solution: if true, it would explain how complex life evolved. However, in solving that problem, Baluška and his colleagues create another, equally formidable problem: how does this primordial sentience work, and where did it come from? 

While there does appear to be evidence that plants, fungi, protozoans, bacteria, and archaea respond to the world in a manner that is much more like “thinking” than we are typically taught to believe, there is a lot of mystery about how they do it. The following explanation, from the first paper, is typical:

The plasma membrane provides all cells with a sheltered space, allowing exotic biophysical phenomena based on charged ions, reactive oxygen species, and bioelectric as well as biomagnetic phenomena.

Throw in a random assortment of poorly understood phenomena, and boom! you have consciousness. Of course, the authors would admit that the exact mechanisms of cellular consciousness are still poorly understood. That’s fine. But do they really think that once they uncover the details of these primordial minds, those minds will be easier to explain naturalistically than, say, the bacterial flagellum?

A Cure Worse than the Disease

The thing is, if we ever came down to hard details about what Baluška et al. are proposing, all the old design arguments would still be waiting to be dealt with. There is no reason to hope that “cellular cognition,” “plant neurons,” or a “fungal mind” is less likely to be irreducibly complex or require foresight in its engineering than any other biological system. Actually, it would probably be much more complex than most. 

Essentially, what these researchers are doing is taking the most advanced and perplexing system in biology, the brain, and putting it at the beginning of the evolutionary process instead of the end. That’s a fascinating theory, and they are to be commended for their courage and willingness to think outside the box. If true, it’s revolutionary. But it’s not going to make things easier on unguided evolution.

For now, it might make things easier on scientists who prefer to hide from design arguments rather than face them head on. But in the end, there is no escaping the fact that if this theory is true it speaks to a level of design in nature far more exquisite and improbable than anything hitherto dreamt of. 

Notes

Baluška, František, William B. Miller Jr., and Arthur S. Reber. “Cellular Basis of Cognition and Evolution: From Protists and Fungi Up to Animals, Plants, and Root-Fungal Networks.” In Evolution “On Purpose”: Teleonomy in Living Systems, edited by Peter A. Corning, Stuart A. Kauffman, Denis Noble, James A. Shapiro, Richard I. Vane-Wright, and Addy Pross. 33-58. Cambridge, Massachusetts: MIT Press, 2023. 

Synergies did it?

 Synergies All the Way Down 

Daniel Witt

The turn of the 21st century saw the publications of several works that challenged the theoretical basis of Darwin’s theory, notably Darwin’s Black Box (1996), by Michael Behe, and The Design Inference (1998) and No Free Lunch (2001) by William Dembski. The books were generally ignored or disparaged in the evolutionary biology community. Yet around that time (no doubt by coincidence) the search began for a “grand unified theory” of evolution, that would provide “some single principle or some small set of principles” to explain the tendency of life to become more complex. 

Of course, “natural selection and random variation” was supposed to be that single principle. But unofficially, Darwin’s unifying theory had been deemed inadequate, and the quest was on for something that actually worked. 

Evolutionary biologist Peter Corning seems to be rather annoyed by this quest. After giving a summary of the state of things (including the quotes above), Corning writes that there already is such a unifying theory, and he invented it.1 It was proposed decades ago in his 1983 book The Synergism Hypothesis: A Theory of Progressive Evolution. 

This is how Corning explains his theory:

Synergistic selection refers to the many contexts in nature where two or more genes/genomes/individuals have a shared fate; their combined effects are functionally interdependent…Although it may seem like backwards logic, the thesis is that functional synergy is the cause of cooperation and complexity in living systems, not the other way around.

The idea is that pre-existing systems combine to make more complex systems, and the whole is greater than the sum of the parts. Examples of synergy cited by Corning include: self-replicating molecules enclosed in cell walls; chromosomes linking those self-replicating molecules together relationally; the genetic code connecting RNA, DNA, and proteins; eukaryotes created by the absorption of one prokaryote into another; multicellularity; sexual reproduction; emperor penguins huddling together for warmth. 

Foresight, or Synergy? 

If you survey this list, you may notice something. Most of the examples are used by ID proponents, but for a different purpose — to point to the principle of planning or foresight in living systems. When a system requires many complex interworking parts to function, this can’t be explained by minor innovations building up over time, except perhaps by an insanely lucky fluke; another principle besides Darwin’s mechanism is needed, and that principle is design. 

Or perhaps it isn’t. Perhaps it’s “synergy”?

Corning believes that this principle explains the complex interdependency of living systems, without the need for a designer. He sees his model as a Darwinian theory. It’s not that Darwinism needed replacing: it was just missing an ingredient, and synergy is that ingredient. 

Solving the Problem, or Just Describing It?

Okay, that’s a theory… or is it? Is synergy an explanation, or merely a description? The term “synergy” points to the reality that organisms are wholes much greater than the sum of their parts, with the parts working together in a symphony of complex relationships. It does not, in and of itself, explain how that came to be. The final cause is left unspecified. 

You can see this in the fact that Corning mixes up cases of synergy that are clearly caused by an identifiable intelligent mind (e.g., emperor penguins huddling together for warmth) with cases where no such mind is apparent (e.g., the appearance of chromosomes to connect genes together). In the case of the emperor penguins, penguin intelligence is the explanation for the penguin huddle. The synergy happens because they decide they want it to happen, using their intelligence. Can RNA, DNA, proteins, and cell membranes do the same? 

Yes or no? Neither answer helps Darwinian evolution out much. If the answer is yes, that’s truly remarkable, and itself requires intelligent design, since all the usual design arguments would apply to this undoubtedly complex (though apparently hidden) molecular intellect. If the answer is no, Corning has done nothing but describe the situation. He has not explained it. Yes — RNA, DNA, proteins, and cell membranes work together in beautiful synchronization to create a system greater than the sum of its parts — well and good, but how did this come to be?

Without foresight, why should two complex, compatible systems be sitting there, ready-made and waiting to be combined in intricate ways to form something greater? There is no reason implicit in the laws of nature why they should be. And the odds of it happening by chance, through a single random variation at a time, are not likely to be any better than the odds of simply building the whole system that way. If, on the other hand, the systems are not designed to be compatible, how are they to come together? How could evolution do the necessary random tinkering, a vast amount of it, without destroying the functionality of one or both systems?

If you doubt the difficulty of this, take a couple of man-made machines and try to combine them, preserving function in every step of the process. It’s not easy, even though you are using intelligent design to do it — unless the two machines were intentionally designed to be compatible.  

The funny thing is, these are the standard arguments for intelligent design in biology. Corning only calls attention to the problem. He does not solve it, because in the end his explanation just backs the question. He deals with the improbability of design by explaining it through synergy, not caring that this synergy is itself a design marvel in need of explanation. And why should he care? No doubt that design marvel can be explained by synergy, too — and on and on, back into the misty dawn of life where nothing is visible and therefore nothing needs to be explained.

“It’s Turtles All the Way Down”

Corning concludes his paper with a familiar story. He writes:

There is a story attributed to the famed twentieth century philosopher Bertrand Russell about a public lecture in which he discussed various properties of the Solar System. At the end of his lecture, an elderly woman in the audience approached him and told him he was wrong. The sun is held up on a turtle’s back, she said. A startled Russell responded by asking her, so what holds up the turtle? “You think you’re so clever,” she replied. “It’s turtles all the way down.” So what explains the rise of complexity in evolution? From the perspective of the Synergism Hypothesis and Synergistic Selection, it’s synergies all the way up.

Honestly, it’s a bit perplexing that he would choose such an example to sum up his views. The tone of his writing here is triumphant, but doesn’t he realize that the old woman is supposed to be either foolish, crazy, or pulling Russell’s leg?

I’m also not quite sure why he substitutes “up” for “down” in the phrase “synergies all the way up.” There is no logical reason to do so. You can envision the process of evolution from either direction, just as you can look at a stack of turtles from either above or below. Our actual perspective, however, is from the top, and we are looking down into the past in search of the final cause of complex systems. So the original phrasing is really more fitting. 

One has to wonder if Corning changed the word due to a subconscious realization that there was a rhetorical risk in drawing attention to the parallel between himself and Russell’s crazy turtle lady. But mixing up the phrasing isn’t going to solve that problem, because the logic is the same. “Synergies all the way down” may be good enough for Corning, but some of us would like to know what it all rests on.

Notes

Corning, Peter A. “Teleonomy in Evolution: “The Ghost in the Machine”.” In Evolution “On Purpose”: Teleonomy in Living Systems, edited by Peter A. Corning, Stuart A. Kauffman, Denis Noble, James A. Shapiro, Richard I. Vane-Wright, and Addy Pross. 11-31. Cambridge, Massachusetts: The MIT Press, 2023.

Naturally selecting what exactly?

 

The fossil record sides with devolution?

 Fossil Friday: New Study Confirms “Feathered Dinosaurs” Were Secondarily Flightless Birds

Günter Bechly

This Fossil Friday features one of the most well-known fossils of all, the famous Berlin specimen of the ancient bird Archaeopteryx from the Late Jurassic Solnhofen lithographic limestone in Bavaria. This iconic fossil was often considered to be a missing link between dinosaurs and birds, and thus a poster-child for fossil evidence in favor of Darwinian evolution.

In several past articles at Evolution News I have discussed the work of paleo-ornithologist Alan Feduccia, who courageously challenged the current consensus view that birds evolved from dinosaurs, as first suggested by Yale paleontologist John Ostrom in the mid 1970s with his Birds-are-Maniraptoran-Theropods (BMT) hypothesis. Feduccia elaborated his opposing views in numerous technical articles and four popular books titled “The Age of Birds“ (Feduccia 1980), “The Origin and Evolution of Birds” (Feduccia 1996), “Riddle of the Feathered Dragons” (Feduccia 2012), and most recently “Romancing the Birds and Dinosaurs” (Feduccia 2020). In a highly recommended review of the latter book, James (2021) wrote that “Every school child knows that birds are dinosaurs. Numerous magazine articles and popular books on the topic are available,” which is a remarkable success of selling a relatively recent scientific hypothesis to a wide general audience as an established fact. James continues that “in spite of all this confidence that the problem of the origin of birds has been solved, strong grounds exist for regarding the issue as unsettled, … Surely, admitting that the hypothesis that birds are maniraptoran theropods has serious problems would be better than to defend it so strongly.”

Three General Objections

In a review of Feduccia’s earlier book on the “Riddle of the Feathered Dragons,” Leigh (2014) listed three general objections by Feduccia to Ostrom’s dinosaur-to-bird hypothesis:

1.Most of the fossils used to support the theropod ancestry of birds are 20 million or more years younger than Archaeopteryx [this was famously labeled by Feduccia as a “temporal paradox”].

2.Theropod dinosaurs, Deinonychus included, were runners. It is much more reasonable to believe that, like bats and pterosaurs, birds descended from arboreal animals that evolved flight via the ability to glide.

3.The fossil record suggests that feathers evolved in connection with gliding and flying, rather than as insulation, or as part of an apparatus for catching insects, as Ostrom had suggested.

James (2021) listed several further problems that Feduccia has identified in his most recent book, which support his alternative view:

Neoflightless problem: Some flying and flightless birds are being misclassified as theropods.

Data analysis problem: Standard phylogenetic analyses are unable to detect complex evolutionary processes like convergence. Flightless birds converge on the body plan of theropods. To estimate basic similarities (homologies), anatomical studies are needed before the phylogenetic analysis.

Reduced forelimb problem: Complex characters, once lost, are unlikely to reevolve. Dollo’s Principle.

Protofeather problem: “Protofeathers” may be degraded collagen fibers.

Digit problem: The frame shift is a verificationist explanation, designed to fit the BMT.

Behavior problem: Studies that infer bird-like behavior in dinosaurs are about misidentified birds.

Confirmation problem: Scansoriopterygids have no distinctive theropod characters. An assumption that they are theropods is a form of confirmation bias. 

Geist (2022) commented in his review of the same book:

Feduccia leads readers through case after case where scientists, to accommodate the cladograms supporting the BMT hypothesis, have gone to extraordinary lengths to work around data that directly contradict their conclusions. Such efforts violate another bedrock, though not ironclad, philosophy of science: Occam’s Razor, stating that given multiple hypotheses, the simplest of competing theories be preferred over the more complex. Feduccia elegantly illustrates cases where conclusions drawn from cladistic analysis that dictate the connection between birds and dinosaurs violate this principle. At the very least this book might convince supporters of BMT to reevaluate the data.

This failure of cladistics was admitted by John Ostrom (1994: 172) himself, who commented that “reasoning of such dubious quality demonstrates a fundamental flaw in cladistic methodology. Preoccupation with compilation of lengthy lists of shared derived characteristics at the expense of a well-reasoned analysis will result in an erroneous phylogeny every time.”

Responding to Feduccia

So, how did the proponents of the dinosaurian ancestry of birds respond to Feduccia’s profound challenges? They did as Darwinists always do when their pet hypotheses are challenged with actual data: they ridicule and marginalize the critique or reduce it to a straw-man caricature. Here is what Ruben (1997) wrote in his review of Feduccia’s second book:

Specialists who are concerned with avian origins, especially those advocating a dinosaur-bird lineage, will be forced to confront a variety of previously ignored data that argue against this lineage. Thus, it hardly comes as a surprise that the book has been dismissed in recent reviews by several particularly zealous, cladistically oriented paleontologists. However, readers should not be misled by such shenanigans.

Zealous shenanigans? This is quite revealing for an alleged unbiased quest for scientific truth.

The Neoflightless Hypothesis

But, how does Feduccia explain the indisputable great similarity between vane-feathered bipedal dinosaurs (called Pennaraptora) and true birds? Actually, he does not dispute a close relationship at all, but suggests that Pennaraptora were not theropod dinosaurs but rather secondarily flightless birds, which he called the neoflightless hypothesis. Incidentally, the same claim has been made by skeptics of Darwinian evolution.

Now, a new study by Kiat & O’Connor (2024) published in the Proceedings of the National Academy of Sciences provides strong additional support to the neoflightless hypothesis (also see the press releases by Field Museum 2024 and Koumoundouros 2024). The scientists studied the wing feathers in hundreds of different living bird species of all major orders, and detected a simple pattern that reliably distinguishes secondarily flightless birds from those that can fly: the latter always have 9-11 asymmetrical flight feathers called primaries, while the former have either significantly more or none at all. Furthermore, the degree of primary vane asymmetry turned out to be strongly related to flight. This allowed the researchers to look at 65 species of fossil birds and feathered dinosaurs to estimate their ability to fly. Unsurprisingly, Archaeopteryx and the four-winged Microraptor passed the litmus test for flight.

Much more surprisingly, the study suggests that feathered dinosaurs like “Caudipteryx possessed the correct number of primary feathers but they were almost completely symmetrical, ‘almost certainly’ ruling out flight” (Koumoundouros 2024). The authors concluded that “applying these data to extinct pennaraptorans suggests that anchiornithines and the oviraptorosaur Caudipteryx are secondarily flightless. The phylogenetic position of these species suggests that volant abilities are plesiomorphic to Pennaraptora.” In other words, all those feathered dinosaurs originally had wings like birds and could fly, and thus do not represent transitional stages in the evolution of avian flight from cursorial dinosaurs. They are no help at all to explain the origin of pennaceous feathers and wings. This also makes very recent studies obsolete, which proposed scenarios to derive the bird wing from more primitive structures in maniraptoran dinosaurs, such as the propatagium in Caudipteryx and Microraptor (Uno & Hirasawa 2023, also see University of Tokyo 2023). As new data accumulate at an ever faster rate, the shelf life of evolutionary story telling is plummeting from decades to only months.

Trust the Science?

Should you really just trust the science (but not too long)? Alan Feduccia can rightfully claim an important empirical confirmation of his theory, and Darwinists may have to say goodbye to some cherished assumed transitional forms and the evolutionary just-so stories built upon them. But there is more: Kiat & O’Connor (2024) explicitly admit that “the results of these analyses support a single origin of dinosaurian flight and indicate the early stages of feathered wing evolution are not sampled by the currently available fossil record.” It looks very much like flying vertebrates with feathered wings appeared fully formed and abruptly in the Jurassic, which resonates perfectly with intelligent design theory, but with Darwinism (in the sense of unguided gradual evolution) not so much.

References

• Feduccia A 1980. The Age of Birds. Harvard University Press, Cambridge (MA), ix+196 pp.
• Feduccia A 1996. The Origin and Evolution of Birds. Yale University Press, New Haven (CT), 420 pp. 
• Feduccia A 2012. Riddle of the Feathered Dragons: Hidden Birds of China. Yale University Press, New Haven (CT), x+358 pp.
• Feduccia A 2020. Romancing the Birds and Dinosaurs: Forays in Postmodern Paleontology. Brown Walker Press, Irvine (CA), 336 pp.
• Field Museum 2024. The hidden rule for flight feathers and how it could reveal which dinosaurs could fly. Phys.org February 12, 2024. https://phys.org/news/2024-02-hidden-flight-feathers-reveal-dinosaurs.html
• Geist N 2022. Romancing the Birds and Dinosaurs: Forays in Postmodern Paleontology. Ornithology 139(3), 1–2. DOI: https://doi.org/10.1093/ornithology/ukac013
• James FC 2021. How Many Dinosaurs Are Birds? Bioscience 71(9), 991–994. DOI: https://doi.org/10.1093/biosci/biab060
• Kiat Y & O’Connor JK 2024. Functional constraints on the number and shape of flight feathers. PNAS 121(8): e2306639121. DOI: https://doi.org/10.1073/pnas.2306639121
• Koumoundouros T 2024. Scientists Discover an Ancient Pattern Hidden in The Feathers of Birds. ScienceAlert February 25, 2024. https://www.sciencealert.com/scientists-discover-an-ancient-pattern-hidden-in-the-feathers-of-birds
• Leigh EG 2014. Alan Feduccia’s Riddle of the Feathered Dragons: what reptiles gave rise to birds? Evolution: Education and Outreach 7: 9, 1–3. DOI: https://doi.org/10.1186/s12052-014-0009-0
• Ostrom JH 1994. On the origin of birds and of avian flight. pp. 160–177 in: Prothero DP & Schoch RS (eds). Major Features of Vertebrate Evolution. University of Tennessee Press, Knoxville (TN), 270 pp.
• Ruben J 1997. The fuss over feathers. BioScience 47(6), 392–395. DOI: https://doi.org/10.2307/1313154
• University of Tokyo 2023. How birds got their wings. Phys.org February 24, 2023. https://phys.org/news/2023-02-birds-wings.html
• Uno Y & Hirasawa T 2023. Origin of the propatagium in non-avian dinosaurs. Zoological Letters 9: 4, 1–8. DOI: https://doi.org/10.1186/s40851-023-00204-x