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

On the iconoclasm unleashed by the four horsemen.

 Dawkins, Dennett, and the Taste for Iconoclasm

William A Dembski

I’ve had two memorable encounters with Richard Dawkins and Daniel Dennett, one with Dennett alone, the other with both together. The first was with Dennett alone. In 1999, my good friend Paul Nelson and I were doing some tag-team talks on intelligent design in the Boston area at MIT and Tufts. The talk at Tufts, Dennett’s university, was in the evening, so we had some time beforehand. We therefore decided to attend Dennett’s philosophy of science seminar, which was taking place late that afternoon. 

The Aquatic Ape

Dennett was hosting Elaine Morgan, an evolutionary anthropologist. In her talk, she described her “aquatic ape hypothesis.” According to this hypothesis, in the evolution of humans from hairy ape-like ancestors, we had an aquatic phase in which we lived primarily in water. Our water phase is supposed to account for a number of human characteristics, including our smooth skin. 

Dennett didn’t accept Morgan’s aquatic ape hypothesis, but he did give her a forum. He saw it as helpful to his students and colleagues to engage her. And he himself has defended her view in his 1995 book Darwin’s Dangerous Idea:

Many of the counterarguments seem awfully thin and ad hoc. During the last few years when I have found myself in the company of distinguished biologists, evolutionary theorists, paleo-anthropologists, and other experts, I have often asked them just to tell me, please, exactly why Morgan must be wrong about the aquatic ape theory. I haven’t yet had a reply worth mentioning, aside from those who admit, with a twinkle in their eyes, that they have often wondered the same thing

In her talk at Tufts, Morgan was affable, and she made a detailed case for her position. She also made available for sale at the talk her then recently published book The Aquatic Ape Hypothesis, which I bought and had her sign (it remains somewhere in storage). 

Near the start of the seminar, Dennett noted that Paul and I were in the audience and would be speaking at Tufts that evening on intelligent design. He then remarked: “If your taste for iconoclasm exceeds even mine, attend their talk tonight.” It was an amusing shout-out. Dennett clearly regarded Elaine Morgan as an iconoclast. Yet to his mind, her iconoclasm was far less than Paul’s and mine in advancing intelligent design.  

To my mind, Morgan is the bigger iconoclast, and intelligent design is sound sober theorizing about biological origins and complexity. Yet as Dennett could rightly note in reply, the taste for iconoclasm is a matter of taste. For whatever reason, Dennett didn’t attend our talk that night.

“The Deniable Darwin”

My second story involves both Richard Dawkins and Daniel Dennett, and occurred in 2003. I was editing for ISI Books an anthology titled Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. I wanted to include not just David Berlinski’s article “The Deniable Darwin” that had appeared in Commentary in June 1996 but also the some of the letters that had been written in response to the article in the September 1996 issue. (The links here give you everything that appeared in Commentary!)

David’s piece was 10 double-columned pages. The responses took up 30 double-columned pages. The responses ranged from pro-ID people who were favorable to David’s piece (notably Phillip Johnson and Michael Behe) to a who’s who of Darwinists opposed (notably Richard Dawkins and Daniel Dennett). There was also a closing response to all the letters from Berlinski himself.

The anthology I was editing didn’t have room for all the letters, but I wanted a representative sampling of letters by the Darwinists. In particular, I wanted to reprint the letters by Dawkins and Dennett. So I contacted them to ask permission. Note that Commentary would have been happy to grant permission, but the copyright for the letters belonged to the letter writers. 

Both Dawkins and Dennett refused to grant permission to reprint their letters. I asked them to reconsider, but they refused again. Finally, I decided that the anthology would be richer if, even without their actual letters, the substance of what was in those letters were reprinted. I therefore paraphrased the letters and sent my paraphrase to Dawkins and Dennett to ask whether they thought I had represented their original letters accurately.

Instantly both got back and gave me permission to reprint their letters, preferring their words to mine. There’s no doubt a lesson here: we prefer our own words to those of others who would speak for us.

Darwinism's LVPs continue to double down on the argument by misrepresentation and name calling

 “Creation Myths” Misquotes and Misrepresents Junk DNA Video

Casey Luskin

A YouTube channel called Creation Myths put up a new offering that claims, “Discovery Institute recently put out a video on junk DNA that contains all the usual lies about junk DNA, plus a few other tricks to make their audience think they’re on the up-and-up. We’re going to talk about it.” This is in reference to our new Long Story Short video:

Sure, Let’s Talk About It

Before I get too far into this, I need to say that it’s probably best to be cautious when dealing with “Creation Myths,” who also identifies as “Dr. Dan” and is a genuine PhD biologist at Rutgers. He’s an anti-ID YouTuber who has exhibited an unfortunate unwillingness to acknowledge black-and-white facts that are in favor of intelligent design. To be specific, two years ago I did a debate on the Unbelievable show, and Creation Myths left a comment stating that the ID research program “Hasn’t advanced past where it was in 2004/2005. Where’s the research program? Where are the papers?” Well, I had already provided this evidence in spades throughout the debate. He was just unwilling to accept these realities.

During the debate I discussed multiple ID 3.0 research projects that we fund, and discussed multiple papers that have been published through this research program. I don’t usually speak like this, but it’s important to get a sense of what we’re dealing with here: Creation Myth’s unwillingness to acknowledge the simple fact that the ID research program has advanced since 2004/2005 — and is publishing papers — does not inspire confidence in his ability to handle this debate fairly. He’s welcome to disagree with ID, but to deny our research program exists or that it’s publishing papers is simply to deny reality. He invited me to go on his channel, but I’m sorry, I don’t think it’s fruitful to dialogue with people who cannot acknowledge unambiguous facts. So it’s important to understand the temperament of debaters and their tactics before engaging with them. 

What We Actually Said

With that, my first point provides another disturbing example of how Creation Myths operates. He has now left another comment, this one on our YouTube Channel, which directly misquotes the new Long Story Short video on junk DNA. His comment claims the video says “it was assumed that the other 98 percent was junk.” Those are words that Creation Myths puts in quote marks but they were never stated in the video! 

Here’s what we actually said: it was “assumed that it was largely junk.” Words matter and we did not say it was assumed that the entire other “98 percent was junk.”

So did evolutionists say the genome was “largely” junk? Of course they did! Creation Myths recommends Laurence Moran’s book that says “90 percent” of the genome is junk, and then there’s Richard Dawkins who said 95 percent is junk. In other words, “largely” junk. What we said is accurate and defensible.

In fact, had we used the more aggressive language that Creation Myths falsely claims we did, there might even be authorities to support such a claim. As I recently noted, a 2021 article in American Scientist said that “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA”! So it’s clear that we are accurate in saying that many evolutionists view the genome as “largely” junk — if anything, that may be an understatement.

Creation Myths has overstated our argument in order to make it look unreasonable. This is a common tactic from junk DNA defenders. 

Second, Creation Myths wants to have it both ways — he wants to essentially say evolutionists never said DNA was largely junk, but that nonetheless the genome really is largely junk. So there’s an internal contradiction in his framing.

The Bigger Issues

With that, my first point provides another disturbing example of how Creation Myths operates. He has now left another comment, this one on our YouTube Channel, which directly misquotes the new Long Story Short video on junk DNA. His comment claims the video says “it was assumed that the other 98 percent was junk.” Those are words that Creation Myths puts in quote marks but they were never stated in the video! 

Here’s what we actually said: it was “assumed that it was largely junk.” Words matter and we did not say it was assumed that the entire other “98 percent was junk.”

So did evolutionists say the genome was “largely” junk? Of course they did! Creation Myths recommends Laurence Moran’s book that says “90 percent” of the genome is junk, and then there’s Richard Dawkins who said 95 percent is junk. In other words, “largely” junk. What we said is accurate and defensible.

In fact, had we used the more aggressive language that Creation Myths falsely claims we did, there might even be authorities to support such a claim. As I recently noted, a 2021 article in American Scientist said that “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA”! So it’s clear that we are accurate in saying that many evolutionists view the genome as “largely” junk — if anything, that may be an understatement.

Creation Myths has overstated our argument in order to make it look unreasonable. This is a common tactic from junk DNA defenders. 

Second, Creation Myths wants to have it both ways — he wants to essentially say evolutionists never said DNA was largely junk, but that nonetheless the genome really is largely junk. So there’s an internal contradiction in his framing.

The Bigger Issues

Third, and this bring us to the bigger issues, let’s look at the paper he cites, Kellis et al. (2014). It’s authored by quite a few prominent ENCODE scientists, and despite what Creation Myths asserts, this paper does not “walk back” central claims of their major 2012 Nature ENCODE paper. That 2012 paper is cited by our video because it reported evidence that 80 percent of the genome is biochemically functional. As the 2012 paper stated, “These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions.” 

And note what our video says — we did not claim that the 2012 Nature paper said 80 percent MUST be functional. Our video correctly states that the 2012 Nature paper from ENCODE “found 80 percent of DNA shows evidence of functional biochemical activity.” That’s absolutely true and totally consistent with what the 2012 ENCODE paper said and what the evidence says. And no one has walked that claim back. 

I’d like to ask Creation Myths to provide the exact statement where Kellis et al. (2014) denies or “walks back” ENCODE’s claim that 80 percent of the genome shows evidence of biochemically functionality. He won’t find it because they never retracted that evidence.

Fourth, Kellis et al. (2014) does cite the major 2012 Nature ENCODE paper — not to retract it but rather it cites this paper very affirmatively. But we’ll get to that in a moment. Before we delve into the paper, here’s a revealing question:

If ENCODE was really “walking back” their claims, then why did lead ENCODE researcher Ewan Birney — who is a co-author on Kellis et al. (2014) — say the following just a couple of weeks before the Kellis paper was published: “There is not a single place in the genome that doesn’t have something that you might think could be controlling something else.”

That quote from Birney came from his comments in Bhattacharjee (2014), an article published in the journal Science as a response to ENCODE critic Dan Graur who had claimed that the genome is largely junk. So it’s totally on point and in context.

Birney is effectively saying that the entire genome appears to be functional — i.e., “There is not a single place in the genome that doesn’t have something that you might think could be controlling something else.” And he said what he did around the same time he co-authored the Kellis paper (the statement was published on March 21, 2014, and Kellis et al. came out on April 29, 2014, but was probably submitted months earlier). So Ewan Birney cannot be understanding his own paper to be walking back the claim about 80 percent functionality because clearly he thinks the genome is almost entirely functional.

Creation Myths Is Bluffing. How Do I Know?

Fifth, you have to understand what kind of paper Kellis et al. (2014) is. It’s a perspectives or review paper that compares and contrasts three different methods of investigating genome function: evolutionary, genetic, and biochemical. They set up this framing in the introduction, stating: “Geneticists, evolutionary biologists, and molecular biologists apply distinct approaches, evaluating different and complementary lines of evidence.”

The paper then discusses the strengths and weaknesses of each method, and discusses estimates of function for the genome for each method, offering pros and cons for each estimate and the methods used to infer those calculations. No method is perfect or foolproof, and they look at strengths and weaknesses of the evolutionary method and of the biochemical method. That’s what you do in a review paper. Well, what method do they ultimately favor? We’ll get there in just a moment. 

Now, the biochemical method is the method that ENCODE used to find evidence of function for 80 percent of the genome. Kellis et al. (2014) note that the evolutionary method, in contrast, predicts that no more than 20 percent of the genome is functional, and the rest is junk: 

The estimated mutation rate in protein-coding genes suggested that only up to ∼20% of the nucleotides in the human genome can be selectively maintained, as the mutational burden would be otherwise too large. The term “junk DNA” was coined to refer to the majority of the rest of the genome, which represent segments of neutrally evolving DNA.

So which method does Kellis think is the most reliable? You guessed it — they strongly favor the biochemical method. Here’s the conclusion of the paper:

In contrast to evolutionary and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease (14, 35, 69, 111, 112). The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far more important than any interim estimate of the fraction of the human genome that is functional.

They are saying that the “biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act” and that ENCODE’s application of this method provides reliable data that “is far more important than any interim estimate of the fraction of the human genome that is functional.” They affirmatively cite five papers in saying this. Guess which citation is #69? It’s the major 2012 ENCODE paper in Nature which said that 80 percent of the genome is biochemically functional. They are citing it to say that the approach taken in that paper gives results that are “far more important than any interim estimate of the fraction of the human genome that is functional.”

So it’s true that in this particular paper they aren’t asserting any particular fraction of the human genome that is functional — but neither are they denying or “walking back” the 80 percent statistic either. They are clearly endorsing the biochemical approach in ENCODE’s 2012 paper. That means they don’t think the evolutionary approach is going to give you the best answer. Instead, they prefer the biochemical method, which uncovered evidence of function for 80% of the genome. 

Critical of Evolutionary Estimates

Sixth, also noteworthy is that the Kellis paper is highly critical of evolutionary estimates of the fraction of the genome that is functional. Here’s how it describes the evolutionary view:

[T]he biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Many examples of elements that appear to have conflicting lines of functional evidence were described before the Encyclopedia of DNA Elements (ENCODE) Project, including elements with conserved phenotypes but lacking sequence-level conservation, conserved elements with no phenotype on deletion, and elements able to drive tissue-specific expression but lacking evolutionary conservation. … A high level of sequence conservation between related species is indicative of purifying selection, whereby disruptive mutations are rejected, with the corresponding sequence deemed to be likely functional.

They are saying that the “biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act” and that ENCODE’s application of this method provides reliable data that “is far more important than any interim estimate of the fraction of the human genome that is functional.” They affirmatively cite five papers in saying this. Guess which citation is #69? It’s the major 2012 ENCODE paper in Nature which said that 80 percent of the genome is biochemically functional. They are citing it to say that the approach taken in that paper gives results that are “far more important than any interim estimate of the fraction of the human genome that is functional.”

So it’s true that in this particular paper they aren’t asserting any particular fraction of the human genome that is functional — but neither are they denying or “walking back” the 80 percent statistic either. They are clearly endorsing the biochemical approach in ENCODE’s 2012 paper. That means they don’t think the evolutionary approach is going to give you the best answer. Instead, they prefer the biochemical method, which uncovered evidence of function for 80% of the genome. 

Critical of Evolutionary Estimates

Sixth, also noteworthy is that the Kellis paper is highly critical of evolutionary estimates of the fraction of the genome that is functional. Here’s how it describes the evolutionary view:

[T]he biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Many examples of elements that appear to have conflicting lines of functional evidence were described before the Encyclopedia of DNA Elements (ENCODE) Project, including elements with conserved phenotypes but lacking sequence-level conservation, conserved elements with no phenotype on deletion, and elements able to drive tissue-specific expression but lacking evolutionary conservation. … A high level of sequence conservation between related species is indicative of purifying selection, whereby disruptive mutations are rejected, with the corresponding sequence deemed to be likely functional.

We will address this objection head-on in a forthcoming Long Story Short video on junk DNA that’s been in production since long before Creation Myths posted its objections. The objection is fallacious because it assumes DNA can only be functional if it is “evolutionarily conserved.” But that view further assumes that evolutionary processes are the only way to produce function in the genome. If you can have function outside of “conserved” regions because evolution isn’t what generated the genome, then the argument falls apart. So this evolutionary argument effectively assumes the truth of evolution and boils down to a circular argument. 

Kellis et al. (2014) offers some additional arguments against the “evolutionary approach” to discerning function:  

has limitations. Identification of conserved regions depends on accurate multispecies sequence alignments, which remain a substantial challenge. Alignments are generally less effective for distal-acting regulatory regions, where they may be impeded by regulatory motif turnover, varying spacing constraints, and sequence composition biases (17, 49). Analyzing aligned regions for conservation can be similarly challenging. First, most transcription factor-binding sequences are short and highly degenerate, making them difficult to identify. Second, because detection of neutrally evolving elements requires sufficient phylogenetic distance, the approach is well suited for detecting mammalian- conserved elements, but it is less effective for primate-specific elements and essentially blind to human-specific elements. Third, certain types of functional elements such as immunity genes may be prone to rapid evolutionary turnover even among closely related species. More generally, alignment methods are not well suited to capture substitutions that preserve function, such as compensatory changes preserving RNA structure, affinity-preserving substitutions within regulatory motifs, or mutations whose effect is buffered by redundancy or epistatic effects. Thus, absence of conservation cannot be interpreted as evidence for the lack of function.”

That’s a potent critique. It says some sequences cannot be compared or aligned because they are TOO different, and those differences might in fact encode functions! The evolutionary approach might be missing some of the sequences that encode differences between species. And it notes that “absence of conservation” does not mean “lack of function.”  

So Kellis et al. (2014) gets the logic right: while conservation strongly implies function, the converse is not necessarily true: absence of conservation does not necessarily mean lack of function. In other words, they blew the “If it ain’t conserved you can’t say it’s functional” objection out of the water.

Seventh, there are additional noteworthy statements from the Kellis et al. (2014) showing they did not walk back the claim about 80 percent of the genome:

“[T]he noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse gene regulatory and other functions.”

They still see the non-coding genome as having a “rich array of functionally significant elements.” This is NOT the traditional evolutionary view.

“[F]unction in biochemical and genetic contexts is highly particular to cell type and condition, whereas for evolutionary measures, function is ascertained independently of cellular state but is dependent on environment and evolutionary niche.”

This suggests that something can still be functional in a biochemical context, though in an evolutionary sense it can be hard to determine if it’s “functional.”

“The methods also differ widely in their false-positive and false-negative rates, the resolution with which elements are defined, and the throughput with which they can be surveyed.”

So genetics and molecular biology, on one hand, and evolutionary measures on the other have different rates of “false negatives” for function. This is a polite way of saying that the evolutionary approach often wrongly says things aren’t functional.

But the junk DNA advocate will say that the biochemical approach might lead to false positives of function. The paper acknowledges this: “[A]lthough biochemical signatures are valuable for identifying candidate regulatory elements in the biological context of the cell type examined, they cannot be interpreted as definitive proof of function on their own.”

That’s fair. We haven’t studied in detail every single time that the genome is transcribed to see what it’s doing, and there could be some “transcriptional noise” — the “junk RNA” view. We’ve also addressed this in the earlier Long Story video. Is this tantamount to “walking back” the 80% statistic? Not in the lease. 

Random Noise or “Reproducible Biochemical Activity”

To defeat the 80 percent statistic, junk DNA defenders need there to be a huge amount of random noise in transcription. It’s possible that some transcription is random noise. But if much or most or nearly all of this transcription is noise, then cells are wasting colossal resources, and that would be highly deleterious to an organism, and would likely be selected against. So we have good reason off the bat to doubt that this transcription is largely random. 

Indeed, the paper has an opinion on this and it prefers the view that transcription is non-random and functional. Kellis et al. (2014) note that even if there is some transcriptional noise, there’s far more going on in cells than we would expect if most of the genome were genetic junk:

Thus, unanswered questions related to biological noise, along with differences in the resolution, sensitivity, and activity level of the corresponding assays, help to explain divergent estimates of the portion of the human genome encoding functional elements. Nevertheless, they do not account for the entire gulf between constrained regions and biochemical activity. Our analysis revealed a vast portion of the genome that appears to be evolving neutrally according to our metrics, even though it shows reproducible biochemical activity, which we previously referred to as “biochemically active but selectively neutral” (68). It could be argued that some of these regions are unlikely to serve critical functions, especially those with lower-level biochemical signal. However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional. Despite these limitations, all three approaches are needed to complete the unfinished process of inferring functional DNA elements, specifying their boundaries, and defining what functions they serve at molecular, cellular, and organismal levels.

The key words there are “reproducible biochemical activity.” 

ENCODE’s results suggest that a cell’s type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As another Kellis et al. co-author, John Stamatoyannopoulos, observed in a 2012 paper, ENCODE found that “the majority of regulatory DNA regions are highly cell type-selective,” and “the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types” studied increases. Or, as two other ENCODE researchers explain in a 2013 paper, “Assertions that the observed transcription represents random noise … is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell-and tissue — specific transcription in human cells.”

Stamatoyannopoulos (2012) further finds that repetitive DNA (often called “transposable elements”), which comprises over 50 percent of our genome, is active only in specific cell types. This nonrandom transcription of repetitive DNA into RNA suggests that transposable elements have functions whose importance are on par with other gene regulation mechanisms. He writes:

In marked contrast to the prevailing wisdom, ENCODE chromatin and transcription studies now suggest that a large number of transposable elements encode highly cell type-selective regulatory DNA that controls not only their own cell-selective transcription, but also those of neighboring genes. Far from an evolutionary dustbin, transposable elements appear to be active and lively members of the genomic regulatory community, deserving of the same level of scrutiny applied to other genic or regulatory features.

The vast majority of our genome — including repetitive DNA — is transcribed into RNA in nonrandom, cell-type-specific ways. These non-random processes strongly point against transcription being noise and provides strong evidence of function.

Indeed, individual RNA molecules then form networks in a cell, interacting with DNA, proteins, and other RNAs to control which genes are turned on and off, and which genes are expressed as proteins, thereby playing a crucial role in determining the cell’s type. As Stamatoyannopoulos puts it, this complex system exudes function:

More of the human genome sequence appears to be used for some reproducible, biochemically defined activity than was previously imagined. Contrary to the initial expectations of many, the overwhelming majority of these activities appear to be state-specific — either restricted to specific cell types or lineages, or evocable in response to a stimulus. … [B]iochemical signatures of many ENCODE-defined elements exhibit complex trans-cellular patterns of activity. … Together, these observations suggest that the genome may, in fact, be extensively multiply encoded — i.e., that the same DNA element gives rise to different activities in different cell types.

These consistent and predictable cell-type-specific patterns of RNA expression, and stimulus-specific patterns of transcription, show that mass genomic transcription of DNA into RNA is not random, but has important functional purposes.

In other words, transcription isn’t random — it happens over and over again in predictable patterns — and there’s a lot more non-random transcription going on than what you would expect from an evolutionary view of “constrained regions” of the genome. We may not yet have definitive proof of what every genomic element that’s transcribed is doing, but this evidence tells you that ENCODE’s data shows real evidence of function. Organized, reproducible, predictable transcription across the vast majority of the genome is far more compatible with the mass-functionality view of the genome, and highly incompatible with the “transcriptional noise” view promoted by junk DNA defenders. And the Kellis et al. authors think this biochemical evidence of function is more important than evolutionary predictions.

Bottom line: As for the rest of what Creation Myths has to say, there’s really not much there. Our video backs up what it says with clear quotes and references. We’ve provided more documentation here. Creation Myths, in contrast, is inventing quotes. Whether you celebrate Easter or not, may you enjoy this weekend and spend it quoting people carefully and accurately — not inventing quotes to suit your own purposes.