Paul Gosselin (7/6/2024)

This is not a book review, but rather an article review of an article by American biologist and geneticist James A. Shapiro entitled Evolution Is Neither Random Accidents nor Divine Intervention: Biological Action Changes Genomes. Now why “Sad Shapiro”? Well, as we shall see, Shapiro finds himself between a rock and a hard place...

In his introduction Shapiro briefly looks at pre-Darwinian scientists such as Linnaeus and Cuvier who did research on living or extinct organisms. (2024: 48)

No thought was given to the idea that living organisms could change their fundamental natures. Even a scientist dedicated to analyzing the nature and classification of life forms, Carl Linnaeus (1707-1778), and one who documented the extinction of fossil organisms, Georges Cuvier (1769-1832), both believed in the fixity of species.

Unfortunately this is typical evolutionary misinformation (not very subtly) implying that, because of their acceptance of Genesis, pre-Darwinian scientists were blithering idiots incapable of basic observation. Here is a similar instance of evolutionist spin from the Linnaeus estate Museum (managed by Uppsala University) regarding Carl von Linnaeus' plant research (2024):

In 1744, Linnaeus heard of a flower nobody had ever seen before. It had many similarities with toadflax (Linaria vulgaris), but the flower looked completely different, with radial symmetry instead of the normal zygomorphic symmetry of toadflax. Linnaeus was curious about this plant and asked one of his students to collected one which he planted in the University garden (the Linnaeus Garden). Unfortunately it soon withered, but not before Linnaeus had time to discover something interesting. Despite the strangeness of the flower, the plant itself was essentially identical to toadflax. He concluded that it was a hybrid of toadflax and some other unknown flower. His discovery was momentous: it appeared to show that new species could arise in nature. He chose to call his new plant Peloria, Greek for ”monster” or ”prodigy”.

While such comments are copy-pasted on a regular basis in evolutionist literature, I've never encountered them accompanied by direct quotes from pre-Darwinian scientists actually expressing dismay that new discoveries had refuted Genesis and turned their world upside down[1]. One would be tempted to conclude this is evolutionist spin and nothing else...

Here's the thing, pre-Darwinian scientists and animal breeders knew of variation within species. Not only that but even ordinary farmers were well aware that beef, sheep, horses, pigs, chickens display a wide range of variations within their species and that selection for specific traits could widen the range of variation. Furthermore in Darwin's time, Dutch tulip growers or English pigeon breeders knew a thing or two about species variation and how to spin new varieties into cash revenue. So when Europeans encountered biological variation on other continents[2] that was unknown in Europe, such discoveries were not the “world-shaking surprise” the evolutionary narrative portrays, but simply objects of curiosity. Of course part of the interest in biological novelty was the prestige (and privilege of naming a species) that went along with the discovery of some new plant or animal. In some cases, pre-Darwinian biologists called unusual variations in plant morphology “sports”.

Dogs are perhaps the most extreme example with variations in height, body weight, body shape, fur length, fur colour, fur texture, head shape, ear shape[3]/length, tail shape/length. Wiki mentions that “Dogs are the most variable mammal on earth, with around 450 globally recognized dog breeds.” Wiki notes: These [dog] breeds can vary in size and weight from a 0.46 kg (1.0 lb) teacup poodle to a 90 kg (200 lb) giant mastiff. So in terms of weight, there is a 1/200 ratio of lightest to heaviest dogs. And regarding the range of height in dogs, the (shortest/tallest) ratio seems to be around 1/5 at least. Naïve early 20^th century proponents of scientific racism regarded human variation as so significant that such were considered “proof” that blacks and other races were viewed as so different that they had to have a origin separate from that of more “advanced races” such as European whites. Yet if phenotype variations in humans are compared to those in dogs (who are known to be of the same origin), then it soon becomes apparent that human variation is extremely limited.

Veterinarian Jean Lightner rejects as disinformation the claim that preDarwinian biologists were locked into the belief that species were completely fixed, excluding any variation. She notes (2018) one must “recognize that species fixity (in the taxonomic sense) was not the view expressed by eminent creation field biologists of the past, despite the fact that Darwin sets it up as the view he is opposing.” It is clear that the British preDarwinian botanist, William Herbert came to reject the species fixity concept (1837: 18)

For the purpose of assisting our view of nature, we arrange them in groups, to which however no distinct limits were assigned by the Creator; and, though we are trying to find out the ways of nature, our classifications, by whatever name we may call them, are artificial, and if we proceed beyond one step at a time, we must be liable to find ourselves baffled by the reality. When I began, many years ago, to write concerning vegetables, I had to combat an idea that the Almighty had created each species of our botanical catalogues as it now exists, and that plants being able to breed together was the test of their identity as species. It has since been ascertained beyond dispute, as I then anticipated, that in some genera all the species are capable of easy intermixture; and that even some, which botanists had erroneously placed in different genera, could produce a fertile cross-breed.

Further into Shapiro's article, regarding the state of the origins debate, we are provided with additional disinformation as he claims (2024: 49):

The conflict persists to the present day among a significant fraction of the U.S. population, and there are serious movements to ban the teaching of evolution in schools.

Of course Shapiro provides no proof to back up his claim of “serious movements to ban the teaching of evolution in schools”[4], but one could suppose the purpose of such bogus claims is to insinuate that evolutionists are the “beleaguered martyrs” of Science. In point of fact, the only “serious movements” going down in the 1980s were attempts to allow criticism of evolution as well as the freedom to explore other explanations of origins in the education system. We all know how that ended. The evolutionary ideological monopoly in education could not be touched. Evolutionists enrolled sympathetic judges and freedom of debate and thought in education regarding origins was squashed. The holy dogma of the materialistic origins myth[5] could not be questioned... Criticism of evolution was locked out of the education system. But perhaps what Shapiro meant by "movements to ban the teaching of evolution in schools" was simply heretical movements that had the audacity to criticize the evolution narrative. In any case the shutting down of serious debate by evolutionists is the sort of behaviour that drew the contempt of philosopher of science, Paul K. Feyerabend (1975/1979: 46):

Unanimity of opinion may be fitting for a church, for the frightened or greedy victims of some (ancient or modern) myth or for the weak and willing followers of some tyrant. Variety of opinion is necessary for objective knowledge. And a method that encourages variety is also the only method compatible with a humanitarian outlook.

Feyerabend was well aware of the political dimension of theory dominance in science and wrote (1975/1979: 197):

A research programme is now dropped not because there are arguments against it, on the basis of the standards, but because its defenders cannot go on. Briefly, but not at all unjustly: research programmes disappear not because they get killed in argument but because their defenders get killed in the struggle for survival.

Shapiro goes on to polish his somewhat tarnished street-cred as an orthodox evolutionist with a typical evolutionary jab at critics of evolution such as creationists and ID proponents. As a result, Shapiro's colleagues will confide to their undergrad students that they can still buy and safely use manuals published by him in their classes. But Shapiro will probably irritate some of his colleagues as he concedes (2024:49-50):

The ID argument has a valid point with regard to the explanatory limits of neo-Darwinism, still widely regarded as the only legitimate scientific explanation of evolution. ID falls down by assuming (as do mainstream evolutionists) that genome change occurs from outside the boundaries of life itself. Within the scientific community, there is agreement that the hereditary variation necessary for evolutionary change occurs by natural means. But significant difference exists between scientists about what constitutes “natural means.”

While Shapiro doesn't come out and say this explicitly, he seems to be implying that evolutionists need to accept that genetic variety is not caused solely by mutations, but that much of it is due to “genetic programming”. Yet despite having taken this step, Shapiro would still deny the reality of a “Genetic Programmer”...

Why “Sad Shapiro”?
Well it seems clear that Shapiro finds himself between a rock and a hard place. Over the years Shapiro has demonstrated the (rare) courage to openly discuss the shortcomings of Neo-Darwinism that has become dogma throughout universities in the West. Such a step outside the herd does require real courage. Shapiro is clear, Neo-Darwinism, with it's mechanisms of mutations and natural selection are insufficient to produce all the organisms we find in the biosphere. Genetics in particular is more complex than anything Neo-Darwinism ever envisaged. In Shapiro's view “mutations did it!” is not a good/sufficient explanation for biological variation. Many epigenetic processes need to be added to the evolutionary toolkit.

For example, in 2001 Shapiro did a conference entitled “Natural genetic engineering: the toolbox for evolution, prokaryotes)”. During this conference, it is almost funny to hear Shapiro reminding his audience that many aspects of genetic variation are programmed, not random. In addition Shapiro noted that high speed Eukaryote replication occurs with VERY low error rates, because such processes are backed up by multiple proof-reading systems to correct any errors, systems which includes check-point mechanisms (present in yeast in and higher organisms as well). While DNA is being corrected, a cell-division inhibitor blocks cell division until error correction is completed. Shapiro notes that in traditional evolutionary theory genetic variation is always thought to be due to random mutations and natural selection. Shapiro says that evolutionists must now face the fact that epigenetics (internal programming) is the source of much observable genetic variation and not random mutations. Unsurprisingly, Shapiro neglects to add that epigenetics (internal programming) is a further mechanism that evolutionary theory MUST explain and provide a source for.

That said, Shapiro's faith in the materialistic origins myth is unshaken and as a result any consideration of an Intelligent Agent as a cause of the myriad biological organisms we see on Earth along with the mind-boggling variety of coordinated mechanisms (with VERY specific and identifiable functions) which such organisms include is vorboten. Yet everywhere biologists and microbiologists look there are multitudes of mechanisms (with recognizable functions) staring at them... While early 19^th century evolutionists could examine one-celled organisms in their microscopes and chortle: “Look at the SIMPLE organism!”, scientists can no longer do so now as it is well known that these simple organisms are in fact astoundingly complex entities and that the simplest of these organisms is capable of accomplishing a task unreachable by the apex of human engineering (the massively parallel super computer) that is producing a functioning copy of itself without any outside intervention. This is an issue that bugged Francis Crick, British biophysicist, co-discoverer of DNA and Nobel Prize winner, who observed that empirical biology can sometimes lead in unexpected directions (1988: 138): "Biologists must constantly keep in mind that what they see was not designed but rather evolved." What Crick says seems to suggest that biologists and geneticists must constantly think "happy thoughts" in order to avoid falling into the cunning traps laid by the empirical world.

Now here's the thing, while Shapiro rejects the efficacy of mutations and natural selection as a mechanism sufficient to drive Evolution, he does not provide other mechanisms capable of doing so. He merely describes epigenetic processes as adding to our understanding of observable genetic variety, but does NOT explain how evolution could have produced these specific epigenetic processes (and the intricate programming[6] they involve) in the first place. One could get the impression that Shapiro assumes “POOF, they (conveniently) appear!”. Since science is about examining observable processes, this raises the question: how would one go beyond speculation and go about observing the origin of the epigenetic processes that Shapiro thinks are so important?

The materialistic origins myth has always been playing catch-up with real science. When Mendelian genetics gained acceptance in the early 20^th century, Darwinist were stuck with an outdated theory. The “New Synthesis” or “Neo-Darwinism” was the answer, that is Darwin with a Mendelian genetics spin thrown in. Now Shapiro is forcing evolutionists to face genetic mechanisms that Neo-Darwinists never dreamed of (or attempted to ignore). As Shapiro points out[7], the Junk Genes claim[8] previously made by Neo-Darwinists is now quite embarrassing as it is now widely know that this claim was completely wrong and that this category of genetic material does in fact have function. Shapiro seems to be (implicitly) claiming here that Evolution is a Theory in Crisis, a crisis similar to that faced by Darwinists in the early 20^th century before Neo-Darwinism was proposed. It would appear that we are due for the proposal of a “New-And-Improved-Synthesis”. Of course this is a rather clumsy label, but I'm sure Evolutionists will come up with something more elegant. Their marketing department has always proven effective and reliable.

After the genetic code (DNA) common to all living organisms had been discovered by British scientists Watson and Crick in the 1950s, shock set in as evolutionists were forced to face the full implications of DNA as the physical basis for a genetic CODE. Just coming out of WWII, the British were well aware of the critical part that understanding coded messages had played in the recent war[9]. Thus if DNA was a medium for sending coded messages, then this immediately raised the question WHO was the Message Sender of the genetic code and WHO had invented this code in the first place? Even before even the simplest life forms could appear, DNA had to be produced and a genetic code invented. This was compounded by the fact that Earth had an oxidizing atmosphere and delicate molecules such as DNA quickly disintegrate under such conditions. Even the co-discoverer of DNA, Francis Crick, was unsettled by such matters and thought the issue so intractable that he proposed an odd escape hatch called Directed panspermia which conveniently swept all such issues under the carpet and assumed life had not originated on Earth, but had appeared elsewhere and then been brought here by aliens. British astronomer Fred Hoyle came to a similar conclusion, but eventually recognized that such proposals were only hand-waving attempts to push the problem out of sight. Since then evolutionists have ignored such issues and all is well...

But getting back to Shapiro, the problem here is that while there can be no doubt about Shapiro's faith in the materialistic origins myth, contrary to early 20^th century “New Synthesis” proponents such as Ernst Mayer, he offers no mechanism to actually drive evolution and produce the astounding mechanisms and systems we discover every day. Shapiro's main contribution is to add new layers of genetic complexity to the mix which he says evolutionists must integrate into evolutionary theory (and spin of as part of the evolutionary process), all the while Shapiro side-steps the problem of providing an empirically verifiable materialistic explanation for the origin of these new layers of genetic complexity. As a result he finds himself condemned to spouting interesting descriptions of previously unknown genetic mechanisms and sprinkling in the word “evolution” here and there, hoping this will suffice to resolve the issues facing Neo-Darwinism. Here's an example as Shapiro discusses interspecific hybridization (2024: 54):

When the hybrids reproduce, they can become progenitors of totally new species[10] with new traits and new genome configurations in just a few generations. Thus, long periods of selection are not essential to taxonomic divergence. In self-pollinating plants in particular, but also in animals, hybrid speciation is often accompanied by whole genome duplication events, which stabilize the genome and increases fertility. It also expands the DNA sub-strate available for further evolutionary development of new functionalities because one copy of each locus can be repurposed without endangering existing functions encoded by another copy. The evolutionary history[11] of eukaryotes, ranging from yeast and fungi to flowering plants and animals, is marked by a succession of WGD[12] events. It is difficult to imagine a process further from random mutations than WGD, which involves control of complex cell cycle and nuclear division processes. It is not hard to see repeated doubling in genome coding capacity as one source of greater organismal complexity with ongoing evolution.

It would appear that rather than offering an explanation of (or a mechanism providing a plausible cause for) the multiple layers of additional genetic complexity he explores, Shapiro (unintentionally) only adds to the mass of problems Neo-Darwinists face and resorts to hand-waving as a solution. So sad.

This situation reminds me of an old quote by the UK physicist Arthur Eddington. At the time, the Heat Death of the universe implied by the Second Law of Thermodynamics (Entropy) was a real preoccupation. Scientists were wondering how Order began. Eddington observed (1931: 450):

We are unwilling to admit in physics that anti-chance [or order -PG] plays any part in the reactions between the systems of billions of atoms and quanta that we study; and indeed all our experimental evidence goes to show that these are governed by the laws of chance. Accordingly, we sweep anti-chance out of the laws of physics - out of the differential equations. Naturally, therefore, it reappears in the boundary conditions, for it must be got into the scheme somewhere. By sweeping it far enough away from our current physical problems, we fancy we have got rid of it. It is only when some of us are so misguided as to try to get back billions of years into the past that we find the sweepings all piled up like a high wall and forming a boundary - a beginning of time - which we cannot climb over.

And then replace the anti-chance expression in the quote above with genetic complexity and chew on that... All of this is enough to think that Pink Floyd's song The Wall might be a favourite of Shapiro as he seems to have spent much of his career adding many bricks to the Wall (of complexity) that Evolution needs to overcome to get life going. In closing his article Shapiro has very generously supplied us a list of genetic phenomena that were unexpected (and unexplained) by Neo-Darwinism (2024: 56):

Since the formulation of the neo-Darwinian Modern Synthesis in the 1940s, many unexpected surprises have emerged from genetics research and from novel molecular techniques that define evolutionary genome changes. These include:

1. mobile genetic controlling elements;
2. discontinuous coding of proteins;
3. protein evolution by domain/exon swapping;
4. horizontal DNA transfers between unrelated taxa;
5. complex eukaryotic cells have molecular and cellular processes for major genome restructuring and new sequence creation;
6. there is widespread rapid speciation by interspecific hybridization;
7. ncRNAs encoded partly by repetitive DNA elements fill major regulatory roles in cell and developmental biology, and;
8. DNA that codes for ncRNA instead of proteins comprises the majority of genomes in the most complex organisms.

Still the odd thing is that Shapiro apparently thinks he is helping the cause of the materialistic origins myth by making all these problems known.

References

-- (2024) Peloria – Linnaeus's monster. Linnaeus' Hammarby – Uppsala University

Crick, Francis (1973/1981) Directed Panspermia. Icarus July p. 341; Life Itself. Simon & Schuster New York

Crick, Francis (1988) What Mad Pursuit: A Personal View of Scientific Discovery. Basic Books New York xiii-182 p.

Eddington, Arthur (1931) The End of the Physical World: From the Standpoint of Mathematical Physics. pp. 447-453 in Nature Vol. 127

Feyerabend, Paul K. (1975\1979) Against Method. Verso London 339 p.

Gosselin, Paul (1979) Myths of Origin and the Theory of Evolution. Samizdat

Gosselin, Paul (2024) A Forgotten Issue with Evolution and Mutations. Samizdat - 17/5/2024

Herbert, William (1837) An Attempt to Arrange the Monocotyledonous Orders, followed by a Treatise on Cross-Bred Vegetables. James Ridgway & Sons - London 428 p.

Hoyle, Fred & Wichramasinghe, Chandra (1981) Evolution From Space: A theory of cosmic creationism. Simon and Schuster New York 175 p.

Lightner, Jean K. (2018) Hybridization shaking up the evolutionary Tree of Life—what does it mean for creationists? Journal of Creation 32(1): pp. 10–13, May 2018

Shapiro, Jim (2001) Presentation title : Natural genetic engineering : the toolbox for evolution, prokaryotes) - Chicago, ITP, 15 March 2001. Drawn from: ITP Program on Statistical Physics and Biological Information (January 16 - June 15, 2001- UC Santa Barbara) Coordinators: W. Fitch, T. Hwa, L. Peliti, G. Stormo, C. Tang - Part2

Shapiro, James A. (2020) All living cells are cognitive. Biochemical and Biophysical Research Communications - Volume 564, 30 July 2021, Pages 134-149

Shapiro, James A. (2024) Evolution Is Neither Random Accidents nor Divine Intervention: Biological Action Changes Genomes. pp.48-56 In Academic Questions 37 (1): 36 April 2024 [special issue: The State of Evolution] DOI: 10.51845.37.1.7

Wasmann, Erich (1904/1910) Modern Biology and the Theory of Evolution, translated from the third German edition by A.M. Buchanan, Kegan Paul, Trench, Trübner & Co. Ltd., London, , p. 292

Wiki: note on “Dog”

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Thanks to Jean Lightner for her input.

Notes

[1] - Erich Wasmann, who was born the year The Origin of Species was published, was a field biologist who believed in the doctrine of creation and recognized species change. While Wasmann used the term evolution, he used it in the original sense, that is solely as describing variation within a created kind. In his Modern Biology and the Theory of Evolution, Wasmann pointedly observes the limits to variation (1904/1910: 292):

All honest supporters of the theory of evolution, who pay due attention to the facts, acknowledge further that the grounds for assuming the existence of a real relationship between the forms in question become more scanty when the higher divisions are considered. For the species of one genus these grounds often amount to great and even irrefutable probability, and the same may be said in not a few cases of the genera of one family, and occasionally for the families of one order, but it can seldom be maintained of the orders in one class. The evidence afforded by natural science for the theory of common descent becomes steadily weaker the higher we ascend the system...

This of course is the elephant in the room that evolutionists cannot explain and avoid. To escape this problem, the evolutionist strategy is to refuse to distinguish between observable variations and the fantasy of universal common descent. This is the trick that sweeps (contradictory) evidence under the carpet.

[2] - Such as beak variations in Galapagos Finches....

[3] - Including ear rigidity floppy/erect.

[4] - Since the 1925 Scopes Trial, this has been totally out of the question...

[5] - The detailed argument for this claim appears in our book: Flight For the Absolute, volume 2. The Reference section above provides a brief article (Gosselin 1979) giving an introduction to the issues involved.

[6] - In a recent 2020 article Shapiro side-steps this issue claiming “All living cells are cognitive”. Using the term “programming” instead would of course be rather problematic for a devout evolutionist...

[7] - In this regard Shapiro says specifically (2024: 51)

Today, we recognize that most of this repetitive DNA is made up of transposable elements and other repeats needed for various aspects of genome function, especially developmental regulatory networks controlling cellular differentiation.

[8] - The claim was that so-called Junk Genes were the non-functional and discarded genetic residue of past evolution. This was good evolutionary spin while it lasted... It is clear now that this claim has since been refuted. The Junk Genes concept gained popularity when geneticist Susumu Ohno published a 1972 paper titled "So much 'junk' DNA in our genome".

[9] - Just look at the British war effort at Bletchley Park to crack the encryption code of the Enigma machine. Wiki notes “During the war, British cryptologists decrypted a vast number of messages enciphered on Enigma. The intelligence gleaned from this source, codenamed "Ultra" by the British, was a substantial aid to the Allied war effort.”

[10] - “Totally new species”?? This is a meaningless claim unless you lay your cards down on the table and spell out which particular species definition you are talking about. Would Spiro buy into Ernst Mayr's Biological Species Concept (BSC) for example where fertility to the 2^nd generation is the trait defining membership in a species (and not morphology)? Depending on which definition of species is adopted, one could look at the same evidence Shapiro evokes and just as easily claim “new variations (within a species) were observed”. Ho hum... But seeing no evolutionary spin is gotten from such an interpretation, this inevitably pushes most evolutionists into the splitter camp. Discussing the views of William Herbert, Jean Lightner underscores the repercussions of one's choice of species definition (2018):

Herbert recognized that the variation seen between different varieties in a single species of domestic plant was essentially the same as that seen in different species in the wild. He pointed out that if fertility of offspring was the criteria for the species designation, many plant species recognized at that time would disappear, as morphologically distinct species would be grouped together. He also provided specific examples demonstrating that obvious morphological differences can be a poor predictor of whether or not fertile offspring can be produced when hybridizing.

This is of course part of the history of the long-running lumpers/splitters debate regarding the species definition in biology. Seeing a splitters definition (based primarily on morphology) is good spin for evolutionists (seeing the appearance of “new species” can be readily quoted as “proof” of evolution), despite Mayr's stellar scientific reputation, evolutionists are not fond of his BSC definition, which is squarely in the lumpers camp, despite it's strong grounding in biological reality (reproduction). A splitters definition, on the other hand, while it provides great fodder for evolutionary spin, is a more arbitrary concept, being grounded in a number of factors susceptible to bias, the whims of scientific consensus and subjective or commercial interests. The primary issue here is that a lumpers species definition leaves the decision to nature as opposed to arbitrary (and changeable) human judgements in the case of a splitters definition. Perhaps a dissuasive factor regarding a lumpers definition is that it requires more (observational) work to sort things out... It also demands intellectual discipline and restraint in recognizing that classification is never entirely fixed.

[11] - Or imaginary stories...

[12] - WGD = “whole genome duplications”.