NEO-DARWINISM – R.I.P
I predict that the overturning of Neo-Darwinism will be the teaching example of the Kuhn theory as to how paradigms are replaced by the avant-garde of the scientific community in which the paradigm has existed for many, many decades. Somewhat unique in the annals of interring old paradigms is the clear demonstration of motivation for clinging to a crumbling paradigm – religion. In late Twentieth Century, there arose a political component in the evangelical community, or the young earth creationists as the fundamentalist Darwinists brand them. Together with social conservatives they scared the daylights out of the evolutionists – and all progressive liberals. The progressives had conflated their atheism with their Darwinism. Of course, the creationists’ rejection of evolution per se enraged them. The creationist position, proudly and blatantly anti-science, preferring God as an explanation for existence, drove the Darwinists deeper and deeper into defense of evolution until they became obsessed with the Enlightenment. Evolution became a religion
Many of these secular critics of evolution concentrated their focus, not on descent with modification but at the core of Darwinian evolution – natural selection, the only true contribution of Darwin as he readily admitted. Natural selection explains change as the occurrence of random mutations of DNA and then the selection of organisms with the mutated genes. Thus the theory became gene-centric – gene-based evolution became not merely the leading component of the mechanism for change, but the only one. Meanwhile, general science was progressing by leaps and bounds in the period after Darwin. Science became for many the only epistemological basis for existence. Atheists claimed science as their own. Not the hard and empirical sciences, but the historical sciences such as anthropology and of course evolution. They manipulated the argument for the existence of God into a framework of this historical science. If evolution could prove that the development of life could be explained without any God, it would decimate religion and banish God from the world. Posturing evolution as science attracted many atheists. Thus, evolution became the battering ram for breaching the ramparts of religion. But many biologists refused to join in a crusade against religion insisting that Darwinism was not good science. Its tenets were faulty and frail and lacked a satisfying explanation life.
The players that represent the defense of the Darwinism paradigm include Richard Dawkins (of “selfish gene” ignominy) and Jerry Coyne (of “Faith vs. Fact” regurgitated atheism), Kenneth Miller, Philip Kitcher, John Avise. J. B. S. Haldane. Sydney Brenner. Sean B. Carroll. Steve Jones. PZ Meyers. With a few philosophers such as Daniel Dennett, Christopher Hitchens and Sam Harris they assumed the mantle of the New Atheists – new in the sense that their atheism relied upon the pseudo science of evolution, rather than the abstruse arguments typical of their trade.
To demonstrate how such an august group of Darwinians could be so spectacularly wrong, I offer as proof of error, not of Darwinism in its entirety, but in a not insignificant facet of DNA technology. I refer to so-called “junk DNA.” Over-simplified, after the genome was established as comprising 25-30,000 genes, and three billion base pairs of nucleotides, the Darwinists pointed out that the protein coding genes constituted only 1.5% of the genome, the rest was junk. And, in characteristic bioatheist hubris, pointed out that no God would have created so much junk in the human genome. Kitcher referred to the junk as “whimsical tolerance of bungled designs.”
Unfortunately, science marched on. It turns out that the non-coding regions of DNA, denominated “pseudo-genes,” perform myriads of functions in the cell. They were no less important to life development than the genes – they were not without function. Indeed, critical functions. Below, I discuss the new paradigm that is very much based on the evidence that genes are “not the thing.” Genes are merely gears in a mechanical transmission, a passive database waiting to be transcribed and translated by proteins and other cell features. The pseudo-genes are not genes at all, they form a network the extent and scope of which we have just begun to understand but recognize as critical elements of development.
For the past fifty years, the pursuit of real science, not pseudo-science solely in the service of atheism, has engaged in fruitful denouncement of reductionism of the mechanics of life development. Long gone are the philosophers, like Daniel Dennett, who discovered the word algorithm late in life believing it was an alchemical explanation for the mechanism of evolution. His inability to grasp the idea of an algorithm as explained brilliantly by his nemesis, David Berlinski (The Advent of the Algorithm: The Idea That Rules the World), is the stuff of legend. His great metaphor, the sky crane, smacks more of Marvel comics than science. Or Jerry Coyne who mocked current religious thought in his book titled Faith vs. Fact. An example of what John Gray refers to as “a tedious re-run of a Victorian squabble.” A rehash of atheistic criticism of religion with an evolutionary spin.
The world’s favorite atheist, Richard Dawkins, a zoologist with scant knowledge of evolutionary biology, and even less of religion, created the selfish gene concept that had no support other than a fertile imagination. These fundamentalist Darwinists, as Stephen Jay Gould, a Darwin defender, characterized them, struggled to save Darwinism from a long line of Darwin critics of gene-centrism and natural selection. The struggle has been to no avail.
The Old Paradigm
The first task in creating a new paradigm is to destroy, or at least to severely circumscribe, the existing one. The former is of course more difficult. The latter is exemplified by the circumscription of the Newtonian paradigm by Einstein’s theory of relativity. In a similar manner, the idea of the gene as the determiner of life is wrong, but that does not mean that the gene concept must be destroyed. It is a component of the new paradigm – natural genetic biology. But it clearly is not the “selfish gene” that has led to the gene-centric view of the development of life.
The old paradigm is constructed upon the gene as “the” identifiable hereditary element underlying the evolutionary process. It is the infrastructure. Change is carried out by a random mutation of the gene. This change affects the animal phenotype. The new phenotypic animal is then subject to selection – if the change was advantageous (it adapts the animal to its environment), the animal will survive while its co-species will die. The change is propagated to its progeny by this “selected” animal since it is the survivor. Thus the principal tenets of the theory are: the gene, random mutation, adaptation, and selection = Neo-Darwinism, or for our purposes, just plain Darwinism.
Darwinism has been criticized, contested, and questioned from the outset. The attacks have been leveled at the various supports for the theory as set forth below. They were, by and large, not substitutes or alternatives for the theory. But many went to the core of the evidence that Darwinians relied upon. For nearly a hundred years, even after the word “gene” was coined, the hereditary element was vague, undefined, hypothetical. I think of the attacks on the theory prior to the discovery of the tangible gene, that is, before the discovery of DNA, as the pre-molecular genetics criticism or attack. Only in the last 15-25 years has the criticism based on molecular processes that effect the changes risen to the fore. It also disputes the old paradigm, but offers an alternative theory of evolution. We need to trace both to fully understand why Darwinism is dying, if not dead.
The deconstruction task is carried out spectacularly by Denis Noble, a physiologist and one of the natural genetics advocates, in the Department of Physiology, Anatomy and Genetics at Oxford. In his layperson book, based on a metaphor of music (though he properly limits the scientific value of metaphors), The Music of Life: Biology Beyond Genes, and a 2013 article entitled Physiology is rocking the foundations of evolutionary biology, Experimental Physiology, 98:8 (2013), pp. 1235-1243 he extirpates the gene-centric view of the present paradigm. And that requires an analysis of the gene-only theory propounded by Richard Dawkins in his book The Selfish Gene.
Dawkins states as his theory:
“Now they swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and me; they created us, body and mind, and their preservation is the ultimate rationale for our existence.”
(p 21). This is not a statement of a metaphor. It is a bold statement that genes “create” humans. Alone. Physical and mental. And with a flourish of nihilist existentialism. This is raw determinism. Noble attempts to exculpate Dawkins from this gene-determinist position but that flies in the face of the millions who interpret the statement as just that.
Simply stated, Noble states that the genes are merely a database. It is inert. It does not program the system. It depends on other elements of the system. Genes code for proteins. It is plainly erroneous to state that genes are “for” some function, a point made clear by Massimo Pigliucci and Gerd Muller in: Evolution: The Extended Synthesis. Noble states: “This is that there is no one-to-one correspondence between genes and biological function. Strictly speaking, therefore, to speak of a gene as the ‘gene for x’ is always incorrect.” (Emphasis in original) There are many ways to read a genome; exons may be combined in various ways. It is the “pattern” of expression that determines a step in the building of functionality. “Selection” does not depend on genes – it depends on the entire organism. Gene-centrism is no more than a metaphor and metaphors are seducers for pseudo-science; they too often polemically extended beyond their application, taken too literally, and are rarely scientifically correct. Many functions are expressed only by a coordinated combination of genes and the proteins they create – not by competition between genes as promulgated in the selfish gene theory.
As cogently stated by Lenny Moss:
“The empirical fruits of several decades of research in molecular, cell, and developmental biology have revealed that what distinguishes one biological form from another is seldom, if ever, the presence or absence of a certain genetic template but rather when and where genes are expressed, how they are modified, and into what structural and dynamic relationships their ‘products’ become embedded.”
What Genes Can’t Do, p. xvii. The gene-centric paradigm is again badly wounded.
Fissures in the Old Paradigm
The pseudo-science of evolution based on the gene as the center of all things biological has been the major supporting actor for atheism. It served no other purpose, surely not as science. The “just so” stories constructed in anthropology to prove natural selection, in retrospect, are comedic. Once molecular biology came on stage the entire play required a massive rewrite. Ptolemaic cosmology served as pseudo-science to support a religious narrative confirming that the Earth was the center of the universe. Now gene-centrism similarly supports a theory, this time an anti-religion one, as an explanation for the development of life. The history of science produced Copernicus and Galileo to displace the Earth-centric theory of cosmology. Today there are an increasing number of scientists who support the displacement of gene-centrism, by genetics based on molecular chemistry.
It is the common understanding that genes are protein-coding segments of the DNA molecule that purport to control heredity. People believe that DNA causes life. This has been referred to as DNAmania by the French historian of science Andre Pichot. It is embarrassingly naïve. The avant-garde now know that DNA is passive. It is the proteins that do all the work. The idea of heredity determined by genes is defunct and must be retired.
What is referred to as “genes,” are protein coding DNA sequences. However, the term is misleading because the function and the very nature of this alleged fount of life is a merely a recognition site where DNA is formatted for transcription, replication, restructuring and many other processes. Here is how James Shapiro explains the DNA- protein process:
“In some aspects, genome formatting can usefully be compared to data file formatting in computer systems because they are essential in both cases to accurate utilization of stored information. The realization that all aspects of genome function involve formatting elements is one of many reasons that the term ‘gene’ has become impossible to define rigorously.”
Evolution: A View from the 21st Century (p. 10) It is changes in formatting the genetic sequence that is as important as changes in the coding elements with respect to genome expression and therefore the organism phenotype. In short, the entire edifice of gene-centrism, with its religious commitment to the gene as the sole or primary driver of evolution is erroneous.
For some time it has been accepted that the gene per se does not have a coherent definition permitting an explanation of the extent of its role in the development processes. Shapiro identifies the true source of change by referring to the Lac Operon discovery by Monod and Jacob as a recognition site for relating DNA to proteins. He states: The description of the first of these recognition sites . . . was revolutionary in our understanding of the genome because such sites are fundamentally different in nature and function from the protein coding sequences conventionally believed to constitutes ‘genes’.” (p. 10) These sites “format” the DNA – without formatting, DNA is useless.
It is highly desirable to banish the term gene from the lexicon of evolutionary biology. Here is why:
“Throughout the book, the term ‘gene’ appears in quotation marks to indicate its hypothetical nature. It has been used to designate countless different features of genome organization. In other words, the use of ‘gene’ gives the false impression of specifying a definite entity when, in fact, it can mean any number of different genomic components. In some cases, such as when ‘gene’ is used to indicate a continuous human sequence encoding a specific protein, it actually means something that has no real existence in nature. This is because the genomic DNA coding regions usually comprise several separated exons and are only joined at the level of the RNA transcript.”
(Shapiro, p. 29) Here in one fell swoop the entire structure and process of evolution as conventionally understood, confined to the all-powerful magical “gene,” is obliterated. Darwin confronted the question of how heredity worked and conceived of the term “gemmule,” a hereditary transmission element. It has long been discredited as an imaginary entity. Now is the time for the term “gene” to be assigned a similar fate. Science disrupts with new technology, new insights, and deeper understanding. Old players refuse to retire. Much worse, when they have a hidden agenda for clinging to the old theory, they are scientifically dishonest.
A gene is not well defined. At one time it was thought that a gene is a continuous segment of the base pairs that comprise DNA, like beads on a string. Now it is known that a gene may be composed of different and spatially located base pairs that provide the template for proteins that are the active elements in a cell. The gene has been poignantly described, metaphorically, as a CD or more to my liking, a database. Although static, it can, but only with the active elements, proteins, create new proteins and thus new life. Think of the gene as a segment of data that with powered hardware and a software program can manipulate the database. The power, hardware and software are the living cell, mitochondrion power, multiple interacting components comprised of proteins, and the database provided by the gene. No one denies that the gene is a necessary component of the machinery of life, but no one should be fooled into believing it causes the development of life. How critical is the gene? The answer is that it depends on your point-of-view and the current fast-advancing state of molecular biology. The development of life is a complex integrated system. The gene does not build proteins, cells, tissues, and organs of the body. It is a lesser player in an exceedingly complex score of a great symphony.
Of course, the proteins are the result of transcription and translation of genes. Nothing exposes the statement as erroneous – that proteins are gene products and therefore it is the gene that is deterministic – more than the origin of life. If there was a warm pond, what was created first – the gene or the protein. A gene cannot create a protein without the help of proteins. The problem is insoluble. Only the RNA theory of the beginning of life acknowledges that there would have to be some molecule that was both a gene and a protein. That theory failed. But it points up the fact that the gene alone is recognized as incapable, at the origin of life as well as at the most advanced state of life, of creating life.
Pre-molecular Challenges to Darwinism
In modern times, I identify Michael Denton in his book Evolution: A Theory in Crisis as leading the attack with a detailed critique of every manner of support for natural selection from homology, to lack of transitions, to inexplicable speciation, uniformitarianism, to say nothing of the complete ignorance of the origin of life and consciousness. The echo heralded an avalanche from a wide variety of evolutionists and outsiders. David Stove. Karl Popper. Brian Goodwin. Ohtoo Kimura. James Doolittle. Carl Woese. Jan Sapp. Barabara McClintock. Lynn Margulis. Eva Jablonka and Marion J. Lamb. Eugene V. Koonin. Michael Behe. Stephen Rothman. Perry Marshall. And, James Shapiro and Denis Noble.
The focus of criticism prior to the advent of molecular genetics was multifold: hereditary variation was stochastic. It is not. Natural selection is the sole vector for adaptation. It is not. Quantitative population genetics was fully explanatory of diversity. It does not. Geological uniformitarianism was equally applicable to evolutionary change – slow, incremental, and cumulative. It is not. Random mutations were the full explanation of the process – mutational change of DNA components. They are not. Even after it was shown that the gene was a passive entity and could do nothing without the supporting cast – the entire organism and its environment – the physiological process was ignored. Each assumption of the classical Darwinism theory was simply incorrect. But each was not individually discredited. Moreover, focus on negative critiquing of Darwin’s various arguments for support of his theory did not address the Darwinists’ taunt: What alternative do you have to offer? The criticism missed the important point that advances in molecular genetic science was rapidly accumulating evidence and establishing a new paradigm. Not merely a critique, a substitute. (p.125)
Paleontology and Random Mutations
Shapiro goes so far as to say that: “The key evolutionary questions no longer center on whether we can establish relationships between different organisms.” (p.4) This is a startling statement that essentially dismisses the shackling of paleontology finds that catalog differences in morphological features to a relationship of these organisms that is explainable only through natural selection. Paleontology is a fascinating record of the development of life while archaeology is an equally interesting record of the material aspects of culture. Neither can form the basis for explaining how and why the development took place. They are at best historical sciences. And at worst, are subject to unsupportable and speculative inferences and ultra-imaginative unfalsifiable hypotheses.
Development of life is not the selection-biased random process that is the basis for natural selection. Indeed, as Perry Marshall in his book, Evolution 2.0, explains, the world-class mathematician Gregory Chaitin has shown that it is impossible to prove that any event is random. In other words, there are unavoidable natural environmental and exogenous conditions that affect heredity. If there is direction, purpose, then selection is redundant. The phenotype is by definition a survivalist.
What Darwin fundamentalists mean by “random” is that the mutation is not directed toward a specific functional change. In other words, alleles (mutated genes) do not directionally accumulate so as to create a new phenotypic feature. Each mutation is independent of the past mutational accumulations. Darwin often referred to “chance” variations; in Neo-Darwinism, chance is tied to DNA mutations. Thus, random or chance mutations. Elliott Sober clarifies what is meant by random in the Darwinian context: “There is no physical mechanism (either inside organisms or outside of them) that detects which mutations would be beneficial and would cause those mutations to occur.” But fundamentalist Darwinists adhere to a different definition – that the cause of mutations is unguided and purposeless. They do so in order to exclude the possibility that a natural phenomenon or extraterrestrial being could be guiding the process. But whatever the motive, it is scientifically wrong.
“It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change, and sequence studies confirm distinct biases in location of different mobile genetic elements.”
(p. 82) In other words, the changes are guided physically and functionally toward a purpose. This is what is meant by “natural genetic engineering,” as explained below.
The gene-centric concept as a metaphor for the developmental system is simply too crude, too basal, too imaginary to correctly describe the system. As Shapiro states: “Thinking about genomes from an informatics perspective, it is apparent that systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations.” (p. 6) This is a wholesale rejection of the Dawkins’ selfish gene theory, that however denied, is genetic determinism, a science suffocating simplicity.
On metaphors, it is erroneous to think of the genetic code as “like a code.” It is a code. As Perry Marshall explains, there are four features of a code: (a) a set of rules that are established in advance, (b) an encoder with the encoding rules, (c) a digital message that transmits information according to the rules, and (d) a decoder with the rules. Schemes such as html, bar codes, postal codes and Morse code all fit this description. It was a fruitless effort of the bioatheist community to turn the genetic code into a mystical concept that occurs and functions without intelligence. To the contrary there must be an “encoder,” a super-intelligent entity. Some call it God.
Central dogma of molecular biology
More than a half-century after the central dogma was originally announced by Francis Crick, the gene deterministic process is bankrupt. Shapiro states: “The cognitive, informatics view of how living cells operate and utilize their genomes is radically different from the genetic determinism perspective articulated most succinctly, in the last century, by Francis Crick’s famous ‘Central Dogma of Molecular Biology’.” (p. 24) Like some other dogmas, this one is wrong, or at least misleading if construed as the sole manner in which the DNA to RNA to protein is a one-way process. Reverse transcription such as a retrovirus like the HIV virus is a direct violation of the Central Dogma; it imposes the RNA genome on the DNA genome. RNA viruses, as opposed to DNA viruses, may act in the same manner as messenger RNA and translate to proteins, such as the influenza virus. In this case the process is not reversed but rather disrupts the sequential DNA to RNA to protein process. Still another disruption of the process is the existence of non-coding RNA denominated ncRNA. ncRNA does not translate to proteins but acts directly in the cell as RNA that has not been coded from DNA. Examples include transfer RNA and ribosomal RNAs. Again, not so simple.
Cynically speaking, no science, other than Darwinism, has hid behind the excuse that a critical tenet of its theory is that the time required to confirm whether an observation supports the theory is so long that confirmation is impossible. Darwin adopted a natural concept called uniformitarianism that was established in geology as that science took root. It simply means that change takes place at a glacial pace. Slowly. Incrementally. Successively. And it surely is correct as an explanation of how the earth develops. Darwin was a friend of Charles Lyell who followed in the footsteps of James Hutton, known as the father of geology. Darwin held that the development of life was analogous to the geologic changes in the earth surface.
Darwin was fond of metaphors as he developed his theory of evolution. But uniformitarianism was a two-edge sword. Because progress was incremental, observable changes in fossils should be minor. However, the fossil record is so episodic with no smoothly graded minor transitions from one species to another that it failed to support the theory of life development as slow and with small steps. From one point-of-view, critics argued that change was so slow that the enormous variety of life could not have developed if the pace was so slow – there was not enough time. From a counter critical perspective if there was such small modifications from one species to another, there should be some evidence of a near continuous species development so that even minor changes would be apparent. But the fossil record does not cooperate. It exposes embarrassing gaps.
More importantly, the fossil record showed that there were not small incremental changes, but significant morphological leaps from one animal to another in the same germ line. This idea was termed saltation, meaning sudden development that is evidenced by large discontinuities from one generation to another. An entire school that lasted for many decades advocated saltation and included prominent evolutionists such as deVries, Lamarck, Cuvier, Etienne Geoffrey Saint-Hilaire, Bateson, and others. Not only did the Darwinists crush the saltationists that rejected natural selection because changes were not minor, they mocked their theory as stupid.
But recently, molecular genetics has shaken if not destroyed the idea of uniformitarianism as applied to evolution. Barbara McClintock, a Nobel prize winner, discovered what are now called mobile genetic elements, or transposons as well as other forms of genetic mobility . While ignored for years as limited to plants (McClintock worked on corn), over two-thirds of the human genome is derived from mobile genetic elements. These genomic changes are not slow processes. James Shapiro is unequivocal in his dismissal of slow, numerous, slight and successive variations:
The data are overwhelmingly in favor of the saltationist school that postulated major genomic changes at key moments in evolution. Only by restricting analyses to certain classes of genomic DNA, such as homologous protein encoding sequences, can conventional evolutionists apply their gradualist models. Moreover, we will see from genome sequencing that protein evolution itself often proceeds in relatively large steps. Contrary to the views of Linnaeus and Darwin, nature does indeed make leaps, and we now have molecular evidence of how some leaps occurred.
(pp. 89-90) He cites to Darwin’s own doubts: In a letter to his friend, the botanist, J. D. Hooker, on July 22, 1879, Darwin called the rapid diversification of flowering plants (angiosperms) in the fossil record of the Lower Cretaceous “an abominable mystery.” (p.122)
Once again Shapiro explains:
“It is important to note that selection has never led to formation of a new species, as Darwin postulated. No matter how morphologically and behaviorally different they become, all dogs remain members of the same species, are capable of interbreeding with other dogs, and will revert in a few generations to a common feral dog if allowed to go wild. The way we make new species synthetically is by interspecific hybridization. The importance of interspecific hybridization [hybrids involving different species within the same genus] has been mentioned by many early evolutionists, including Lamarck . . . .” (p.121)
The New Paradigm
It is difficult to assign a date for the start of the new paradigm for it is not a cataclysmic event but an evolutionary one. A major event however was the publication of the book Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life by Eva Jablonka and Marion J. Lamb in 2005. The title speaks for itself. And it is a lively read:
“Our basic claim is that biological thinking about heredity and evolution is undergoing a revolutionary change. What is emerging is a new synthesis, which challenges the gene-centered version of neo-Darwinism that has dominated biological thought for the last fifty years. . . . We will be arguing that:
there is more to heredity than genes;
some hereditary variations are nonrandom in origin;
some acquired information is inherited;
evolutionary change can result from instruction as well as selection.”
Indeed, Eugene Koonin is blatantly frank:
“The edifice of the Modern Synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. . . . The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.”
Trends Genetic, November, 2009, 25(11): 473-475.
In biochemistry, reductionism has reached rock bottom– nucleic acids and amino acids. In evolutionary biology, the fuzzy gene is the bottom. It has led only to a simplicity that can be lapped up by the masses in the bunny stories of anthropology and gene-centrism. Heredity cannot be explained only by the genetic code. The paradox of heredity is brilliantly delineated by Carl Zimmer in his recent book: She Has Her Mother’s Laugh, The Powers, Perversions, and Potential of Heredity. In the book he explores a puzzling array of natural idiosyncrasies involving heredity. But he also focuses on the new science that has demoted genes from their central position in how heredity occurs. (pp. 426-444)
In what was thought to be a very simple genetic linkage – the gene for height – when the researchers looked for the gene – were startled to find: “In 2017, a decade after the first genome-wide association study of height, GIANT [the acronym for the study] published a study on more than 700,000 people bringing the total number of genes influencing height to almost eight hundred.” (p.280) Moreover, those 800 genes accounted for only 27% of the heritability of height. The human genome project, a very expensive endeavor, intended to be dispositive of all questions genetic, turned out instead to merely open a Pandora’s box. While geneticists have always acknowledged that some traits are polygenic, the height study suggests that the more appropriate word may be totallygenic. So much for “gene (singular) for.”
Like wars, religions, and football seasons, there is always a few battles, dogmas, or games that determine the winner. So it is with paradigm transitions. The battleground for the correct paradigm for the development of life is called epigenetics. That is, the study of the heritable changes in organisms caused by modification of gene expression without a change in the genome. Denis Noble states in his scientific paper:
“Evolution theory itself is already in a state of flux (Jablonka & Lamb, 2005; Noble, 2006, 2011; Beurton et al. 2008; Pigliucci & Mueller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). In this article, I will show that all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproved. Moreover, they have been disproved in ways that raise the tantalizing prospect of a totally new synthesis, one that would allow a reintegration of physiological science with evolutionary biology.”
(p.1235) It strikes at the heart of the gene-centric theory. It effects changes in the phenotype without a change in the genotype. The word “epigenetic” was coined almost 75 years ago, forgotten but then revived and reconstructed in the 1990’s. The full scope of the concept is yet to be determined but as with flying cars it has created a playground for pseudo-science. From mind control over cancer to other radical absurdities – the hype is thick in the air. But there are also real truths and more to be discovered.
At the risk of being overtaken by the latest research, there are three to six (depending on how the specialties are defined) main areas of science-based epigenetics: (1) DNA methylation; (2) histone modification; (3) transcription factors; (4) non-coding RNA (ncRNA) and micro-coding RNA (miRNA); (5) chromatin re-modeling; and (6) nuclear location. More importantly, these individual processes do not work alone but in various combinations. Combinatorial analysis is always mind-boggling. It is not my purpose to explain the vast and exceedingly complex research establishing the regulatory effects of epigenetic elements. One source I found that was not overwhelmingly technical is at: https://www.whatisepigenetics.com/fundamentals/. My point is to show that the epigenetic revolution is a prime candidate for retiring the gene-centric paradigm. It is robust and empirical. It is attracting significant research money and players that are always evidence of credibility. It is not influenced by religious advocacy. It is carceral reform of paleontological based evolutionary biology. It is natural. It is early but gaining. Molecular biology versus anthropology.
Even more heretical to the fundamentalist Darwinians is the reprise of Lamarckism whose theory of the passing of acquired characteristics to progeny became a standard jape of the bioatheists. They ignored that Lamarck did not conceive of acquired characteristics – that concept was ancient. Moreover, Darwin was frustrated by the concept but was an adherent causing him to find a mechanism that he named pangenes that moved from somatic to sex cells. It is unnecessary to resurrect Lamarckism in name, but molecular genetics has established that exogenous factors including acquired characteristics are undoubtedly a component of the developmental process.
The other pillar that supports Neo-Darwinism is natural selection. That misguided tautological concept has been under fire for decades. Genetic drift, neutral mutations, spandrels, or simply the maladaptive mutation. But epigenetics undermines natural selection simply because it shows that the random mutation tenet, a key element of natural selection, is false. Natural selection is “fundamental” to Darwinism in the sense that even if change occurs primarily by gene mutations, the mutations are guided by non-gene factors that lead to a designer or to factors that are controlled by the environment within the cell, tissues, organs, the complete organism, and its environment.
The development of life is guided by natural genetic engineering. The cell is capable of recognizing its relation to the external world and makes goal-directed decisions based on those observations properly comprehended. To be sure, epigenetics per se is not teleological. Shapiro states: “It is possible that DNA-based heredity will ultimately find a more modest role in our thinking about inheritance in the course of the [21st] century.” (p. 4) But it will never dominate as it does today.
The work of McClintock damaged the Tree of Life metaphor; transposons rearranged chunks of the DNA thus unsettling the Darwinian concept that gene mutation was the dominant driver of evolution. But more startling, as Margulis, Woese, and Doolittle, among others, have shown, is a process called symbiogenesis, in which the entire genome of a different species may be transferred. It is the mechanism by which the eukaryote evolved from the prokaryote – a horizontal gene transfer of the prokaryote into a eukaryotic cell. For example, mitochondria within the eukaryotic cell was once a free-standing prokaryote. This proof upset the entire tree that Darwin and his followers had constructed and undermined the “common ancestor” theory of Darwinism. Inheritance is not simply vertical.
Still another blow came from phylogenetics as explained by Jan Sapp:
“The new phylogenetics marks a new beginning with concepts that fundamentally contradict the principal tenets and assumptions of Darwinian theory: (1) The concept of species as discrete objective entities . . . confronted with evidence of extensive lateral gene transfer between taxa. (2) The notion that gene mutation and recombination within species are the principal fuels of evolutionary change is denied. (3) That evolutionary change is gradual – that evolution does not take leaps – is refuted by evidence of saltational changes resulting from the inheritance of acquired genes and genomes. (4) The fundamental conception of evolution itself as descent with modification . . . is contradicted by evidence that most genes are transferred laterally.”
The New Foundations of Evolution: On the Tree of Life, p.317.
The 21st Century view of the development of life is an ongoing research project attempting to break the manacles that have stultified evolutionary progress. In addition to advancing our knowledge of how life develops, it will inter the idea of bioatheism that is only supported by the Darwinian paradigm. I do not wish to suggest that the new synthesis is supportive of a God. Rather, bioatheism was based squarely on Neo-Darwinism and in particular the genecentric hypothesis that became a theory but only by gross over-simplification, easy for the non-biologist to grasp and embrace, while distorting science. More generously, the Dawkins obsession with using genecentrism to prove atheism was laid out in his 1976 book, The Selfish Gene, over forty years ago, before the current molecular revolution began to gather adherents. Dawkins never changed his evolutionary views – he could not because genecentrism was not created as a biological concept but as a anti-religion jihad. It is ironic that the millenials who now boast “no religion,” assuredly encouraged by secondary school biology classes that inculcated and idolatrized genecentrism, have been left with no evolutionary theory to support their agnosticism, atheism and satanism. May Darwinism, as the modern atheists have transmogrified it, rest in peace.