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The first Darwin Day I started writing just for this day, I wrote about (and defended Darwin’s words) how both Creationists and evolutionists who are themselves evolutionary progressionists twist Darwin’s words for their own gain. Darwin never wrote in The Descent of Man that the ‘higher races’ would take out ‘the lower races’, but that doesn’t stop Creationists and evolutionists—who I presume have not read one sentence in Darwin’s words from one of his books—from taking what Darwin meant out of context and attributing to him beliefs he does not hold. This year, though, I am going in a different direction. The Modern Synthesis (MS) has causation in biology wrong. The MS upholds the ‘gene’ as one of the highest seats in evolutionary biology, with a sort of ‘power’ to direct. Though, as I will show, genes do nothing unless transcribed by the system. Since the MS has causation in biology wrong, then we either need to extend or replace the MS.

To begin, Darwin, without knowledge of genes or other hypothesized units of inheritance, had a theory of inheritance in which things called ‘gemmules’ (what Darwin called heritable molecules) were transmitted to offspring (Choi and Mango, 2014). It’s ironic, because Darwin’s theory of inheritance was one of the more Lamarckian theories of inheritance in his day, and Darwin himself sympathized with the Lamarckian view of evolution—he most definitely did not discard it like modern-day Darwinists do. Darwin suggested that these gemmules circulated in the body and that some were used for the regeneration of some bodily tissues, but most aggregated in the reproductive organs (Jablonka and Lamb, 2015: 23). Further, according to Darwin, gemmules were not always immediately used but could reappear later in life or even be used in future generations. Darwin even said that “inheritance must be looked at as a form of growth” (Darwin, 1883, vol 2, p. 398; quoted by Jablonka and Lamb, 2015: 24).

The crux of the MS is the selfish gene theory of Dawkins (1976). Dawkins (1976, 2006) writing “They are in you and me; they created us, body and mind; and their preservation is the ultimate rationale for our existence.” “They”, of course, being genes. The gene has been given a sort of power that it does not have, but has been placed on it by overzealous people, quick to jump to conclusions while we still have yet to understand what ‘genes’ do. The MS—with the selfish gene theory—is at the forefront of the neo-Darwinist revolution, that evolution is gene-centered, with genes playing the starring role in the evolutionary story.

Though, numerous researchers are against such simplistic and reductionist viewpoints of evolution, mainly the gene-centered view of evolution pushed by the MS. There is no privileged level of causation in biology (though I will state later in this article that I think ATP comes close to it) (Noble, 2016).

Neo-Darwinists, like Richard Dawkins, overstate natural selection’s importance regarding evolution. They elevate the gene’s overall importance. In the quote from Dawkins above, where he stated that “they” (genes) “created us, body and mind”, he is implying that genes are a sort of ‘blueprint’, like a ‘plan’ or ‘recipe’ for the form of the organism. But this was taken care of by Susan Oyama in her 1985 book The Ontogeny of Information where she writes on pages 77:

“Though a plan implies action, it does not itself act, so if the genes are a blueprint, something else is the constructor-construction worker. Though blueprints are usually contrasted with building materials, the genes are quite easily conceptualized as templates for building tools and materials; once so utilized, of course, they enter the developmental process and influence its course. The point of the blueprint analogy, though, does not seem to be to illuminate developmental processes, but rather to assume them and, in celebrating their regularity, to impute cognitive functions to genes. How these functions are exercised is left unclear in this type of metaphor, except that the genetic plan is seen in some peculiar way to carry itself out, generating all the necessary steps in the necessary sequence. No light is shed on multiple developmental possibilities, species-typical or atypical.“

The genes-as-blueprints canard is one that is heavily used by proponents of the MS. Oyama also writes on page 53 “Just as traditional thought placed biological forms in the mind of God, so modern thought finds many ways of endowing the genes with ultimate formative power, a power bestowed by Nature over countless millennia.” This same sentiment from Oyama is also echoed by developmental systems theorist and psychologist David Moore in his book The Dependent Gene: The Fallacy of “Nature VS. nurture”, where he writes:

Such contextual dependence renders untenable the simplistic belief that there are coherent, long-lived entities called “genes” that dictate instructions to cellular machinery that merely constructs the body accordingly. The common belief that genes contain context-independent “information”—and so are analogous to “blueprints” or “recipes”—is simply false. (p. 81) (Quoted from Schneider, 2007)

Environmental factors are imperative in determining which protein-coding exons get read from a cistron, when and how often. So the very concept of a gene depends on the environment and environmental inputs, and thusly gene ABC does not code for trait T on its own.

When it comes to epigenetics (defined here as inherited changes in gene expression with no genetic change to the genome), this completely changes how we view evolution.

The underlying nucleotide sequence stays the same but differences are inherited due to environmental stressors. I’ve stated in the past that these inherited marks on the genome (through histone modification, DNA methylation, which then alter the chromatin structure of the DNA. Further, this would show up on heritability estimates as ‘genetic’ when the ’cause’ was ‘environmental’ in nature (which is also yet another reason that heritability estimates are inflated).

DNA methylation, histone modification and noncoding RNA all can affect the structure of chromatin. As of now, the mechanisms of mitotic inheritance aren’t too well known, but advances in the field are coming.

If you want to talk the P and F1 generations regarding transgenerational epigenetics, then you must realize that these changes do not occur on the genome, the genome remains the same, just certain genes are expressed differently (as I’m sure you know). Though mi-MRNA signals can change the DNA methylation patterns in the F2 sperm which then is replicated in meiotic and mitotic cycles (Trerotola et al, 2015).

For another similar process on how DNA methylation persists, this (semiconservative) replication of DNA methylation occurs on both strands of the DNA which then become hemimethylated DNA which can then become fully methylated by methylase maintenance. So chromatin structure affects the genetic expression of the eukaryotic genome which then becomes the basis for epigenetic effects. Xist RNA also mediates the X-chromosome deactivation. This doesn’t even get into how and why the microbiome can also affect gene expression (which has also been called ‘the second genome’ (Zhu, Wang, and Li, 2010) with other authors calling it an ‘organ’ (Clarke et al, 2014; Brown and Hazen, 2015) this can also affect gene expression and heritable variation that becomes the target of selection (along with the other modes of selection) (Maurice, Haiser, and Turnbaug, 2014; Byrd and Segre, 2015). This shows that gene expression in the F2 and F3 generations is not so simple, and that other factors such as our gut microbiota can also affect gene expression and stressors experienced by parents and grandparents can also be passed to future generations, and may have a chance of becoming part of heritable variation that natural selection then acts on (Jablonka and Lamb, 2015).

The point of the debate with neo-Darwinists is over causation: do genes hold this ‘ultimate formative power’ as people like Dawkins contest? Or are genes nothing but ‘slaves’, passive, not active, causes as Denis Noble writes in his 2016 book Dance to the Tune of Life. (Noble, 2008 discusses genes and causation, again showing that there is no true causation, but getting technical, ATP is up there in the ‘chain’, if you want to get literal. The point is that genes do not have the ‘power’ that the neo-Darwinists think they do, they’re just slaves for the intelligent physiological system.)

When discovering the structure of DNA, Francis Crick famously announced to his drinking companions in a Cambridge tavern that he had discovered ‘the secret of life’. The director of his Institute, Max Perutz, was rather more careful than Crick when he said that DNA was the ‘score of life’. That is more correct since a musical score does nothing until it is played, DNA does nothing until activated to do so. […] Recent experimental work in biological science has deconstructed the idea of a gene, and an important message of this book is that it has thereby drthroned the gene as a uniquely privileged level of causation. As we will see, genes, defined as DNA sequences, are indeed essential, but not in the way in which they are often portrayed. (Noble, 2016: 53)

A 2017 paper titled Was the Watchmaker Blind? Or Was She One-Eyed?, Noble and Noble (2017) write that organisms and their interacting populations have evolved mechanisms so that they can harness blind stochasticity, thereby generating functional changes to the phenotype as to better respond to environmental challenges. They put forth a good argument, though it really makes me think because I’ve been such a staunch critic against evolution having a ‘direction’ and against the ‘teleological view’ of evolution: “If organisms have agency and, within obvious limits, can choose their lifestyles, and if these lifestyles result in inheritable epigenetic changes, then it follows that organisms can at least partially make choices that can have long-term evolutionary impact.”

Noble and Noble (2017) argue (using Dawkins’ analogy of the Blind Watchmaker) that humans are the only Watchmakers that we know of. Humans evolved from other organisms. The ability to become a Watchmaker has evolved. Ergo, there is no surprise that there is directed agency for other organisms that directs their evolution too. There are several processes, they conclude, that could account for directed evolutionary change which are “targeted mutation, gene transposition, epigenetics, cultural change, niche construction and adaptation” (Noble and Noble, 2017). Niche construction, for instance, is heavily pushed by Kevin Laland, author of the book Darwin’s Unfinished Symphony: How Culture Made the Human Mind who has a few papers and featured it heavily in his new book. Either way, these ways in which organisms can in a way direct their own evolution are not covered by the MS.

Though I couldn’t end this article without, of course, discussing Jerry Coyne who goes absolutely crazy at people pushing to either extend or replace the MS. His most recent article is about Kevin Laland and how he is “at it again” touting “a radically different view of evolution”. It seems as Coyne has made up his mind and that the MS is all there is—he believes it is no problem for our current understanding of evolutionary theory to absorb things such as niche construction, epigenetic inheritance, stochasticity, and even (way more controversially) directed mutations. Coyne has also criticized Noble’s attacks on the MS, though Noble came back and responded to Coyne during a video presentation.

Lastly, Portin and Wilkins (2017) review the history of the gene, and go through different definitions it has been given over the decades. They conclude in this paper that they “will propose a definition that we believe comes closer to doing justice to the idea of the “gene,”

in light of current knowledge. It makes no reference to “the unit of heredity”—the long-standing sense of the term—because we feel that it is now clear that no such generic universal unit exists.” Writing on page 1361-1362:

A gene is a DNA sequence (whose component segments do not necessarily need to be physically contiguous) that specifies one or more sequence-related RNAs/proteins that are both evoked by GRNs and participate as elements in GRNs, often with indirect effects, or as outputs of GRNs, the latter yielding more direct phenotypic effects. [GRNs are genetic regulatory networks]

This is similar to what Jablonka and Lamb (2015: 17) write:

Although many psychiatrists, biochemists, and other scientists who are not geneticists (yet express themselves with remarkable facility on genetic issues) still use the language of genes as simple causal agents, and promise their audience rapid solutions to all sorts of problems, they are no more than propagandists whose knowledge or motives must be suspect. The geneticists themselves now think and talk (most of the time) in terms of genetic networks composed of tens or hundreds of genes and gene products, which interact with each other and together affect the development of a particular trait. They recognize that whether or not a trait (a sexual preference, for example) develops does not depend, in the majority of cases, on a difference in a single gene. It involves interactions among many genes, many proteins and other types of molecule, and the environment in which an individual develops.

The gene as an active causal actor has been definitively refuted. Genes on their own do nothing at all, until they are transcribed by the intelligent physiological system. Noble likens genes as slaves that are used by the system to carry out processes by and for the system. So genes are caused to give their information by and to the system that activates them (Noble, 2011). Noble’s slave metaphor makes much more sense than Dawkins’ selfish metaphor, since genes are used like slaves by the system, the genes are then caused to give their information by and to the system that activates them, which shows how they are a passive, not active, cause, completely upending the MS and how it views causation in biology. Indeed, Jablonka and Lamb state that one of their problems with Dawkins is that “Dawkins assumes that the gene is the only biological (noncultural) hereditary unit. This simply is not true. There are additional biological inheritance systems, which he does not consider, and these have properties different from those we see in the genetic system. In these systems his distinction between replicator and vehicle is not valid.”

So, both Gould and Dawkins overlooked the inheritance of acquired characters, as Jablonka and Lamb write in their book. They argue that inherited variation had a large effect on the evolution of species, but admit that evidence for the view is scant. They write on page 145 “If you accept that heritable epigenetic variation is possible, self-evidently some of the variants will have an advantage relative to other variants. Even if all epigenetic variations were blind, this would happen, and it’s very much more likely if we accept that a lot of them are induced and directed.” Not everything that is inherited is genetic.

DNA is found in the cell, and what powers the cell? ATP (adenosine triphosphate). Cells use and store ATP to carry out their functions (Khakh and Burnstock, 2016). Cells produce ATP from ADP and Pi. Cells use exergonic reactions to provide the energy needed to synthesize ATP from ADP and Pi. The hydrolysis of ATP provides the energy needed to drive endergonic actions.So the cells continuously produced more ATP from ADP and Pi to then carry out diverse functionings across the body. So, in a way, you can argue that one of the ultimate causes is ATP since it has to power the cell, then you can look at all of the other reactions that occur before ATP is created and privilege that part of the chain, but there will never be some ultimate causation, since, as Noble argues in his book Dance to the Tune of Life, there is no privileged causation in biology.

In conclusion, evolution, development, and life, in general, is extremely complex. Paradigms like the selfish gene—a largely reductionist paradigm—do not account for numerous other factors that drive the evolution of species, such as targeted mutation, niche construction etc. An extended evolutionary synthesis that integrates these phenomena will better be able to describe what occurs to drive the evolution of species, and if the directed mutation idea has any weight, then it will be interesting to see how and why certain organisms have evolved this ability. It’s ironic how the MS is being defended as if it is infallible—like it can do no wrong and that it does not need to be added to/extended or replaced by something else that incorporates the phenomena brought up in this article.

Either way, a revolution in modern biology is coming, and Darwin would have it no other way. The Modern Synthesis has causation in biology wrong: the gene is not an active agent in evolution, it only does what it is told by the intelligent physiological system, and so we must look at whole organisms and not reduce organisms down to genes, but we must look at the whole organism—a holistic view of the organism, not one that is reduced down to just ‘the genes’, because there is no privileged level of causation in biology (Noble, 2016).