Toward a Biology Worthy of Life

Genes and the Central Fallacy of Evolutionary Theory

Is DNA the Decisive Heritable Material?
Stephen L. Talbott

This essay is part of a larger work in progress entitled: “Toward a Biology Worthy of Life”. Original publication of this article: February 28, 2013. Date of last revision: February 2, 2015. Copyright 2013, 2015 The Nature Institute. All rights reserved.

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“EVOLUTION”, BY COMMON UNDERSTANDING, is almost synonymous with “survival of the fittest”. The idea is that, over time, more organisms of any species are produced than could possibly subsist upon available resources. So there must be a competitive struggle: those organisms better adapted to their environments — fitter organisms — will tend to survive and produce more progeny of their own. As a result, their characteristics become more prominent in the population as a whole. The population evolves.

But two other ideas must be added to that of a struggle for survival before we can have evolution. One, obvious enough, is that there must be variation among the competing organisms. Otherwise, we could hardly declare some to be fitter, or better adapted for survival, than others. And it is clear that there is variation within any given species.

The second additional idea may require a moment’s reflection. Even if organisms differed in their fitness, leading to the preferential survival of some, there couldn’t be anything like evolution as we think of it today unless offspring tended to inherit the traits of their parents. Not that there must be an absolute rule to this effect; but if offspring didn’t at least tend to resemble their parents more than other members of the species, then any superior fitness of a given parent over those other members would not likely be propagated down through the generations. The offspring of the fittest members of the species could just as well resemble the least fit members. Change would become arbitrary, and therefore we would be very unlikely to see any consistent accumulation of useful variations yielding a new, complex adaptation.

According to the standard formulation, then, evolution is guaranteed to occur under three conditions — conditions summing up what is often presented as the core logic of evolution:

Variation, inheritance, and survival of the fittest: there is something irresistible and self-evident about the way they testify to the idea of change. And yet, “self-evident” may also mean “with little empirical significance”. It’s easy to forget that the three conditions tell us only in the vaguest possible way that some sort of change might possibly occur. They say nothing at all about the kind of change to expect, what evolutionary significance (if any) it may have, or why the actual history of life on earth looks the way it does.

A great deal depends, for example, on what sort of variation is possible: How does it come about, and what role, directed or otherwise, does the organism play in generating it? How does the variation influence the environment and how is it in turn influenced by the environment? What constraints govern its combination with previous and future variation? As for differential survival: in what respects and at what levels of observation, from pairs of organisms to the biosphere as a whole, does life turn out to be competitive or, on the contrary, cooperative? And most generally: what, if any, principles of structure, order, and harmony should we expect to find in individual creatures and their various groupings?

Our three conditions, in other words, give us no concrete understanding, and therefore no real theory of the sort scientists normally look for — not until we import additional principles. These, unfortunately, may prove far less compelling and far less self-evident than the familiar trio of variation, inheritance, and differential fitness.

Evolution as a Genetic Narrative

The independence of the three conditions from material contingencies is so great that philosopher Daniel Dennett, in his influential book, Darwin’s Dangerous Idea, was happy to celebrate the conditions as elements of a purely logical structure (“algorithm”) whose truth requires no particular sort of physical embodiment (1995, pp. 50-1*; Talbott 2007a*). We can hardly expect such skeletal logic, shorn of subtlety, detail, and empirical substance, to tell us anything very specific about the real organisms available to us for study. We will never come to understand how and why this organism differs from that one merely by looking at a universal logic applying equally to both.

Even when we turn from philosophers to biologists, finding a science of evolution rather than a mere toying with logically self-contained and empirically detached algorithms may prove difficult. We can glimpse the difficulty by observing how the three conditions listed above are thought to connect most directly to actual physical organisms. DNA — whose individual “letters” (nucleotide bases) are widely construed as “atoms” of programmable logic — appears to be almost the entire conventional story:

DNA sequencesprotein-coding genes, with the more recent and increasingly prominent addition of DNA regulatory sequences — constitute the one unquestioned material foundation and efficient cause upon which, from the organism’s side, the modern edifice of evolutionary theory has been erected. As defined in a classic introductory text, the process of evolution “includes all mechanisms of genetic change that occur in organisms through time...” (Hartl 1988, p. 143; emphasis added*). Evolution, in this view, looks very much like a matter of genes and their fate — and not much more.

Yet the hollowness of the evolutionary “algorithm” — its detachment from concrete scientific insight — is hardly improved by harnessing the three principles to gene destinies. Consider:

Variation. Genetic mutationsmutations that are supposed to account for evolutionarily significant variation — are assumed to be random. But the appeal to randomness — however it may be employed within a larger context of explanation — is in itself the antithesis of scientific explanation1. If we are to gain clarity about any particular evolutionary lineage — which we call a “lineage” only because it exhibits a coherent and recognizable (that is, nonrandom) trajectory begging for a principled understanding — this clarity must come from something other than random variation.

Differential fitness. We find little more clarity when we turn to the organism’s fitness-determining observable features (phenotype), and try to understand them based on DNA. No serious biologist today would claim that we can, in general, look at the genotype, or genetic constitution, of a zygote and “read off” from it the developing organism’s morphology, physiology, or behavior, let alone the associated fitness implications.

The imprecision and ambiguity of the concept of fitness shouldn’t need to be argued today — although I have argued it (Talbott 2011a*). University of Missouri philosopher André Ariew and Harvard geneticist Richard Lewontin (2004*) summarized the situation when they wrote that “No concept in evolutionary biology has been more confusing” than that of fitness. The “consensus view,” as Roberta Millstein and Robert Skipper, Jr., have written in The Cambridge Companion to the Philosophy of Biology (2007*), is that “biologists and philosophers have yet to provide an adequate interpretation of fitness.”

Without a workable concept of fitness or its relation to DNA — and, which makes the matter vastly more complicated, without an understanding of how the environment might “channel” fitness changes, whatever they are, into the distinctive unity and unique structures and capabilities of the organisms in radically different evolutionary lineages — we don’t have much that practically relates to evolution at all.

Inheritance. Finally, there is the idea that DNA is the decisive heritable substance so far as evolution is concerned. It is the burden of this paper to show how misconceived this is. But first we need to ask why the idea carries so much weight with evolutionary biologists.

Why DNA Seems So Central to Evolution

You will recall the principle of inheritance, part of the core logic of evolution: offspring must generally tend to resemble their parents more than they resemble others. The fact of such resemblance is not disputed, and for the past several decades biologists have accepted that genes, or DNA sequences, provide the overwhelmingly dominant “mechanistic basis” for the fact. Three lines of thought prove particularly effective in solidifying the hold of the heritable gene upon the imagination of evolutionary theorists:

Transgenerational digital fidelity. The complex adaptive features produced over long ages by evolution must — so it is assumed — be assembled step by step, by adding part to part, as when we build a machine. And therefore it is natural to expect that the heritable foundation for this building process must likewise evolve in a stepwise fashion involving the aggregation of distinct parts. Evolution will depend on stable, though alterable, structures that pass reliably from parents to offspring.

This is taken to mean, in the first place, that heritable elements should be discrete — particulate or atom-like. They must not interpenetrate or blend into one another. If they did blend, we would not be able to evolve new features sequentially. It would be as if we were trying to build an edifice from Lego blocks, but every time we added, removed, or changed one block, all the other blocks shifted their position or melted together into different forms. The stability necessary for the evolution of a coherent structure — for preserving and extending specific changes in it — would be missing.

A closely related requirement is that heritable elements should be accurately replicated when passed on to offspring. Without this accuracy, we would again find additive, step-by-step evolutionary change impossible.

DNA, it seems, could scarcely fulfill these requirements more neatly. It consists of discrete nucleotide bases, as well as higher-order constructs, such as genes, that we have long conceived as distinct, well-defined entities subject to occasional mutations. And during the reproductive process an organism’s entire DNA sequence is (ignoring certain reshuffling processes and other dynamic changes mentioned below) replicated with remarkable fidelity.

The ideal suitability of DNA as the transgenerationally stable material of inheritance is summed up in the conviction, widely shared among biologists, that DNA is an essentially digital medium. Each element of DNA is an all-or-none, yes-or-no sort of thing — it is unambiguously this letter or that one, with no fuzziness of definition, just as a Lego block has a particular color and shape selected from a fixed collection of alternatives. This unambiguous choice between well-defined alternatives is what enables us (in principle, at least) to reproduce digital song recordings — but not analog ones — countless times without loss of fidelity.

DNA, then, gives us discrete particles of inheritance with near-perfect digital fidelity of replication. It gives us exactly what we’re told evolution needs as a reliable medium for cumulative and constructive change.

In light of all this, we can understand why Richard Dawkins assures us that “Bodies don’t get passed down the generations; genes do” (2006a, p. 79*). We do not find a child to be an atom-like, digital, precisely replicated version of either of its parents. But genes, as the evolutionist conceives them, do get reliably passed on, generation after generation. This contributes greatly to the centrality of genes in evolutionary theory.

The explanatory primacy of genes. Genes have long been thought of as the fundamental explainers of the organism, acting as a kind of First Cause. This seemingly ineradicable conviction is too obvious to require documenting here2. I do wish to mention, however, that even those aspiring to a radical re-think of evolutionary theory continue to claim final grounding in DNA. For example, Andreas Wagner, professor at the University of Zurich’s Institute of Evolutionary Biology and Environmental Sciences and author of The Origins of Evolutionary Innovations, has no doubt that, “ultimately, evolutionary innovations are caused by genotypic change” (2011, p. 3*). At the same time he repeatedly assures us — as if the matter were too obvious to require justification — that, in the individual organism, genotypes “form” phenotypes, “map” to them, “determine” them, and so on.

Likewise, systems biologists Marc Kirschner and John Gerhart, in articulating their theory of “facilitated phenotypic evolution”, take it for granted that “genotype generates the phenotype” and assume that there is an “ultimate map between genotype and phenotype” (2005, p. 33*). And the late Stephen Jay Gould, who in some respects strongly opposed one-sided, gene-centered thinking, nevertheless accepted both that “genes lie at the base of a causal cascade in the development of organisms”, and “only genes act as nearly ubiquitous recorders of all evolutionary alterations” (2002, pp. 634, 636*).

The belief that genes somehow provide the ultimate ground of explanation for what organisms become certainly strengthens the conviction that genes are the paramount heritable material accounting for the evolution of those organisms.

The divorce of evolution from development. One way to guarantee the gene’s supremacy as the evolutionarily significant inherited material is simply to ignore everything else. And this becomes easier when, in your thinking, you forcibly separate the gene, as it passes immaculately down through the generations, from all the close-knit processes in individual organisms with which it is bound up.

During much of the past century many observers have commented on the strange disconnection of evolutionary from developmental biology, the former dealing with the origin of species (phylogeny) and the latter with the life cycle of the individual organism (ontogeny). The disconnection was no doubt encouraged by the fact that DNA, with its precise sequence, offered the evolutionist a wonderfully convenient material for strict analysis, whereas the developmental biologist could not avoid reckoning, for example, with the dynamic complexities of the “heaving and churning” cellular sea (Weiss 1973, p. 40*) surrounding every organism’s chromosomes. It proved irresistibly attractive to isolate the calculable aspects of evolutionary theory, however artificial, from the discouragingly non-algorithmic cauldron of life.

There was a related idea conducing to the detachment of evolution from the reality of the developing organism. In animals (although not in plants) the germline consists of a distinct cellular lineage traceable from zygote to gametes. This germline has been thought to pursue its own destiny more or less insulated from all the non-germline (“somatic”) cellular lineages leading to the various other tissue types of the body. So biologists pictured a germline sequestered from the rest of the organism, and within each cell of the germline they imagined a causally decisive genome faithfully maintaining its own sequential identity regardless of changes in the rest of the cell.

Students of evolution — disregarding the plant world and believing that genes somehow manage to act as causes of the developing organism without being affected in turn by that organism — were now free to restrict their attention to the all-important germline and, in particular, its DNA.

This helps us to understand why a certain idea has long been anathema among evolutionary biologists. I mean the idea that acquired characters (features or traits) of the organism can be inherited. And it is true, for example, that the enlarged biceps of the blacksmith are not passed on to his descendants, and similarly with the slightly stretched neck of a giraffe, who, we might imagine, spends much of its life straining upward to feed on higher leaves (Holdrege 2005*).

The reason for rejecting the inheritance of acquired characteristics seems perfectly reasonable, given the causal primacy of the gene, the isolation of the germline from the rest of the organism, and the kind of acquired characters usually considered. Things like biceps enlarged from exercise, and necks lengthened by stretching, have no way to be impressed upon well-insulated germ-cell DNA. As the generally accepted rule has it: only rare fortuitous mutations in germline cells can contribute to something like the long neck of the giraffe.

If traits acquired during the lifetime of an organism cannot be inherited, then there seems all the more reason to pursue evolutionary studies without bothering oneself unduly about all the achievements and unpredictable “quirkiness” of development3. No one has more forcefully refused such bother than Richard Dawkins. Whatever the complexities of individual development, he sees these complexities as having a disturbing effect upon discussions of evolution by natural selection. Too many people, he fears, get carried away by the intricacies of development and thereby lose sight of the definitive role of genes in evolution — a mistake he derisively equates to the lament, “Dear oh dear, development is a terribly complicated nexus, isn’t it?” (2004, p. 392*).

He himself prefers “frankly facing up to the fundamental genetic nature” of Darwinian evolution (2008, p. 28*). Development may be a “complicated nexus”, but evolution (again we see the habit of abstraction at work) is merely a matter of pristine bits or bytes in an informational DNA sequence.

No one, incidentally, is saying that the organism’s phenotype is irrelevant to evolution. It’s just that the relevance has to do only with the fact that certain genes have contributed to this phenotype and therefore to the survival capabilities of the organism and its offspring. This in turn influences which genes will be passed down the line and survive in the larger population. But beyond this question of survival, in which they themselves have a say, genes are not otherwise affected by the particulars of an organism’s life. They follow their stable, independent path, remaining just what they are except for the occasional mutation. They constitute, according to Dawkins, a “river of information”. This river “passes through bodies and affects them, but it is not affected by them on its way through” (Dawkins 1995, p. 4*).

The point, then, is this: the insulation of the transgenerationally replicated gene from the complexities of the individual organism’s development — an insulation emphasized by the non-inheritance of acquired characteristics — further strengthens the gene’s imperial position as the heritable entity whose changes constitute the main substance of evolutionary transformation.

rule

Genes as a stable, faithfully replicated medium for cumulative, step-by-step adaptation and evolutionary change; genes as the ultimate explainers of the organism; genes as insular entities unaffected by acquired characters or developmental processes in general — these ideas have all provided aid and comfort to those who see evolution as a selective process whose ultimate significance lies in the way it acts (whether directly or indirectly) upon the digital logic encapsulated in heritable DNA sequences . I have no intention here to disentangle the historical relations among these various ideas. I aim only to show how much untruth lies in them insofar as they inform contemporary thinking about evolution.

In short, I wish to say a few things about what we might (with admitted presumption) call the “Genetic Dogma of Evolutionary Theory”:

Genetic Dogma: The tale of evolution is, in one sense or another, the tale of a single, overwhelmingly dominant, stable heritable substance slowly changing over time and explaining the organism. This heritable substance is DNA.

To recognize the gross misunderstandings embedded in this dogma will be to jettison nearly the entire modern version of evolutionary theory4. But it will help us with the misunderstandings if we first ground our thinking in the life of the organism.

Plasticity, stability, and DNA (“Dear oh dear, development is a terribly complicated nexus, isn’t it?”)

If I were to tell you that scientists have sequenced the genomes of two entirely distinct organisms — say, a flying creature such as a bird or bat, and a crawling one such as an earthworm or lizard — and had found the two genomes to be identical, you’d be sure I was joking. Surely such differently structured forms and behaviors could not possibly result from the same genetic instructions!

Like a phoenix rising from its pyre. Well, the fact is that no organisms result from genetic instructions (Talbott 2012*). And, to reinforce the point, there are flying and crawling creatures with the same genomic sequence. A monarch butterfly and its larva, for example. Nor is this an isolated case. A swimming, “water-breathing” tadpole and a leaping, air-breathing frog are creatures with the same DNA. Then there is the starfish: its bilaterally symmetric larva swims freely by means of cilia, after which it settles onto the ocean floor and metamorphoses into the familiar form of the adult. This adult, bearing the same DNA as the larva, exhibits an altogether different, radially symmetric (star-like) body plan.

Millions of species consist of such improbably distinct creatures, organized in completely different ways at different stages of their life, yet carrying around the same genetic inheritance. Isn’t it a truth inviting the most profound meditation by every biologist? The picture is so dramatic that it deserves an extended sketch. I draw from a description of the goliath beetle offered by British physician and evolutionary scientist, Frank Ryan:

Rather than a den of repose, we see now that the enclosed chamber of the goliath’s pupa really is a crucible tantamount to the mythic pyre of the phoenix, where the organic being is broken down into its primordial elements before being created anew. The immolation is not through flame but a voracious chemical digestion, yet the end result is much the same, with the emergence of the new being, equipped with complex wings, multifaceted compound eyes, and the many other changes necessary for its very different lifestyle and purpose.

The emerging adult needs an elaborate musculature to drive the wings. These muscles must be created anew since they are unlike any seen in the larva, and they demand a new respiratory system — in effect new lungs — to oxygenate them, with new breathing tubes, or tracheae, to feed their massive oxygen needs. The same high energy needs are supplied by changes in the structure of the heart, with a new nervous supply to drive the adult circulation and a new blood to make that circulation work. We only have to consider the dramatic difference between a feeding grub or caterpillar and a flying butterfly or a beetle to grasp that the old mouth is rendered useless and must be replaced with new mouthparts, new salivary glands, new gut, new rectum. New legs must replace the creepy-crawly locomotion of the grub or caterpillar, and all must be clothed in a complex new skin, which in turn will manufacture the tough new external skeleton of the adult. Nowhere is the challenge of the new more demanding than in the nervous system — where a new brain is born. And no change is more practical to the new life-form than the newly constructed genitals essential for the most important new role of the adult form — the sexual reproduction of a new generation. The overwhelming destruction and reconstruction extends to the very cells that make up the individual tissues, where the larval tissues and organs are broken up and dissolved into an autodigested mush . . . To all intents and purposes, life has returned to the embryonic state with the constituent cells in an undifferentiated form. (Ryan 2011, pp. 104-5*)

The supplemental text, “Free Life and Confining Form”, points briefly to one aspect of the special place of DNA in the life of the organism.

None of this is to say that DNA counts for nothing. It is no doubt as crucial in its special role as many other elements of the cell are in their roles. The larger picture may look something like this (from the DNA vantage point, at least; there are other worthy perspectives): the organism and its cells actively play off the genomic sequence within a huge space of creative possibility. Or, I should say (since the sequence as such is a denuded abstraction): the organism both modifies and plays off the dynamically sculpted chromatin, thereby converting the sequence into an active, meaningful, three-dimensional chromosomal structure (Talbott 2010a*).

The power of differentiation. But we don’t need the mystery of metamorphosis to make the point at hand. As adults we humans embody ourselves in over ten trillion cells, commonly said to exemplify at least 250 major types. Moreover,

different parts of the body have different subtypes of the major categories of cell type . . . [Also,] many transient cell types exist in embryonic development. ... When all these cell types are enumerated, there may be thousands or tens of thousands of kinds representing different stable expression states of the genome, called forth at different times and places in development. (Kirschner and Gerhart 2005, pp. 179-81*)

Actually, the emerging story today is even more extreme. Every cell is, to one degree or another, its own cell type. “A growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type” (Loewer and Lahav 2011*). For example, “identical” genomes in “identical” cells can assume altogether different three-dimensional configurations in their respective nuclei, with potentially dramatic implications for divergent gene expression (Krijger and de Laat 2013*). That is, every cell is in one way or another “doing its own thing”. Strikingly, however, the cell does its own thing only while heeding the “voice” of the surrounding context. It is disciplined by the needs of its immediate cellular neighborhood as well as those of the entire developing organism in its larger environment.

The vast majority of cells in the body at all stages of development have (more or less exactly) the same DNA sequence5. Yet the path from the singular zygote through the many stages of cell differentiation to a particular mature cell type is a path that, for every such type, takes a novel course. Each path of differentiation represents a distinct cellular “evolution”, or active unfolding of potential.

There are, for example, cells (neurons) that send out extensions of themselves up to a meter or more in length while being efficient at passing electrical pulses through the body. There are contractile cells that give us our muscle power. There are the crystalline-transparent fiber cells of the lens of the eye; their special proteins must last a lifetime because the nucleus and many other cellular organelles (prerequisites for protein production) are discarded when the fibers reach maturity. There are cells that become hard as bone; as easily replaceable as skin; as permeable as the endothelial cells lining capillaries; and as delicately sensitive as the various hair cells extending into the fluids of the inner ear, where they play a role in our hearing, balance, and spatial orientation.

So the same DNA sequence sits contentedly within the unique phenotypes of hundreds or thousands of mature cell types. Some of these are as visibly and functionally different, in their own way, as the phenotypes of any two organisms known to the evolutionary biologist. And in order to reach these mature phenotypes, this DNA must have yielded itself to the finely choreographed yet flexible and adaptive sequence of transformations along each cellular path of differentiation — transformations that are “remembered” (inherited) from one cell generation to the next, and take their place within a smooth trajectory of change.

The whole cell: stable, yet capable of elaborate change. Who, in light of all this, will dare to claim: the numerous divergent pathways from the zygote to the various cell types of the body are explained by the one thing in the cells that remains more or less the same, namely, the bare DNA sequence, unstructured by the organism’s developmental processes?

For further examples of the subordination of DNA to the intentions of the broader context, see the supplemental texts, “Putting Genes in Perspective”, and “The Seat of Power: Nucleus or Cytoplasm?”.

Moreover, once the “end point” of differentiation of a particular cell lineage is reached, the recognizable character of that cell type can be maintained indefinitely throughout the life of the organism and through all subsequent cell divisions. Or, in some cases, it can be changed further at need, as when certain cells in the liver transform into an entirely different cell type during wound healing (Yanger et al. 2013*). Or, as with neurons and lens fibers, a cell can remain itself without further division over the several decades of a human life.

The power of the cell to remain itself in any one of many radically different configurations signifying radically different activities and conditions, has no particular temporal limit. Both this stable character and the power of differentiation during development are guaranteed only by the qualities of the cell as a whole in its organismal context, rather than by a fixed sequence of nucleic acids.

All these truths of development have yet to be taken with due seriousness by students of evolution. The individual organism expresses itself with almost incomprehensible eloquence, insistent aim, and aesthetic sensibility as it passes through the integral stages of unified metamorphosis or transformation — transformation involving much more than DNA. Yet this organism is somehow supposed to be rendered mute and directionless when engaged in the intricate, creative processes through which it contributes dynamic potentials to its offspring and shapes a space for their lives.

Life Is an Activity, Not a Collection of Things

In every empirical science, our abstractions must be disciplined and shaped by observation, not the other way around. So, too, our overly secure evolutionary logic must be brought into connection with the actual life of organisms. That is why I offered the preceding glimpses of individual development.

At every one of the cell divisions leading from a human zygote to, say, a hematopoietic (“blood-forming”) stem cell in the bone marrow, and from there to a mature red blood cell circulating in our arteries and veins, the cellular DNA is replicated. But we cannot track the dramatic transformations of cell type along this pathway of differentiation by looking for anything like step-by-step changes, or “mutations”, in the bare DNA sequence. There may be occasional mutations — and they will have their consequences — but no one will claim that they progressively add up to an explanation of the trajectory of the cell lineage.

But neither is there any other cellular constituent, whether simple or complex, whose discrete changes would by themselves spell out the destiny of this particular lineage. For all the talk of “master regulators” of this or that, the entire literature of molecular biology today is pregnant with a momentous truth: context matters in every biochemical transaction. The significance of those transactions is qualified by what is going on around them, so that we can trace the development of a cell only as the thorough-going transformation of a whole.

In other words, there is no construction process in the cell corresponding to a Lego-block project. Contrary to the nonblending and digital conditions laid down above, altering any one part of the cell would in fact very likely change the configuration of many others, even blurring their identities. There is, to be sure, a more or less stable DNA sequence, but there is no foundational explanatory power offered by some fixed structure to which molecular nuts and bolts, gears and levers — or informational “particles” — can be neatly added, subtracted, or substituted for each other in isolation from larger processes.

Yet every lineage of cells proceeds along its path in a perfectly coherent, well-organized way, with transformations occurring in a proper, adaptable, and fluent order. The cell is an activity, with its own spatial and temporal patterns of behavior. And these patterns of behavior, situated within the choreography of the larger organism and its environment, are what hold the cell lineage together as a unified and well-directed process of differentiation.

Actually, cumulative or directional change is possible in development only because the organism does not have to add or alter one piece after another successively in the way we build machines. It happens because every change is already a functional modification of other parts. Changes occur as in an improvisational symphony, where a shift in one instrumental part immediately lends a different harmonic significance to other parts and sends them in new directions. The organism functions integrally, and if it could achieve its harmonious unity of performance only by individually altering many other parts in response to every change in any one part — and if it had to do so in discrete, “mutational” steps — the task would prove impossible.

I am, as you will see below, intentionally blurring the overly rigid distinction between the development of organisms and their evolution. The truth of the developing organism is the truth we see in every direction, and at whatever level we choose to examine. And it is the only truth seen by any evolutionist who looks at life itself, at any time scale. Cells, organisms, and ecological communities are living processes whose distinctive patterns of activity give them the only definition they have. No cell is a mere bag of chemicals, no organism is a mere assemblage of cells, and no ecological community is a mere cohabitation of organisms.

The error at the core of the Genetic Dogma of Evolutionary Theory is this: it posits DNA as a clearly definable and static thing6, a single substance that can be analyzed out of an almost infinitely complex, functioning whole and treated in this disconnected state as if it held the decisive causal explanation for the canonical form and character of that whole.

But the organism does not consist of things. It is an active agent (Moss 2011*) whose activity must be understood as such — which is to say, must be grasped as meaningful, contextualized, adaptive intent. And it would be a strange hope if we expected to comprehend the nature of this activity and its evolutionary potentials without first looking at the activity itself in the one place where we find it concretely embodied — in organisms, in their development, and in their life together. Here, then, is the position I am defending:

Against the Genetic Dogma of Evolutionary Theory: The organism is an activity rather than a thing. It is a living agent whose life as a whole is a pursuit of its own ends and meanings. Its significant bequest to future generations consists of an elaborately chosen projection of its own life — not some single “controlling” molecular element — into a nascent life that is never less than a complete organism. This organism, as a physical entity, is without a beginning in any absolute sense. Its life is a continuation and transformation of the directed development of its progenitors. The heritable substance is never anything less than an entire organism.

There is nothing in actual organisms to suggest anything remotely like the standard evolutionary narrative. There is no single heritable substance as opposed to living cells or zygotes, no exclusive explanatory burden carried by DNA, and no rigid barrier separating the individual organism’s life history from its contribution to evolutionary change7.

DNA, Inheritance, and the Whole Organism

Something went horribly wrong in biology. The fact that organisms are living — that their existence is, in the case of each species, a characteristic doing — is neither obscure nor esoteric, neither on the fringe of science nor remote from the day-to-day researches of the biologist. It is a fact that not only stares us in the face, but one that, when it is pointed out (as it has been for centuries by the most reputable of biologists), draws little criticism. A child can recognize it.

When the eminent twentieth-century cell biologist and Medal of Freedom recipient, Paul Weiss, wrote, “Life is a dynamic process [and] logically, the elements of a process can be only elementary processes, and not elementary particles or any other static units” (1962, p. 3; emphasis in original*), his colleagues discharged no cries of disbelief. One gets the feeling that the truth, while routinely recognized upon reflection, is one that materialistically trained biologists simply don’t quite know what to do with. And so (if they are in a generous mood) they nod their heads and move on, still gripped by their traditional modes of thought. However that may be, it does not bode well for any science when fundamental principles are routinely ignored.

And the principle that life, while capable of being frozen and analyzed to whatever degree we choose must yet be grasped as an active unity could hardly be more fundamental. When you recognize that there is no single substance in the cell whose step-by-step changes, stably maintained and added one to another, account for or uniquely map to the remarkable transformative powers of that cell — well, then, the entire gene-centered edifice of evolutionary theory outlined above begins to fade into nothingness like a forgotten enchantment.

Brief remarks on a few themes should be enough to make this point more explicit.

What is inherited? When Dawkins wrote that “Bodies don’t get passed down the generations; genes do” (2006a, p. 79*), he could not possibly have missed the truth by a wider margin. Genes, as biologically meaningful entities rather than as abstract and inherently meaningless sequences (assuming, unreasonably, that they can be defined as “entities” at all) do not get passed unchanged down the generations — certainly not in the literal sense Dawkins intended8. And bodies — complete organisms — are exactly what do pass from one generation to another, not indeed as precise replicas of their parents, but with the continuity of active process and typical character that matters for evolutionary change9.

Dawkins’ point, repeated in many places, is that “alterations in [the individual organism] are not passed on to subsequent generations” (1982*). Taken at face value, the statement would be a monstrosity. Virtually everything in the gametes and the zygote is “custom-made” by the parents for their next-generation heir, all the way down to the detailed chromatin structure of the chromosomes. (Or, I should say, everything is custom-made in cooperation with the next-generation heir — for where, exactly, does the life of the parents end and that of the newborn begin?) Dawkins can say what he does only because he has no interest in organic change; he refuses to speak of anything other than alterations in what he imagines to be static, unlifelike structures that persist for many generations. He is interested in “replicators” that can be acted on by natural selection; he is not interested in the agency of an organism that is itself always responding to its environment and to its own internal imperatives — an organism “going somewhere”, telling a story, even at the molecular level.

We know that the zygote10 is capable of all the transformations along the pathway from single, fertilized cell to mature organism, and we have seen that this maturation process is an activity of the entire cell and entire organism. Life scientists, from molecular biologists to naturalists, routinely describe the organism’s life in narrative terms (Talbott 2011c*), and it is the character of the narrative that must change in a coherent manner from generation to generation if evolution is to occur. It must change in the only way an integral narrative context can change, through a continual mutual adjustment of directed activities — an adjustment that may secondarily lead to altered structures (Talbott 2010b*). These structures are often where our study must begin. But they are coagulations of an ongoing activity — more like residues of that activity than causes of it, just as a spluttering cauldron of magma is continually clotting here and there into partially hardened rock.

Consider the rapidly growing interest in transgenerational epigenetic inheritance (Lim and Brunet 2013*). This inheritance is commonly thought to be mediated by methyl groups attached to DNA nucleotide bases, by chemical modifications of the protein histones around which much of our DNA is wrapped, and by various small RNA molecules. But concerning all these factors the literature today is shrill with warnings that their effects are context-specific. So it is the context, and no particular thing as such, that “carries” the heritable effect.

Why, then, should we restrict our attention to these particular factors — or to other material elements that likewise can be more or less repeatably and reliably tracked? Such factors may indeed serve as suggestive markers for us, but what is fundamental for both the functioning of the organism and for inheritance is the context as such. And the functioning of this context — by the very nature of contextuality — cannot be rigidly equated with particular local configurations of elements that may happen to reappear in successive contexts.

In slightly different words: what we need is not so much the stable transmission of thing-like replicators as the stable intention of the organism itself. Here “stable intention” is not too mysterious for biologists to face. It refers to something like the directedness and adaptive stability we already witness in individual development. And this individual development is not separable from the processes at work in evolution. After all, the individual’s physical body is potentially “immortal”, inasmuch as it passes alternately through an expansionary phase of development and then a contraction into the still living germ cell, followed by another expansion. There is never anything but continuous life in this ongoing narrative. The living, directed capacities we see in the passage from adult to germ cell and zygote are no less living and directed than the capacities we see in the passage from zygote to mature adult, and, at least in physical terms, there is no radical disconnection between the successive movements.

The one-celled zygote, as a whole organism, is as much a bearer of this narrative as is any other phase of the living cycle. This zygote is the heritable substance. It does not develop into an organism under the autocratic control of just one of the contents it effectively coordinates; it already is the whole organism. This is why it can so deftly execute the subsequent spatial re-organizations, cell divisions, normal developmental processes, and adaptations to unforeseeable disturbances, all in order to produce the orderly stages of its own existence. The passage of this directive capacity down through the generations is the essence of inheritance, and any evolutionary process must derive in the first instance from changes in the overall character of the activity.

Inheritance of acquired characteristics. You can now see how the discussion of “Lamarckism” — the inheritance of acquired characteristics — has been distorted out of all usefulness. The characters, or traits, at issue have been taken in a wooden sense to be the finished products of a specific life rather than the productive capacities of that life. How the experience and character of an organism livingly plays into the inheritance of its offspring is a topic we hardly know how to approach as yet — because we have hardly thought of it as yet. The one thing we can be sure of is that the primary secret of inheritance will not be found in the transmission of fixed, already achieved features — things like the blacksmith’s muscled arm or the giraffe’s slightly stretched neck. Or, for that matter, any particular state of the organism’s chromosomes, whether in somatic cells or the germline.

To argue the issue in these terms is to assume that the organism is not an organism, but rather a collection of things lacking organic activities and relations. The fact that particular acquired11 features of a developing organism are in general not replicated in offspring — never at all exactly replicated in a biologically meaningful sense — should only redirect our attention to the far-from-static life of the organism.

While it’s unsurprising that the blacksmith’s muscled arm cannot find its way into his gametes, the longstanding belief has been that not much else can, either. The heritable substance of the germline is supposed to be more or less insulated from goings-on elsewhere in the organism. But when we realize that the heritable substance is not DNA but rather the germ cell as a whole, and when we recognize in turn that germ cells participate in the organism as a whole (on their way to becoming organisms in their own right), then the picture begins to look different. Especially when we glance at current research developments.

The organism manages its own germline. Before we claim that the organism’s embodied wisdom and experience in pursuing its own development can have nothing to do with heredity and evolution, we might want to ask ourselves whether any creature should be less expert at managing its reproductive organs and gametes in relation to their distinctive purposes and environmental context than it is at managing its heart, lungs, and legs.

When a sexually reproducing organism such as a mammal undertakes to establish and maintain its germline, it must employ its powers of differentiation to the fullest. The end product of this differentiation is a type of cell — a gamete — at least as specialized as any other cell of the body. At the same time, this gamete, along with the entire lineage leading up to it, must retain the potential to yield the totipotent zygote. That is, despite its commitment to a highly specialized, reproductive function unlike that of any other cell type in the body, the germline cell must at the same time preserve within itself the flexibility and freedom that will be required for producing every cellular lineage of a new organism.

It’s an extraordinary mandate, and the organism must focus extraordinary powers of development upon the task. For example, “germ cells exhibit highly unusual chromatin states that are vastly different from other cell types” (Rando 2012*). In general, “global epigenetic regulation of germline gene expression and germ cell-specific posttranscriptional regulation are essential both for specifying, maintaining, and protecting the germline during its life cycle and for ensuring transgenerational success” (Lehmann 2012*).

Both sperm and egg will have placed certain epigeneticmarks” (chemical groups) on their DNA and chromatin, ensuring that particular genes in the offspring will be active (or repressed), depending on which parent the gene was inherited from. Other marks, widespread throughout the egg and sperm genomes, will (for the most part) be erased immediately after fertilization, allowing the new organism an opportunity to establish marks according to its own developmental intentions. These modifications play a large role in structuring the spatial, electrical, and chemical characteristics of the chromosomes, and therefore dramatically affect gene expression.

And of course, there is the elaborately orchestrated “meiotic ballet” (Page and Hawley 2003*) that produces both sperm and egg, each with only half the number of chromosomes found in somatic cells, and with those chromosomes reshuffled and otherwise modified (Talbott 2011b*) according to a logic and via activities that are still largely beyond our understanding. But one thing is sure: the rearrangement (recombination) of chromosomes during meiosis is now showing itself to be highly regulated. Multiple protein-DNA complexes and epigenetic modifications function combinatorially, with synergism, antagonism, and redundancy: “The newfound multiplicity, functional redundancy and [evolutionary] conservation” of these regulatory factors “constitute a paradigm shift with broad implications. They provide compelling evidence that most meiotic recombination is, like transcription, regulated by sequence-specific protein-DNA complexes” (Wahls and Davidson 2012*).

Then, too, the nucleoplasm and voluminous cytoplasm of the egg cell (and, we are now learning, also the minimal nucleoplasm and cytoplasm of the sperm cell) will play vital roles in helping to direct development of the embryo at its very earliest and most sensitive stage, before the embryo’s genes come into play. Indeed, many traits, including diseases, have been shown to be influenced powerfully by inherited cytoplasm (Rando 2012*).

The organism’s replication and transshipment of its DNA, in other words, is not merely a replication and transshipment of DNA. That activity is caught up within, and inseparable from, the coordinated, goal-directed processes we see at work throughout the rest of the developing organism. Researchers are now uncovering ever more evidence for communication between somatic cells and germline cells, including communication with powerful implications for inheritance. “This is a problem”, write molecular biologists Shan Gao and Yifan Liu of the University of Michigan, “that needs to be fully explored due to its potentially huge implications in biology”. They wonder aloud (with a certain anachronism12) what conclusions Lamarck and Darwin would have drawn “had they known about all of the messages being passed between the germline and soma” (Gao and Liu 2012*).

The independence of the germline from the rest of the organism that we spoke about above — the independence supposedly rendering the wisdom and experience of the body as a whole irrelevant to inheritance — is an illusion. The illusion was encouraged by a misplaced emphasis on the inheritance of things or discrete traits rather than the dynamic potentials of an overall activity from which no cell, tissue, or organ can be insulated.

I have focused in this article only on the issue that seems to me most fundamental, and most ignored within the community of biologists: the organism is an activity, not a collection of things. But what I have called the “genetic dogma of evolutionary theory” collapses under the weight of many other considerations as well. For pointers to two of those considerations, see the supplemental texts, “Missing Heritability — Or Whole-Organism Inheritance?” and “Indefinable Genes and the ‘Wild West’ Genomic Landscape”
One aspect of the work by Gao and Liu, which was conducted on flatworms, shows how a worm modulates its gene expression by carrying a memory of the genes it expressed in previous generations. In this way, the changing conditions a species may be experiencing over time can be reflected in the inheritance of offspring produced by members of that species. According to Craig Mello, an investigator at the Howard Hughes Medical Institute and 2006 Nobel prizewinner, this “could accelerate evolutionary change by increasing heritable phenotypic variation (without the need for DNA mutations). There is growing evidence that many organisms can track and respond epigenetically to gene expression patterns” (quoted in Physorg 2012*).

And so, just as genetically identical cells within a single organism can differentiate into many different cell types, so, too, researchers are now learning how an entire organism with a given DNA sequence can have any of many dramatically different patterns of gene expression — and therefore dramatically different phenotypes — depending on its ancestral history (Ashe et al. 2012*; Lee et al. 2012*; Shirayama et al. 2012*).

None of this is to belittle the role of inherited DNA. It obviously has a very special role to play. But, merely as a particular substance, it is far from embodying a biologically significant narrative. Such a narrative can never be anything less than a whole-organism performance carried over from one generation to the next.

A Story We Have Not Yet Learned to Narrate

I remarked at the outset that, by itself, the widely advertised core logic of evolution tells us little if anything about what to expect from the history of life on earth. Stephen Jay Gould made a similar point, acknowledging that while he taught this logic for thirty years, it says nothing concrete about “the sciences of natural history”. He added, however, that the compelling force of the logic (which he called the “syllogistic core”) can at least “rebut charges of hokum or incoherence at the foundation [of evolutionary theory]” (2002, pp. 125-6 fn.*).

I hope you can see by now that the “compelling” syllogistic core is itself hokum. It is hokum for two reasons. First, it has been founded upon particular static entities (genes), that are incapable of doing anything — entities, moreover, that cannot even be defined in a meaningful, functional sense, and that in any case are subject, during processes of development and reproduction, to the almost unimaginably sophisticated governance of the cell and organism. The living activity of the cell and organism can never be understood except contextually, which is to say, holistically.

In the second place, the core logic of evolution completely ignores the organism as agent — an active, dynamic, adaptable agent pursuing a highly directed path in all its affairs, including when it makes its own, meticulously composed contribution to future generations.

But there is supposed to be a problem here. Anyone who argues for a holistic approach to the organism is bound to hear, as I have heard, this objection: “How can we possibly understand the potentials hidden in a whole cell with its infinitely complex and integral processes, let alone in a whole organism? You have no right to speak of such wholes, because you can offer us no program for understanding them as such. Our only methods for understanding are grounded in the causal analysis of parts”.

Well, I am sorry if life makes things difficult — if cellular substance really is rather more like the “vibrant, throbbing gels and oozes” from which Richard Dawkins recoils (2006a, p. 159*) than like a machine or digital device. But life is what it is, and if little or no attention has been given to the real issues — if these issues demand ways of looking for which we have received no training, or (to use Goethe’s phrase) for which we have not yet even cultivated the necessary “organs of perception” — this can only be reason for trying to develop the relevant cognitive capacities and for learning some new approaches, not for sticking to what we have done because it’s the only thing we know.

And if any spur to our learning is needed, perhaps the most effective would be to realize that, with the demise of the gene as the single, decisive heritable substance, virtually the entire conventional and logically compelling structure of evolutionary theory, as outlined in the early part of this article, is shown to be an empty shell, disconnected from living activity.

Supplemental texts associated with (and cited in) this article:

Notes

1. Do not take the word “random” here to imply anything beyond the widely sanctioned usage among evolutionary biologists. See Evolution and the Illusion of Randomness (Talbott 2011a*).

2. It is true that “interactionist” ideas — for example, the idea that organisms result from the interaction between genes and environment, or between nature and nurture — are almost universally avowed in one form or another. But this rarely seems to undermine the sense of certainty that, fundamentally, genes are the essential, enduring definers of the canonical form of the organism. For a brilliant dissection of the genocentrism implicit in a wide range of “interactionist” theses across the life sciences, see Oyama 2000a* and Oyama 2000b*.

3. It’s a healthy sign, however, that overcoming the divorce of evolution from development has become a hot topic today, yielding the relatively new discipline known as “evo-devo” — evolutionary developmental biology. The problem is that gene-centered thinking continues to dominate the field. (See, for example, Sean Carroll’s Endless Forms Most Beautiful [2005*] and my own early essay, Can the New Science of Evo-Devo Explain the Form of Organisms? [Talbott 2007b*].)

4. This is not at all to discount the value of all the empirical studies inspired by current theory. The authors of those studies may see themselves as providing evidence for the reigning theoretical abstractions, but often — if we strip out the obligatory references to “survival strategies” and all the rest — we find wonderful additions to the naturalistic tradition whereby we get to know the organisms themselves.

5. This is turning out to be less true than was long thought, as I point out in Natural Genome Remodeling (Talbott 2011b*). It’s not only that many cells of the immune system contain uniquely rearranged portions of DNA, yielding overall a huge diversity of immunological proteins. In neurons, so-called “jumping genes” are active during development; this “high level of mutagenesis . . . suggests that each neuron is genetically unique” (Thomas 2012*). And Yale University’s Dr. Flora Vaccarino leads a team of researchers who have shown that, in her words, “humans are made up of a mosaic of cells with different genomes”. In particular, “at least 30 percent of skin cells harbor different deletion[s] or duplication[s] of DNA” (quoted in Peart 2012*).

But even a DNA sequence varying drastically from cell lineage to cell lineage (which is not what we actually see) would only reinforce my contention here that DNA must be understood as subject to the governance of the whole cell and developing organism. That is, the organism would have to manage the patterning of the various DNA sequences in different tissues, starting from the single sequence given in the zygote. And, in fact, when we shift our attention (as we should) from DNA as mere inert sequence to DNA as functional structure and activity, then we find that it does vary drastically from cell lineage to cell lineage — and even from cell to cell within the same lineage. The organism’s contextual management of its DNA never ceases.

6. Actually, DNA is often conceived as if it were an informational abstraction. But this abstraction is nevertheless imagined and treated (as materialists are bound to imagine and treat any abstraction) in a thing-like way.

7. And, looking beyond our immediate purposes here: there is no foundational role for randomness in generating change (Talbott 2011a*), and no complex, adaptive outcomes creatively shaped by “mindless” environmental factors acting via natural selection (Talbott forthcoming*).

8. Remember that the genes pursued by researchers today are complex, often non-contiguous stretches of DNA bound together with all the material of chromosomes. They do not function like computer codes, but are expressed (the technical phrase, “gene expression”, is well-chosen) through a dynamic sculptural, or acrobatic, performance of the larger context. Molecular biologists can hardly restrain themselves from referring to this performance in the cell nucleus as a “dance”, and the character of the dance changes from cell type to cell type, from one stage of the cell cycle to another, and from one contextual situation to another.

I make this point throughout the current series. See, for example, Getting Over the Code Delusion (Talbott 2010a*) and the section, Eloquent Form in “The Poverty of the Instructed Organism” (Talbott 2012*). Also see the accompanying article, “Indefinable Genes and the ‘Wild West’ Genomic Landscape”.

9. If one speaks of the replication of bodies (whole organisms), there is no alternative to the idea of active process. No single stage of development between conception and death could reasonably be selected over all the others as if it were the basis for a “true” replica of the organism. It is the life of the organism, with all its potentials, that must be reproduced. Dawkins’ thought seems so removed from the actual organism that he cannot conceive of replication in living terms. His definition of “replicator” as “any entity in the universe of which copies are made” (1982*) leaves no doubt — as if it were not already clear in virtually everything he says — that his entire interest in evolutionary change is an interest in statically defined objects disconnected from context, process, and the intentions of agents. Disconnected, in other words, from life.

10. I am, of course, speaking of sexual reproduction. The whole-body continuity from generation to generation is even more obvious in asexual reproduction.

11. The notion of acquired characters versus inherited ones cannot even be made coherent. Regarding this fact, and the meaning of “inheritance” in general, see the excellent work of the developmental system theorists (Oyama 2000a*; Oyama 2000b*; Oyama, Griffiths and Gray 2001*). However, while their focus on “heritable resources” of all sorts — not merely genetic resources — has been extremely useful, I do not have the impression that they have yet reckoned fully with the vital distinction between the organism as an activity and the organism as a collection of things (or resources). In any case, statements like this are helpful reminders in the current intellectual climate:

Many nongenetic resources are reliably passed on across the generations. ... Developmental systems theory applies the concept of inheritance to any resource that is reliably present in successive generations, and is part of the explanation of why each generation resembles the last. This seems to us a principled definition of inheritance. It allows us to assess the evolutionary potential of various forms of inheritance, rather than immediately excluding everything but genes and a few fashionable extras” (Griffiths and Gray 2001).

Heritable resources in this sense can range from the microorganisms carried in the gut of certain insects and passed on to their progeny (without which those progeny could not live) to behavioral traits such as the particular plant upon which an insect chooses to lay its eggs, and upon which the progeny therefore also choose to lay their eggs. In the latter case, an “accident” whereby an adult chooses the “wrong” plant may result in a changed habit of egg-laying, and therefore many other differences in the organism, propagated indefinitely down through the generations.

12. Neither Lamarck nor Darwin, in their day, had any reason to imagine the germline and soma as separate things in the first place. A clear distinction between the two didn’t emerge until later.

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Steve Talbott :: Genes and the Central Fallacy of Evolutionary Theory