On The Form Of Species: ‘Dance To The Tune Of Life’ by Denis Noble Reviewed

Calm, calm

Due to the length of yesterday’s and today’s post, there will be no post tomorrow. Video at bottom.

There are two ways to review a book like Denis Noble’s Dance to the Tune of Life: Biological Relativity: long versus short. I struggled with the long version, because once you start describing just what you mean by “evolution”, given the subject’s notoriety, one damned thing leads to another, because all experience shows ill-considered arguments are acrimony are sure to follow unless one can be perfectly specific, and being perfectly specific takes great amounts of space.

In the end, I opted for short (rather, shorter; I’ll still have to beg the reader’s patience). We’re going to have to split the discussion of the nature of life and biological change into several parts. Feel free to get needlessly angry in the meantime.

The Review

Denis Noble was giving a talk on the weakness and errors of Neo-Darwinism, and suggesting possible alternate mechanisms by which biological change occurs, all outlined in his new book, a talk where he expected, and got, the usual default sniffy rejection of professional scientists exposed to new ideas. But what surprised him was

a very distinguished neuroscientist who confided in me during the coffee break [said]: ‘I would go along with you, Denis, except that what you are arguing would let God back in.’ This was very revealing to me, since I certainly did not think that conclusion followed at all. Yet he clearly did, and had no doubt about it. In fact, I suspect for many scientists, defending reductionism, including particularly Neo-Darwinism, was a necessity in order to counter the claims of creationist religions or supernatural intelligent design.

The “distinguished” scientist willed himself to be ignorant in his fear of God. So much for the vaunted scientific method.

Now Noble himself is no theist; it pleases him in his book to call God “she”, among his other enlightened opinions. But it is evident he has taken pains to reduce the skew his prejudice brings when thinking on biology. In any case, Noble ought not to have been surprised. Mention evolution in debate, a word with no fixed meaning, a point which is paramount, and Calm Rationality puts on its tennis shoes and flees. If there are disagreements, opprobrium and judgments of mental acuity are never long in appearing.

Noble says the word “seems to bring out very strong passions in people — positive and negative. It is almost as though the less illumination there is on how [biological change] happened, the greater the heat of the debate.” Not almost, dear Denis, not almost.

Sadly, Noble himself often adopts the flawed shorthand of using “evolution” badly, saying things like “evolution could use such mechanisms”, when evolution is not a cause nor a power, “during evolution”, when he meant “over time”, and so on. This is an occupational hazard of any writer growing weary having to spell out complex processes when a one-word substitute is at hand (like “IQ” for “intelligence”, as we saw). It is clear Noble, and you and I dear reader, ought to reject any implication “evolution” is a power or cause.

Noble’s central argument is that Neo-Darwinism is, at best, incomplete, and is wrong in many details. Neo-Darwinism is a fully reductionist, mechanistic theory. It is Democritian: all is atoms and the void. Neo-Darwinism brings, says Noble, the “Hope that chance brings this part to this wet widget, multiplied by a number with many zeros, and in the end you get this animal.” Theorists are fond of evoking “randomness” here, in a causal sense, as the explanation for how change occurs. This is always wrong. “Random” is with respect to knowledge, not things.

Change, says Noble, is “not random with respect to location in the genome”, noting that “If all locations in the genome were equally open to changes, there would be no possibility for functionally relevant change.” There is change in “the genome by combinatorial selection [of alleles], not selection of new random mutations.”

In other words, we have to look for causes, and not wave hands and bluff about “randomness”.

Many are recognizing difficulties with the theory: “[W]hat went wrong with Neo-Darwinism? In a single word: hubris….[T]he Modern Synthesis became hardened into dogmatism…Darwin himself did not think natural selection was the only mechanism…Neo-Darwinism and twentieth-century biology reflected highly reductionist philosophical and scientific viewpoints, the concepts of which are not required by the scientific discoveries themselves.”

What is Noble’s new synthesis? In essence (a terrific pun), Noble (and peers) have rediscovered substance, albeit in rough form (another good pun!). He rejects reductionism, also known as the machine metaphor, the idea that everything is “just” a machine, composed somehow of parts that work together “blindingly” following the “laws” of physics, and which result in things, including organisms, that are no greater than the sum of their parts. But it has long been clear Nature is not like that.

In discussing substance and physical change, I like the example of water, while Noble uses salt. Both are creations which are more than the sum of their parts—H2 + O or Na + Cl—they are new substances which are unlike their components. The substance of water is different in form and powers than the substance of hydrogen or the substance of oxygen, and similarly for salt. The wholes are greater, by far, than the sum of their parts.

Classically, it is said the components of each of these substances exist only virtually in substance, and not independently as in a machine. We, too, are substances and not machines. Water, and salt, and everything, disproves reductionism: the machine metaphor is false, and should have always been obviously false.

This is fundamental, because one of the classic objections to “evolution” was the truth that effects cannot be greater than their cause. How can animals of species A produce an animal of species B, when B is not the same in essence of A? That difference is what makes them different species. To make B requires a power in A that does not exist. If A could be B, then there is no difference between A and B! What is surprising is that while this is a revealing objection, it was rarely applied elsewhere outside “evolution”. Water is clearly greater than hydrogen or oxygen. Which shouldn’t be possible (if the machine metaphor of Nature were right), yet is!

The efficient and material cause of bringing the two substances H and O together is not the whole of the cause. The final cause is the powers of water, but consider the formal cause. The form (essence) of hydrogen is not the form of oxygen is not the form of water. To get water from the others, because the efficient and material cases were insufficient, requires the form of water to be pre-existing. Put it this way: you cannot make a substance which is impossible to make. You cannot create a form, an essence. You can only occupy one. Biological change fills pre-existent forms—which are not material, of course.

Noble understands the reductionist philosophy of science gets cause wrong. It recognizes only material and efficient causes, but wrongly ignores formal and final causes. The latter is also called teleology. That’s the one that frightened his neurologist so badly. He thought final causes allowed God to sneak back into science. This is an ignorant—the most appropriate word—fear, because though the final cause can involve will, including God’s will, that is limited view of what final cause is. It merely describes the purpose of reason for the rest of the causes.

The real mystery is in the formal cause. Coding is a formal cause, for instance. The late Wolfgang Smith well recognized this in his Cosmos and Transcendence. We’ll review that book another day.

Classical thought (and men like Smith and even Rupert Sheldrake to an extent) say forms reside in the mind of God. This is why I always say “intelligent design” is trivially true. So far from science disproving the existence of God, biological change positively and loudly corroborates it. As do water and salt. Which wasn’t seen because of that pesky false reductionist machine metaphor.

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What about biological change in particular? No one (that I know of) disputes what philosophers call “accidental” changes to essences, which some scientists call “micro-evolution”. These are small changes to organisms which do not effect their fundamental forms (essences, or natures). Humans have noses: the size and shape, two “accidents” of noses, which can vary widely while still being noses.

The machine metaphor says all life is “nothing but” chemicals at the command of DNA—or the genes of which it is made.

Noble says no. That the center of life is DNA is, he insists, “illusory”: “The illusion has become so strong that many people think we know exactly what a gene is and how genes control the body…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 dethroned the gene as a uniquely privileged level of causation.” Causation to Noble is “relative”, meaning not only bottom-up, hence his subtitle.

Genes are entirely passive and do nothing except when the organism itself calls on them. Calls on itself, that is. Genes don’t command. Organisms command. The machine metaphor says genes are “selfish”, and we are their Dawkinsian slaves, their goal being only self-production. Yet if this is true of genes, and we are made of and by genes, then it must be even truer for molecules, because genes are made of molecules. It’s molecules that are responsible for all we see. They seek only their perpetuation, harnessing genes, DNA, tissue, organs, organisms as their slaves. None of those higher-order systems have a purpose: they only follow orders from molecules.

And not even molecules, because those are made of atoms. It’s blind atoms which ruthlessly seek only their own selfish survival. But not atoms, because, etc., etc. all the way down. The machine metaphor never could stand on its own feet.

The gene-centric machine metaphor should have been obviously wrong in higher organisms. Take specialization of cells: “All these cells in our body have almost exactly the same DNA in their genomes! That should already warn you that it cannot be the DNA alone that determines what happens in cells, tissues, and organs. The same genome can be interpreted in completely different ways.” But of course.

“A single stretch of DNA cannot ‘know’ when to trigger mitosis. No single gene, or even set of genes, can possibly have this kind of natural dynamic purposiveness.” That purposiveness comes from the organism itself, which “necessarily emerges at a level that has the degree of dynamic complexity necessary for it to be instantiated.” Noble reminds us “…most changes in DNA do not necessarily cause a change in phenotype. Organisms are very good at buffering themselves against genomic change.” By phenotype he means, though maybe he didn’t know it, essence, quiddity.

Most “single genes contribute very little to complex functions, which is why the correlations between genes and complex diseases have been found to be a matter of large numbers of small effects.” He reminds of what some said (Follow the Science!) was “junk DNA”: “As we have seen from Waddington’s [on fruit flies] and other experiments, the whole pattern of the genome is relevant to inheritance. The real problem with the gene-centered view is that it ignores the properties of the genome as a whole.”

Genes are templates; they are called upon, they do not command. “If the word ‘instruction’ is useful at all, it is rather the that the cell instructs the genome. As Barbara McClintock wrote…the genome is an ‘organ of a cell’, not the other way around.” “…passive causality by DNA sequences acting as otherwise inert templates, and active causality by the functional networks of interactions that determine how the genome is activated.” I think Noble would agree accessed is a better word here. In any case, the “code” of genes is insufficient.

Genes are not active causes, and cannot be. Cells can continue to function without DNA. Like blood cells. “Others, such as isolated nerve axons, fibroblasts or any other enucleated cell type, can do so in physiological experiments.”

Butterflies used to be caterpillars: “It is as though the genome contains the templates for two completely different organisms.” More than “as though”! Noble goes to great length to demonstrate how certain regulatory genes in fruit flies, and man, if removed, find other processes to step up to replace the broken system. It’s rare single genes are for one thing and one thing alone. We covered this before, so instead of repeating all that, please refresh your memory with “Limitations of Biological Determinism“, and the Steve Pettelli article “The Question That Must Be Asked: Is Behavioral Genetics a Null Field?” The answer, Pettelli says, is yes:

Determinist scientists are ever hopeful: “there is a never-ending sense, in the moment, that the latest study is more evidence for a genetic basis for one trait or another, despite the fact that so many studies in the past were accepted as true findings, then faded from consciousness when they could not be consistently replicated.”

Genes are not in charge, insists Noble. Organisms are. “Nothing is isolated”, like genes; organisms are wholes, they are systems. They are substances. Which is as we have been saying, they have an essence, a form. Here is a good cartoon, taken from Noble’s book, using my superb photographic skills, demonstrating how the organism acts as a whole. Genes and cells and etc. are in organisms the same way hydrogen is in water: there but not there, only there independently virutually.

Everything works together, at once, not as a machine, but as a whole, a substance. Noble: “there is no global frame of causality in organisms”. When we analyze a system a machine metaphor can be, and obviously has been, fruitful. But once that metaphor has given us all it can, it serves only to bind and restrain thought.

In the first part of Noble’s book, which serves as an introduction to biology, Noble demonstrates there is no “privileged” level of causation, which is what he means by “biological relativity”. This is obviously true in the case of man, who can will causes. But it is true, too, for the lowest bacterium.

Onto the methods and causes of change, the book’s main argument. I do not present full defenses of any of these mechanisms, except to insist on the plural. Doubtless new causes and conditions will be discovered, different emphasizes given in time. Some will be discovered to work here and and in these certain circumstances, whereas others can only work there and in different conditions. The point should always be to discover the full cause and conditions of any change.

Rather than proceed by arguing for each mechanism, for there are many, I think it best to reverse Noble’s presentation and start at the end. Here is his diagram for the Integrated Synthesis of biological change (copied Noble’s similar paper “Evolution beyond neo-Darwinism: a new conceptual framework“):

The bits on the left outside the Integrated Synthesis are wrong, says Noble. Inheritance is not via DNA or gene-selection only.

Take the so-called so-called Weismann Barrier, which is said to keep the germ line “Sealed off from the outside world” (Dawkins). But the barrier has been seen to be breached: environments can change germ cells. Which means, yes, Noble defends, up to a point, a sort of Lamarckism.

Tracy Sonneborn in the 1960s “showed changing the orientation of swimming cilia in a part of the animal by surgery produced an inherited characteristic, transmitted down at least two subsequent generations.” Noble: ‘The idea is that Lamarckian inheritance may occur in a functional interaction between the organisms and their environment, through the use and disuse of the organism’s structures and functions”.

Getting direction of cause right is ever the key. Cutting off tails “clearly does not achieve [change] since it is extremely unlikely that natural plasticity should respond to non-functional surgery.” Certain plasticity is already present in some populations (with my emphasis): “That strongly suggests that all alleles (gene variants) necessary for the inheritance of the [acquired] characteristic were already present in the population, but not initially in any particular individuals in the correct combination.” Change happens but “not in a way that requires any new mutations.”

Moving inside the Modern Synthesis, nobody questions gene mutation, or even Mendelian inheritance. Everybody agrees with contingency, which is that changing circumstance affects life. Population genetics is only controversial for equalitarians and only in man, hence is a political and not biological question. Something has to account for the rise of species, which all agree, but here there is much dispute how minute, nearly entirely deleterious, singular gene mutations can lead, or even if they can lead, to the variety in species we see in the time required.

How new biological forms are occupied is outside anybody’s knowledge: no one has seen it happen. As in no one.

Inside strict Darwinism, obviously variation exists, and, as any parent or farmer will tell you, so does inheritance. Natural selection is a truism: that which survives, survives. We can let the rest pass.

This leaves the less well known causes on the right. Briefly and incompletely, they are these. I can do no more than bullets here, for to explain all of them would require a book-length treatment, which (of course) Noble provides. Again, our point is not to defend any of them, at least because I am not qualified. My point is only to insist that where current theory fails (such as predicting the behavior of man) it is well to look for replacements.

Evo-devo theory: “change has occurred as a result of changes in genetic expression patterns or through genes acquiring different roles in new functions…phenotype change can occur before genotype change.”

Plasticity & accommodation: From Sommer: “Phenotypic plasticity is defined as the property of organisms to produce distinct phenotypes in response to environmental variation.” Crudely, it’s not “genes” alone, nor even “gene+environment”, but organism+environment.

Epigenetic inheritance: Inheritance outside genes, which also kills any “selfish gene” notions. Changes to the germline can and have occurred, as above.

Epigenetics has already been proved in that cells with the same genome can have radically different phenotype. “More usually, epigenetics refers to additional control mechanisms, including marking using methlyation of some nucleic acids, and binding to the tails on the histone proteins. When this kind of epigenetics was first discovered it was thought that these chemical marks were always removed in the germ line before transmission to the next generation…this is not always true.” And “Robust inheritance of an acquired epigenetic characteristic has been demonstrated in mice by Joe Nadeau’s group in Seattle. They worked on a family of proteins that can insert mutations in DNA and RNA to show inheritance of epigenetic marking.”

Multilevel selection: This means extra-organism changes, such as to the environment which triggers changes in several organisms, which then pass on these changes. Some stretch this to say “group selection”, but this is a metaphor apt to be abused.

Genomic evolution: More or less than standard theory you know. But take Barbara McClintock: the genome is a “high sensitive organ of the cell…sensing the unusual and unexpected events, and responding to them, often by restructuring the genome.”

For instance: “Retrotransposons are DNA sequences that are first copied as RNA sequences, which are then inserted back into a different part of the genome using reverse transciptase…[which may sometimes] not require an RNA intermediate.”

Niche construction: This especially applies to man, who changes his environment to suit himself, which in turn can change him. Same with ants, and so forth.

Replicator theory: This is like the idea of inclusive fitness, given below. The danger here is the Deadly Sin of Reification.

Evolvability: Wokepedia: “Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.”

I think you can see that through new synthesis is groping its way toward understanding its whole organism and their environments that are crucial. Organisms as living complete systems, which are not machines. And environments which are the conditions under which the powers of the organism are expressed, places which can never be escaped! Organisms have to live somewhere.

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Inclusive fitness. Here is a prime example of the Deadly Sin of Reification, a mistaking of epistemology with ontology. Altruism is observed, in man and other species, and there are certainly causes of it. That cause is not and cannot be selfish genes. One can model the closeness of relatives as a function of genes, but that model is not a cause. Noble:

It is of course true that close kin often act altruistically towards each other. But there are nevertheless two obvious problems with this explanation. The first is that it clearly doesn’t explain altruistic behavior towards other organisms that are not closely related. The second and even more serious problem is that it conflates the concepts of selfishness and altruism at different levels. This is a mistake since selfish or altruistic behavior at one level does not automatically guarantee such behaviour at another level.

The fad in man, at the moment, are males who enjoy sodomy (which is far from altruism or indeed any notion of reproductive success) adopting (paying un-genetically related women to produce for them) young males. If you class this as altruism, then it clearly cannot be because of genes. And that is even stronger for actual couples who adopt, often outside what is considered their own race. Nor would man have pets. Nor would man allow the purposeful killing of their own genes before the escape their would-be mothers’ wombs. Et cetera.

Inclusive fitness is a correlation, a model which might be useful to make some predictions, but it does not speak of causes.

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Let us accept that Neo-Darwinism is flawed, and that something like what Noble advocates better explains the causes and conditions of biological change. Even so, this has not solved speciation, let along biogenesis. We haven’t answered how new forms—which is to say, new species—are occupied.

Yet there are hints. It “is impossible to explain” the rise of eukaryotes “as simply the outcome of chance mutations in the genomes of prokaryotes followed by natural selection. Before the evolutionary threshold was passed, it was impossible for organisms with separate germ lines to exist. The Weismann Barrier and the original basis of Neo-Darwinist theory would have been irrelevant. Yet the great majority of time which life has evolved on Earth occurred before this threshold.”

Speculation is a bacteria ate something, assimilated it instead of digesting it, and so developed mitochondria. “We also know that much of the DNA of bacterial origin subsequently moved to the nuclear genome, presumably by the transposition mechanisms…” This has been observed, not in history, but presently: “Transfer of DNA between green algae and a sea slug has been shown to be responsible for the remarkable ability of the sea slug to photosynthesise. Algal DNA has not only been transferred to the host, but has been incorporated into the sea slug’s genome.”

The key questions are still largely not fixed. The debate is not over. Even this small (it only seemed long) description does not come close to exhausting the subject. We’ll return to the idea of forms, and how they might be filled, another day.

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