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For a summary treatment of certain themes of the book, see the article, Evolution As It Was Meant To Be — An Overview.
All the contents listed below are subject to change and reorganization, whether minor or major. This caveat extends to titles and even to the existence of particular chapters. I am discovering the proper shape of the book only as I write it. Please note: the currently available chapters may contain dead links to chapters not yet written.
Chapter 1: The Keys to This Book
This introductory chapter offers a brief summary of the central themes of the book: 1) every organism comprises more than a set of physical and chemical interactions, but possesses an agency through which it weaves a life story; and 2) biologists suffer from a kind of blindsight through which they are unable to incorporate much of what they actually know about organisms into their scientific explanations. It is also explained that the book rests on a fundamental conviction that the world, by nature, manifests itself in thought.
Chapter 2: The Organism’s Story
Organisms are purposive (“teleological”) beings. Nothing could be more obvious. The fact of the matter is so indisputable that even those who don’t believe it really do believe it. Philosopher of biology Robert Arp speaks for biology as a whole when he writes,
Thinkers cannot seem to get around [evolutionary biologist Robert] Trivers’ claim that “even the humblest creature, say, a virus, appears organized to do something; it acts as if it is trying to achieve some purpose”, or [political philosopher Larry] Arnhart’s observation that … “Reproduction, growth, feeding, healing, courtship, parental care for the young — these and many other activities of organisms are goal-directed”.
And yet, despite his acknowledgment that we “cannot get around” this truth, Arp again speaks for almost the entire discipline of biology when he tries, with some delicacy, to take it all back: “with respect to organisms, it is useful to think as if these entities have traits and processes that function in goal-directed ways” (his emphasis). This as if is a long-running cliché, designed to warn us that the organism’s purposive behavior is somehow deceptive — not quite what it seems. The goal-directedness is, in the conventional terminology, merely apparent or illusory. Certainly it must not be seen as having any relation at all to human purposive activity — an odd insistence given how eager so many biologists are to make sure we never forget that the human being is “just another animal”.
Others have commented on this strange reluctance to acknowledge fully the purposiveness that is there for all to see. The philosopher of science, Karl Popper, said that “The fear of using teleological terms reminds me of the Victorian fear of speaking about sex”. Popper may have had in mind a famous remark by his friend and twentieth-century British evolutionary theorist, J. B. S. Haldane, who once quipped that “Teleology is like a mistress to a biologist; he cannot live without her but he’s unwilling to be seen with her in public”.
We find — and will later explore further — this same unwilling yet inescapable conviction of purposiveness at the foundations of evolutionary theory. The theory, we are often told, is supposed to explain away the organism’s purposes — “naturalize” them, as those who claim to speak for nature like to say. But at the same time the theory is itself said to be grounded solidly in the fact that organisms, unlike rocks, thunderstorms, and solar systems, struggle to survive and reproduce. If they did not spend their entire lives striving toward an end, or telos, in this way, natural selection of the fittest organisms (those best qualified to survive and reproduce) could not occur. So it is not at all clear how selection is supposed to explain the origin of such end-directed behavior.
This double stance — believing and not believing, acknowledging and explaining away — constitutes, you could almost say, the warp and woof of biology itself. Look for “purpose” in the index of any biological textbook, and you will almost certainly be disappointed. That term, along with others such as “meaning” and “value”, is effectively banned. There is something like a taboo against it. Yet, in striking self-contradiction, those textbooks are themselves structured according to the purposive activities, or tasks, of organisms. Biologists are always working to narrate goal-directed achievements. How is DNA replicated? How do cells divide? How does metabolism supply energy for living activity? How are circadian rhythms established and maintained? How do animals arrive at the evolutionary strategies or games or arms races through which they try to eat and avoid being eaten?
Such questions are endless, and their defining role is reflected on every page of every textbook on development, physiology or evolution. A research question is biological, as opposed to physical or chemical, only when it is posed in one way or another by the organism’s purposive, future-oriented activity. The puzzle is that the answers biologists are willing to offer, on the other hand, are rooted with equal consistency in the assumption that organisms have no purposes. The reigning conviction is that explanations of physical and chemical means effectively remove any need to deal scientifically with the ends that alone could have prompted our search for means in the first place.
My larger argument in this book will be that this conviction about the adequacy of physical and chemical descriptions is misbegotten, with devastating effects upon many fields of biological understanding, and particularly evolutionary theory. It hardly needs emphasizing that if organisms really are purposive beings — if the fact of purposive activity is not an illusion — then a biological science so repulsed by the idea of purpose that its practitioners must avert their eyes at the very mention of it … well, it appears that these practitioners must feel threatened at a place they consider foundational. And with some justification, for admit to what they actually know about organisms would be to turn upside down and inside out much of the science to which they have committed their lives.
“Purpose” — an idea that will need careful qualification in different biological contexts — gives us but one of several intimately related avenues of approach to what is distinctive about the life of organisms. In the remainder of this chapter I will briefly sketch a few of these avenues.
Chapter 3: What Brings Our Genome Alive?
Throughout most of the twentieth century, genes were viewed as the “agents” responsible for an organism’s development, activity, and evolution. Their agency was said to lie in their ability to “regulate”, “organize”, “coordinate”, and “control” physiological processes. DNA, the bearer of these genes, became the “Book of Life” — the essential maker of organisms and driver of evolution. And this view remains stubbornly entrenched today, despite many changes in our understanding. A leading behavioral geneticist has recently written a book entitled, Blueprint: How DNA Makes Us Who We Are.
Nevertheless, the idea that genes are the decisive “first causes” of life — and, more generally, that molecules at the “bottom” ultimately explain everything that happens at larger scales — has come in for a great deal of criticism in recent years. This criticism, as we will see, is fully justified. But the issues can be subtle, as is suggested by an apparent paradox. Philosopher of biology Lenny Moss, who wrote the valuable book, What Genes Can’t Do, has remarked:
“Where molecular biology once taught us that life is more about the interplay of molecules than we might have previously imagined, molecular biology is now beginning to reveal the extent to which macromolecules [such as DNA], with their surprisingly flexible and adaptive complex behavior, turn out to be more life-like than we had previously imagined.”
In a similar vein, I myself wrote a decade ago:
Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate. The explanatory task at the bottom is essentially the same as what we faced higher up.
But if all this is true, what are we to make of Harvard geneticist Richard Lewontin’s declaration, itself hardly disputable, that “DNA is a dead molecule, among the most nonreactive, chemically inert molecules in the living world. That is why it can be recovered in good enough shape to determine its sequence from mummies, from mastodons frozen tens of thousands of years ago, and even, under the right circumstances, from twenty-million-year-old fossil plants … DNA has no power to reproduce itself. Rather it is produced out of elementary materials by a complex cellular machinery of proteins. While it is often said that DNA produces proteins, in fact proteins (enzymes) produce DNA … Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of ‘making’ anything else.”
Many astute observers have echoed Lewontin’s remarks, and I have never seen anyone question them, including those who remain enamored of the “Book of Life”. So which is it? When we peer at DNA, do we see a dead molecule or the secret of life? As it happens, there is a simple answer: if we are looking at a molecule conceived in the usual way as a bit of mindless, inherently inert stuff, then, according to our own conceptions, we see only dead stuff. But if we observe the molecule as a system of forces and energies capable of participating and being caught up in the creative life of the cell and organism, then we can hardly help recognizing — and perhaps even reverencing — the living performance unfolding before our eyes.
Saying this is one thing; making it both meaningful and profound is quite another — and that is one task of the present book. So let us begin.
Chapter 4: The Sensitive, Muscular Cell
Throughout a good part of the twentieth century, cell biologists battled over the question, “Which exerts greater control over the life of the cell — the cell nucleus or the cytoplasm?” From mid-century onward, however, the badge of imperial authority was, by enthusiastic consensus, awarded to the nucleus, and especially to the genes and DNA within it. “Genes make proteins, and proteins make us” — this has been the governing motto, despite both halves of the statement being false (which will become ever clearer as we proceed).
The question for our own day is, “Why would anyone think — as the majority of biologists still do — that any part of a cell must possess executive control over all the other parts?” We have already caught our first glimpse of the performances in the nucleus (see Chapter 3), and these hardly testify to domination by a single, controlling agent. Now we will broaden our outlook by making a first approach to the rest of the cell — the cytoplasm, along with its organelles and enclosing membrane.
It would be well to remind ourselves before we proceed, however, that, whatever else it may be, an organism is a physical being. Its doings are always in one way or another physical doings. This may seem a strange point to need emphasizing at a time when science is wedded to materialism. And yet, for the better part of the past century problems relating to the material coordination of biological activity were largely ignored while biologists stared, transfixed, into the cell nucleus. If they concentrated hard enough, they could begin to hear the siren call of a de-materialized, one-dimensional, informational view of life.
The idea of a genetic code and program proved compelling, even though the program was never found and the supposedly fixed code was continually rewritten by the cell in every phase of its activity. So long as one lay under the spell woven by notions of causally effective information and code, problems of material causation somehow disappeared from view, or seemed unimportant. And so, freed from “mere” material constraint, programmatic Information became rather like the Designer of the intelligent design advocates.
Surely, even if they are not the decisive causes usually imagined, genes do connect in some manner with the features they were thought one-sidedly to explain. But this just as surely means they must connect physically and meaningfully, via movements and transformations of substance testifying to an underlying narrative (Chapter 2) — not merely logically, through the genetic encoding of an imagined program. And what we saw in Chapter 3 about the significant movements and gesturings of chromosomes is only the beginning of the story.
Chapter 5: Our Bodies Are Formed Streams
In this materialist era, we like our reality hard and our truths weighty and rock solid. We may accept that there are states of matter less substantial than rocks, but in our imaginations we turn even fluids and gases into collections of tiny particles more or less closely bound together. Similarly, in our reconstructions of physiological processes, material structures come first, and only then can movement, flow, and meaningful activity somehow occur.
How, after all, can there be movement without things to do the moving? (It’s easy to forget that energy, fields, and forces are not things!) Ask someone to describe the circulatory system, and you will very likely hear a great deal about the heart, arteries, veins, capillaries, red blood cells, and all the rest, but little or nothing about the endless subtleties of circulatory movement through which, for example, the structured heart first comes into being (Chapter 0).
Yet there is no escaping the fact that we begin our lives in a thoroughly fluid and plastic condition. Only with time do relatively solid and stable structures precipitate out as tentatively formed “islands” within the streaming rivers of cells that shape the life of the early embryo. As adults, we are still about seventy percent water.
One might think quite differently based on the scientific rhetoric to which we are daily exposed. This could easily lead us to believe that the real essence and solid foundation of our lives was from the beginning rigidly established inside those very first cells. There we find DNA macromolecules that, in a ceaseless flood of images, are presented to us as crystalline forms in the shape of a spiraling ladder — a ladder whose countless rungs constitute the fateful stairway of our lives. So, too, with the all-important proteins and protein complexes of our bodies: we have been told for decades that they fold precisely into wondrously efficient molecular machines whose all-important functions are predestined by the DNA sequence.
The trouble is, biological researches of the last few decades have not merely hinted at an altogether different story; they have (albeit sometimes to deaf ears) been trumpeting it aloud as a theme with a thousand variations. Even the supposedly “solid” structures and molecular complexes in our cells — including the ones we have imagined as strict determinants of our lives — are caught up in functionally significant movement that the structures themselves can hardly have originated. (See Chapter 3, “What Brings Our Genome Alive?”, and Chapter 4, “The Sensitive, Muscular Cell”.)
Nowhere are we looking either at a static sculpture or at controlling molecules responsible for the sculpting. In an article in Nature following the completion of the Human Genome Project, Helen Pearson interviewed many geneticists in order to assemble the emerging picture of DNA. One research group, she reported, has shown that the molecule is made “to gyrate like a demonic dancer”. Others point out how chromosomes “form fleeting liaisons with proteins, jiggle around impatiently and shoot out exploratory arms”. Phrases such as “endless acrobatics”, “subcellular waltz”, and DNA that “twirls in time and space” are strewn through the article. “The word ‘static’ is disappearing from our vocabulary”, remarks cell biologist and geneticist Tom Misteli, a Distinguished Investigator at the National Cancer Institute in Bethesda, Maryland.
Everywhere we look, shifting form and movement show themselves to be the “substance” of biological activity. The physiological narratives of our lives play out in gestural dramas that explain the origin and significance of structures rather than being explained by those structures.
Hannah Landecker, a professor of both genetics and sociology at UCLA, having looked at the impact of recent, highly sophisticated cellular imaging techniques on our understanding, has written: “The depicted cell seems a kind of endlessly dynamic molecular sea, where even those ‘structures’ elaborated by a century of biochemical analysis are constantly being broken down and resynthesized.” And she adds: “It is not so much that the structures begin to move, but movements — for example in the assembly and self-organization of the cytoskeleton — begin to constitute structure”.
And in a paper that appeared as I was writing this chapter, a team of biochemists from Duke and Stanford Universities point out how inadequate is our knowledge of the action of biomolecules when all we have is a frozen structure of the sort commonly reported in the literature. “In reality”, they say, “all macromolecules dynamically alternate between conformational states [that is, between three-dimensional folded shapes] to carry out their biological functions”:
Decades ago, it was realized that the structures of biomolecules are better described as “screaming and kicking”, constantly undergoing motions on timescales spanning twelve orders of magnitude, from picoseconds [trillionths of a second] to seconds.
Why, after all, should we ever have expected our physiology to be less a matter of gesturings than is our life as a whole?
Chapter 6: Context: Dare We Call It Holism?
The centrality of living wholes within biology seems beyond argument. These have not been “put together” or built by an external agency. They are never the results of a physical activity that starts with non-wholes. Biology gives us nothing but beings that have never existed except as wholes possesssing the formative powers that enable them to pass through further stages of physical development.
The one-celled zygote is already a functioning whole. It does not gain further cells through the addition of “building blocks” assembled by an engineer or designer, but rather through an internal power of reorganization and subdivision in which the entire organism participates. All the parts are orchestrated in a unified performance that yields new cells, and particular kinds of cells, just where they are needed. The orchestrating power of the whole can hardly be determined by the particular parts it is bringing into being and orchestrating.
Where the physicist may prefer unambiguous, isolated, and well-defined “point” causes, the biologist never has such causes to theorize about. A biological whole is never absolute, and never perfectly definable as distinct from its environment. Further, its actions are always multivalent, like the meaning of a sentence in a profound and complex text. Its activities interpenetrate one another, like the events of a story.
The wonderfully insightful twentieth-century botanist, Agnes Arber, captured well the polar tension between organic wholeness, on one hand, and contextual embeddedness, on the other:
The biological explanation of a phenomenon is the discovery of its own intrinsic place in a nexus of relations, extending indefinitely in all directions. To explain it is to see it simultaneously in its full individuality (as a whole in itself), and in its subordinate position (as one element in a larger whole.
Every ecological setting, every organism within that setting, every organ within the organism, and every cell within the organ is a whole providing a context for its own interrelated parts, and at the same time is itself contextually embedded within larger wholes. “Context”, “whole”, and “part” can never be rigid, absolute terms in biology. They are bound up with interweaving spheres of activity.
We need to gain some practice in thinking, not with the single, distinct point-causes of the physicist (or at least the classically minded physicist), but rather with the actual narrative qualities of biological activity. The perplexing issues surrounding attempts at holistic thought may thereby lend themselves more easily to our efforts at understanding.
Chapter 7: All Genetics Is Epigenetics
You and I harbor trillions of “sub-creatures” in our bodies. I am not referring to the microorganisms in our guts, but rather the cells we consider our own — the constituents of our muscles and brains, our livers and bones, our lenses and retinas. Each of these cells, embedded in its supportive environment, sustains a dauntingly complex and unique way of life. If we had first discovered such cells floating singly in a pool of water and had observed them through a microscope, we would have judged them to be distantly related organisms. Phenotypically (that is, in visible form and function) one cell type can differ from another as much as an amoeba differs from a paramecium.
All the cells in the human body have descended from a single cell (zygote) with a single genome. And just as hundreds of different cell types have arisen from that one zygote, so, too, have the multicellular, intricately organized entities we know as lung, heart, eye, kidney, and pancreas, along with all our other organs. Supremely interdependent as these are, each is nevertheless a functioning organic world of altogether distinctive character.
For the past century these facts of development have been thought to present a (largely ignored) problem for the gene-centered view of life. The developmental biologist Frank Lillie, who had directed the prestigious Marine Biological Laboratory at Woods Hole, Massachusetts, and would go on to become president of the National Academy of Sciences, remarked in 1927 on the contrast between “genes which remain the same throughout the life history” of an organism, and a developmental process that “never stands still from germ to old age”. In his view, “those who desire to make genetics the basis of physiology of development will have to explain how an unchanging complex can direct the course of an ordered developmental stream.”
This ordered developmental stream, of course, includes generation of the hundreds of different cell types in our bodies. It is hard to understand how a single genomic “blueprint” — or any other way of construing a fixed genetic sequence — could by itself provide the definitive causal basis for these hundreds of radically distinct ways of living. If the blueprint is compatible with all of them, do we have compelling grounds for thinking that it fundamentally determines any one type of cell, or organ, let alone all of them together? One might reasonably expect that other factors direct the developmental process toward particular outcomes of such different sorts.
A more balanced understanding arises when we watch how every cell displays its character through its life as a whole. That character, in all its qualitative richness, somehow seems decisive. DNA is caught up in a seamless and integral way of being. When we grasp this integral nature, we quickly realize that the idea of DNA as the crucial causal determinant of the whole is an impossible one. As a specific kind of liver cell passes through its developmental lineage, it must sustain its entire organization in a coherent and well-directed manner from one cell generation to the next — including, for example, the cytoskeletal and cell membrane organization described in Chapter 4. It must also bring about and orchestrate the elaborate performances of its chromosomes we saw in Chapter 3 — performances that are unique to this type of cell and that chromosomes themselves have no way to set in motion.
Every individual part, including DNA, is shaped by, and gives expression to, the character of a larger whole. As functional participants in diverse physiological processes, our genes do not in fact “remain the same throughout life”. They, like all parts of a cell or organism, gain their identity and meaning only within the context of innumerable, interpenetrating, living narratives (Chapter 2).
Chapter 8: The Mystery of an Unexpected Coherence
We heard in “The Organism’s Story” that living activity has a certain future-oriented (“purposive” or “intentional” or end-directed) character that is missed by causal explanations of the usual physical and chemical sort. This is true whether the end being sought is the perfection of adult form through development, or the taking of a prey animal for food.
An animal’s end-directed activity may, of course, be very far from what we humans know as conscious aiming at a goal. But all such activity nevertheless displays certain common features distinguishing it from inanimate proceedings: it tends to be persistent, so that it is resumed again and again after being blocked; it likewise tends to be adaptable, changing strategy in the face of altered circumstances; and the entire activity ceases once the end is achieved.
This flexible directedness — this interwoven play of diverse ends and means within an overall living unity — is what gives the organism’s life its peculiar sort of multi-threaded, narrative coherence. Life becomes a story. Events occur, not merely from physical necessity, but because they hold significance for an organism whose life is a distinctive pattern of significances.
The idea of narrative coherence, like the related idea of a governing context (Chapter 6), is a mystery for all attempts at purely physical explanation. This is why even the explicit acknowledgment of an organism’s striving for life — central as it may be for evolutionary theory — is discouraged whenever biologists are describing organisms themselves. It sounds too much as if one were invoking inner, or soul, qualities rather than material causes — acknowledging a being rather than a thing. And it is true that our physical laws, however combined, nowhere touch the idea of striving.
Biologists much prefer to identify single, definitive causes. The cell nucleus with its genome has long been viewed as the seat of such causation. But, as we saw in our discussion of epigenetics, the single-minded pursuit of genetic causes has forcibly redirected our attention to epigenetics, where we have discovered that genes are circumscribed and given their meaning by the narrative life of the entire cell and organism.
In what follows below we will consider this narrative coherence in a more detailed way — first, in relation to one of the many activities of the cell that can be considered under the heading of “epigenetics”. Then we will look more briefly at a startling phenomenon that, already on its face, renders absurd the idea of central genetic control. In both cases we will be focused on molecular-level activity, which is precisely where we have been most strictly trained to expect the absence of any coherence other than that of “blind mechanism”.
Chapter 9: Biology’s Missing Ideas
Readers may be forgiven if, having been patiently reading the book to this point, they have experienced a growing frustration. This frustration, as I imagine it, might go like this:
“You have talked about the organism’s story as if it were a meaningful narration, full of purposes. You have talked about chromosome organization in the nucleus, the dynamics of the cytoskeleton, and the identity-preserving role of the cell membrane as if they all held some secret of a more-than-physical coordination of events. You have claimed that the context-dependence of biological processes implies a play of governing ideas. And you have celebrated epigenetics as if it represented an activity of the organism as a whole, which can hardly mean anything less than: the organism as a being or entelechy. A more conventional biology restricts itself to tracing the causal relations among physical parts.
“So, enough with your coy suggestion of some beyond-physical, mystical reality! Isn’t it time to acknowledge that you have a huge problem relating all this to the magnificent body of biological knowledge established on strictly materialistic grounds during the past couple of centuries? This knowledge seems to leave no place for the peculiar terms of your presentation.”
And I agree at least this far: it is time to bring to a focus the decisive questions that seem to lie behind everything I have been talking about. To begin with, then, let us quickly recall how certain key questions have so far been most explicitly raised.
Chapter 10: A Mess of Causes
The difficulties in talking about causes in biology have been recognized for at least two centuries. It’s just that the issues were largely set aside in the era of molecular biology due to the expectation that our rapidly growing powers of minute analysis would bring full causal understanding. Biology would soon be rid of its troublesome language of life in favor of well-behaved molecular mechanisms. And yet today, after several decades of stunning progress in molecular research, the struggle to fit our understanding of living activity into the comfortable garb of familiar causal explanation looks more hopeless than ever.
On one hand, most biologists seem unaware that there is a problem here — or, at least, they are unwilling to betray their awareness in professional circles. On the other hand, their scientific descriptions could hardly signal more dramatically the failure of the usual causal explanations. We seem to be looking here at another illustration of blindsight (Chapter 2).
In a previous chapter we considered epigenetics, which is commonly taken to be about the way epigenetic “marks” on chromosomes alter gene expression. But no sooner did epigenetics gain biologists’ attention than researchers began puzzling over the question, “Do epigenetic marks alter gene expression, or do changes in gene expression alter the marks?” And (as we will see in Box 10.1), the question is still with us. According to Luca Magnani, a cancer researcher at Imperial College London,
It’s an absolutely legitimate question and we need to address it. The answer is either going to kill the field [of epigenetics], or make it very important.
“Either kill the field or make it very important”. The comment expresses absolute confidence that we can discover unambiguous causation, which will in turn settle the matter: either epigenetic changes cause gene activity (in which case they are very important), or they are mere effects of that activity, with little significance. It must be one way or the other. The general idea is that, if something is to contribute to scientific understanding, it must be the indisputable cause of an indisputable effect. And yet, as we will now see, this stubborn insistence on causal clarity continually prods biologists to offer embarassingly incoherent explanations.
Chapter 11: All Science Must Be Rooted in Experience
In previous chapters we have seen how organisms, as centered agents, present us with rich, narrative contexts — mortal performances that proceed, with characteristic expressiveness and intention, through the stages of a life drama unique to a particular species. And yet, as we have also seen, a powerful urge drives biologists to ignore, as far as they can, every living feature of those performances.
They ignore, for example, what it must really mean when they say that animals “strive” to maintain their life, or that a wound “heals” itself, or that an organism “adapts” to its environment, or that it “perceives” a threat and “responds” to it. (Physical objects in general — stones, clouds, and dust storms — do not strive, heal, adapt, perceive, or respond.) But it is all too easy for any scientist to side-step such meanings and analyze the organism’s story into lifeless sequences of precisely lawful molecular interactions. And since there appear to be no gaps in the molecular-level picture, the resulting explanations seem complete. Only the organism is missing.
In other words, seamless as they may be in their own impoverished terms, such explanations are not in fact complete. They miss the simply observed fact that molecular-level interactions in an organism are always caught up in, and governed by, the higher-level pattern of a life story. We always find ourselves watching the meaningful coordination of causal processes in an extended narrative — an end-directed coordination that cannot be explained by the processes being coordinated. This is why explanations that never move beyond physics and chemistry stop short of biology.
Non-living explanations do, however, have one advantage: they conveniently avoid all those troublesome words I use throughout this book in discussing organic contexts and life stories — words such as intention and purposiveness, idea and thought, agency and end-directedness, interests and meaning. Most biologists prefer to have nothing to do with such terms.
One problem with those words is that they evoke features of our own inner lives — our human experience. It is, of course, healthy to avoid an anthropomorphic projection of human experience upon other organisms, where it does not belong. But we, too, are organisms, and we have good reason to ask: Where does living human awareness belong in our biological science? If we ignore the character of our own life and experience, can we fully understand a world that has been capable of producing us? Where can we gain our scientific ideas, if they are not empirical — if they are not expressions of our most rigorously considered experience? And can we reasonably assume that our own experience has nothing at all in common with that of our evolutionary forebears?
Chapter 12: What Is the Problem of Form?
It is well known that amphibians such as frogs and salamanders have a remarkable ability to regenerate severed limbs. What may not be so commonly realized is that, if you graft the tail bud of a salamander onto the flank of a frog tadpole at the place where a limb would normally form — and also near the time when metamorphosis of the tadpole into a frog will occur — the grafted organ first grows into a salamander-like tail, and then, in some cases, more or less completely transforms into a limb, albeit a dysfunctional one. Among other changes, the tip of the tail turns into a set of fingers.
The experiment can remind us, in passing, how biologists commonly try to learn about life by severely disrupting it. But the current thing to note is that, in this particular experiment, the transformation of the tail into an approximate limb cannot be the result of local causes, since the local environment of the fingers-to-be is a tail, not a limb. The power of transformation is, in a puzzling manner, holistic. The part is caught up within the whole and moves toward its new identity based, not merely on local determinants, but also on the form and character of a whole that is not yet physically all there.
In a rather different vein, Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the currently unrealized form of the limb as a whole is the ruling factor, redefining the parts according to the larger, developing pattern. Lewontin went on to remark:
Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development.
But how can this be? How can spatial position within a not yet fully realized form physically determine not only the future and proper sculpting of that form, but also the identity of its parts?
Chapter 13: Why We Cannot Explain the Form of Organisms
Questions of form have seemed oddly resistant to the biologist’s quest for explanation. Darwin himself seemed to sense the difficulty in that famous instance where he recoiled from contemplating the subtle perfections in the form of the eye: “To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree”.
Of course, as Darwin quickly added, his theory convinced him that he was merely suffering from a lack of imagination. All that was really needed were the creative powers of natural selection acting through eons upon an endless supply of small, helpful changes. But his underlying malaise was not so easily vanquished: “It is curious”, he wrote to the American botanist Asa Gray in the year following publication of the Origin, “that I remember well [the] time when the thought of the eye made me cold all over, but I have got over this stage of the complaint, and now small trifling particulars of structure often make me very uncomfortable. The sight of a feather in a peacock’s tail, whenever I gaze at it, makes me sick!”
We can assume that Darwin got over that stage of the complaint as well. But, thankfully, the biologist is still now and then allowed, if not a complaint, at least an honest expression of wonder.
Additional chapters in Part 1 will be forthcoming.
Technical Supplement to Part 1
If your understanding of genetics comes from your newspaper’s science section, or a popular science magazine, or any other source intended for the general public, then you will not have been given the remotest glimpse of what actually goes on with the genes in our bodies. In fact, geneticists themselves have been known to lament how limited their knowledge of gene-related activity is, simply because the demands of professional specialization scarcely allow a wide field of view.
But it turns out that a wide field of view is the one critical prerequisite for any adequate understanding of genes. Only a broad survey can illustrate how every gene, like a significant word in a text, receives its full meaning only through the interweaving and converging influences issuing from all the elements of its context.
My aim here is to offer such a wider, “epigenetic” view — and to do so in the briefest space possible. If I succeed, you will begin to sense a biological landscape that reconfigures many long-standing assumptions, not only about genetics itself, but also about the character of living processes.
Chapter 15: Puzzles of the Microworld
Einstein, so it is said, was led to his theory of special relativity due in part to his having imagined what it would be like to “ride on a light beam”. Might we possibly discover equally strange things if we tried to imagine what it would be like to dwell within an individual living cell?
Unlike Einstein with his task, ours would be much simpler. It would not require bold new understandings in physics, but simply a willingness to imagine the changing play of already recognized physical laws at different dimensions. And, fortunately, we have at least one scientific paper, written thirty years ago, that has already done much of the work of imagining the startlingly different conditions of life at the scale of the cell.
That 1990 paper was written by Guenter Albrecht-Buehler of the Northwestern University Medical School in Chicago. He began his professional life as a physicist before moving into cell biology. However, unlike what you might expect of a physicist, one of his larger concerns was rooted in the conviction that we cannot build up an understanding of organisms by starting from the molecular level. His paper, titled “In Defense of ‘Nonmolecular’ Cell Biology”, has not, in my judgment, received the attention it deserves. The present article represents my effort to summarize only that part of the paper dealing with the wildly unexpected consequences of differences of scale, and then to offer a few additional comments of my own.
Chapter 16: Gene Regulation: A Partial Outline
Following is the bare outline of a rather massive collection of notes I have haphazardly collected during the past decade from the technical literature on gene regulation. That collection is available under the title How the Organism Decides What to Make of Its Genes.
So why supply in this book the mere outline — the headings — under which those notes were collected? The main reason is that it gives the reader at least a vague sense for the remarkable variety of means (more than 250 major topics are listed below) by which the cell and organism decisively determine how their genes shall be used. Here I have in mind not only the general reader (who deserves to be spared all the technical details), but also the molecular biologist and geneticist. For I have found, rather to my surprise, that even these latter tend to be so narrowly focused on their own specialities that they have no clear idea of the full breadth of gene regulatory activity.
You will find various caveats about the original document at the link given above.
A special tip: much of the technical language found here can easily be looked up in the glossary, which you may want to keep open in a separate window as you browse the descriptions below.
[Additional chapters in Part 1, not shown here, will be interleaved with the chapters listed above. Some of the chapters in Part 2 (the list below is also not complete) will not be posted for some time.]
Chapter 17: Let’s Not Begin With Natural Selection
Evolutionary theorists tend to become frustrated when many of the rest of us fail to “get” the revolutionary and convincing simplicity of natural selection, that primary engine of adaptive evolution also known as “the survival of the fittest”. For example, Niles Eldredge, a paleontologist and, for several decades, a curator at the Museum of Natural History, has wondered, “Why do physicists, who have the reputation of being among the best and the brightest, have such a hard time with the simple notion of natural selection? For simple it is”. He then quotes Charles Darwin:
As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring Struggle for Existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected.
“The concept”, Eldredge writes, “is definitely simple enough. This description of natural selection may be a bit longer than the elegantly brief F=MA [force equals mass times acceleration — Newton’s second law of motion]. Conceptually, however, it is hardly more complicated.”
Chapter 18: Evolution Writ Small
One might think that the natural place to look for an understanding adequate to the evolutionary history of life would be the powers of self-transformation we observe in the evolving organisms themselves. But it can be dangerous to look in a clear-eyed manner at the creative potentials of living beings. One risks having to acknowledge the evident wisdom and agency so vividly on display. In an era of institutionalized materialism, any suggestion that these inner powers are vital to the entire evolutionary story can only produce the sort of discomfort associated with a taboo and what I have been calling the biologist’s blindsight (Chapter 2).
On the other hand, Stephen Jay Gould ran afoul of no taboo when he effectively ascribed this same wisdom and agency to natural selection. Countering the questions we heard voiced in Chapter 17 about what sort of creative principle could explain the “arrival of the fittest”, he asked (referring to several giants of twentieth-century evolutionary biology), “Why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley?”
The answer, Gould said, is that the allusions to poetry, musical composition, and sculpture helpfully underscore the “creativity of natural selection”:
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. It preserves favorable variants and builds fitness gradually.
On its face, Gould’s argument was a puzzling one. His answer to the question how creative variation arises amounted to saying nothing more than “It is everywhere” (“variation is ubiquitous”) — which, one might have thought, only added urgency to the need for an explanation. He seemed to suggest that, because organisms are so expert and prolific at producing new possibilities of life, the evolutionist can simply take their powers of achievement for granted. Because organisms so abundantly provide raw materials for creative work, we are somehow free to declare natural selection the agent performing this work. It need only preserve all those wonderfully effective new traits.
How easy it is, apparently, to forget that the so-called “raw materials” being preserved are never merely raw materials! At the first appearance of any beneficial change, the creative work has already been accomplished. We find ourselves looking, not at random raw materials, but at a viable feature harmoniously incorporated into all the tightly interwoven complexity of a living being. The only power we know to be capable of such incorporation is that of the organism telling its own story, a story always reflecting the qualitative, dynamic character and developmental potentials of a particular species.
This harmonious incorporation of new features, founded upon whole-cell inheritance and manifested in whole-organism processes of development, is the only place where we see creative evolutionary change originating. The spreading of an already-existing change through a population — almost the only thing those dominant evolutionary theorists known as “population geneticists” have attended to — is not where we see evolutionary novelties arising.
So Gould’s response shows us that one of the evolutionist’s strategies for coping with taboo agency is immediately to turn the question, “How does creative change arise?” into the different question, “How does creative change, once arisen, spread through a population?” The switch of topics is not hidden, but occurs in plain sight. Only a habit of blindsight relative to the organism’s agency seems able to explain the prevailing inattention to such an obvious evasion of a real biological question.
None of this means we need to doubt whatever is true in the idea of natural selection. As philosopher Ronald Brady summed it up, “simple selective pressure has never been seriously in question. That certain conditions can cause selective mortality means only that some alleles [genes] can be weeded out, not that this action can combine with variation in order to optimalize adaptation”. Eliminating problematic traits (or defective organisms) is not the same thing as profoundly transforming the integral unity that every organism is.
The point is not terribly subtle. There is simply nothing in the idea of natural selection that points to the creative capacities necessary for producing new adaptive features — for producing, say, a four-chambered heart (with all its organism-wide implications) from a three-chambered one. There is only the living being whose agency and activity natural selection necessarily assumes and which, as a result of blindsight, evolutionists have unconsciously transferred to a mystical “mechanism” of selection somehow operated by the inanimate world.
So here is our main question for this chapter: What do organisms show us, directly, compellingly, and uncontroversially, about their own powers of organic transformation? Much of the first half of this book contributes to an answer, especially at the physiological and molecular levels of observation. But in the present, evolutionary context, it will be well to look at the organism from a new angle.
Every organism is continually dying in order to live. Breaking-down activities are prerequisites for building up. Complex molecules are synthesized, only to be degraded later, with their constituents recycled or excreted. In multicellular organisms such as vertebrates, many cells must die so that others may divide, proliferate, and differentiate. Many cancers reflect a failure to counterbalance proliferation with properly directed tearing-down processes.
You and I have distinct fingers and toes thanks to massive cell death during development. The early embryo’s paddle-like hands give way to the more mature form as cells die and the spaces between our digits are “hollowed out”. In general, our various organs are sculpted through cell death as well as cell growth and proliferation. During development the body produces far more neurons than the adult will possess, and an estimated ninety-five percent of the cell population of the immature thymus gland dies off by the time the mature gland is formed.
Despite all this life and death, I doubt whether anyone would be tempted to describe an embryo’s cells as “red in tooth and claw”. Nor do I think anyone would appeal to “survival of the fittest” or natural selection as a fundamental principle governing what goes on during normal development. The life and death of cells appears to be governed, rather, by the form of the whole in whose development they are participating.
But this has been a truth hard for biologists to assimilate, since it has no explanation in the usual causal sense. One way to register the problem is to ask yourself what you would think if I suggested that organisms in an evolving population thrive or die off in a manner governed by the evolutionary outcome toward which they are headed — that the pattern of thriving and dying off becomes what it is, in some sense, because of that outcome. It is not a thought any evolutionist is likely to tolerate.
But perhaps the occasional intrepid researcher will be moved to inquire: “Why not?” After all, we can also ask about the cells populating our bodies: do they thrive or die off in a manner governed, in some sense, by the forthcoming adult form? And here the answer appears to be a self-evident “yes”.
Perhaps, when we have come to accept what we see so clearly in individual development, we will find ourselves asking the “impossible” question about evolutionary trajectories: Does natural selection really drive evolution, or is it rather that the evolving form of a species or population drives what we think of as natural selection? Are some members of an evolving species — just as with the cells of an embryo’s hands — bearers of the future, while other members, no longer being fit for the developing form of the species, die out?
What makes this idea seem outrageous is the requirement that inheritances, matings, interactions with predators, and various other factors in a population should somehow be coordinated and constrained along a coherent path of directed change. Unthinkable? But the problem remains: Why — when we see a no less dramatic, life-and-death, future-oriented coordination and constraint occurring within the populations of cells in your and my developing bodies — do we not regard our own development as equally unthinkable?
Few would imagine that our own well-directed development from embryo to adult is owing to an external guiding power or to a conscious “aiming” or planning. Nor need we think that the “developmental path” of evolution is owing to guidance such as an external breeder might supply. Rather, the idea would be that the evolutionary narrative, like the developmental one, arises from the agency and developmental powers of cells, organisms, and communities of organisms, as they express their own character and realize their potentials in the presence of the prevailing environmental challenges and opportunities.
So the question is this: do we have any less reason to expect a coordinating agency at play in a population of organisms pursuing an evolutionary trajectory than we do to expect a coordinating agency at play in a population of cells pursuing a developmental trajectory?
Our answer will depend on our willingness to take seriously a plain fact of our experience — a fact stressed throughout the first half of this book: agency and intention, wisdom and meaning, are given expression by organisms in a way that belies our expectations for collected bits of inanimate matter.
Chapter 20: Development Writ Large
We have found throughout the preceding chapters that all biological activity, including at the molecular level, is thoroughly and irreducibly directive. Some biologists explicitly acknowledge the fact, and all biologists implicitly recognize it in their choice of descriptive language (see Chapter 2, “The Organism’s Story”).
This leads naturally to the central conclusion of this book — a conclusion I will develop in this chapter — which is that we already know more than enough to say that evolution is a purposive, or directive, or telos-realizing, process. Many readers, I suspect, will have difficulty coming to terms with this conclusion. But, as we will see, it is simply a matter of admitting to ourselves what we in fact know quite well. After all, an understanding of the directiveness of living activity, however repressed, is the only thing that lends to existing theory any appearance of plausibility.
The essence of this “unacknowledged knowledge” lies in the striking truth that living activities are quite unlike inanimate processes. Whether conscious or unconscious, they are, simply as a matter of observable fact, effective preparations for the future. In this sense they are purposive, and the purposes are carried out with an incomprehensible wisdom and facility. A cell replicating its DNA, proceeding through division, and intricately coordinating its ever-changing patterns of gene expression; higher animals mating and providing for their young; a zygote undergoing all the “miraculous” transformations of embryonic development — these activities are, in terms of the prevailing principles of biological explanation, all but out of reach. Processes we conventionally accept as “causal” do not explain a developing organism’s living narrative — its ceaseless adjustment and coordination of causal activity so as to move directively toward a characteristic future that is not yet there.
But such telos-realizing narratives are also so “boringly” familiar that we cannot help taking them for granted. We assume their decisive role in every biological context we look at, and cannot “un-know” them even when we are theorizing from a position that ignores or denies them. And so we have the two sides of biology today: an uneasy, theoretical disregard of what seems ungraspable or dangerously mysterious, and a carefree, unexamined taking-for-granted of the powers at work in those all-too-familiar mysteries.
My aim in this chapter — an aim grounded in all the preceding chapters — is to facilitate the changed angle of vision that can enable the reader to grant full recognition to what is already known. I want to jog evolutionary thinking out of its customary pathways.
Additional chapters are not listed here.
Chapter 22: The Evolution of Consciousness
This chapter is not yet written. You will, however, find an earlier article that might be considered a fairly substantial “prelude” to this chapter: “A Physicist, a Philologist, and the Meaning of Life — Do We Have a Home in the Vast Cosmos?”
About the Author
This document: https://bwo.life/bk/index.htm
Steve Talbott :: Evolution As It Was Meant To Be