“What Do Organisms Mean?”

Finally we’re on to part 3/3 of this New Atlantis series I’ve been reading over the past two days (part 1, part 2), roughly about whether the mechanics of life are quantifiable; whether physics can fully explain biology. The series took a slide from scientific and agreeable to me to philosophical and disagreeable to me, but I stuck through it in the search of something convincing.

This third essay, “What Do Organisms Mean?”, basically expands on the arguments presented in the second one, and I feel the same way about them – his arguments are very god of the gaps-like, and he seems to give scientists’ pathetic fallacy significance that it doesn’t have.

A main thing that confuses me about his arguments is that he insists that he is not arguing for a non-material life force, while saying that physics cannot explain biology because there’s some greater organizing force at work in organisms. He addresses this discrepancy below; for context, his general argument is that there’s some sort of meaning inherent in living organisms, some overarching goal or thought process not encapsulated in its physical composition.

The accusation of vitalism seems inevitably to arise whenever someone points to the being of the organism as a maker of meaning. This is owing to a legacy of dualism that makes it almost impossible for people today to imagine idea, meaning, and thought as anything other than ghostly epiphenomena within human skulls. So the suggestion that ideas and meaning are “out there” in the world of cells and organisms immediately provokes the assumption that one is really talking about some special sort of physical causation rather than about a content of thought intrinsic to organic phenomena…

But ideas, meanings, and thoughts are not material things, and they are not forces. Nor need they be to have their place in the world. After all, when we discover ideal mathematical relationships “governing” phenomena, we do not worry about how mathematical concepts can knock billiard balls around. If we did, we would have made our equations into occult or vital causes. But instead we simply recognize that, whatever else we might say about them, physical processes exhibit a conceptual or thought-like character. And so, too: the meanings that give expression to the because of reason do not knock biomolecules around, but — like mathematical relations — are discovered in the patterns we see. The thought-relations we discover in the world, whether in the mathematical demonstrations of the physicist or the various living forms of the biologist, need to be genuinely and faithfully and reproducibly observed, but must not be turned into mystical forces.

From this I think I can succinctly state where I disagree with him: he claims that “physical processes exhibit a conceptual or thought-like character,” instead of recognizing that we assign conceptual or thought-like character to physical processes. To borrow my analogy from my previous post on this series, a protein that we call a master regulator isn’t analogous to a boss at work intrinsically; there’s nothing intrinsic about it that indicates that it relays orders or interprets feedback. That’s a purely human invention meant to explain a physical phenomenon through analogy, because we assign agency to things left, right and center.

Our unavoidable tendency to assign agency led people to create pantheons of gods in the past to explain the conscious motivations of nature, and leads us to anthropomorphize molecules now. The difference is that at this point we consciously acknowledge this fallacy, and embrace it as a part of human perception, not as part of reality. I think the author’s error is in failing to separate this feature of perception from the objective reality it tries to describe.

I think I’ve said about as much as I can about this series of essays; they are long and a bit dense, but I hope you’ll take a look at them too, to challenge how you think about biology and reality. I can’t capture all of it, but I’ll quote some of the meaty parts of this third essay below: 

We commonly explain occurrences by saying one thing happened because of — due to the cause of — something else. But we can invoke very different sorts of causes in this way. For example, there is the because of physical law (the ball rolled down the hill because of gravity) and the because of reason (he laughed at me because I made a mistake). The former hinges upon the kind of necessity we commonly associate with physical causation; the latter has to do with what makes sense within a context of meaning…

Here, then, is the point. What distinguishes the language of biology from that of physics is its free and full use of the because of reason. Where the inanimate world lends itself in some regards to application of a “deadened,” skeletal language — a language that perhaps too easily invites us to think in terms of mechanisms — the organism requires us to recognize a full and rich drama of meaning.

And so when we ask whether a protein has folded correctly, we’re not suggesting it may have rashly disregarded the laws of physics. Its respect for the syntax of a physical law is not the issue we’re addressing. We want to know something much more plastic — more plastic in the way that meaning is more plastic than a rigid grammar or mathematical formula. That is, we want to know whether the folding is consistent with — serves the needs of and is harmonious with — the coherence and the active, self-expressing identity we recognize in the surrounding context. It’s a context and an identity whose qualities and intents differ greatly from a snake to a lion, from a German shepherd to a golden retriever, or from a lung to a kidney. Likewise, when we inquire into the communication between cells, we are not merely curious about the physical impact of molecular projectiles fired from one cell to another; we are trying to clarify a context of meaning. The one cell is saying something to the other, not just pushing against it…

A context of meaning can be thought of in various terms. We can take it, for example, to be the organism’s unified form in the fullest sense — not only its bodily form (as a flexible, dynamic trajectory of development), but also the “shape” of its pattern of activity, its recognizable and irreducibly qualitative way of being, distinct for every species. Every organic form is a gesturing, which is also to say, a kind of speaking or an expression of meaning. And we could just as well say that the organism’s gesturing manifests the character we recognize in the organism as a whole.

Gesture, character, significant form, a tapestry of meaning — these terms all point to the “something more” that, as we found earlier, makes the language of physics and chemistry inadequate to describe the organism. They also typify our way of thinking about beings, as opposed to things. That is, they require a language of directed intention (responddevelopadaptregulate, and so on); an aesthetically colored language (everything relating to health and diseaseorder and disorderrhythm and dysrhythmiaharmony and disharmony); and a language of wholeness (unitycoordinationintegrationorganization). In fact, just about all the kinds of meaning we express in our words, thought, and activity find their analogue in our descriptions of organisms. Not surprisingly, then, the biologist directly invokes meaning itself in terms such as messageinformationcommunication, andsignal.

The biologist’s reliance upon the because of reason — a because that resonates so intimately with the meaning of our own lives — is no small thing. It is no small thing, that is, to find ourselves living together with all our fellow creatures in a community of meaning. For in the realm of meaning, there can be, finally, only one community; a hermetically sealed compartment of meaning wholly disconnected from all other meaning is an impossibility. If this truth of community hasn’t been loudly proclaimed from the research laboratories to the wider public, it is only because biologists have gone on for decades using the language of meaning while remaining content never to reckon with it — and even effectively denying it with a contradictory language of mechanism and control. It is past time for the reckoning…

Meaning need not be thought of solely in terms of our own human consciousness. Everyone accepts that neither the bird building a nest nor the embryo “constructing” a heart is self-consciously realizing its own purposes and meanings. Likewise, the directed nature of cellular processes does not imply conscious, human-like purpose, and, more generally, the meaning I have been referring to need not involve anything like our own conscious awareness.

This is not to suggest, however, that meaning is no longer meaning. Our knowledge of ourselves informs us that the because of reason can play out in less than full consciousness. We know that it weaves throughout the psyche, conscious or otherwise, all the way down through subconscious urge and habit to biologically rooted instinct and even to physical reflex. It is not so unexpected, then, to discover meaning-governed activities also at the molecular level, where they manifest as regulation, organization, signaling, responsiveness, and all the rest. Organisms, so far as the biologist has been able to determine, are alive and whole and engaged in activity shaped by relations of meaning — a meaning whose signature is recognizable all the way down…

It will be important to keep in mind these distinct aspects of the physical sciences: on the one hand, precise, invariant relationships — the fundamental laws — implicit in whatever happens; and, on the other hand, the much less precise, never absolute, never infallible notion of a cause, which is supposed to tell how one thing makes another happen, that is, how one event, or set of conditions, brings about another event or set of conditions.

Many people, when they speak of the world’s “causal regularity,” are actually referring to its lawfulness. This conflation of law and cause — this illegitimate bestowal upon physical causes of the regularity, predictability, and certainty associated with physical laws, as if the causes had the same necessity as the laws — yields a great deal of mistaken thought. Among other things, it lends to any science guilty of it the illusion of vastly greater explanatory power than it in fact possesses. This helps us to understand why so many biologists see a determinate machine where there is in fact a living being; the physical lawfulness discoverable in the organism is unthinkingly equated in their minds with a collection of causal mechanisms

No biologist today will deny that fundamental physical laws continue to apply without exception to organisms. But what about causes? We have just now noted that, by means of carefully designed closed systems more or less immune to contextual interference, it is possible to say one thing “causes” another, with due caveats. Machines are such systems. But what happens when the biologist attempts to see the organism in the same mechanistic light, making a closed system of it?

The effort fails miserably. For in biology a changing context does not interfere with some causal truth we are trying to see; contextual transformation is itself the truth we are after. Or, you could say: in the organism as a maker of meaning, interfering is the whole point. The ongoing construction and evolution of a context, with its continually modulated causal relationships, is what the biologist is trying to recognize and do justice to. Every creature lives by virtue of the dynamic, pattern-shifting play of a governing context, which extends into an open-ended environment. The organism gives expression, at every level of its being, to the unbounded because of reason, the tapestry of meaning, the form and character I referred to earlier. It can change its proximal goal from moment to moment, thereby also changing the contextual significance of the details of its life…

One would think that biologists might pause and consider the possibility that the kind of stable causal relationship they’ve been looking for simply isn’t there — the possibility that they’ve defined their task in misleading terms. Yet when researchers find, for example, that patterns of nuclear organization are implicated in cancer, an almost automatic exhortation follows: “However, it is crucial to determine the extent to which cancer-associated changes in nuclear organization are cause or effect.”[15] But is it crucial? Are the actual goings-on in the cell in fact proving so clear-cut? Why do we need causes as an addition to lawfulness and meaning? After all, we have no difficulty understanding all the relationships in a meaningful text, even though we cannot say that one part of the meaning causes another part…

The pursuit of causes in biology is something fierce. There is evidently a visceral feeling that without causal mechanisms we have no explanation, and without explanation, no understanding. It is a prejudice so deeply engrained, so resistant to removal, that it has badly distorted the entire field of biology…

It’s not that identifying a so-called gene “switch” — or calculating kinetic energies or measuring mechanical stresses on macromolecules — gives us no understanding. Of course such insights are important. But they become biological insights, as opposed to physical and chemical ones, only insofar as they find their place within the living, metamorphosing form of the organism. They do not explain the form. If anything, we should say that the form explains the physical interactions — in the sense that it gives us an understanding of their pattern, their shape, their direction and place within a functional whole, none of which can be deduced from physical transactions as such. We can observe the patterns by tracing the physical interactions, but what those patterns will turn out to be can never be arrived at merely by working out the implications of the physical laws and substances…

You can’t explain an organism of meaning, and you don’t need to. You need only allow it, like any meaningful text, to speak ever more vividly and clearly, in ever greater detail. The separate processes do not make tidy explanations because they are not really separate and are not just doing one thing; they are harmonizing with everything else that is going on in the organism. We gain understanding when we learn to recognize this harmony in every aspect of the organism. Various analyses can play a crucial role in bringing clarity to our understanding. But the full picture takes shape only when the analytical threads are woven back into the larger fabric of meaning.

We have an increasing appreciation today of the importance of organismal context, and of the organism’s plasticity, and of its dynamism, and of the complexity of its interweaving processes, and of the causal ambiguity of our explanations. For a mindset fixated upon causal mechanisms, all these factors might be viewed as unwelcome complications — detours on the way toward real understanding. But do they really make our descriptions and explanations less revelatory of the organism than what we had before, when gene-mechanisms were supposed to provide a “blueprint” or “instruction set” for the organism as a whole? Shouldn’t we expect that the processes we cannot neatly tie down or capture in mechanisms are precisely what bring the organism alive for us? …

The organism, we have seen, is continually expressing the because of reason. Possessed of a certain inwardness, it is a maker of meaning, a fact most immediately presented to us in our own lives as self-conscious beings, but further evident all the way down to the eloquent and concerted molecular interactions of every living cell. We recognize meaning in the vocalizations, body language, and gestures of animals; in the qualities that make the oak tree a recognizable presence, consistently expressing its own character, distinct from a willow tree; and in the active, directed striving for self-realization in all organisms — a striving that enables us to speak reasonably of their health and disease, wholeness and injury.

And yet, in a baffling show of tolerance for contradiction within science, an entrenched metaphysical dogma assures us that the universe in which these creatures of meaning exist is a universe inherently without meaning, idea, or thought.

The truth of the matter may simply be so close to us — so fundamental and so intimately a part of our nature as understanding beings — that we cannot readily step back and see it. I mean the truth that any understanding of the world, animate or inanimate, must be an understanding — which is to say, it requires a conceptual grasp of things. Whatever is incommensurable with thought and idea will never be contemplated in thought and idea, and therefore will never enter into science. The world we know will always and only be a world in whose inwardness we can participate inwardly — a world whose being can take form as a content of consciousness. Without a truth of things that can at the same time be a truth of word and thought, we could have no scientific conversations or textbooks — no science at all…

The depths of physical reality are, of course, as hidden from us in the living organism as they are in the rest of the physical world. But in the organism we encounter something further: reason and meaning come to much more “visible” and insistent manifestation, narrating the stories of living beings — stories that, evoking as they do the intentional and meaningful patterns of our own lives, are more accessible to us than whatever speaks to us now through the qualities of inorganic substance. It is ironic that the organism has been regarded as a more difficult challenge for science than the world of physics. The truth is that the organism is much closer to us — we are, after all, organisms ourselves — and it offers many informed, articulate responses to our inquiries. We can apprehend it with a richness and depth of comprehension far exceeding the admirable mathematical comprehension of the physicist.

If the world is indeed intelligible — if it speaks meaningfully, as must be assumed by every scientist who tries to capture that meaning in revelatory words and ideas — then the place where we find it speaking most fully and explicitly is presumably the place where we will find its fundamental truths most fully declared. And that is in the living organism.

The “difficulty” of the organism is really just the difficulty of reducing it to mere physics and chemistry. Yes, very difficult indeed — but that’s because the organism is alive, as we are alive, and because every biologist instinctively understands this life as offering more than lessons in physics and chemistry. As for the “nonliving” world: we imagine it is simpler to understand only because we are bewitched by the precision and predictability of the physical laws we find implicit in things — things of whose nature we know almost nothing.

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