This chapter is a commentary on the findings reported in the previous chapter, The Mystery of an Unexpected Coherence, which the reader should be familiar with before attempting the discussion here.

The coherence we observe in RNA splicing, described in Chapter 8, is the coherence of an activity, a narrative performance. In living cells this activity — intricate, complex, and requiring the cooperation of scores of molecules continually reconfiguring themselves in a fluid medium — reliably achieves a desirable result that biologists describe in terms of the momentary needs of the cell. Further, the entire, drawn-out process is clearly directed, in an extemporaneous manner, toward that result. Despite the fact that the process could, with perfect physical propriety, go in an infinite number of different directions, it produces, from among all the present possibilities, the particular result that fits the present storyline of the ever-changing cellular context. The slightest splicing “error” committed by these molecules, which themselves can hardly be said to have a sense of right and wrong, could mean cell death.

It is worth noticing the great distance between, on one hand, what RNA splicing shows us and, on the other hand, the idea of DNA as a decisive cause of the cell’s life (or even DNA as a strict determinant of protein synthesis). The notion of a decisive physical cause immediately comes up against questions such as the following:

Does DNA (or, for that matter, any other cellular feature) have any possibility of determining the specific and crucial, well-timed chemical modifications or changes in form of just one of the proteins involved in the splicing activity, let alone the mutually interacting modifications that must occur in a great number of them as the splicing “surgery” proceeds?

Does DNA enforce the way these proteins (and other molecules) come together in distinct configurations at one point in the process, or dissociate at other points, or come together in a new configuration at yet another point — all in the temporal order required for the success of the overall procedure?

Does DNA ensure that the interaction of the proteins with the RNA they are now reconstructing should occur with a particular variation this time, compared to the splicing effort previously undertaken in the same cell?

It is proper to see all this activity as physically lawful. The problem is that we have a great difficulty distinguishing two things: the physical lawfulness of a process, and the strict determination of its outcome. The difficulty is no puzzle: we create it for ourselves by refusing to accept any explanatory meanings other than those we have conceptualized as physical laws. If there are other explanatory principles, as all biological description implies (see Chapter 2), then the fact that the physical lawfulness of an activity does not determine the activity’s outcome presents no puzzle.

The value in our consideration of RNA splicing — and we could just as well have chosen almost any other molecular-level activity in the cell — is that it may make us more receptive to two truths: (1) The splicing activity, as it transpires moment by moment in the cell’s watery milieu, is impossible to picture as a clockwork mechanism or in any other way as “mechanistically” determined in its outcome by physical conditions immediately preceding the splicing; and (2) when we look at the temporally extended splicing narrative in its larger context, we recognize meanings of a sort that are quite different from those we encapsulate in our formulations of physical law.

Can biologists come
to terms with 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.

We heard, for example, in Chapter 3 from James Wang, who played a pivotal role in discovering various molecular processes through which DNA in the cell nucleus is prevented from becoming a hopeless tangle. Having pictured how certain molecules (enzymes) untie a DNA knot by cutting through the double helix and later putting it back together again — all without disturbing the critical integrity of the original chemical structure — he went on to write:

When we think a bit more about it, such a feat is absolutely amazing. An enzyme molecule, like a very nearsighted person, can sense only a small region of the much larger DNA to which it is bound, surely not an entire DNA [molecule]. How can the enzyme manage to make the correct moves, such as to untie a knot rather than make the knot even more tangled? How could a nearsighted enzyme sense whether a particular move is desirable or undesirable for the final outcome? (Wang 2009).

This is the problem of “unexpected coherence” — unexpected, that is, if we are trying to explain things on a strictly physical basis. It is the same problem we heard University of Massachusetts geneticist Job Dekker alluding to when he cited the “huge number of potentially regulatory elements in a very crowded nucleus”. This led him to ask, “How do cells ensure that genes only respond to the right regulatory elements while ignoring the hundreds of thousands of others?” (Dekker 2013).

And the problem appeared again in the wonder of the editor of Science, who wrote about the task a cell faces in dealing with its billion or so protein molecules:

If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins … Somehow, a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places (Travis 2011).

— a comment that was seconded by Robert Singer of Albert Einstein College of Medicine in New York City: “It’s almost as if every mRNA coming out of the nucleus knows where it’s going” (quoted in Travis 2011).

Perhaps most importantly, there was cell biologist and Medal of Science recipient, Paul Weiss, who described for us (in Chapter 6) how, in the “heaving and churning” cell, “Small molecules go in and out, macromolecules break down and are replaced, particles lose and gain macromolecular constituents, divide and merge, and all parts move at one time or another, unpredictably, so that it is safe to state that at no time in the history of a given cell, much less in comparable stages of different cells, will precisely the same constellation of parts ever recur”.

But Weiss did not merely stare, transfixed, at the problem of order within this cellular “chaos”. He tried to formulate its essence as clearly as possible, often resorting to statements such as this: “The resultant behavior of the population [of cellular constituents] as a whole is infinitely less variant from moment to moment than are the momentary activities of its parts.” And so “the system as a whole preserves its character” (Weiss 1962, p. 6). And again: When we examine the form and physiology of an organism, we see how “certain definite rules of order apply to the dynamics of the whole system … reflected [for example] in the orderliness of the overall architectural design, which cannot be explained in terms of any underlying orderliness of the constituents” (Weiss 1971, p. 286).

What was the constraining power through which all those molecules, possessing all those degrees of freedom at their own level, yielded to a consistent order at a higher level — a physically unexpected coherence? This was the question Weiss’ life-long observation of living cells continually brought him up against. But he was too honest to pretend to an answer he didn’t have. His virtue was in not shrinking from the problem. He spent a long career investigating and describing the material performances of cells, but he did not pretend that, in doing this, he was explaining the order he observed. In this he differed, not only from the others I have cited above, but also from the biological community as a whole.

So, then — returning to the impatience I have imagined in my own readers: yes, there is a looming question — what I have called the “mystery of an unexplained coherence”. It is not a mystery about some thing. Coherence refers, not to a thing, but rather to the ideas that meaningfully hold a collection of things together in a conceptual unity. And it is certainly true that to speak of such a unity raises deep questions for biology. Yet these questions, which might seem the most obvious ones for biologists to pursue if they want to make fundamental progress, are oddly absent from biological texts.

So you see: I am not the one ignoring the questions. Biologists have known about them — have even given voice to them, as the quotations above show. But, with the exception of a few intrepid scientists such as Paul Weiss, they have chosen to sweep the issues under the rug and pretend, if only by their inattention, that everything is fine. Their assumption seems to be that, if only we continue tracing local, isolated causes and effects, this tracing just must add up to the larger story.

But notwithstanding the assumption, no one has actually shown how any possible sequence of physical causes could explain “The Organism’s Story” (Chapter 2). It is hard even to know what such an explanation might look like — hard to know how the lawful physical interactions we are so expert at isolating are related to the overall, meaning-rich, narrative outcomes that researchers cannot help recognizing, but refuse to touch in their theoretical work. It is as if they fear that addressing the matter might threaten the stability of their science.

My own role here is to attempt to bring the refused questions into the light, and to suggest a sensible approach to them. The peculiarity of my presentation is not my personal deviation from “proper biology”. It is my effort to keep biology’s native problems in view, instead of evading them.

In what follows I offer a condensed summary of what I take to be the deep significance of the issues swept under the rug. We will have to take these issues up more expansively in later chapters.

There is no escaping the
centrality of distinctively
biological meaning

Notice the centrality of idea and meaning in everything I have described so far. For example, I mentioned in Chapter 6 that a chessboard is one sort of context if the game is chess, and a different sort of context if the game is checkers. Although the physical board remains the same, a decisive difference lies in the system of ideas establishing how the events on the board hold together in a meaningful pattern. If, as observers of the game, we try to understand what we are seeing, our only hope lies in grasping the ideas conveying the meaning of what is going on. A context can be said to govern and unify — give contextual significance to — its constituent activities.

I have also spoken of biological wholes, each of which is just such a context. Here, too (as with the chessboard, if much more profoundly) idea and meaning are keys to any understanding of what transpires within the context. A cell preparing to divide mobilizes all its resources in a meaningful pattern radically different from what we observe in a cell entering a quiescent state. Those are two distinct contexts.

Similarly, all my references to end-directed or purposive activity amount to implicit recognitions of the idea of the end or purpose, which is what holds together and gives meaning to the part-processes through which the end is realized.

And, finally, it hardly needs arguing that the narrative unfolding of a story, to which I have compared the organism’s life throughout these several chapters, just is a temporally ordered interweaving of idea- and meaning-laden events. That organisms give us all manner of stories is a truth enshrined in thousands of books published every year.

So it turns out that everything I have been saying so far is rooted in a claim about the importance for our biological understanding of highly contextualized, narrative ideas, including ideas of end-directedness or purposiveness. If you want to know how I deal with the problem of the unexpected coherence of biological activity — the problem I have intentionally raised throughout the presentation of the preceding chapters — the answer lies in the simple fact that principles of coherence just are what scientific explanations consist of. In other words, there really isn’t a problem here at all. If some of the principles of coherence in organisms cause puzzlement or offense, it is only because the scientist prefers not to see them, having been convinced that the only possible explanatory principles applying to living beings are those governing inanimate phenomena.

In sum:

I take biological ideas seriously. I accept them at face value. The “unexpected” coherence in the life of organisms is the coherence of biological — as opposed to merely physical — ideas. And the ideas are really there, which is why we so readily recognize them and assume them in our descriptions.

That statement is the heart of this book. I do not see any alternative to it for the scientist trying to theorize on the basis of accurate and thorough description. Biological description as we actually have it concerns nothing but the kinds of living, end-directed, narrative ideas I am talking about (Chapter 2). There is no coherent biological description without them.

This characteristic description of animate beings is not a problem. Like all proper scientific description, it is the empirically given foundation upon which biological understanding must be established. The scientist should have no trouble at least starting with whatever is immediately given. There is, after all, no other sensible place to start.

By “whatever is given” I mean: whatever seems manifestly there. We have no right to refuse this reality — not until, after further investigation, it shows itself to be manifestly other than what it first seemed to be. The biologist’s “data” consists of whatever has become manifest to observation.

Every organism is an entity in which certain ideas and intentions are manifest — observably expressed and realized. We have to be willing to say, as everyone does say, “This cell is preparing to divide.” We would never say (as I mentioned earlier), “This planet is preparing to make another circuit of the sun.” The organism obviously gives us a reality different from planets and suns. Shouldn’t this manifest difference be front and center in the biologist’s attention — all the more if there exists a prejudicial urge to approach biological explanation solely in the causal style we bring to planets and suns?

I am fully aware that what I have just said comes at the contemporary scientist from a strange and, at this point, probably objectionable, direction. But perhaps this initial statement will at least intrigue some readers. We will pursue the ideas further throughout the remainder of the book.

Thinking versus thoughts:
a vital distinction

Meanwhile, one potential misunderstanding can at least be alluded to right away. It would suggest to us that if we really recognized an idea livingly embodied in the behavior of an amoeba, we would have to say that the amoeba was itself thinking the idea. But this is not the case. It overlooks the distinction between an act of thinking and the resulting thought (Barfield 1971, chapter 1).

The difference becomes clear enough in our own experience. We can recall an earlier thought without having to repeat the experience through which we originally gained the thought and understood it. It is as if the original act of thinking leaves certain memory traces that are easily recollected. The traces of the act are not the act. This is why we can so easily entertain ideas in a rather mechanical fashion — for example, out of habit or association, or in reverie — without any deep or new thinking.

Here is a different angle on the matter. In designing and building a new kind of washing machine, an engineer organizes and functionally integrates the parts according to a system of ideas. The ideas are really there, implicit in the form of the finished and performing machine. We are in a position to recognize those ideas when we look at the machine’s functioning. But this does not lead us to conclude, “The machine is thinking the ideas.” No, the thinking was the act of the engineer, but the machine nevertheless bears in its functioning the undeniable imprint of the engineer’s thoughts.

We will not forget that the designed machine is only the most remote image of an organism, in whom ideas work in a more living way. But the point holds: we can recognize a play of ideas through a material form without ascribing to that bit of material the kind of centered, autonomous agency allowing it to carry out its own act of thinking — let alone the power to consciously intend acts of thinking.

There exist, we might reasonably assume, different degrees of autonomy and centeredness in organisms. And there is reason to think that different degrees obtain at different points in the evolutionary panorama (Rosslenbroich 2009; 2014). We will have occasion later to note among organisms the different possible balances between acts that we might, in one sense or another, consider the organisms’s own, and those that might better be said somehow to play through the organism from the wisdom of its living environment, whether visible or invisible.

It is indisputable that organisms are effective agents. But we have good reason to keep in mind the distinction embedded in our common use of the word “agent”, which can refer either to that which is “capable of its own activity”, or that which is a “mediator of activity”.

We can, in any case, rightly say that the ideas we recognize as empirically given in the life of an organism are really there. “This amoeba really is directing its activity so as to engulf a particle of food and sustain its own life.” But we cannot also say that this idea is directly observable as the amoeba’s own act — certainly not in anything like the sense in which we can feel ourselves as the authors of our own thinking. We can, in general, recognize ideas at play,¹

This, of course, raises many questions — all the better for provoking further consideration.

Today’s biology celebrates
(perversely) the explanatory
value of thought and idea

There is, one might think, no need to remark upon the objective reality of distinctively meaningful ideas in the phenomena of life. Biologists themselves seem to make the same point almost obsessively. Notions such as information, communication, signaling, code, instruction, and program — all related to thought and language — are fundamental to a great deal of contemporary biological explanation, from molecular biology to evolution.

We could also look, as we did in Chapter 2, at the entirely different explanatory terms applied to a living dog and its corpse. These differences testify as loudly and explicitly as they possibly could to the biologist’s belief in the thoughtful, rational, and meaningful lives of animals.

Or, again, as I remarked in the chapter, Chapter 6, whenever we speak of beings rather than things, we necessarily turn to a language of directed intention (respond, develop, adapt, regulate, and so on); a normative and aesthetically colored language (everything relating to health and disease, order and disorder, rhythm and dysrhythmia, harmony and disharmony, error and error correction); and a language of wholeness (context, coordination, integration, organization).

So, yes, biologists can hardly draw a breath without ascribing to organisms a character that is somehow akin to our own inner life of thought, intention, and meaning, however great the differences may be between human experience and and that of a sloth or worm. The pathology of it all lies in the fact that the affirmations of this meaning take the paradoxical form of denials of it. That is, despite the obvious meaning of their terms, biologists help themselves to this meaning “under the table”, and in such a way as to barricade themselves against any unpleasant awareness of what they are doing.

The programmed computer-organism

The most egregious example of this kind of thing is the genetic program. Ernst Mayr — like Paul Weiss, a National Medal of Science recipient, and a towering figure in twentieth-century evolutionary biology — wrote that “the program for the [organism’s] behavior computer” is provided by the “DNA code”, yielding “a purely mechanistic purposiveness” (Mayr 1961). Further, “The existence of a genetic program … constitutes the most fundamental difference between living organisms and the world of inanimate objects, and there is no biological phenomenon in which the genetic program is not involved” (Mayr 1982, p. 629).

How easy it is to overlook the fact that a computer program is pure thought! We can impress the structure of that thought upon any number of different media — magnetic tapes, silicon memory, optical disks, and so on. Yet the program as such remains quite independent of the arbitrary choice of medium. The medium does not affect what we think of as “the program” at all, because the program is simply a record of the programmer’s thought. It is not altogether unlike the way a book is a record of its author’s thoughts.

So Mayr was urging an appeal to a pure structure of thought as fundamental to biological explanation. The difference between what he was saying and what I am saying, is that the thoughts to which I would appeal, unlike the ideas constituting a program, are really there — observably so — and are intrinsic to the organism.

If we really wanted a program-executing computer that we could analogize to an organism, we would not so blithely focus on the notion of a program while forgetting the material computer. We would, that is, expect to observe the play of the programmatic ideas in the continual transformation of the parts of the computer — in their “embryonic” growth from a single, microscopic piece of hardware to a complex, mature machine; their healing in the case of injury; their changing conformation and arrangement in the face of various environmental stresses; their metabolism; and much, much more. It would be in this material development of the computer that we recognized a dynamic, ever-changing “program”. The program would be the inner aspect of all the physical elements of the computer — not an unrelated disk that we slip into a slot like a Designer slipping a soul into an inert form of dust.

In other words, we would discover the ideas animating the computer in the material performances of the machine itself, where the parts, through their own nature and the ideas informing that nature, were held together in a living structure.² If we had such a program and such a computer, then, yes, we might want to analogize them to an organism. But, of course, we would have something so improbably different from computers and their programs as we actually know them today that we would hardly think of the two kinds of devices as the same sort of thing. Our currently familiar computers would no more be comparable to the hypothetical new “machines” than they are now to organisms.

But, as we saw before, one can always retreat into the “double stance” I spoke of in Chapter 2 — implying belief while not believing, acknowledging while explaining away. Those biologists who speak of programs have no difficulty ignoring the fact that they are really talking about thoughts, even as their metaphorical descriptions gain effectiveness only through our human experience of the thoughtfully contrived performances of program-executing computers.³ It is easy enough, when one is in the grip of a powerful philosophical commitment, to imagine that a programmer’s thoughts are really just a pattern of pits in an optical disk. It is as if we claimed that the writing in a book was nothing but a pattern of meaningless marks, while at the same time we were enjoying the story.

My hope is that we all can continue enjoying the organism’s story while also recognizing its scientific legitimacy. Given the rather scandalous role of the word “program” in today’s biological literature (along with related terms such as “information”), there would seem to be a startling level of unawareness and recklessness in any charge that my acknowledgment of the organism’s narratively meaningful life evidences a “mystical” or “vitalist” point of view.

Notes

1. Actually, there is no seeing things at all except by virtue of the ideas that constellate each thing for us as this particular sort of thing. Anyone who doubts this can put his doubts to rest by reading the three chapters by philosopher Ronald Brady in the freely available online book, Being on Earth: Practice In Tending the Appearances. but we cannot see the acts of thinking through which those ideas have come into play.

2. All this — not merely the fact that no one has ever shown where we find a computer-like program in a cell or organism, nor merely the fact that the organism lacks computer-like hardware for executing such a program — is why the proposal of an even vaguely computer-like program in the organism has never made the slightest sense. How would we even begin to apply the idea of such a program to the molecular activities of RNA splicing discussed in Chapter 8?

3. Projecting our experience of computers onto organisms is one of the ways in which today’s biology becomes lamentably anthropomorphic.

This document: https://bwo.life/bk/idea.htm

Steve Talbott ::