Biology’s Missing Ideas
This is a preliminary draft of one chapter of a book-in-progress
tentatively entitled, “Evolution As It Was Meant To Be — And the Living Narratives That Tell Its Story”.
You will find
a fairly lengthy article serving as a kind of extended abstract of major
parts of the book. This material is part of the
Biology Worthy of Life
Project. Copyright 2017-2021
The Nature Institute.
All rights reserved. Original publication: May 31, 2019.
Last revision: May 31, 2019.
This chapter is a commentary on the findings reported in the previous
The Mystery of an Unexpected Coherence,
which the reader should be familiar with before attempting the discussion
The coherence we observe in RNA splicing, described in
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”
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
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
“The Organism’s Story”),
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
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?
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?”
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.
— 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
Perhaps most importantly, there was cell biologist and Medal of Science
recipient, Paul Weiss, who described for us (in
“Context: Dare We Call It Holism?”)
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
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
(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
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
Notice the centrality of idea and meaning in everything I have described
so far. For example, I mentioned in
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.
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
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
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
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
(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
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, 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
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
but we cannot see the acts of thinking through which those ideas have come
This, of course, raises many questions — all the better for provoking
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
“The Organism’s Story”,
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,
“Context: Dare We Call It Holism?”,
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
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”
(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
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
But, as we saw before, one can always retreat into the “double stance” I
spoke of in
“The Organism’s Story”
— 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
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.
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.
Emphasis in original.
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
Projecting our experience of computers onto organisms is one of the ways
in which today’s biology becomes lamentably anthropomorphic.
holism/versus mysticism and vitalism
inwardness (intention, idea, meaning)
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Steve Talbott :: Biology’s Missing Ideas