Quotes of the Week

July 28, 2025

Whatever the level we analyze, from macromolecular complexes, to organelles, to cells, to tissues, to individual organs, to the organism as a whole, we find the same principle: we cannot reconstruct the pattern at any level of activity by starting from parts and their interactions. There are always organizing principles that must be seen working from the whole into the parts. (See the discussion of Weiss in Chapter 6, “Context: Dare We Call It Holism?”)

(from Chapter 10, “What Is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 21, 2025

[Regarding the problem of form in organisms:] A key feature of holistic, end-directed, living processes is that the end plays a role in shaping the means. Tadpoles with faces engineered to be highly abnormal “nevertheless largely become normal [adult] frogs: the craniofacial organs move in abnormal paths until a proper frog face morphology is achieved” (Levin 2020). In other words, the means are modified, even becoming entirely unprecedented if necessary, in order to achieve a characteristic result.

We find the same principle when we look at cascades of gene expression, such as the sequential expression of the various genes that have been said to “determine” left-right asymmetry of the vertebrate body. The normal expectation would be that if one blocks or changes the expression of earlier genes in the sequence, the disorder should accumulate and be magnified, perhaps explosively, in downstream gene expression, since proper cues for the later steps are missing. But:

“Surprisingly, this is not actually what occurs: each subsequent step has fewer errors than the previous step, suggesting that the classic linear pathway picture is importantly incomplete. Embryos recognize transcriptional deviations from the correct pattern and repair them over time ... The existence of corrective pathways in embryogenesis and regeneration raises profound questions about the nearly ubiquitous stories our textbooks and ‘models’ tell about the molecular explanations for specific events” (Levin 2020).

All this may remind us of E. S. Russell’s remark that in biology “the end-state is more constant than the method of reaching it”. We also see here the principle that cell biologist Paul Weiss enunciated so clearly at mid-twentieth century, when he pointed out that the whole “is infinitely less variant from moment to moment than are the momentary activities of its parts.” At the lowest level of biological activity, molecules in the watery medium of a cell have degrees of freedom (possibilities of movement and interaction) that would spell utter chaos at higher levels if it were not for the fact that the lower-level activity is “disciplined” from above.

(from Chapter 10, “What Is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 14, 2025

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 (Farinella-Ferruzza 1956).

The experiment can remind us how biologists commonly try to learn about life by severely disrupting it. But the current point 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.

(from Chapter 10, “What Is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 7, 2025

It is important to get clear about the nature of causation in biology. It differs from the problem of causation in the physical sciences. Organisms manifest a fluid, integral, harmonizing sort of causation that is more like a play of the multi-dimensional reasons for things than a set of one-dimensional mechanical interactions. It is more like the rich interplay of meaning in an unfolding poem than a rigid syntax or logic.

And yet, despite all this, biologists seem fixated on the “fundamental issue” of distinguishing clear-cut cause from clear-cut effect in the usual physical sense. That’s why we hear statements to the effect that “despite intensive studies of genome organization in the past decade, a fundamental issue remains regarding genomic interactions and genome organization as a cause or a consequence of gene expression. This problem is also pertinent to RNAs, which may have regulatory functions in transcription rather than being simply products of transcription” (Li and Fu 2019).

Unfortunately, there is little if any effort to elucidate just what hangs upon this “fundamental issue” — or what might be the implications of the fact that the issue appears irresolvable so long as we insist upon unambiguous physical causation as the basis for biological understanding.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 30, 2025

When a cell enters into mitosis, just about every detail of its physiology and chemistry takes on an altered meaning in light of the changing narrative context. Everything is now heading toward a different outcome. Molecules that had been participating in one set of interactions (and could easily still do so in purely physical terms) now enter into very different intermolecular relations. Similarly with a cell experiencing heat shock, oxygen deprivation or other stress, a cell coming into contact with new neighbors, or a cell proceeding along a path of embryonic differentiation.

Certainly we can still identify unambiguous causes in the organism. It is always possible to narrow the conditions of our experiments so severely that a consistent “causal arrow” for a particular interaction emerges under those conditions. But the whole point of life’s adaptability is to seek (or help create) altered conditions according to present needs and interests. This is why there can be no fixed syntax, no mechanical constancy of relations among the parts. The organism is forever abandoning the coordinating principles of its old context in favor of a new and ever-changing meaning. Its story is always evolving.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 23, 2025

The powerful compulsion to identify decisive causes, even at the expense of painfully self-contradictory language, strongly suggests that a one-sided and unrealizable ideal of biological explanation is at work. Under its influence we aim to discover a physical lawfulness reflecting, above all, our experience with machines — a lawfulness of precise, unambiguous control, where one thing can be said, without unwelcome qualification, to make another thing happen.

Think of a machine. Having conceived what we want it to do, we design it to be a closed system whose intended functioning is more or less immune to contextual interference. And we try to do much the same in many scientific demonstrations. For example, we can create a vacuum in a chamber, and then release a leaf from the top of the chamber. It falls like a stone.

Of course, leaves in nature often travel upward. But the experiment in the chamber enables us to observe the singular and lawful play of gravity, without any disturbing “interference” from the resistance or movement of air. We can then — and only then — say that gravity appears to make the leaf fall, just as the simple laws governing the gears and springs of a mechanical watch make the watch perform as a reliable keeper of time.

But when the biologist tries to see an animal in the same mechanistic light, as a closed system without interfering factors, the attempt fails miserably. This is because, for the animal, contextual interference is the whole point. As the meaning of its activity shifts from moment to moment, so, too, does the contextual significance of all the details of its life. For example, when a deer is grazing in a meadow, its glimpse of a vaguely canine form in the distance changes the meaning of everything from the flowers and grass the deer was eating, to its own internal digestive processes, to the expression of its genes. This happens, not because the distant form is exerting some strange physical force upon the deer, but because that form becomes part of a now suddenly shifted pattern of meaning.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 16, 2025

Not only are the elements of an individual signaling pathway extremely flexible and adaptive; the individual pathway itself, once thought of as discrete and well-defined, doesn’t really exist — certainly not as a separate “mechanism.” Researchers now speak of the “multi-functionality” or “functional pleiotropism” of signaling nodes, pointing out that signaling networks have “ways of passing physiologically relevant stimulus information through shared channels” (Behar and Hoffmann 2010).

Whenever we imagine a biological process aimed at achieving some particular result, we need to keep in mind that every element in that process is likely playing a role in an indeterminate number of other significant, and seemingly goal-directed, activities. The mystery in all this does not lie primarily in isolated “mechanisms” of interaction. The question, rather, is why things don’t fall completely apart.

In sum: messages do not fly back and forth as metaphors or disembodied abstractions. They move as dynamically sculpted currents of force and energy. Their meanings are mimed or gestured — neither translated into, nor reduced to, a kind of expressionless Morse code, nor impelled along precisely incised channels like computer instructions. And what holds them together amid the ceaseless flows and crosstalk and molecular transformation is the unity of meaning that is the whole organism.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 9, 2025

In the conventional machine model of the organism, signaling pathways were straightforward, with a clear-cut input at the start of the pathway leading to an equally clear-cut output at the end. Not so today, as a team of molecular biologists at the Free University of Brussels found out when they looked at how these pathways interact or “crosstalk” with each other. Tabulating the cross-signalings between just four such pathways yielded what they called a “horror graph,” and quickly it began to look as though “everything does everything to everything” (Dumont et al. 2001).

Perhaps a horror graph is what a flow of contextualized meaning looks like when we are expecting one-dimensional, reduced, carefully coded, mathematically analyzable information. By contrast, some researchers now imagine (if rather fancifully) the “collaborative” reality of signaling pathways “as a table around which decision-makers debate a question and respond collectively to information put to them” (Levy et al. 2010).

Even considering a single membrane receptor bound by a hormonal or other signal, you can find yourself looking, conservatively, at some two billion possible states, depending on how that receptor is modified by its interactions with other molecules. Despite previous belief, there is no simple binary rule distinguishing deactivated receptors from those activated by some combination of signals in a particular context. “The activated receptor looks less like a machine and more like a ... probability cloud of an almost infinite number of possible states, each of which may differ in its biological activity” (Mayer et al. 2009).

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 2, 2025

If there was any place where biologists expected a causal explanation of the organism to emerge clearly, it was in the study of Caenorhabditis elegans, a one-millimeter-long, transparent roundworm whose private molecular and cellular affairs may have been more exhaustively exposed than those of any other organism. The adult hermaphrodite has exactly 959 cells, each precisely identified as to origin and type: for example, 302 cells belong to the nervous system. The developmental fate of every somatic cell, from egg to adult, had already been mapped out by 1980. But this mapping and the associated molecular studies did not produce the expected explanations.

Sydney Brenner — who received a 2002 Nobel prize for his work on C. elegans — acknowledged that development “is not a neat, sequential process ... It’s everything going on at the same time.” Even regarding the carefully mapped cell lineages of this “simple” roundworm, “there is hardly a shorter way of giving a rule for what goes on than just describing what there is.” In other words, the only “rule” for the development of this worm is the entire developmental description of it.

When critics suggested he had not really come to an understanding of the worm, but had “only” described it, Brenner wisely responded, “I’m not sure that there necessarily is anything more to understand than what it is.” British science writer Roger Lewin quoted this remark by Brenner in an article titled, “Why Is Development So Illogical?” with the subtitle, “The more biologists learn about development, the less it appears that organisms are assembled by neat, sequential processes; we should not be surprised”. Actually, it’s not even true that organisms are assembled from pre-existing parts. They grow from within through processes of self-transformation, not mechanical assembly.

The difficulties of linear, causal explanation encountered by the C. elegans researchers were not accidental. 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 profoundly, in ever greater detail, so as to yield up its unique and unrepeatable story.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 26, 2025

What we’re gaining from all this research [into circadian rhythms] is a wonderful portrait of the organism as a rhythmic being. Investigators have not found controlling mechanisms that single-handedly establish or govern the circadian rhythms of the organism, but rather are discovering how those rhythms come to expression at every level and in every precinct of the organism — perhaps more centrally here and more peripherally there, but altogether in a single, organism-wide harmony that is also linked to environmental rhythms. There is no sensible way, as a scientist, to speak of particular mechanisms that explain this harmony. Instead, every isolated “mechanism” is found to be a reflection of the harmony, and we thereby gain further, detailed understanding of how the whole organism functions as a being in time.

Is any of this a surprise? Should we expect, say, that a “master regulator” of digestion exists? Would it be the stomach? The small intestine? The large intestine? The pancreas? The liver and gall bladder? The metabolism taking place in every cell? The brain that sends various coordinating nervous signals to different organs? The mouth that initiates everything? We would certainly look more to the stomach than, say, to the heart, but the fact remains that the organism as a whole is the closest thing we have to a “master regulator.” What we see in the separate, “mechanistic” clocks and regulators of circadian rhythms is simply the functioning of those rhythms in the most recognizable or most focal places. But they merely put on more obvious display the rhythmic functioning of the entire body.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 19, 2025

Pick any topic in biology and you will encounter an egregious failure to “tie down” biological causes. Clockwork mechanisms are nowhere to be found — a fact that becomes particularly poignant in the investigation of “biological clocks” such as the circadian (daily) rhythms that figure so prominently in human and other forms of life. Biologists, of course, set out to identify the “master clock mechanism” that was presumed to “control” these rhythms, and, yes, they found a rhythmic feedback loop involving genes and transcription factors in a certain area of the brain that seemed the perfect candidate. It quickly came to be viewed as the decisive governor of circadian rhythms in the body:

“In mammals, the anatomical structure in the brain that governs circadian rhythms is a small area consisting of approximately 15,000 neurons localized in the anterior hypothalamus, called the suprachiasmatic nucleus (SCN). This ‘central pacemaker’ in the SCN receives signals from the environment and, in turn, coordinates the oscillating activity of peripheral clocks, which are located in almost all tissues (Berger and Sassone-Corsi 2016).”

And yet (as this statement already indicates), ongoing research has revealed distinct “clocks” in different mammalian organs and tissues, and indeed in every cell. These “clocks,” it turns out, are not merely on the receiving end of a central, governing coordination, but rather are themselves participants in that coordination, and also, it now seems, are interwoven with just about all aspects of the organism’s physiology — metabolism, reproduction, cell growth and differentiation, immune responses, central nervous system functions ...

In each of these areas the quest for causes and master controllers leads to the usual perplexity about who’s doing what to whom. For example: “Although metabolism is thought to be primarily downstream of the cellular clock, numerous studies provide evidence that metabolic cycles can operate independently from or even influence circadian rhythms” (Kumar and Takahashi 2010). At the molecular level, one research team remarks that the enzymatic function of a certain clock protein “may be controlled by changing cell energy levels, or conversely, could regulate them” (Doi et al. 2006). In general: “It seems that connections between the circadian clock and most (if not all) physiological processes are bidirectional” (Yang 2010).

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 12, 2025

What we see once we start following out all the interactions at a molecular level, is not some mechanism dictating the fate or controlling an activity of the organism. Rather, we observe an organism-wide, narrative coherence — a functional, end-directed, story-like coherence that we cannot elucidate in terms of strictly physical interactions that make no reference to the meaning of events. Only so far as they are caught up in and sensitive to this functional story do the individual molecular players find their proper roles.

The misrepresentation of this organic and rational coherence in favor of supposed controlling mechanisms is not an innocent inattention to language; it is a fundamental misrepresentation of reality at the central point where we are challenged to understand the character of living things.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 28, 2025

In the era of molecular biology the expectation was that our rapidly growing powers of minute analysis would bring a full causal understanding of life. 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.

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 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 causal significance of their own. 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 biological researchers (we will focus on molecular biology) to offer embarrassingly incoherent explanations.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 21, 2025

We have arrived at a simple truth: the biologist’s sense of threatening mystery (or “mysticism”) when confronted with the intentional, purposive, and meaningfully expressive aspects of an organism’s life typically arises from the unshakable conviction that there needs to be an essentially inanimate explanation of animate beings. As an insistence, this is mere dogma. The requirement of science is that we open-mindedly describe every aspect of every phenomenon in its own terms. It does not require a lot of reflection to see, for example, that organic processes of development and self-realization do not have strictly physical descriptions. Inanimate objects do not persistently and directively engage in efforts to develop and realize themselves.

But this does not mean we are headed toward some kind of mystical conception of the organism. As we will see increasingly in coming chapters, the different aspects of the organism (including the more-than-physical — ideal or archetypal — aspects) require only what all science requires: description in terms that are faithful to the phenomena themselves. To describe the marvelous living coherence of molecular processes in an organism’s cells is no more mystical than to describe the very different but just as marvelous coherence of the laws of physics. It merely requires a willingness to embrace what we see, rather than recoil from it.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 14, 2025

It would be strange if the initially surprising discovery of living and coherent order in the cell persisted as a problem; another name for the discovery of order is, after all, “science”. I suppose that the unexpectedness of at least some forms of order has been part of the scientist’s experience all along. But when we live with it long enough, the unexpected becomes expected. In the end, it simply further strengthens our inalienable sense that we live in a world of coherent meaning.

But this happy ending will not be fully realized in biology until we acknowledge that there are many different ways phenomena can add up to a coherent picture in this cosmos of ours. A sloth is not a lion (Holdrege 2021), ice is not water vapor, and an animal is not a rock. Reductively forcing one sort of coherence into the mold of another by violence is never the answer.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 7, 2025

Paul Weiss (Chapter 6, “Context: Dare We Call It Holism?”) in addressing the larger coherence of the “heaving and churning” cell, did not merely stare, transfixed, at the problem of order within “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” ...

I suspect that, with continuing observation and faithful description, the “problem” of order and wisdom (thought-fullness) in cells will more and more fade into nothingness. It is indeed only the effort at reductionism that creates the problem. Cease that effort, and all we have left is the routine scientific task of accurate conceptualization and description. Physicists, after arriving at concepts of law, force, field, and all the rest, do not often complain, “Those are not material things; how can we possibly deal with them?” They simply continue investigating, describing, and thinking until an overall, coherent picture is formed. That is what making sense of the world means.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 31, 2025

Efforts at reductionism — efforts to reduce biological meaning to the terms of physical lawfulness — never make any progress. Yes, we have dramatically extended our tracing of physical lawfulness in the cell. But, for all the flood of physical data today, the needs, interests, tasks, intentions, and meanings of the organism never become less necessary for structuring our understanding.

What actually tends to happen, however, is not particularly helpful. Once the clarification of physically lawful processes reaches a certain point, the biologist’s deeply ingrained habit of ignoring all questions of meaning leads to the conviction that nothing remains to be understood. And this occurs despite the continuing use, “right under the biologist’s nose”, of a vocabulary of life and meaning well designed to bridge (and conceal) the gap between lawfulness and adequate understanding. (See, for example, the discussion in Chapter 2 of the different vocabularies applied to living and dead dogs — or see below.)

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 24, 2025

Is the entire matter really so vexing? The mystery of the unexpected coherence that molecular biologists confront, for example, in RNA splicing and DNA damage repair is, from a perfectly reasonable point of view, neither a mystery nor unexpected. The problem arises only at the moment when we refuse to accept life as a foundational fact of the universe and unreasonably demand that an organism’s living performances be explained in an inanimate manner. Then, and only then, do we find it difficult to make sense of things.

But, fortunately, researchers never can wholly resist the urge to make good sense of things. They seek an understanding of whatever issue they are working on by looking for the coherence and meaning of events. This is necessary in order to provide at least some minimal context for their physical analyses. And it is so natural that it easily occurs without any conscious effort. What then happens, and what so badly distorts the practice of biology, is that this recognized coherence and meaning must be squeezed out of any ultimate explanation, which is allowed to proceed solely in terms of physics and chemistry. The result is rarely pretty.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 17, 2025

The University of Massachusetts geneticist, Job Dekker, once asked, “How do cells ensure that genes only respond to the right regulatory elements while ignoring the hundreds of thousands of others?” It’s a good and obvious question. An editor of Science amplified it this way: “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”. A given cell, he noted, may make more than 10,000 different proteins under any particular set of conditions, and it typically contains more than a billion individual protein molecules at any one time. “Somehow, a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”.

It would help if we could get clear about the fact that there are two profound, and profoundly different, descriptive challenges posed by a cell’s impressively coherent activities. One has to do with the underlying physical and chemical processes. The other concerns the coordination of those processes as an expression of the organism’s needs and interests, intentions and meanings — its entire qualitative way of being. Severe confusions arise when we say that science must concern itself only with the first challenge, while assuming that the second one, if it can even legitimately be referred to, is automatically taken care of by our answer to the first.

Biologists, in their own fashion, do notice the second question. They notice it in their putting of questions to themselves (“How does the cell do X?”), where the question generally refers to a meaningful accomplishment. They notice it in their acknowledgment that organisms behave and undertake tasks, something solar systems and lake-bottom sediments never do. And they notice it when they grant that every organism acts as if it were a purposive being, even if they immediately feel compelled to explain away this purposiveness by appealing to natural selection (Chapters 2, “The Organism’s Story”, and 18, “Teleology and Evolution”). What is not so often noticed is the fact that an organism’s purposive way of being and its pursuit of its own interests require a distinctive manner of understanding that cannot be assimilated to our understanding of inanimate objects.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 10, 2025

The information we conceive as statically encoded in DNA is a kind of bland abstraction from the living intelligence at work in cellular processes. When we occupy ourselves one-sidedly with genocentric information, it is (to employ a rough analogy) as if we elevated a notebook containing selected words, phrases, definitions, and grammatical hints to a pinnacle high above Moby Dick or Faust or War and Peace, worshipping the former as “information” while ignoring the informed and meaningful activity through which inert words and phrases are woven into soul-stirring tales.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 3, 2025

Damage to DNA is not, in the most direct sense, what proves lethal about radiation. The primary issue, instead, is damage to proteins. As long as its proteins remain functional, a cell can reassemble even a badly fractured genome; but with damaged proteins, a cell is done for, with or without an intact genome.

D. radiodurans employs a number of strategies for preserving its rather commonplace “proteome”, or total inventory of proteins. These strategies include (1) preventing the oxidative damage that results from radiation, a goal it achieves in good part by means of an especially rich supply of antioxidants; (2) eliminating, before they can cause mischief, any proteins that do get damaged, while recycling their constituents; (3) scavenging amino acids and peptides (protein constituents) from the local environment, a capability that, together with the recycling, supports (4) newly synthesizing any proteins that need replenishing.

The proteome thus preserved is then able to go about the task of reconstructing a shattered genome — a task whose complexity at the molecular level is stunning. (Many a bright but befuddled graduate student has twisted his imagination into knots while trying to picture the various textbook processes of DNA damage repair in human cells.) Nevertheless, the task is accomplished in the cells of all organisms. What distinguishes D. radiodurans is its ability to carry out this task to an exceptional degree by maintaining its store of proteins intact under extreme duress.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 24, 2025

A dose of ionizing radiation equal to 10 grays (a measure of absorbed radiation) is lethal to the human body. Most bacteria cannot survive 200 grays. But then there is the bacterium known as Deinococcus radiodurans: it can endure over 17,000 grays and get along just fine. Never mind that its genome is thoroughly shattered by the assault.

Here’s what happens. Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the double helix. The familiar bacterium, E. coli, not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans, by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into many hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting ask, to say the least.

Deinococcus radiodurans is one of a small class of single-celled organisms with extreme radiation tolerance. Actually, it tolerates various other extreme conditions as well — some of which, such as dessication, likewise reduce its DNA to genomic shards. It can, for example, survive in a waterless desert for years until moistened again — which could happen, for example, when winds lift it in a cloud of dust from the Sahara, high into the atmosphere (where it is exposed to damaging ultraviolet radiation 100 to 1000 times that on earth’s surface), and across the Atlantic ocean to the South American jungles. D. radiodurans can be found on Antarctic ice, on dry frozen marble, and in the farthest depths of the sea.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 17, 2025

The discovery of RNA splicing in the late 1970s was one of the transforming moments in the history of molecular biology. To put it in informal terms: the cleanly autocratic mastery of DNA gave way to massive presumption by various scruffy elements of the cellular “rabble”. The idea had originally been that a molecule of messenger RNA (mRNA) was produced as a direct image of the “instructions” in a protein-coding gene and was then exported from the cell nucleus to the cytoplasm. There it yielded passively to translation, a process whereby a protein was supposedly produced according to the exact specifications of the “genetic code” previously copied from DNA into the mRNA.

Our growing knowledge of RNA splicing has, together with many other developments in molecular biology, exploded just about every aspect of this picture. We now know that, via an elaborately orchestrated improvisational drama, many so-called epigenetic elements in the cell (Chapters 7, “Epigenetics: A Brief Introduction”, and 14, “How Our Genes Come to Expression”) converge to decide what use will be made of any particular gene.

In particular, the cell has innumerable ways to obtain and sculpt its proteins. RNA splicing is just one of these — a massive reconfiguration process whereby a cell decides which portions of an initially produced (precursor) RNA to cast aside for other uses, and which ones to “splice” together into a mature mRNA. As we have come to expect by now, these choices are strongly context-dependent, with different protein variants being produced in different kinds of cell or tissue, or under different cellular conditions.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 10, 2025

We hear from the authors of one paper that the epigenome involves a “re-wiring of transcription factor circuits”, as if there were some fixed and standard genetic wiring scheme waiting to be rewired. But — as if biology as a discipline were somehow “of two minds” about such things — the authors of this paper healthily refer to the rewiring as “context-dependent” and “dynamic”. So the terminology appears to be impossibly conflicted. If in fact the governing context is always to some degree fluid, dynamic, and shifting, where do we ever see anything remotely analogous to wires constraining all the relevant molecules to go where they need to go, and to do so in the right time, in the right quantities, and with the right molecular partners?

The picture of a wired cell may sound conveniently causal, but it makes no sense. Biologists are sooner or later going to have to decide which half of their descriptive language they are going to side with — the “wired” half or the “dynamic and context-dependent” half. Meanwhile, those of us trying to decipher what “epigenetics” really means can usefully remind ourselves that the deeper issue has to do with the overall terms of the description ultimately decided upon.

Nothing is merely genetic. Every so-called genetic activity is an expression of its entire context, and therefore is altogether epigenetic. Genetics cannot be abstracted from the rest of the organism. So we can safely say, “All genetics is epigenetics”.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 3, 2025

Rather than think of epigenetics as the application of incidental “marks” on chromosomes, we could conceive it more realistically as encompassing all the ways DNA is caught up in the activity of its larger context and brought into service of the whole. I say “more realistically” because there is, in fact — as two molecular biologists have phrased it in the journal Nature — “an avalanche of biochemical evidence revealing a complex and versatile array of molecular mechanisms that regulate gene expression without changing DNA sequences”.

In other words, what genes mean to the organism is not merely a matter of the DNA sequence or a “genetic code”. It is more a question of the many different ways an organism can employ its genes.

So the word epigenetics may usefully remind us that what is “on top of” DNA is nothing less than the functioning organism as a whole. But a word that threatens to encompass just about everything begins to lose its value as a special term. And this in turn suggests that we could just as well retire the word “epigenetics” and get on with describing how organisms carry out their organically integrated lives — express their own character — in part by “reconceiving” their genes in terms of that character.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 27, 2025

The Human Genome Project and its successors surprised many by revealing an unexpectedly low number of human genes relative to many other organisms — roughly the same number, for example, as in the simple, one-millimeter-long, transparent roundworm, Caenorhabditis elegans. Many began to ask: If genes really do account for the organism in all its complexity, how can it be that a primitive worm boasts as many genes as we do? “As far as protein-coding genes are concerned”, wrote Ulrich Technau, a developmental biologist from the University of Vienna, “the repertoire of a sea anemone ... is almost as complex as that of a human”.

A further revelation only compounded the difficulty: our own genome was found to have a great deal in common with that of many animals. It was reported, for example, that we share about 98.5% of our genome with chimpanzees. A good deal of verbal hand-wringing and chest-beating ensued. How could we hold our heads up with high-browed, post-simian dignity when, as the New Scientist reported in 2003, “chimps are human”? If the DNA of the two species is more or less the same, and if, as nearly everyone seemed to believe, DNA is destiny, what remained to make us special? Such was the fretting on the human side, anyway. To be truthful, the chimps didn’t seem much interested.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 20, 2025

The ordered developmental stream of a mammal includes generation of the hundreds of different cell types in its body. 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, contextual 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. In the case of each cell type, 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 (”The Sensitive, Dynamic Cell”). It must also bring about and orchestrate the elaborate performances of its chromosomes we saw in Chapter 3 (”What Brings Our Genome Alive?”) — performances that are unique to each 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. Only when we recognize that genes participate in a living whole can we find an answer to Lillie’s challenge “to explain how an unchanging complex can direct the course of an ordered developmental stream”. The answer — so we will find — is that there is no unchanging complex. Genes, like all parts of a cell or organism, gain their identities and meanings only within the context of innumerable, interpenetrating, living narratives expressing diverse physiological characters.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 13, 2025

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 (which is impossible) 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 in the human body can differ from another as much as an amoeba differs from a paramecium.

And yet, 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”.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 6, 2025

So long as we are content to look only at the sum of physical causes, we miss the organism’s narrative of its life. The same would be true if we read a novel while attending only to the physical causes underlying all the events. If we then said that the unbroken connection of these causes proves the absence of the narrative — the absence of the meaningful living activity and the ideas that the story is actually about — then we would merely be asserting our fierce determination to see nothing but physical causes.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 23, 2024

It is impossible to fit the idea of context-dependence into the biologist’s usual style of causal explanation. Where do we locate a causal arrow pointing from the contextual whole to a particular part? The arrow needs to originate everywhere. The fact is, we cannot locate it in space at all. We recognize it, not as a link in a linear causal chain, but rather in the way we recognize a possible implication of a broad understanding. When biologists speak of context-dependence, they are speaking of a play of ideas. It is one of the ways they import the organism’s interior into their thinking “under the radar”.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 16, 2024

Cruise missiles — and, for that matter, kitchen blenders, electric hand drills, and textile looms — consist of materials we articulate together for use as tools in accomplishing our own tasks. The “top-down” ideas guiding assembly are ours; they do not come to expression through holistically active developmental processes in which all the growing parts participate. Our ideas are not native to the collection of parts. Our ideas are not active at the very root of material manifestation in the way that physical laws and biological principles are inseparable from the substance in which they work. We merely rearrange, in an external manner, materials already given to us. We cannot penetrate to the inherent lawfulness of physical materials with the force of our wills, except in moving our own bodies. (And even there, the doing is currently inaccessible to our understanding.)

When we want to explain the operation of a kitchen blender (or a missile), we require no reference to its intentions, or to any striving toward a future state. When we do make such reference, we are really talking about our own purposes in structuring the device for employment in service of our interests. There is no more an immanent end-directness in a cruise missile than in a blender. Both devices are simply put together in accordance with our purposes.

By contrast, a developing organism’s living “trajectory” results from its growing directionally into its mature functioning. We never see a designing power or force that assembles an organism from pre-existing parts in anything like the way we build tools and machines. Organisms are not designed and tinkered with from without, but rather are enlivened from within. The wisdom we find at play in them is intrinsic; it is their own in a sense wholly untrue of the external intelligence with which our mechanical inventions are structured.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 9, 2024

[On likening organisms to cybernetic machines:] Surely it is difficult to find much commonality between the transformation of a single zygotic cell into a mature eagle, on one hand, and the “development” of a cruise missile, on the other. If, before venturing upon its flight, the missile were to “mature” from a single transistor (or circuit board) into the totality of a functioning, deadly efficient vehicle; and if, during its flight, all its physical constituents were metabolizing and metamorphosing as an essential part of the overall operation; and if, instead of a single goal, there were a massively interwoven and nearly infinite collection of goals governing each of the missile’s “organs”, each “cell”, the entire missile as a whole, and all its environmental relations — well, as you can see, taking the comparison with living beings seriously could get silly fast.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 2, 2024

In the summer of 2011 a team of researchers at Tufts University produced a startling, time-lapse video of a developing tadpole embryo. Due to the use of special dyes reporting the electric potentials across cell membranes, areas of the embryonic surface successively lit up brightly and then went dark. For a few seconds of the time-lapse film (representing the events of several hours), the featureless part of the embryo that would eventually become the animal’s head flashed the image of a tadpole face.

But no actual face had yet developed. Nevertheless, the electrical pattern did “signal” where key elements of the tadpole’s face, such as its eyes, would eventually appear. Regional changes in electric potential, these scientists concluded, “regulate expression of genes involved in craniofacial development”.

According to Michael Levin, head of the laboratory where the tadpole research was performed, “Ion flows and the resulting [membrane voltage] changes are components of long-range conversations that orchestrate cellular activities during embryonic development, regeneration, and … tumor suppression”. He adds that “bioelectric cues are increasingly being found to be an important regulator of cell behavior”, controlling the proliferation and death of cells, their migration and orientation, and their differentiation into different cell types ...

Levin’s team quickly went on to manipulate the distribution of membrane voltages in developing embryos so as to provoke the generation of eyes in decidedly unexpected places — for example, on the back and tail, and even in the gut, of a frog embryo. The results were fragmentary and rather chaotic — the ectopic (“out of place”) eyes were partial or deformed — but the result was nevertheless as startling as it was monstrous.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 25, 2024

[Regarding various healing processes:] Of course, researchers have traced all sorts of molecular syntheses, movements, and interactions. We can be sure that everything in the entire picture proceeds lawfully, and in this very constricted sense every local event looks necessary. And yet we can find no combination of physical laws capable of “enforcing” the proper form of all the different parts of the body of this or that animal. In the case of a wound, there is no purely physical necessity to achieve the “proper” form in the face of wildly variable conditions.

In other words, the mere fact of physical lawfulness does not explain the coordination of events along an extended timeline in the narrative of healing, from infliction of the wound to the final restoration of normalcy. Nor does it explain the narrative of RNA splicing, from the occurrence of an RNA molecule in need of reconfiguration, to the final product of those scores or hundreds of participating molecular “surgeons”. We can watch the molecules performing in a way that gives expression to the overall sense, or meaning, of the activity, but we do not have even the barest beginnings of a purely physical explanation for their commitment to that meaning.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 18, 2024

Here is a description offered by English biologist Brian Ford:

“Surgery is war. It is impossible to envisage the sheer complexity of what happens within a surgical wound. It is a microscopical scene of devastation. Muscle cells have been crudely crushed, nerves ripped asunder; the scalpel blade has slashed and separated close communities of tissues, rupturing long-established networks of blood vessels. After the operation, broken and cut tissues are crushed together by the surgeon’s crude clamps. There is no circulation of blood or lymph across the suture.

“Yet within seconds of the assault, the single cells are stirred into action. They use unimaginable senses to detect what has happened and start to respond. Stem cells specialize to become the spiky-looking cells of the stratum spinosum [one of the lower layers of the epidermis]; the shattered capillaries are meticulously repaired, new cells form layers of smooth muscle in the blood-vessel walls and neat endothelium; nerve fibres extend towards the site of the suture to restore the tactile senses …

“These phenomena require individual cells to work out what they need to do. And the ingenious restoration of the blood-vessel network reveals that there is an over-arching sense of the structure of the whole area in which this remarkable repair takes place. So too does the restoration of the skin. Cells that carry out the repair are subtly coordinated so that the skin surface, the contour of which they cannot surely detect, is restored in a form that is close to perfect.”

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 11, 2024

During development, the lens of an amphibian eye derives from the outer layer of cells in the developing head, at the point where an outgrowth of the brain comes into contact with the epidermal cells. But if an already developed lens is removed from one of these animals, something truly remarkable happens: a new lens forms from the upper edge of the iris, a structure that has nothing to do with lens formation in normal development. The procedure runs like this (Gilbert 1994, p. 40):

1. Cells from the upper part of the iris — cells that have already reached an endpoint of differentiation — begin multiplying;
2. these multiplying cells then proceed to dedifferentiate — that is, to lose their specialized character, including the pigmentation that gives the iris its color;
3. the newly multiplied, iris-derived cells migrate so as to form a globe of dedifferentiated tissue in the proper location for a lens; and finally,
4. they start producing the differentiated products of lens cells, including crystallin proteins, and are thereby transformed into transparent lens cells — all in the nuanced spatial pattern required for the formation of a proper lens.

And so, lacking the usual resources and the usual context for formation of a lens, the animal follows an altogether novel path toward the restoration of normal form and function.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 28, 2024

[Regarding cascades of gene expression, such as the sequential expression of the various genes that have been said to “determine” left-right asymmetry of the vertebrate body:] The normal expectation would be that if one blocks or changes the expression of earlier genes in the sequence, the disorder should accumulate and be magnified, perhaps explosively, in downstream gene expression, since proper cues for the later steps are missing. But

Surprisingly, this is not actually what occurs: each subsequent step has fewer errors than the previous step, suggesting that the classic linear pathway picture is importantly incomplete. Embryos recognize transcriptional deviations from the correct pattern and repair them over time … The existence of corrective pathways in embryogenesis and regeneration raises profound questions about the nearly ubiquitous stories our textbooks and “models” tell about the molecular explanations for specific events (Levin 2020).

All this may remind us of E. S. Russell’s remark that in biology “the end-state is more constant than the method of reaching it”. We also see here the principle that cell biologist Paul Weiss enunciated so clearly at mid-twentieth century, when he pointed out that the whole “is infinitely less variant from moment to moment than are the momentary activities of its parts”. At the lowest level of biological activity, molecules in the watery medium of a cell have degrees of freedom (possibilities of movement and interaction) that would spell utter chaos at higher levels if it were not for the fact that the lower-level activity is “disciplined” from above.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 21, 2024

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 how biologists commonly try to learn about life by severely disrupting it. But the current point 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.

(from Chapter 10, “What is the Problem of Form?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 14, 2024

When a cell enters into mitosis, just about every detail of its physiology and chemistry takes on an altered meaning in light of the changing narrative context. Everything is now heading toward a different outcome. Molecules that had been participating in one set of interactions (and could easily still do so in purely physical terms) now enter into very different intermolecular relations. Similarly with a cell experiencing heat shock, oxygen deprivation or other stress, a cell coming into contact with new neighbors, or a cell proceeding along a path of embryonic differentiation.

Certainly we can still identify unambiguous causes in the organism. It is always possible to narrow the conditions of our experiments so severely that a consistent “causal arrow” for a particular interaction emerges under those conditions. But the whole point of life’s adaptability is to seek (or help create) altered conditions according to present needs and interests. This is why there can be no fixed syntax, no mechanical constancy of relations among the parts. The organism is forever abandoning the coordinating principles of its old context in favor of a new and ever-changing meaning. Its story is always evolving.

The nature of causation in biology differs from the problem of causation in the physical sciences. Organisms manifest a fluid, integral, harmonizing sort of causation that is more like a play of the multi-dimensional reasons for things than a set of one-dimensional mechanical interactions. It is more like the rich interplay of meaning in an unfolding poem than a rigid syntax or logic.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 7, 2024

When a deer is grazing in a meadow, its glimpse of a vaguely canine form in the distance changes the meaning of everything from the flowers and grass the deer was eating, to its own internal digestive processes, to the expression of its genes. This happens, not because the distant form is exerting some strange physical force upon the deer, but because that form becomes part of a now suddenly shifted pattern of meaning.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 30, 2024

Think of a machine. Having conceived what we want it to do, we design it to be a closed system whose intended functioning is more or less immune to contextual interference. And we try to do much the same in many scientific demonstrations. For example, we can create a vacuum in a chamber, and then release a leaf from the top of the chamber. It falls like a stone.

Of course, leaves in nature often travel upward. But the experiment in the chamber enables us to observe the singular and lawful play of gravity, without any disturbing “interference” from the resistance or movement of air. We can then — and only then — say that gravity appears to make the leaf fall, just as the simple laws governing the gears and springs of a mechanical watch make the watch perform as a reliable keeper of time.

But when the biologist tries to see an animal in the same mechanistic light, as a closed system without interfering factors, the attempt fails miserably. This is because, for the animal, contextual interference is the whole point. As the meaning of its activity shifts from moment to moment, so, too, does the contextual significance of all the details of its life.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 23, 2024

Messages [within cells] are not physically discrete, and they do not fly back and forth as elements of a predefined cellular logic. They move as dynamically sculptured, interwoven patterns of force and energy. Their meanings are mimed or gestured — neither translated into, nor reduced to, a kind of expressionless Morse code, nor impelled along precisely incised channels like computer instructions. And what holds them together amid the ceaseless flow and crosstalk and molecular transformation of the cellular plasm is the unity of meaning that is the whole cell and whole organism ...

The powerful compulsion to identify decisive causes, even at the expense of painfully self-contradictory language, strongly suggests that a one-sided and unrealizable ideal of biological explanation is at work. Under its influence we aim to discover a physical lawfulness reflecting, above all, our experience with machines — a lawfulness of precise, unambiguous control, where one thing can be said, without unwelcome qualification, to make another thing happen.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 16, 2024

Signaling pathways help to maintain a coherence of meaning within and between cells. Take, for example, the work by a team of molecular biologists at the Free University of Brussels. They investigated how signaling pathways interact or “crosstalk” with each other. Tabulating the cross-signalings between just four such pathways yielded what they called a “horror graph”, and quickly it began to look as though “everything does everything to everything”, much like the way any given term in a meaningful text can modify the meanings of many other terms. Other researchers speak of a “collaborative” process that can be “pictured as a table around which decision-makers debate a question and respond collectively to information put to them”.

Even considering a single membrane receptor bound by a hormonal or other signal, you can find yourself looking, conservatively, at a billion possible states, depending on how that receptor is modified by its interactions with other molecules. Despite previous belief, there is no simple binary rule distinguishing deactivated receptors from those activated by some combination of signals in a particular context. “The activated receptor looks less like a machine and more like a … probability cloud of an almost infinite number of possible states, each of which may differ in its biological activity”.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 2, 2024

Should we expect, say, that a “master regulator” of digestion exists? Would it be the stomach? The small intestine? The large intestine? The pancreas? The liver and gall bladder? The metabolism taking place in every cell? The brain that sends various coordinating nervous signals to different organs? The mouth that initiates everything? We would certainly look more to the stomach than, say, to the heart, but the fact remains that the organism as a whole is the closest thing we have to a “master regulator”. What we see in the separate, “mechanistic” clocks and regulators of circadian rhythms is simply the functioning of those rhythms in the most recognizable or most focal places. But they merely put on more obvious display the rhythmic functioning of the entire body.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

August 12, 2024

What we’re gaining from all this research is a wonderful portrait of the organism as a rhythmic being. Investigators have not found controlling mechanisms that single-handedly establish or govern the circadian rhythms of the organism, but rather are discovering how those rhythms come to expression at every level and in every precinct of the organism — perhaps more centrally here and more peripherally there, but altogether in a single, organism-wide harmony that is also linked to environmental rhythms. There is no sensible way, as a scientist, to speak of particular mechanisms that explain this harmony. Instead, every isolated “mechanism” is found to be a reflection of the harmony, and we thereby gain further, detailed understanding of how the whole organism functions as a being in time.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

August 5, 2024

What we see, that is, once we start following out all the interactions at a molecular level, is not some mechanism dictating the fate or controlling an activity of the organism. Rather, we observe an organism-wide, narrative coherence — a functional, end-directed, story-like coherence that we cannot elucidate in terms of strictly physical interactions that make no reference to the meaning of events. Only so far as they are caught up in and sensitive to this functional story do the individual molecular players find their proper roles.

The misrepresentation of this organic and rational coherence in favor of supposed controlling mechanisms is not an innocent inattention to language; it is a fundamental misrepresentation of reality at the central point where we are challenged to understand the character of living things.

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 29, 2024

By now every biologist knows how regulatory processes extend outward without limit, connecting in one way or another with virtually every aspect of the cell. But this only underscores the undisciplined terminological confusion continuing to corrupt molecular biological description today. When key regulators are in turn regulated, and controllers have their fates underwritten or redirected by other players, where within the web of mutual interaction can we single out a master controller capable of dictating cellular fates? And if we can’t, what are reputable scientists doing when they claim to have identified such a controller, or, rather, various such controllers?

(from Chapter 9, “A Mess of Causes”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 22, 2024

I suspect that, with continuing observation and faithful description, the “problem” of order and wisdom (thought-fullness) in cells will more and more fade into nothingness. It is indeed only the effort at reductionism that creates the problem. Cease that effort, and all we have left is the routine scientific task of accurate conceptualization and description. Physicists, after arriving at concepts of law, force, field, and all the rest, do not often complain, “Those are not material things; how can we possibly deal with them?” They simply continue investigating, describing, and thinking until an overall, coherent picture is formed. That is what making sense of the world means.

It would be strange if the initially surprising discovery of living and coherent order in the cell persisted as a problem; another name for the discovery of order is, after all, “science”. I suppose that the unexpectedness of at least some form of order has been part of the scientist’s experience all along. But when we live with it long enough, the unexpected becomes expected. In the end, it simply further strengthens our inalienable sense that we live in a world of coherent meaning.

But this happy ending will not be fully realized in biology until we acknowledge that there are many different ways phenomena can add up to a coherent picture in this cosmos of ours. A sloth is not a lion, ice is not water vapor, and an animal is not a rock. Reductively forcing one sort of coherence into the mold of another by intellectual violence is never the answer.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 15, 2024

It would help if we could get clear about the fact that there are two profound, and profoundly different, descriptive challenges posed by a cell’s impressively coherent activities. One has to do with the underlying physical and chemical processes. The other concerns the coordination of those processes as an expression of the organism’s needs and interests, intentions and meanings — its entire qualitative way of being. Severe confusions arise when we say that science must concern itself only with the first challenge, while assuming that the second one, if it can even legitimately be referred to, is automatically taken care of by our answer to the first ...

Is the entire matter really so vexing? The mystery of the unexpected coherence that molecular biologists confront, for example, in RNA splicing and DNA damage repair is, from a perfectly reasonable point of view, neither a mystery nor unexpected. The problem arises only at the moment when we unreasonably demand that an organism’s living performances be explained in an inanimate manner. Then, and only then, do we find it difficult to make sense of things.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 8, 2024

The problem of what it actually means to say, “Molecules accomplish the work of splicing and DNA reconstruction” presents us with one of those vast blanks in scientific understanding that are easily papered over today with informational generalities and convenient pictures of tiny machines busily, and in a “mechanistically” respectable fashion, carrying on the work of a cellular factory.

We already heard about the essential problem from cell biologist Paul Weiss, who spoke about the many degrees of freedom possessed by the cell’s constituents in their watery medium, and about how these degrees of freedom are so remarkably constrained and disciplined toward the expression of biological order at higher levels of observation. The University of Massachusetts geneticist, Job Dekker, was apparently nodding toward the same problem when he asked: “How do cells ensure that genes only respond to the right regulatory elements while ignoring the hundreds of thousands of others?”

It’s a good and obvious question. An editor of Science amplified it this way: “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”. A given cell, he noted, may make more than 10,000 different proteins under any particular set of conditions, and it typically contains more than a billion individual protein molecules at any one time. “Somehow, a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 1, 2024

The work on Deinococcus radiodurans [a bacterium whose proteins can stitch back together a genome that has been shattered into countless fragments; see Quote of the Week immediately below] can remind us that the activity of an organism always reflects something like an immanent “sense of the whole”. Surely the protein molecules in this bacterium do not “know” what their “goal” should be in dealing with all those disordered snippets of DNA. But if the overall living context (Chapter 6) remains sufficiently intact, then the mysterious power of self-realization that we have been gently stalking in these several chapters — the power sustaining the coherent storyline of a life — continues to assert itself. The narrative, whatever its unexpected twists and turns, remains unbroken. If parts can be more fully constituted from their shattered fragments, it is because a functioning whole, with its innate intelligence, was already there.

The information we conceive as statically encoded in DNA is a kind of bland abstraction from the living intelligence at work in cellular processes. When we occupy ourselves one-sidedly with genocentric information, it is (to employ a rough analogy) as if we elevated a notebook containing selected words, phrases, definitions, and grammatical hints to a pinnacle high above Moby Dick or Faust or War and Peace, worshipping the former as “information” while ignoring the informed and meaningful activity through which inert words and phrases are woven into soul-stirring tales.

A phrase-book or dictionary can be an essential resource, but it is the organism (Deinococcus radiodurans in the case we have been considering) that uses the dictionary to weave its own story — and even reconstructs the dictionary when the pages fall into a disorganized heap on the floor.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 24, 2024

A dose of ionizing radiation equal to 10 grays (a measure of absorbed radiation) is lethal to the human body. Most bacteria cannot survive 200 grays. But then there is the bacterium known as Deinococcus radiodurans: it can endure over 17,000 grays and do quite well, thank you. Never mind that its genome is thoroughly shattered by the assault.

D. radiodurans employs a number of strategies for preserving its rather commonplace “proteome”, or total inventory of proteins. These strategies include (1) preventing the oxidative damage that results from radiation, a goal it achieves in good part by means of an especially rich supply of antioxidants; (2) eliminating, before they can cause mischief, any proteins that do get damaged, while recycling their constituents; (3) scavenging amino acids and peptides (protein constituents) from the local environment, a capability that, together with the recycling, supports (4) newly synthesizing any proteins that need replenishing.

According to Anita Krisko and Miroslav Radman, researchers at the Mediterranean Institute for Life Sciences who have been studying D. radiodurans, “biological responses to genomic insults depend primarily on the integrity of the proteome ... This conclusion is the consequence of the fact that dedicated proteins repair DNA, and not vice versa”. Moreover, “this paradigm is fundamental in its obviousness (no living cell can function correctly with an oxidized proteome) and, if it is true, must be universal, that is, hold also for human cells”.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 17, 2024

The idea of narrative coherence, like the related idea of a governing context, 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 as such, however combined, nowhere touch the idea of striving.

(from Chapter 8, “The Mystery of an Unexpected Coherence”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 10, 2024

We hear that the epigenome involves a “re-wiring of transcription factor circuits”, as if there were some fixed and standard genetic wiring scheme waiting to be rewired. But — as if biology as a discipline were somehow “of two minds” about such things — the authors of this remark healthily refer to the rewiring as “context-dependent” and “dynamic”. So the terminology appears to be impossibly conflicted. If in fact the governing context is always to some degree fluid, dynamic, and shifting, where do we ever see anything remotely analogous to wires constraining all the relevant molecules to go where they need to go, and to do so in the right time, in the right quantities, and with the right molecular partners?

The picture of a wired cell may sound conveniently causal, but it makes no sense. Biologists are sooner or later going to have to decide which half of their descriptive language they are going to side with. Meanwhile, those of us trying to decipher what “epigenetics” really means can usefully remind ourselves that the deeper issue has to do with the overall terms of the description ultimately decided upon, not with particular “epigenetic” insights that are too easily assimilated to traditional, machine-based understanding.

Nothing is merely genetic. Every so-called genetic activity is an expression of its entire context, and therefore is altogether epigenetic. Genetics cannot be abstracted from the rest of the organism. So we can safely say, “All genetics is epigenetics”.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 20, 2024

The word epigenetics may usefully remind us that what is “on top of” DNA is nothing less than the functioning organism as a whole. But a word that threatens to encompass just about everything begins to lose its value as a special term. And this in turn suggests that we could just as well retire the word “epigenetics” and get on with describing how organisms carry out their organically integrated lives — express their own character — in part by constraining their genes to serve that character ...

Genes as self-sufficient or definitive First Causes simply don’t exist. They never did have a reasonable place in our conceptualization of living beings — something that early twentieth-century critics of gene theory clearly saw (Russell 1930). Every organic process, including every genetic process, is an expression of the life of the whole cell and whole organism. In other words, the only genetics we have is epigenetics.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 13, 2024

The Human Genome Project and its successors surprised many by revealing an unexpectedly low number of human genes relative to many other organisms — roughly the same number, for example, as in the simple, one-millimeter-long, transparent roundworm, Caenorhabditis elegans. Many began to ask: If genes really do account for the organism in all its complexity, how can it be that a primitive worm boasts as many genes as we do? "As far as protein-coding genes are concerned", wrote Ulrich Technau, a developmental biologist from the University of Vienna, "the repertoire of a sea anemone … is almost as complex as that of a human"

A further revelation only compounded the difficulty: our own genome was found to have a great deal in common with that of many animals. According to the usual way of measuring things, we were said, for example, to share about 98.5% of our genome with chimpanzees. A good deal of verbal hand-wringing and chest-beating ensued. How could we hold our heads up with high-browed, post-simian dignity when, as the New Scientist reported in 2003, “chimps are human”? If the DNA of the two species is more or less the same, and if, as nearly everyone seemed to believe, DNA is destiny, what remained to make us special? Such was the fretting on the human side, anyway. To be truthful, the chimps didn’t seem much interested.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 6, 2024

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 the hundreds of radically distinct ways of living exemplied by the many and varied cell types in our bodies? If the supposed blueprint in our genome is compatible with cell types as different from each other as remotely related species, do we have compelling grounds for thinking that this genome single-handedly determines any one type of cell, or organ, let alone all of them together?

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 29, 2024

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 (which is impossible) 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 in the human body 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”.

(from Chapter 7, “Epigenetics: A Brief Introduction”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 15, 2024

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).

Not surprisingly, then, the biologist finds herself directly invoking the language of meaning in terms such as message, information, communication, and signal. But, again, she usually tries to do so in a mathematized, de-meaned manner intended to conceal the inwardness of the organism. Yet her recourse to the ubiquitous idea of context is a dead giveaway: if the word does not signify an ideational, aesthetic, and directive coherence, it refers to nothing living at all. Things just “being there” without expressing an active ideational unity — things without a role in a story that matters — do not make a living context.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 8, 2024

Let’s not forget: when we say that what happens in a cell is “context-dependent”, we are talking about a watery expanse populated by untold billions of molecules in unsurveyable variety. The need is for just the right combinations of molecules to do just the right things “in the moment” — and to do them in light of the overall state of the entire cell within its particular tissue. Is this cell just now committing itself to cellular division? Then what these molecules here and those molecules over there must do is now being radically redefined. Their new “assignments” depend not only on their location in the cell, but also on their necessary functional participation in lengthy, complex, temporal sequences of interaction that require the choreographing of countless other molecules as well.

Something is always going on contextually, and all the molecular interactions, taken together, must reflect whatever that something happens to be — must reflect the meaning of the encompassing narrative.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 1, 2024

Curiously, “holism” has almost become a dirty word in biology. It commonly signifies loose thinking, vagueness, obscurantism, and perhaps even an unfortunate tendency toward mysticism. I say “curiously” because the fact is that biologists speak incessantly about holism. You might almost think they were, in recent years, becoming fanatical about it. It’s just that they prefer to honor holism under the more acceptable slogan, “context matters”. This latter idea occurs like a mantra in the contemporary technical literature, so that it would be hard to find any physiological or behavioral process that is not routinely (and rightly) said to be “context-dependent” or “context-specific”.

Strangely, despite their almost universal employment of the pregnant term “context”, biologists rarely if ever bother to define it or to examine the meanings implicit in their use of it. Intentionally or otherwise, this protects them from an unwelcome meaning. For the word can hardly mean anything at all if it is not a close synonym for “larger whole”. The frequent appeal to context as a decisive determining factor, then, looks rather like an under-the-table invocation of the unmentionable concept of holism. It allows biologists to import the seemingly inescapable idea of the causal whole into their descriptions and theorizing, while outwardly pursuing a style of explanation that pretends to disdain holism in favor of purely physical analysis into parts.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 25, 2024

[Amid the “drowning thermal noise” of the cell] it’s as if there were an active, coordinating agency subsuming all the part-processes and disciplining their separate variabilities so that they remain informed by, and caught up in, the greater unity. The coordination, the ordering, the continual overcoming of otherwise disordering impacts from the environment so as to retain for the whole a particular character or organized way of being, expressively unique and different from other creatures — this is the “more” of the organism that cannot be had from the mere summing of discrete, causal parts.

So the center holds, and this ordering center — this whole that is more than the sum of its parts — cannot itself be just one or some of those parts it is holding together. When the organism dies, the parts are all still there, but the whole is not.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 4, 2024

[Regarding the preeminent cell biologist, Paul Weiss, whose work extended from the 1920s into the 1970s, when he was awarded the National Medal of Science by President Jimmy Carter:] As a life-long observer of cells and tissues, Weiss pointed out something obvious, simple, and yet revolutionary for today’s biology. 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”.

That is, despite the countless processes going on in the “heaving and churning” interior of the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes come together in a larger unity. The behavior of the whole “is infinitely less variant from moment to moment than are the momentary activities of its parts”.

We might say that a given type of cell (or tissue, or organ, or organism) insists upon maintaining its own recognizable identity with “unreasonable” tenacity, given the untethered freedom, in purely physical terms, of its molecular constituents as they make their way through a watery medium ... Tuning in to this basic picture — if we could really take it seriously — might change just about everything in biology.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 26, 2024

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 form of the limb as a whole is the ruling factor, redefining the parts according to the larger 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“.

A developing organism, Lewontin adds, “is like a language whose elements ... take unique meaning from their context”.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 19, 2024

[Researches studying damaged hair follicle niches where stem cells had been destroyed found that] “hair follicle stem cells are dispensable for regeneration, and that epithelial cells, which do not normally participate in hair growth, re-populate the lost stem-cell compartment and sustain hair regeneration” — provided, however, that “the overall integrity of the niche is maintained” ... Distant epithelial cells flow toward the damaged compartment and go through a transformation of identity enabling them to replace the lost cells. As the authors summarize it, “The overall structure and function of the tissue is maintained because cells are capable of adopting new fates as dictated by their new niche microenvironment”.

Clearly, the different elements of the hair follicle niche are not rigidly fixed entities. Rather, their changing forms and relationships are choreographed by the larger environment. So the goings-on in the hair follicle niche illustrate very well how the context helps to “decide” what sorts of elements it will have, how they will be formed and transformed, and how they will come into mutual relationship. Nothing could be further from the common picture of an organism being constructed, bottom-up, from an available collection of well-defined building blocks capable of determining outcomes. It appears, rather, that the desirable outcome determines the “building blocks”.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 12, 2024

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, and they interpenetrate one another, like the meanings of events in 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)”.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 5, 2024

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 possessing 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 (through division of existing cells) 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 in this way brings into being and orchestrates.

(from Chapter 6, “Context: Dare We Call It Holism?”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 29, 2024

DNA, RNA, and proteins are being reconceived as “biological soft matter”, subject to continually changing form so that molecular performances become more like improvised dances than automatic lock-and-key mechanical interactions. “Disordered” or “unstructured” sequences in proteins are now seen as decisive for coordinated activities throughout the cell, from gene regulation to signaling across membranes.

Still more dramatically, molecular biologists have in recent years become almost transfixed by the novel importance of phase transitions — for example, the forming and dissolving of distinctive, membraneless droplets within the fluid cell, whereby specialized and localized functional capacities are maintained despite the rapid passage of molecules in and out of the droplets.

And perhaps most important of all is the nascent recognition — which still hasn’t taken widespread hold in biology — that the amazing functional plasticity of water may be key to just about everything that goes on in a cell.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 22, 2024

The high era of molecular biology that followed upon discovery of “the” structure of the double helix was indeed the Age of Simplicity. We can be thankful that the feverish enchantment of fixed code and crystal is now giving way to an increasing recognition of movement, flow, dynamically flexible interaction, and the continual transfiguration of form — prime narrative elements in the organism’s story.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 15, 2024

Structural biologists Mark Gerstein and Michael Levitt have remarked, “When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background. We now know that the background in which these molecules exist — water — is just as important as they are”.

That was 25 years ago. More recently, Nature columnist Philip Ball has reflected on the situation this way: “Why should we place so much emphasis, for example, on determining crystal structures of proteins and relatively little on a deep understanding of the [water-related] forces ... that hold that structure together and that enable it to change and flex so that the molecule can do its job?”

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 1, 2024

Structural biologists Mark Gerstein and Michael Levitt (the latter a 2013 Nobel laureate in chemistry) wrote a 1998 article in Scientific American entitled “Simulating Water and the Molecules of Life”. In it they mentioned how early efforts to develop a computer simulation of a DNA molecule failed; the molecule (in the simulation) almost immediately broke up. But when they included water molecules in the simulation, it proved successful. “Subsequent simulations of DNA in water have revealed that water molecules are able to interact with nearly every part of DNA’s double helix, including the base pairs that constitute the genetic code”.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 25, 2023

I have long thought that some day water will be seen as the single most fundamental, “information-rich” physical constituent of life, and that revelations in this regard will outweigh in significance even those concerning the structure of the double helix. Not many biologists today would countenance such a suggestion, and I am not going to mount a serious defense of it here, if only for lack of ability. Time will decide the matter soon enough. But I was particularly pleased to find that the widely read and respected Nature columnist, Philip Ball, once entitled a piece, “Water as a Biomolecule”. In it he wrote:

“Water is not simply ‘life’s solvent’, but rather an active matrix that engages and interacts with biomolecules in complex, subtle and essential ways ... Water needs to be regarded as a protean, fuzzily delineated biomolecule in its own right”.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 11, 2023

Part of the picture [of the cell] that has recently come into focus has to do with the phases of matter and the transitions between these phases. (Think, for example, of the solid, liquid, and gaseous phases of water, or of solutions and gels — matter in different states.) For example, it’s possible for well-defined droplets of one kind of liquid to occur within a different liquid, like oil droplets in water.

We now know that molecular complexes containing both RNA and protein often gather together to form distinctive RNA-protein liquids that separate out as droplets within the larger cytoplasmic medium. Like liquids in general, these droplets tend toward a round shape, can coalesce or divide, can wet surfaces such as membranes, and can flow. The concentration of particular molecules may be much greater in the droplets than in the surrounding fluid, conferring specific and efficient functions upon the assemblies. ...

When things happen in the cell, phase transitions often play decisive roles, as a University of Colorado group discovered when looking at phase transitions in a roundworm. According to the researchers, these transitions “are controlled with surprising precision in early development, leading to starkly different supramolecular states” with altered organization and dynamics. “Reversible interactions among thousands of [these phase-separated] complexes”, the authors found, account for “large-scale organization of gene expression pathways in the cytoplasm”.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 4, 2023

It has become increasingly clear in recent years that, quite apart from its cytoskeleton and membrane-bound organelles, the fluid cytoplasm in each cell is elaborately and “invisibly” organized. Various macromolecular complexes and other molecules, in more or less defined mixes, congregate in specific locations and sustain a collective identity, despite being unbounded by any sort of membrane. Here we’re looking at significant structure, or organization, without even a pretense of mechanically rigid form. How do cells manage that?

The problem was framed this way by Anthony Hyman from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, and Clifford Brangwynne from the Department of Chemical and Biological Engineering at Princeton University:

“Non-membrane-bound macromolecular assemblies found throughout the cytoplasm and nucleoplasm ... consist of large numbers of interacting macromolecular complexes and act as reaction centers or storage compartments ... We have little idea how these compartments are organized. What are the rules that ensure that defined sets of proteins cluster in the same place in the cytoplasm?”

Even more puzzling, a “compartment” can maintain its functional (purposive) identity despite the rapid exchange of its contents with the surrounding cytoplasm. Hyman and Brangwynne ask: “Fast turnover rates of complexes in compartments can be found throughout the cell. How do these remain as coherent structures when their components completely turn over so quickly?”

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 27, 2023

[Regarding the decisive realization in contemporary molecular biological research that many proteins do not, as previously thought, have a fixed, functional structure, but rather have a “molten” or “intrinsically disordered” structure enabling them to play diverse and dynamic roles in the biochemistry of cells:] But the troubling question arises: if unstructured proteins, or unstructured regions in proteins, are not “pre-fitted” for particular interactions — if, in their “molten” state, they have boundless possibilities for interacting with other molecules and even for reversing their effects — how do these proteins “know” what to do at any one place and time? Or, as one pair of researchers put it, “How is the logic of molecular specificity encoded in the promiscuous interactions of intrinsically disordered proteins?”

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 20, 2023

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?

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 13, 2023

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”.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

November 6, 2023

One might easily think that the real essence and solid foundation of our lives was from the beginning rigidly established inside the first cells of our bodies. 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 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.

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.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 30, 2023

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. 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.

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 enduring 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.

(from Chapter 5, “Our Bodies Are Formed Streams”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 23, 2023

The dynamics of [the cell’s holistic performance] are a long way from the clean, informational logic commonly associated with genes. Lenny Moss, a molecular biologist who transformed himself into one of our most insightful philosophers of biology, had this to say about the relation between cellular membranes and genes:

“The membranous system of the cell, the backbone of cellular compartmentalization, is the necessary presupposition of its own renewal and replication. Cellular organization in general and membrane-mediated compartmentalization in particular are constitutive of the biological ‘meaning’ of any newly synthesized protein (and thus gene), which is either properly targeted within the context of cellular compartmentalization or quickly condemned to rapid destruction (or cellular ‘mischief’). At the level of the empirical materiality of real cells, genes ‘show up’ as indeterminate resources ... If cellular organization is ever lost, neither ‘all the king’s horses and all the king’s men’ nor any amount of DNA could put it back together again”.

(from Chapter 4, “The Sensitive, Dynamic Cell”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 16, 2023

In an integral, organic whole, we can assume the “viewpoint” of many parts in such a way as to make each one momentarily seem to be the coordinating “master” element. This is why the cytoskeleton, just as much as our genes, might appear to explain everything that goes on. With wonderful sensitivity it “feels out” the surfaces of the cell and all its organelles. The balance of forces maintained by the fibers shapes the cell, dynamically positions the organelles, and both guides and helps to power the critical movement of the cell within its environment. As we have seen, the cytoskeleton likewise plays a key role in moving substances to their functional locations within the cell. And it is a decisively important regulator of gene activity.

And yet, this does not make the cytoskeleton a master regulator. The truth is simply that, to one degree or another, each part of an organic whole bears that whole within itself — is informed by, and expresses, the whole. The idea of a master regulator arises only when we insist on viewing a specific part in isolation from the whole so as to identify single, local, and unambiguous causal interactions. We then say that this part makes certain things happen. The fact that the part is itself made to happen by the very things it supposedly accounts for then tends to be ignored. We lose sight of the fluidity and physical indeterminism of the living context — an indeterminism whose meaning and coherence become visible only when we allow particular physical causes to “disappear” into the unifying narratives, or stories, of the organism’s life. In much the same way, we experience physical sounds and gestures disappearing into the meaning of the speech we hear.

(from Chapter 4, “The Sensitive, Dynamic Cell”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 9, 2023

[Regarding the filamentary networks within cells comprising the cytoskeleton:] Neither the cytoskeleton’s moment-by-moment dynamics nor the coherent and intelligible aspect of its activity can be ascribed to “instructions” from genes — or even to the physical laws bearing on cytoskeletal proteins. As the matter was summarized by Franklin Harold, an emeritus professor of biochemistry and molecular biology at Colorado State University, “One cannot predict the form or function of these complex [cytoskeletal] ensembles from the characteristics of their component proteins”. And yet, Harold went on, “When seen in the context of the parent cell the arrangement of the molecules becomes quite comprehensible”. He then raised the obvious question: “How is the cytoskeleton itself so fashioned that its operations accord with the cell’s overall ‘plan’ and generate its particular morphology time after time?”

(from Chapter 4, “The Sensitive, Dynamic Cell”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

October 2, 2023

It would be well to remind ourselves 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.

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 — not merely logically, through the genetic encoding of an imagined program. And what we saw earlier (in Chapter 3) about the significant movements and gesturings of chromosomes is only the beginning of the story.

(from Chapter 4, “The Sensitive, Dynamic Cell”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 11, 2023

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.

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?”

(from Chapter 4, “The Sensitive, Dynamic Cell”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

September 4, 2023

Writing about the striking capability of a topisomerase [enzyme] to untie a DNA knot by cutting through the double helix and later putting it back together again — all without disturbing the critical continuity of the original chemical structure — James Wang, the Harvard University molecular biologist who discovered the first topoisomerase, remarked:

“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?”

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

August 28, 2023

The fixation upon an abstract, neatly identifiable, genetic sequence has served well the compulsion among biologists to find precise, unambiguous, logically clean, and satisfyingly deterministic causal explanations. Nevertheless, what’s been happening in rapidly intensifying fashion over the past couple of decades, has been a forced retreat from explanations of this sort. To cite a few key words and phrases from the contemporary literature: everything turns out to be mind-numbingly complex, which means, in part, that context makes all the difference. We are forced to try to understand how regulatory networks, intricate feedback loops, and the frequent difficulty of distinguishing causes from effects bear upon our biological understanding. Ultimately, we seem to be driven toward systems biology, an easily degraded term that many seem to prefer over the embarrassment (and richer meaning) of holistic biology.

What is not generally realized, however, is that this retreat from simplistic “causal mechanisms” suggests a movement toward a kind of explanation biologists have not yet come to terms with ... How might we make sense of the vast coordination of trillions of molecular events in the interest of a larger picture that is subject to continual change, as when a cell initiates the transition leading toward cell division?

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

August 21, 2023

Yes, the use of terms such as “dance” and “choreography” in molecular biology is rather distinctive. Some might call it eccentric. But this particular eccentricity has for some time now been creeping into the conventional technical literature. We have already heard of “genomic origami”, an idea that has almost become a cliché. And we have also been told: “The statement, ‘genomes exist in space and time in the cell nucleus’ is a trivial one, but one that has long been ignored in our studies of gene function” — this according to two leaders of the current work: Job Dekker, head of a bioinformatics lab studying the spatial organization of genomes at the University of Massachusetts Medical School, and Tom Misteli, a research director at the National Cancer Institute. Recent investigations, they say, have taught us that “gene expression is not merely controlled by the information contained in the DNA sequence”, but also by the “higher-order organization of chromosomes” and “long-range interactions in the context of nuclear architecture” ...

It looks very much as if the chromosome, along with everything else in the cell, is itself a manifestation of life, not a logic or mechanism explaining life. This performance cannot be captured with an abstract code. Gene regulation is defined less by static elements of logic than by the quality and force of its various gestures. Brought into movement by its surroundings, the chromosome becomes an expression of a larger context of living activity.

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

August 7, 2023

We have scarcely begun to look at the dynamic aspects of the cell nucleus. Not only do chromosomes fold, loop, coil, and twist rather like a nest of snakes, but they engage in decisive and changing electrical interactions; they relocate from here to there within the nucleus, partly in order to associate with dynamically assembled collections of molecules important for regulating gene expression; and they are influenced by pushes and pulls from the fibers of the extra-nuclear cytoskeleton.

Or again, DNA is said to “breathe” in rhythmical movements as it tightens and relaxes its embrace of the histone core particles mentioned earlier. And again, it breathes in a different sort of rhythm as the two strands of the double helix alternately separate and reunite at particular loci. And yet again, there are many profoundly significant structural novelties to which DNA lends itself, beyond the double helix. All this and much more is the cell’s way of evoking the genetic performance that it needs — a performance that expresses the cell’s own life and that of the organism as a whole.

And so, when researchers refer to the “choreography” of the cell nucleus and the “dance” of chromosomes, as they sometimes do, their language is closer to being literal than many have imagined. If the organism is to survive, chromosomal movements must be well-shaped responses to sensitively discerned needs — all in harmony with innumerable dance partners, and all resulting in every gene being expressed or not according to the meaning of the larger drama. We can hardly help asking: If such choreography is how the organism lives and performs at the molecular level, what does this mean for the nature of molecular biological explanation?

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 31, 2023

Picture the situation concretely. Every bodily activity or condition presents its own requirements for gene expression. Whether you are running or sleeping, starving or feasting, rousing yourself to action or calming down, suffering a flesh wound or recovering from pneumonia — in all cases the body and many of its different cells have specific, almost incomprehensibly complex and changing requirements for differential expression of thousands of genes. And one thing (among countless others) bearing on this differential expression in all its fine detail is the coiling and uncoiling of chromosomes.

With so much concerted movement going on (including the looping we heard about earlier) how does the cell keep all those “twenty four miles of string in the tennis ball” from getting hopelessly tangled? We do at least know some of the players addressing the problem. For example, there are complex protein enzymes called topoisomerases, which the cell employs to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of individual genes or regions of the chromosome and prevent a hopeless mass of knots.

Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases can undo knots by cutting both strands, passing a loop of the chromosome through the gap thus created, and then sealing the gap again.

Imagine trying this with miles of string wrapped around millions of minuscule beads compacted into a few cubic inches of space, with the string all the while looping and squirming like a nest of snakes in order to bring all the right loci together so as to achieve the tasks of the moment. (And how are these tasks “known”?) I don’t think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts have been made to analyze the local forces and “mechanisms” at play in isolated reactions.

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 24, 2023

We have so far hardly done more than hint at the true dynamism that enlivens our genetic heritage. The general picture of complex, three-dimensional organization has certainly galvanized molecular biologists. John Rinn, director of the Rinn Lab at Harvard, has said of the nuclear space and its chromosomal drama, “It’s genomic origami ... It’s the shape that you fold [the genome] into that matters”. According to the authors of another paper, “A loop that turns a gene on in one cell type might disappear in another. A domain may move from subcompartment to subcompartment as its flavor changes. No two cell types [have their chromosomes] folded alike. Folding drives function.” And Suhas Rao, the paper’s lead author and a researcher at Baylor College of Medicine’s Center for Genome Architecture, remarked:

“A loop is the fundamental fold in the cell’s toolbox. We found that the formation and dissolution of DNA loops inside the nucleus enables different cells to create an almost endless array of distinct three-dimensional folds and, in so doing, accomplish an extraordinary variety of functions”.

Every overall configuration (involving many factors we have not yet considered) represents a unique balance between constrained and liberated expression of our total complement of 21,000 genes. Moreover, new features of chromosome spatial and dynamic organization continue to be elucidated on a regular basis, and there appears to be no limit to the variety and scale of these features.

Think about all this dynamic form and movement for a while, and you may find yourself asking, along with me: What possible mechanism could ensure the coherence of all this movement and gesturing in relation to all the requirements of the trillions of cells in your or my body, or the tissues and organs into which those cells are organized, as we go about our endlessly varying activities under endlessly varying conditions?

(from Chapter 3, “What Brings Our Genome Alive”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 17, 2023

Regarding our theory of evolution: If, in reality, every organism’s existence is a live, moment-by-moment, improvisational storytelling — a creative and adaptive, irreversible narrative that is always progressing coherently and contextually from challenge to response and adaptation, from initiative to outcome, from nascence to renascence, from immaturity through maturity to regeneration — then an evolutionary theory rooted in notions of random variation and mindlessness is a theory hanging upon a great question mark. “The answer to the question of what status teleology [‘end-directedness’] should have in biology” — so the influential biologist and philosopher Francisco Varela came to see at the end of his life — determines “the character of our whole theory of animate nature”.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 10, 2023

An organism is not, most essentially, its body. After all, its body at one time is never materially identical to its body at a different time. It is, rather, a unique power of activity. Its body is first of all a result of this activity, while also developing into a further vehicle for it. Organisms, in other words, are doings rather than beings. Or, as the student of holistic thinking, Henri Bortoft, has put it, they are “doings that be”, not “beings that do”.

So it is not that an organism’s material being determines its doings (as is broadly assumed throughout the biological sciences); rather, its doings are what constitute it as a material being. This means that it is never wholly present to our observation in any outward or material sense. The organism’s essential power to act cannot itself be a visible product of its activity.

The preeminence of activity in relation to physical substance and structure would, if taken seriously, give us an altogether new science of life. For example, it might have saved us from an entire century of badly misdirected thinking about DNA and genes. It might also have spared biologists the crude materialism that many physicists long ago gained the freedom to question.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

July 3, 2023

If the organism’s life is an unfolding story, then we might well take the essence of that life to be the storytelling itself, not the particular embodiment of the story at any frozen instant. Organisms, as philosopher Hans Jonas has written, “are individuals whose being is their own doing ... they are committed to keeping up this being by ever renewed acts of it.” Their identity is “not the inert one of a permanent substratum, but the self-created one of continuous performance”.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 26, 2023

I offer no specific hypotheses to explain the existence of [the organism’s] intentional agency and story narration. I only note that the fact of the narrative is immediately demonstrable in every organism. There may be huge differences in the nature of the stories that can be told by different kinds of organism, but from the molecular level on up there are always elements of story that we do not find in inanimate things. The narrative of meaningful activity undertaken and accomplished is there to be seen, and is characterized as such, if only inadvertently, in every paragraph of biological description.

Moreover, our recognition of intelligent and intentional activity does not require us to understand its source. Looking at the pages of a book, we have no difficulty distinguishing written marks from deposits of lint and dust, even if we know nothing about the origin of the marks. We can declare a functioning machine to be engaged in a purposive operation, whether or not we have any clue about the engineers who built a mechanistic reflection of their own purposes into it. And if we find live, intelligent performances by organisms, we don’t have to know how, or from where, the intelligence gets its foothold before we accept the testimony of our eyes and understanding.

Neither should we expect the stories to be predictable — no more than we expect the ending of a half-read novel to be predictable. We can, however, expect the ending to make sense, and even to throw light on everything that went before. The story will hold together in a way that unstoried physical events do not.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 12, 2023

The “end” being approached in an organism’s story is not some particular, discrete accomplishment, distinct from the means of getting there, but rather the wholeness and perfection of the entire narrative movement from “here” to “there”. Assessing this end is much the same as if we were assessing the meaning of a novel: knowing the ending in isolation would have little significance compared to knowing the larger story of which, so we often feel, it is a necessary and proper part.

Note well, then, that when speaking of the organism’s story, we need make no reference to the consciously directed performances of human beings, even though our performances certainly exhibit a narrative character in the sense meant here. When I refer to living activity as “end-directed”, I am not suggesting the formulation of a conscious goal that is “aimed at”. I mean, rather, something like this:

The organism’s life is a continual playing forward of meanings within meaningful contexts. There is a certain directedness to any such play of meaning (as when birds build a nest), but it need not be the directedness of human plan fulfillment.

The directedness of a temporally unfolding play of meaning implies no narrow goal and no conscious planning. But every such play of meaning does have a certain directedness to it. Think of the greatest poems or novels, where nothing is calculated in order to reach the conclusion, but the movement is nevertheless from the beginning to the end, not the reverse. This movement simply expresses the progressive deepening of a meaningful and coherent unity — more like a dance than pursuit of a fixed and predefined goal. And the dance looks ever more improvisational as organisms ascend in the scale of complexity.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

June 5, 2023

The fact of purposive activity; the obvious play of an active agency; the coordination of diverse means toward the realization of countless interwoven and relatively stable ends; the undeniable evidence that animals perceive a world, interpreting and responding to perceptions according to their own way of life; and the coherence of all this activity in a governing unity — this tells us that every organism is narrating a meaningful life story. This is not something that a rock, say, loosened by ice and tumbling down the steep slope of a mountain ravine, does in anything like the same manner. The pattern of physical events in the organism is raised by its peculiar sort of coherence toward something like a biography whose “logic” unfolds on an entirely different level from the logic of inanimate physical causation. When we tell a story, the narrative threads convey the meanings of a life — for example, motives, needs, and intentions — and these are never a matter of mere physical cause and consequence.

So when I speak of the organism’s wise and knowing agency, or its purposive striving, I refer, among other things, to its capacity to weave, out of the resources of its own life, the kind of biological narrative we routinely observe, with its orchestration of physical events in the service of the organism’s own meanings.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 29, 2023

No one will bristle upon hearing that “this cell is preparing to divide”. But we would certainly bristle if we heard that “Mars is preparing to make another journey around the sun”, or “the nebula has ceased its effort after forming the solar system”. A planet moves according to universal laws acting in an unchanging manner. There is no point in its journey when an act is initiated or concluded, but only the playing out of the immediately preceding forces. There is in this sense nothing new to explain. Biological explanation, by contrast, always involves something new, an element of initiative, a response to circumstances not fully necessitated by the preceding play of physical and chemical processes.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 22, 2023

Think of a living dog, then of its decomposing corpse ... No biologist who had been studying the behavior of the living dog will concern herself with the corpse’s “behavior”. Nor will she refer to certain physical changes in the corpse as reflexes, just as she will never mention the corpse’s responses to stimuli, or the functions of its organs, or the processes of development being undergone by the decomposing tissues.

Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.

The corpse will not produce errors in chromosome replication or in any other processes, and neither will it attempt error correction or the repair of damaged parts. More generally, the ideas of injury and healing will be absent. No structures will inherit features from parent structures in the way that daughter cells inherit traits or tendencies from their parent cells, and no one will cite the plasticity or context-dependence of the corpse’s adaptation to its environment.

The language highlighted here is clearly a language of more-than-physical meaning. When investigators do their best to ignore these additional layers of meaning — for example, when they present their findings as if they were merely elucidating physical and chemical interactions — then they are contradicting just about all their own biological descriptions.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 15, 2023

When an animal responds to a physical stimulus, its response is not in any strict way physically enforced, or directly caused, by the stimulus. Rather, the animal “reads” the meaning of the situation in light of its own concerns, including its needs and interests, and then alters that meaning by responding to it. If the animal is physically moved by a stimulus, as when a rolling stone bumps into a leg, we don’t consider the movement to be the organism’s own act. It is not a response, but merely a physically caused result.

As a useful picture of this, we need only consider how the negligible force producing an image on the retina — say, the image of a charging lion — can set the entire mass of a quarter-ton wildebeest into thundering motion. The impelling force comes from within, so that the movement seems to originate within the animal itself in a way that we do not see in inanimate objects.

The wildebeest is not forcibly moved by a physical impact, but rather perceives something. Further, its perception is at the same time an interpretation of its surroundings from its own point of view and in light of its own world of meaning. The “lawfulness” at issue here, such as it is, is far from being universal. It differs radically from one living being to another, so that the retinal image of a charging lion means a very different thing to the wildebeest from what it means to another lion or to a vulture circling overhead. And it produces an altogether different response in these cases.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 8, 2023

Organisms are agents; they do things. The difference between a motionless rock, on one hand, and a motionless cat on the other is that the cat is not merely motionless; it is resting, or perhaps preparing to pounce. When it ceases doing things, it is no longer alive. Whereas a rock may be moved according to universal laws, the cat is self-moved; the needs and interests according to which it moves are not the universal laws of its surroundings. In our routine experience we take self-motivated activity to be definitive of living things. If an object moves unexpectedly — without an evident external cause — we immediately begin testing the assumption that it is living.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

May 1, 2023

My larger argument in this book will be that the biologist’s conscious commitment to purely physical and chemical descriptions — which is to say, her conscious refusal of much that she actually knows — has 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 to admit 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.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 24, 2023

A double and conflicted stance toward end-directedness — 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 and meaningful 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, behavior, 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, having been aroused by such purposive questions, biologists look for answers rooted 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.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 17, 2023

There is a strange reluctance among biologists to acknowledge fully the purposiveness of living beings 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 this same unwilling yet unshakable 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.

(from Chapter 2, “The Organism’s Story”, in Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 10, 2023

We have no reason to think that the intelligence working through the material limitations of, say, bacteria is a “lower” or less capable intelligence than that which is at work in ourselves — or that the intelligence at work in our cells is lower than what works in our conscious minds. Actually, our cellular intelligence quite evidently far transcends our conscious capacities. We can say this without doubting that the arrival of a self-aware sort of consciousness is a pivotal development in the evolution of life. It’s just that we have no grounds for arrogance regarding our current conscious achievements. These achievements are, in the overall context of life on earth, humble indeed!

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

April 3, 2023

In this book I offer no new or revolutionary findings in biology or evolutionary theory — and would lack the qualifications for doing so even if that were my inclination. Instead, I merely ask: What would biology and evolutionary theory look like if we overcame our blindsight and reckoned with the stories of organisms as we actually observed them? Can we allow ourselves to see with restored vision?

And so there will be no occasion for readers to ask, “Where is all the new evidence?” The evidence supporting my contentions here — as I try to show chapter by chapter — amounts to just about everything biologists have already recognized as truth, however much they might prefer not to acknowledge the gifts of their own insight. This is why you will not find me straining toward the fringes of biology, but rather citing, with very few exceptions, one fully accredited researcher and theorist after another. The case for a thoroughly disruptive re-thinking of organisms and their evolution has long been staring us in the face.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 13, 2023

Some people have a very difficult time with any use of the word “meaning” in a scientific context. It’s worth setting this difficulty alongside the simple fact that the only things we know about the world are meanings. The idea that we are dealing with genuine meaning, not meaninglessness, is already implicit in the word “know”. Meaninglessness would not yield itself to knowing articulation, as in science. Meaning cannot be questioned. The effort to question or define it — or just point to it — assumes that the person being addressed already possesses a working understanding of meaning, such as the meaning of a pointing finger. Acting out meanings is pretty much the only thing we do with our lives. The same thing is true of organisms generally, all the way down to one-celled creatures — except that they lack the capacity for conscious awareness of the meanings at work in their lives. The interesting question has to do with the different meanings at work in different kinds of organism.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

March 6, 2023

[Regarding the “integral unity of the organism”:] I use something like this phrase often, and intend it as an active concept in Aristotle’s sense of “being at work staying itself” (in Joe Sachs’ translation of Aristotle’s entelecheia). Through this activity, the parts of an organism arise from and are differentiated from out of a whole, not assembled as pre-existing entities in order to build a whole. The integral unity is actively there from the start, and is not at any point imposed from outside. It is a unity because each part reflects — or participates in and remains consistent with — the nature of the whole from which it arose.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 27, 2023

Humans are agents — we possess agency, because we possess an awareness of our world and can act in it. We help to create the situations in which we live, instead of merely being determined by them. The cells of our bodies clearly can participate in our agency by giving expression to it, as when we move our limbs intentionally. But we would never say of those cells as such that they possess awareness or agency, as opposed to moving with an agency not fully their own. This is suggestive of the kinds of distinction we must make between ourselves and, say, single-celled organisms.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 20, 2023

Biology today suffers from the deepest possible distortions. We end up with living processes theoretically stripped of their life — this despite the fact that we ourselves know this life more directly and intimately than we know anything about the non-living world.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

February 6, 2023

In order to analyze a whole into parts, we must first have recognized each part as significant — as a meaningful whole in its own right. This recognition of wholes, however unconscious it tends to be, is fully qualitative, contrary to our usual ideas of science, and it requires a movement of understanding that runs contrary to analysis.

The synthetic, or holistic, counter-movement to analysis is implicit in the biologist’s frequent reference to the “context-dependence” of biological processes. The problem is that the implication here — the implication that there is a kind of influence or causation running from a collective, complex whole toward its parts — has drawn little reflection and has had little effect on the underlying assumptions of biologists. “Context” is one of the most common words used by geneticists and molecular biologists. But it seems that no one is at all interested in asking what the term means and implies.

In this manner, “holism” — despite its being hardly separable conceptually from “context” — has become a kind of “devil word” in biology, a fact ironically coexisting with a refusal to consider the issues implicit in current, context-centered biological language. In this book “holism” — like the the biologist’s more acceptable and virtually equivalent “context-dependence” — will simply be taken for granted from the beginning. But, unlike “context-dependence”, its meaning will be consciously and explicitly drawn out as we go along.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 30, 2023

If the organism’s life, its biological existence, takes narrative form, then our explanation of its life — contrary to conventional notions of explanation — must also take a narrative form. And since a genuine, living narrative is always a playing out of interior meanings, the explanation must be framed in terms of those meanings.

It could hardly be clearer that the elements of a story, like the elements of an organism’s life, can never be considered adequately in isolation from each other. Nothing is absolutely distinct from everything else. The end of a really great novel will be illuminated by its beginning, and the beginning by the end. This interwovenness of the narrative amounts to a kind of holism, and in this respect might far more appropriately be compared to sketching a portrait than to analyzing a machine into discrete parts and causal relations.

However, it is clear that we cannot have holism without also applying the remarkable analytical skills that we humans have so fruitfully gained. It is hard even to conceive how one might sketch an organic whole without having a lucid and detailed awareness of its parts. The need is to hold together the two movements of thought — the synthetic (holistic) and the analytical.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 23, 2023

Even our descriptions of cellular and molecular “behavior” refuse to be altogether cleansed of interiority. We can always recognize a meaning — what a biological activity is about (synthesis of a protein, or extraction of usable energy from a substance) — when we look at cellular goings-on, and our biological inquiries are guided by this meaning. Meaning itself is never spatial or sense-perceptible, even if spatial structures are required for giving material expression to meaning.

A dramatic fact about contemporary biology is that biologists seem to have a horror of interiority, or the non-spatial and non-sense-perceptible. Given that the life of animals is through and through an interior business, this horror is not only perplexing, but also devastating for the prospects of a truly biological science.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 16, 2023

On one hand, no scientist would — or should — say, with anything like the human meaning and feeling of the words, “The potter wasp takes great care to make thoughtful provision for its young”. On the other hand, we can hardly avoid our scientific responsibility to ask, “How is it that the performance of the potter wasp so forcibly reminds us of what, in our own evolutionary development, has become ‘taking great care to make thoughtful provision for our young’? Do the two kinds of behavior arise from wholly disparate roots in the history of life on earth, despite appearances?”

Perhaps the best place to start answering that question is with a resolve not to compromise any side of the truth merely because we are philosophically uncomfortable with its apparent implications. In particular, we ought not to twist our understanding out of shape due to a historically conditioned revulsion against anything like a purposive dimension to life processes. Nor should we be unwilling to acknowledge the ways in which all organisms behave as more or less centered agents in the world. Nor again ought we to respect any presumed rule in biology that says, “Some human traits are unnatural and cannot be referred to in a properly ‘naturalized’ science”.

Oddly, those who most eagerly remind us that “humans belong to the animal kingdom” often seem the ones most reluctant to embrace the flip side of this truth: all animals have arisen within the same drama of evolving life that, we now know, also happened to be in the business of producing humans. If we want to say that humans share in the nature of all animals, how can we then turn around and ignore the obvious implication that all animals share something of the nature of humans?

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 9, 2023

This difference between living and nonliving is not one that many scientific students of life are fond of. That is why they have invented an abstract evolutionary drama of miraculous character in order to explain the difference away. As Lila Gatlin, a prominent biochemist, mathematician, and shaper of evolutionary theory in the twentieth century, once acknowledged, “The words ‘natural selection’ play a role in the vocabulary of the evolutionary biologist similar to the word ‘god’ in ordinary language”. In effect, the organism’s living wisdom was transferred to an omnipotent “force” of evolution, where it could be kept safely out of sight, obscured behind an elaborate technical and mechanistic terminology.

An aim of this book is to recapture the drama of life in the place where it actually occurs — in organisms themselves — and to lay bare as clearly as possible the failure of the reigning evolutionary theory to explain the special qualities of that drama. This will be a matter of showing that, in a primary sense, the life of organisms explains evolution, rather than being explained by it.

(from Chapter 1, “The Keys to This Book”, of Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

January 2, 2023

I do not expect my efforts here to be adequate. But I do hope they may be of some use to those sympathetic readers seeking a new vantage point upon biology — one that, even if at first it presents an unfamiliar and perplexing landscape, at least does not require us to deny the living experience of all creatures, including ourselves.

(from the preface to the online book, Organisms and Their Evolution — Agency and Meaning in the Drama of Life)

December 19, 2022

Follow any collection of molecules carrying out their appointed task in the organism — for example, the great variety of molecules whose coordinated activity accomplishes the surgically precise operation required for DNA repair or RNA alternative splicing — and, if you try to think the process merely in terms of physical forces, you will find yourself exclaiming, “They can’t do that! Where is the coordination of it all coming from?”

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

December 12, 2022

I have been emphasizing that the organism is a becoming. This fact makes a lie of the overly emphatic conviction that we learn who we are through a study of evolution. Evolution tells us a great deal — but only about our past. It doesn’t tell us about the potentials of our becoming in the present. When we learn that such-and-such a trait of lower animals is recognizable in ourselves in some form, this knowledge immediately changes our relation to that trait. It opens up a space of freedom to do work and act consciously where previously, rather as with the monarch butterlies migrating south, nature was simply acting through us. “The truth will make you free”. Those who delight in pointing out our “lower nature” are actually assisting us — presumably to their great disappointment, should they become aware of it — toward the realization of a higher nature.

(from “Who Are You and Who Am I and Who Are We?”)

December 5, 2022

There is a consensus today that entire organelles of the cell originated in evolutionary history through a kind of cooperative fusion of distinct microorganisms, a process requiring an almost unimaginable degree of intricate coordination among previously independent life processes. Likewise, hybridization involving distinct species — with a corresponding merger of genomes — is being found to play an unexpectedly significant role in evolution. There is also the well-demonstrated reality of lateral gene transfer, which looks like invalidating the image of an evolutionary “tree,” especially at the level of simpler organisms: repeated horizontal exchanges of genetic material between distinct species make large portions of the tree look more like a complex web.

Then, again, there is good evidence that viruses have played a major role in contributing to the genomes of more complex organisms, including mammals. Every human genome is thought to contain several times as much DNA of viral origin than DNA of all the protein-coding genes combined.

In all this we find organisms bringing their separate, highly coordinated life processes to bear upon each other in a symbiotic or other interactive manner that can no more be described as “random” than can, say, the complex and elaborately orchestrated mating processes we see among sexually reproducing organisms. "Our standard model of evolution is under enormous pressure," says John Dupré, philosopher of biology at the University of Exeter, UK. "We’re clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages”.

(from “Natural Genome Remodeling”)

November 28, 2022

It’s fine to say, “Our dealing only with what can be quantified is exactly what leads us from the qualitative world of the subjective observer to the realities of hard science”. But the phrase “what can be quantified” has no content except to the degree we can say something significant about the ”what” we are quantifying. Given a set of quantities, we have to know what they are quantities of if we are to understand anything at all about the actually existent world. And the only way we can know this is by moving in a direction opposite to the one we took when we abstracted the quantity from its phenomenon. We must attend to the phenomenon in its own terms, but very little in science teaches us how to do this.

(from “The Reduction Complex”)

November 21, 2022

Whether in fully conscious thought, or in speaking, or in gesturing, the human individual is a being of speech in the broadest sense — a being of meaningful expression, a logos-being (to use an older term). Our bodies are, at every level of their activity, a gesture; we gesture our life, speak our life. We live in outward forms expressing an inner content.

Even our listening is simultaneously a gesturing — a gesturing by which we “speak” in sympathy with the speaker. William Condon, a Boston University Medical Center professor of psychiatry, pioneered the use of sound films to micro-analyze human interaction during speaking and listening. He described as “surprising and unsuspected” the observation that “listeners move in precise synchrony with the articulatory structure of the speaker’s speech” — and do so “almost as well as the speaker does”:

This is an incredibly precise and delicate tracking process. Metaphorically, it is as if the listener’s whole body were dancing in precise and fluid accompaniment to the speech (Condon 1988).

(from “From Bodily Wisdom to the Knowing Self, Part 2: Psyche, Soma, and the Unity of Gesture”)

November 14, 2022

If, as I have argued, every molecular process in the organism already expresses an active and present wisdom, then it makes no sense to view such processes as bottom-up explanations of how intelligence arises from the non-intelligent. Nowhere do we find non-intelligence in the organism. Far better to strive toward a recognition of intelligence as it plays through all levels of observation and brings them into a unity.

There is little excuse for the largely unquestioned assumption that the mind, or intelligence, is created by the brain. When we consider the fact that undeniable and (for us) still barely penetrable intelligence is already at work in the zygote, evidencing itself in the very processes through which the future brain will be formed and begin to function, it begins to look rather quixotic to ask how the brain produces intelligence, without first inquiring about the intelligence that produces the brain.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

November 7, 2022

[Regarding the excited “discovery” of intelligence in simple organisms, plants, slime molds, crows, human infants, and so on:] We might naturally respond, “What in the world is all the fuss about? Who could ever have doubted the discovery of intelligence anywhere in the biological realm?” After all, we never see anything but intelligence. It’s what biologists are always trying to understand, what they are forever talking about. No organism — when looked at as a living performance rather than a dead weight — is ever not displaying intelligence in every aspect of its being. Whether we speak about instinct, or adaptive processes, or learning, or communication, or behavior in general, or the development of form, or circadian rhythms, or stress responses, or immune responses, or wound healing, or growth processes, or any other organic function — it is impossible to avoid the conviction that we are dealing with the expression of an active intelligence.

We all share this conviction, whether we are playing with a pet cat or trying to shoo away a pesky blackbird diving around our heads during nesting season, or watching a paramecium through a microscope. We know that the creature is aiming at something — that is, trying to accomplish something (or many things at once), enlisting diverse means in the service of diverse ends, telling a kind of life story. The fact that it fails to put its meanings, intentions and intelligent capabilities into the words of a human language is irrelevant to this fundamental and readily observable fact.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

October 31, 2022

[Regarding the evolutionary movement toward individuation:] Does the organism speak, or is it spoken? To what degree does it speak the meaning of its life from its own center, and to what degree does the world breathe meaning into and through it?

Every autumn in North America, migrating monarch butterflies travel southward a couple of thousand miles to a small forest location in Mexico — a location they have never before come near in their lifetime. It seems fair to say in this case that they are moved by the call of their surroundings — surroundings that play into and help define their bodily instincts from without — more than they are moved by any choice of their own. But analogs to choice become more vivid among birds and mammals, and something like true and free choice comes to expression, at least as a potential, in the human being.

One may be dismayed by the centrifugal and chaotic potentials of the one-sided contemporary obsession with the individual and his rights. But, on the other hand, this is the individual who for the first time, standing firmly on his own ground, can behold the planet as a whole — can feel himself belonging to humankind in a way that was inconceivable in earlier eras, can survey the world of nature and become aware of his own dependence upon it and responsibility for it. As Russian philosopher Vladimir Solovyov pointed out in The Meaning of Love, the stronger the independent being of the individual becomes, the greater its capacity for reunion with other creatures — now in freely spoken love rather than as the world’s irresistible urging.

(from “Who Are You and Who Am I and Who Are We?”)

October 24, 2022

Recalling all your experiences of nature, begin to subtract elements from her, one at a time. Take away the storm, with its thunder, wind, and lightning, and how much poorer would our own inner world become? (We would, to begin with, lose a significant portion of the meanings we find in Shakespeare.) Or take away the arching vault of the sky, replacing it, say, with a ten-foot ceiling. Would our minds retain the same ability to form a concept of the transcendent, the exalted, the superior, the sublime — all those ideas that connote the world’s vertical dimension? Or banish the willow and pine from your world, or the swan and heron, or the gurgling stream and powerful ocean wave, or the radiance of sun, moon, and stars ...

It becomes clear, then, why those who count the world meaningless have, with some reason, concluded that most human language is meaningless as well. For our language is the world’s language. But, as the philologist Owen Barfield pointed out, the converse is also true: if our language is meaningful — as everyone in fact vividly pronounces it to be every day of their lives — then the world that bequeaths to us the meanings we speak must also be meaningful.

(from “How Biologists Lost Sight of the Meaning of Life”)

October 17, 2022

All, or nearly all, of us have no difficulty reading the smiles of our spouses, children, and friends as much more than “widenings of the oral aperture, caused by contractions of the cheek musculature”. Some among us develop great skill at understanding the entire range of human expression, learning to commune deeply and sympathetically with the self doing the expressing. This sort of understanding — as every one of us (scientist or otherwise) assumes in daily life — is real and objective, even if it is very unlike our schematic knowledge of machines. It leads to possibilities of conversation and exchange that are as deep as our understanding.

There is, then, one inescapable fork in the road to understanding, and it requires something like a yes-or-no commitment from us. We can, on the one hand, deny our full cognitive potentials, splitting the world's truth down the middle and refusing to accredit half of it as scientific truth. We will then be tempted to equate science with technology and with our ability to manipulate things. But, on the other hand, we can open ourselves to the possibility that the face of the larger world — a face every bit as qualitative and expressive in its own way as the human face — might be read meaningfully and with objective understanding. Then we will find ourselves in a scientific relation to the world that truly enlarges our souls even as we move toward the widening horizons of an ever more ensouled world.

(from “Recognizing Reality”)

October 10, 2022

The organism massively structures, restructures, and regulates its genome through the intricate remodeling of chromatin (the DNA/protein/RNA complex comprising our chromosomes), just as it shapes the dynamic, three-dimensional organization of the cell nucleus, which in turn has a great deal to do with how genes get expressed. Even regarding the bare DNA sequence in the narrowest sense, Italian geneticist Vittorio Sgaramella, after noting the various alterations of the sequence throughout the cells of our bodies, was led to ask, “Which is our real genome?” And he adds, “The human genome seems more complex but less autonomous than originally believed”. Less autonomous because so many concerted activities of the organism are brought to bear on it.

(from “Natural Genome Remodeling”)

October 3, 2022

To analyze is to cleave and distinguish. We answer the question, "What is X?" by pointing to the parts Y and Z of which X is composed. That, of course, raises the question, "What is part Y or Z?" each of which must now in turn be analyzed. The problem here is that, without a countermovement foreign to reductionism, one can never stop to consider a thing in its own terms. The tree resolves into root, branch, and leaf, the leaf into cells, the cells into organelles, the organelles into biochemicals ... and so on without end, down to the most remote subatomic entities.

How, without the largely uncredited countermovement, could there possibly be a satisfactory end? If the part must explain the whole, so that all understanding must be founded upon analysis, and if this analysis were ever to stop at some fundamental, unanalyzable thing, then that thing (upon which the reductionist would erect all else) must, by virtue of its unanalyzability, stand as an incomprehensible mystery, no more approachable than divine fiat. At some point, in a spirit opposite to that of analysis, we have to be able to say in meaningful terms what X is in its own right — the task we have avoided all the way down. To accept this task in its full significance would mean a revolution in science. But, as things stand, the subatomic, almost purely mathematical and probabilistic extreme of our analysis seems to have carried us as far as possible from the goal of knowing what it is we are talking about.

(from “The Reduction Complex”)

September 26, 2022

Spoken words are physical phenomena of sound bearing an inner meaning. But this sound can be infinitely varied, and all such variation is meaningful. Elements, some of which we might call “musical” — loudness, emphasis, rhythm, inflection, timbre, accent, and no doubt many subtleties that may elude awareness — all contribute to our conscious recognition when we say, for example, “He’s using that tone of voice again”. The slightest expressive shift may prove as decisive in its meaning as changing the word “is” to “is not”.

All these elements are physical performances and at the same time expressions of an inner meaning, which is only possible because the physical by its nature is a bearer of meaning. We can distinguish the two aspects of speech — the physical features of sound and the meaning — but they are inseparable. And can we not say the same thing of every outward physical performance of our bodies? What can we do that is not meaningful gesturing? Our walking may suggest heaviness or lightness (in a psychological sense), it may be graceful or awkward, purposeful or ambling, workmanlike or clumsy. If you stamp your foot in any particular context, you are making a statement. Even if you intentionally move so as to suggest random, meaningless activity, then your movement will indeed suggest exactly that intent and meaning ...

There is nothing we can do that is not a gesture — is not a speaking, in the broad sense of that word. The psychiatrist, the stage director, and, indeed, every human being as an attentive conversationalist, knows that the slightest shadow of change flitting across a face carries meaning.

(from “From Bodily Wisdom to the Knowing Self, Part 2: Psyche, Soma, and the Unity of Gesture”)

September 19, 2022

Looking at [the explosively growing literature about the intelligence of organisms] from one angle, we might naturally respond, “What in the world is all the fuss about? Who could ever have doubted the discovery of intelligence anywhere in the biological realm?” After all, we never see anything but intelligence. It’s what biologists are always trying to understand, what they are forever talking about. No organism — when looked at as a living performance rather than a dead weight — is ever not displaying intelligence in every aspect of its being. Whether we speak about instinct, or adaptive processes, or learning, or communication, or behavior in general, or the development of form, or circadian rhythms, or stress responses, or immune responses, or wound healing, or growth processes, or any other organic functions — it is impossible to avoid the conviction that we are dealing with expressions of an active intelligence.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

September 12, 2022

The search for intelligence in other organisms often focuses heavily on skills construed by the investigators as “calculational” or “computational”. Not surprisingly, these happen to be the skills emphasized in our own highly mathematized scientific activities and in our increasingly computerized society. All too often little distinction is made between the skill and tool use of humans and the activities of organisms with no scientific sensibilities, none of the internal structure of computers, and a complete absence of the powers of wakeful abstraction required for mathematics and computation.

“But certainly”, one might reply, “even if the proposed ‘mechanisms’ at work in humans, salmon, and slime molds differ greatly, just as a computer, slide rule, and abacus differ — still, mathematical precision requires something that we can recognize as calculation, does it not?”

Actually, no. Planets do not calculate their mathematically well-behaved pathways around the sun. More to the present point: A frightened young child runs to his mother in the straightest of straight lines. Yet he has never carried out anything like a proof that the shortest distance between two points is a straight line. Nor has any collection of cells in his brain derived such a proof. Nor, in his short life, is he likely even to have considered the bare fact of the matter. The most we can say is that the child’s flawless sentient and muscular performance, with its uncalculated mathematical precision, may suggest something about his future mathematical potentials.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

September 5, 2022

How can we speak of “an organism” when there is no strict dividing line between the organism and its environment? For example, we have more microbial cells in our body than cells we call our “own”, and we could not live without them. Do they belong to us, or to our environment?

Yet we are quite capable of distinguishing where we cannot rigorously divide. Just as the “particle” of the physicist is a center of force interacting with countless other centers of force — yet is still distinguishable as this center — so, too, the organism can be distinguished from its inanimate surround. This doesn’t mean, however, that the line between the individual organism and its ecological/physical context is ever precisely definable.

(from “Who Are You and Who Am I and Who Are We?”)

August 29, 2022

To reconcile ourselves to the full range of meanings we confront in our encounters with living beings is to transform our understanding of life. We discover that our highest capacities — our thinking, our formulation of goals and plans, our strivings and passions, our sense of well-being and illness — are objectively imaged in our own biological organism right down to the molecular activity of our cells, as also in the cells of every other living creature. “Where molecular biology once taught us that life is more about the interplay of molecules than we might have previously imagined”, writes biologist and philosopher Lenny Moss, “molecular biology is now beginning to reveal the extent to which macromolecules, with their surprisingly flexible and adaptive complex behavior, turn out to be more life-like than we had previously imagined”.

But it is hardly just a matter of macromolecules. It is the entire dynamic society of molecules, membranes, and organelles, with all their diverse conversations coordinated from above, that tells us we are looking at the logos of life, even at the molecular and cellular level.

The supposed “taking down” we humans endured when we were made cousins of the apes should actually have been recognized as a rebirth of the old conviction that we are microcosms of the macrocosm — that Man, as Ralph Waldo Emerson perceived, “is placed in the centre of beings, and a ray of relation passes from every other being to him”. We are cousins of all creatures, for in us the reason displayed in every creature flashes forth as conscious understanding. And just as, among humans, to be understood is fully as important as to understand, so, too, our understanding of ape and honey bee and rainforest is today proving decisive for their own being. We have arrived at a time when we can say, consistent with the evolution of a threatened earth: every creature needs our understanding.

(from “How Biologists Lost Sight of the Meaning of Life”)

August 22, 2022

I have not been trying to identify some strange or paranormal or unapproachable reality called a “quality”. We in fact have nothing but qualities. The question should be turned around and thrown at the scientist who does his best to ignore qualities: “Give us a scientific characterization of the physical world that is not qualitative. And remember that mathematical statements by themselves, as pure mathematics, are not statements about the physical world”. If you want obscurantism, just listen to the strange answers you will receive to this request.

What I have been suggesting is that, in our attempts to apprehend the world, we have two polar opposite movements of consciousness. With one gesture we try to take hold of the world's truth, narrowing it down to a sharp focus for ease of comprehension. With the other we yield ourselves up to the truth by allowing its expressive fullness to resonate within us and thereby to shape the entire range of our cognitive faculties — to shape us — in its likeness.

Both are essential. When the former tries to dominate, as it does in reductionist science, it becomes a grasping in order to possess and control. It becomes a demand for certainty and a refusal of ambiguity. When the two movements are in balance — the taking hold and the offering of ourselves — we have exchange, conversation, participation in reality.

(from “Recognizing Reality”)

August 15, 2022

With transposons the organism reshapes its genome through elaborately organized and synchronized processes often affecting considerable stretches of DNA. But even more striking, the geneticist Henrik Kaessmann notes, is the recent discovery of protein-coding genes being composed “from scratch” — that is, from non-protein-coding genomic sequences altogether unrelated to pre-existing genes or transposable sequences. In a famous paper the preeminent French biologist, François Jacob (1977), wrote that the probability for creation of new protein-coding genes de novo (from scratch) by random processes “is practically zero”. Such creation was widely thought to be virtually impossible. And yet, Kaessmann goes on, “recent work has uncovered a number of new protein-coding genes that apparently arose from previously noncoding (and nonrepetitive) DNA sequences”.

If we take seriously Jacob’s “practically zero” probability for random, de novo assembly of functional, protein-coding genes from noncoding DNA sequences, then, given that such assembly does in fact somehow occur, the obvious thing to suspect is that the process is not random. Nor does the scale of the problem, as it is now emerging, look trivial. There is, we’re told by two biologists working in Germany — one at the Max Planck Institute for Evolutionary Biology and one at Christian Albrechts University — “accumulating evidence that de novo evolution of genes from noncoding sequences could have an important role” in a class of genes representing “up to one-third of the genes in all genomes” (Tautz and Domazet-Lošo 2011). The seemingly unbridgeable gap between “practically zero” and this recent, extraordinary claim invites evolutionary geneticists to do a lot of soul-searching.

(from “Natural Genome Remodeling”)

August 8, 2022

You might hope that, if only by association, the invocation of science in a conversation would naturally lead people to relax their grip on hard-and-fast dogma. You might hope that the thought of science would inspire them to consider the rich, many-faceted contexts of the topic under discussion, searching these contexts for new insights — for a deeper and transformed understanding of the issues at hand.

But, no, the desire for the imprimatur of science becomes little more than competition for an authoritative word from on high. It is enough to say, “There is no scientific evidence that...” or “It has been shown scientifically that...” and the conversation is expected to halt at the stark dividing line between certainty and nonsense. If you've already “got” an unarguable truth, why muddy the waters with contextual complication?

The underlying cognitive gesture we are speaking of also helps to illuminate our loss of humanity's earlier, participative relation to knowledge and the world. If we can fix and possess the truth, then clearly it cannot possess us. By keeping a tenacious grip upon the truth — which only seems possible so far as, in good Cartesian style, we imagine the world to exist wholly outside the observing mind rather than in living conversation with it — we spare ourselves the worry that the truth of the world might demand something uncomfortable of us. Reality is no longer something we must follow, no longer a way. Our truth ceases to bring us into a mutual exchange with the world.

(from “The Reduction Complex”)

August 1, 2022

It’s clear enough that many conditions we might naturally think of as purely bodily often rise into conscious experience, whether it be the position, balance, and motion of our bodies and limbs, or the movements of stomach, heart, or bowels, or physical pain or hunger.

More broadly within the animal world, we find instinctual (“innate”) behavior. The dance of honeybees; the newly hatched leatherback turtle’s race toward the ocean; the gaping of young birds being fed by a parent; a great variety of courtship behaviors; the building of nests, burrows, and every imaginable sort of habitation or protective barrier — all this and much more is commonly counted as instinctual and “biologically based”. Yet it is accomplished with a present and active knowing of some sort. The organism always responds more or less improvisationally — which is to say, intelligently — to encountered circumstances.

Even at the molecular and cellular level, biologists routinely employ a language connoting a psychic element, but without any suggestion of self-aware consciousness. Indeed, sensing and responding, communication, information, signal, and message have become part of the core terminology of biologists and are sometimes cited as the terms that make biology a science distinct from physics and chemistry.

The preceding remarks illustrate that there’s a range of consciousness extending all the way from full awareness down to the bodily-unconscious where we still require an inward descriptive language — a language at least partly derived from the psyche. Whatever the nature of the “unconscious consciousness” at work in cells, instinctual processes, and pathological complexes, it manifests in directed, intelligent behavior that shapes much of our lives.

(from “From Bodily Wisdom to the Knowing Self, Part 2: Psyche, Soma, and the Unity of Gesture”)

July 25, 2022

Migrating animals do not calculate according to the stars or the sun or magnetic fields; birds and mammals do not count; and infants do not note the fact that three is greater than two. Actually, we can be quite sure that infants don’t note facts, period. Facts are just not the kind of thing they have in their possession. Nor can they carry out mathematical reasoning — not even the simplest counting. How could they at an age when they have not yet even learned clearly to delimit one thing from another? The projection of adult forms of intelligence onto the child leads only to absurdity. And how much more so when we extend the projection to animals and plants!

The experiments with plants, animals, and human infants certainly indicate that some form of understanding is at work. Biologists refer to the wisdom or intelligence of the organism for good reason. But saying this much is a long way from saying anything very meaningful about the locus of that intelligence, or the manner of its operation, or its relation either to the organism’s own physiological activities or to conscious human intelligence.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

July 11, 2022

Whenever biologists refer to context, they are invoking the parallel with speech, or text. Organic activity is, in fact, always a special kind of contextualized expression, and “context” is another word for “that which has the character of a meaningful whole”. Without some quality of wholeness, it would not be an identifiable context.

The word “meaningful” here points, in part, to an ideational content. A collection of arbitrarily designated things — a collection lacking a unity of idea — does not add up to a context. We call a context a “context” because it has a recognizable and integral character possessing some sort of ideal unity.

An example. Twenty-two people randomly milling about in a field do not make an organic context. But when twenty-two people are arrayed against each other on an American football field, consistently, adaptively, and innovatively performing according to the aims and choreographic requirements of a game — then we have a recognizable context. The context cannot be defined apart from the many ideas making up the aim and the meaning of the game.

(from “Who Are You and Who Am I and Who Are We?”)

June 27, 2022

It would be well for biologists to pull back a little from the religious wars and realize that the truly fundamental problem most people have with much of the biological and evolutionary literature is rather simple and needs respectful addressing. We read stories of organisms whose activity, from the molecular level on up, displays meaningful intricacies and coherent, eloquent plot lines that never cease to surprise us, far outshining the highest literary achievements of a Shakespeare or Goethe or Pushkin.

And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.

(from “How Biologists Lost Sight of the Meaning of Life”)

June 20, 2022

[Regarding geneticist Barbara McClintock:] McClintock’s biographer, Evelyn Fox Keller, tells of the geneticist’s meeting with a group of graduate and postdoctoral biology students at Harvard University. The students were responsive to her exhortation that they “take the time and look”, but they were also troubled. Where does one get the time to look and to think? “They argued that the new technology of molecular biology is self-propelling. It doesn’t leave time. There’s always the next experiment, the next sequencing to do. The pace of current research seems to preclude such a contemplative stance”.

McClintock went on to tell the students how fortunate she had been for having worked with a slow technology, a slow organism. Other researchers disliked corn because you could only grow two crops a year. But she found that even two crops a year were too many. If she was really to observe her plants adequately, one crop was all she could handle.

[McClintock’s "slow" attention to the qualitative nuances of individual corn plants led eventually to discoveries about “jumping genes” among other things for which, tardily, she was awarded the Nobel Prize.]

(from “Recognizing Reality”)

June 13, 2022

When genomic researcher David Haussler of the University of California, Santa Cruz, was asked by the journal Cell what has been most surprising about the human genome, one of the things he cited was “mounting evidence” that transposons [so-called jumping genes] “play a critical role” in the turnover and reinvention of regulatory elements in DNA. And, responding in Science to a report about the work on jumping genes in mammalian brains, Southern Illinois University neuroscientist, David King, wrote that the “dismissive dictum, ‘Mutations are accidents’, has grown obsolete”, adding that protocols for “the spontaneous, non-accidental production of genetic variation are deeply embedded in genomic architecture”.

[The movable DNA elements known as “jumping genes” or “transposons”] exemplify a growing (and, for many biologists, embarrassing) class of cellular constituents that were initially dismissed as more or less functionless simply because they didn’t fit into a kind of neat (but now hopelessly outmoded) digital coding schema linking DNA as Master Cause, to RNA as precisely programmed mediary, to protein as definitive final result. Making up a sizable portion of the human genome, transposons are to this day often referred to as “junk” or “parasitic” elements. Because they play a particularly prominent (and still barely explored) role in the germline, one often hears about the germ cell’s “defensive mechanisms” to protect itself from these highly mobile, “selfish” elements, with their genome restructuring potentials. How this kind of thinking could go on for many years without most biologists suspecting a positive role for transposons as genome remodelers with potentially powerful implications for evolution is, for me, a great mystery. Certainly transposons, like everything else in the cell, are subject to intense oversight by their larger context — and viruses may indeed have played a role in their origin, as many suppose — but this hardly makes them mere parasites in the organisms that have so intently taken them up and put them to use.

(from “Natural Genome Remodeling”)

May 30, 2022

The inner act of isolating something so as to grasp it more easily and precisely and gain power over it is the essential gesture of what I am calling “the reduction complex”. Grasping is indeed a useful description of the cognitive activity I am pointing toward. Of course, we must try to get hold of things in our understanding. But if we are too intense and one-sided in our will to grasp a thing, then we sever it from its relationships to everything else, as when we uproot the plant to study it in the laboratory. This may be helpful in its own way, but requires us to keep in mind how we have falsified and decontextualized the thing we are trying to understand.

To know the reality of the plant in truth, we would have to live with it, experience the conditions of its life, and participate imaginatively as well as physically in its habitat. We would, in other words, have to change, adapting ourselves to a different way of being. In this manner what lives in the form before us also comes to expression within us, and becomes knowledge. In all this we conform to reality with more than just our abstracting minds.

Similarly, to know water, we must learn to flow with it, as when we swim. We must know the water in part as a fish does, by allowing its laws to come to expression within us as our laws. This is not merely to know about water in the abstract, but to participate in its way of being. Our aim in such endeavors is not so much to possess truth as to follow reality and conform to it, remain true to it.

(from “The Reduction Complex”)

May 23, 2022

There are, of course, biological disciplines where the challenge of the mindlike is taken up with great seriousness. Cognitive science — bringing together (at least) psychology, neuroscience, linguistics, artificial intelligence, philosophy, and anthropology — is a field upon which advocates of remarkably diverse points of view often joust in free and bracing intellectual combat. One need only browse the Journal of Consciousness Studies to witness the creative ferment now attracting so many researchers.

But how many molecular biologists today would feel the freedom to wonder aloud whether intention and agency, so difficult to banish from biological description, might be at least as fundamental to biological understanding as the local causal interactions we are so expert at fingering?

Why should the consideration of mindfulness, which presents such a vivid and stimulating conundrum to researchers in a number of respectable sciences, be absent from what are usually considered the core disciplines of biology? Perhaps most molecular, cellular, and evolutionary biologists are prepared to claim — despite their own heavy reliance upon a mentalese dialect, and despite all those kindred disciplines actively wrestling with the problem of mind — that the conundrum merely reflects an unusually persistent confusion that ought to be clarified once for all and dispensed with.

But if it’s this simple, then why a silence that has all the appearance of being taboo-enforced? Let the conversation begin!

(from “Let’s Loosen Up Biological Thinking!”)

May 16, 2022

[As a preface to consideration of the nature of intelligence and consciousness in non-human organisms:] There is no doubt that we can be manipulated by psychic contents we are unaware of — and that we may eventually become aware of them as psychic contents (thereby gaining at least a degree of freedom with respect to them). We also have good reason for believing that, the more coercive and unavailable to us such contents may be, the more deeply and organically we will discover them to have penetrated our lives. The child systematically and cruelly abused by a parent may grow into adulthood with, for example, obsessive anxieties, disturbing thoughts, or compulsive urges that, however “ridiculous”, prove almost miraculously resistant to conscious alteration, even over the course of many years of hard work by extraordinarily intelligent sufferers.

In such cases it is difficult not to believe that the ideational, emotional, and volitional “complexes” have partly rooted themselves in some aspect of the growing child’s corporeal being, forming a kind of psychosomatic organ. And the medical profession’s inability to stabilize a historically oscillating consensus about the best treatment — it is, of course, pharmacological … or, no, is it psychological instead? — testifies to the seemingly inextricable psyche-soma nexus.

(from “From Bodily Wisdom to the Knowing Self, Part 2: Psyche, Soma, and the Unity of Gesture”)

May 2, 2022

The search for intelligence in other organisms often focuses heavily on skills construed by the investigators as “calculational” or “computational”. Not surprisingly, these happen to be the skills emphasized in our own highly mathematized scientific activities and in our increasingly computerized society. All too often little distinction is made between the skill and tool use of humans and the activities of organisms with no scientific sensibilities, none of the internal structure of computers, and a complete absence of the powers of wakeful abstraction required for mathematics and computation.

“But certainly”, one might reply, “even if the proposed ‘mechanisms’ at work in humans, salmon, and slime molds differ greatly, just as a computer, slide rule, and abacus differ — still, mathematical precision requires something that we can recognize as calculation, does it not?”

Actually, no. Planets do not calculate their mathematically well-behaved pathways around the sun. More to the present point: A frightened young child runs to his mother in the straightest of straight lines. Yet he has never carried out anything like a proof that the shortest distance between two points is a straight line. Nor has any collection of cells in his brain derived such a proof. Nor, in his short life, is he likely even to have considered the bare fact of the matter. The most we can say is that the child’s flawless sentient and muscular performance, with its uncalculated mathematical precision, may suggest something about his future mathematical potentials.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

April 25, 2022

You may have heard about the archerfish, found in warmer waters of the far east. This fish “spits” a forceful stream of water sufficient to dislodge an insect from its sticky attachment to a stem or leaf up to at least two meters away. Of course, when looking from the water into the air, the fish must correctly compensate for the same refraction of light that, in our own experience, makes a stick look “bent” at the point where it enters the water.

That itself is mystifying enough. But researchers recently showed that the archerfish’s achievement is even more startling. This cunning hunter emits its lethal jet in such a way that the last water released (the trailing part of the stream) eventually catches up with the water released earlier — and does so right at the distance where the insect is located, making for maximum force of impact. Moreover, the way to do this changes a great deal, depending on whether the insect is 10 cm away or, say, 100 cm.

The gathering of water in the fish’s mouth, its dynamic shaping, and the force of propulsion imparted to the stream in order to achieve the proper result at each distance, are extraordinarily complex — and not fully understood. But researchers, in testing the fish with targets at 20 cm, 40 cm, and 60 cm, reported that “jet tips recorded just before impact were equally well focused, and their shapes bore no information on how long they had traveled before”. That is, the fish adjusted the dynamics and timing elements of its water jet in order to have it “come together” in just the right way at whatever distance the target resided.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

April 18, 2022

When a Pacific Ocean Chinook salmon is prompted by some deep urge to migrate from the open ocean to its natal stream — there to lay its eggs and die — several years may have passed since it left that stream as a juvenile. Supposing it hatched in a central Idaho waterway — and leaving aside thousands of miles of ocean travel so as to reckon only from the mouth of the Columbia River — its return journey could well extend over 900 miles. Struggling against stiff currents and strong rapids, the fish must gain several thousand feet in elevation. Upon reaching its birth stream, the male “knows” to pair up with a female, the female “knows” to dig a depression in the stream bottom in order to lay her eggs, and the male “knows” to fertilize the eggs. Both fish “know” to protect the eggs from predators — and both very likely die before the eggs actually hatch.

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

April 11, 2022

The arctic tern migrates between its antipodal summer residences (from the Arctic and sub-Arctic summer to the Antarctic summer and back) every year. The meandering and partly improvised course of its annual round trip, shaped to take advantage of prevailing winds, amounts to as much as 56,000 miles (90,000 km) — well more than twice the entire circumference of the earth, and mostly over the “pathless” sea. For mating, the tern usually returns time and again to the same northern colony. The slender bird accomplishing these feats, armored against the elements with nothing but delicate feathers, weighs about 4 ounces (110 g).

(from “From Bodily Wisdom to the Knowing Self, Part 3: Where Do Intelligence and Wisdom Reside?”)

April 4, 2022

To discover ourselves in the universe — which is to say, to discover ourselves as discoverers, or knowers, of the universe — tells us something about what the universe is like. It does so fully as much as our discovery of gravitational attraction among objects of the solar system informs us about the reality of gravity in the universe. If we find ourselves to be knowers of a knowable world, then knowing and being known — being cognized, being the stuff of cognition, being meaningful — belong to the world’s and our own character. Speaking and being spoken belong to the very fabric of things.

(from “Who Are You and Who Am I and Who Are We?”)

March 28, 2022

Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, have written: “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type”.

The question they are asking is how cells can do the right thing, cooperating to form the unthinkably complex architecture of a mammal while dealing with the heterogeneity — the continual fluctuation — of their molecular “components”. There is no determinate mechanical or computational rigidity here, no interaction of the parts of a smoothly running machine. Where is the sequence of reliable causes that can account for the predictable outcome of the process as a whole, when all the causal details are so variable and so obviously being shaped to living purposes?

We need to understand all those physical connections. But we get to the living processes only when we raise ourselves above the causal web and view it from a different level of meaning — a level where we can ask: “What is going on from the organism’s point of view”. It’s always that way with meaning. The movements of a ballet dancer can be analyzed in terms of the play of force in muscle, bone, and flesh, but we read the movements only when that play becomes effectively transparent to us — only when we look through it to another level of meaning. This is the kind of thing biologists will always notice themselves doing, if only they observe themselves.

(from “How Biologists Lost Sight of the Meaning of Life”)

March 21, 2022

The recognizable expressiveness of things is not something added to their “real” content. It is the fullness of the content itself. Without it, all content disappears. Abstract schemata in general and measurements in particular do not give us reality. Painfully obvious as this is, it remains widely ignored. But our measurements have to be measurements of something, and we have no scientific understanding until we can speak intelligibly about what this something is. Nor can we do this in any terms except qualitative ones. Simply filling in our quantitative notions with unexamined, almost unnoticed qualitative mental pictures does not make our work worthy of science.

(from “Recognizing Reality”)

March 14, 2022

With remarkable nuance, the organism contextualizes its genome, and it makes no sense to say that these powers of contextualization are under the control of the genome being contextualized. Thus, the human genome yields itself to a radical and stable “redefinition” of its meaning in the extremely varied environments of some 250 different cell types found in brain and muscle, liver and skin, blood and retina. It is well to remember that the genes in your stomach lining and the genes in the cornea of your eye are supposed to be the “same” genes, and yet the immediate context makes very different things out of them. An especially revealing case of contextualization occurs when a genome fit for the needs of all the varied cells of a worm-like larva is subsequently pressed into perfectly adequate service for the entirely different cell types — and different bodily organization and different overall functioning — of a graceful, airborne butterfly. The genome, it appears, is to one extent or another like clay that can be molded in many different ways by the organism as a whole, according to contextual need.

(from “Natural Genome Remodeling”)

March 7, 2022

Here are 5 features of what I am calling “The Reduction Complex”, by which I refer not only to reductionism, but also to materialist and mechanistic thinking:
(1) There are a few, simple, fundamental constituent elements of the material universe.
(2) These elements relate to each other externally, like the parts of a machine.
(3) The fundamental elements and the laws governing them can be precisely characterized mathematically and logically.
(4) The fundamental elements and laws account for and ultimately explain everything that happens. This explanation proceeds unidirectionally, "from the bottom up".
(5) The constituent elements and laws of the world possess no intrinsic character of mind.

We can discover the coherence of our five reductionist propositions by recognizing in them the operation of a single gesture of the cognizing mind. The gesture itself is not pathological; rather, its singleness — its operation in conjunction with a suppression of the necessary counterbalancing gesture — is alone what renders it and its reductionist results pathological. Reductionism, at root, is not so much a body of concepts as it is a way of exercising (and not exercising) our cognitive faculties.

The cognitive gesture I'm alluding to here is the inner act of isolating something so as to grasp it more easily and precisely and gain power over it. We want to be able to say, "I have exactly this — not that and not the other thing, but this". The ideal of truth at work here is a yes-or-no ideal. No ambiguity, no fuzziness, no uncertainty, no essential penetration of one thing by another, but rather precisely defined interactions between separate and precisely defined things. We want things we can isolate, immobilize, nail down and hold onto.

(from “The Reduction Complex”)

February 28, 2022

Molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself.

(from “Let’s Loosen Up Biological Thinking!”)

February 21, 2022

Every cell of our bodies behaves such that, if we knew it to be conscious, we would naturally assume that its behavior issued from thoughts and intentions. Of course, no one would attribute consciousness to cells, unless perhaps at an unimaginably primitive level. But the fact of mind-like (intended, reasoned) behavior is already given in the character of the behavior itself, quite apart from the assumption of conscious awareness. We needn’t remain blind, even in ourselves, to thoughts and intentions operating beneath the level of consciousness.

And we shouldn’t forget that while the bacterium may have no conscious awareness of what it is doing, the scientist is fully capable of raising its behavior to full consciousness, and in doing so cannot help experiencing that behavior, if not actually acknowledging it, as an expression of mind-like intent and reason.

(from “Psyche, Soma, and the Unity of Gesture”, Part 2 of “From Bodily Wisdom to the Knowing Self”)

February 14, 2022

Our understanding necessarily alternates between narrow focus on the parts of an activity viewed separately, and receptivity to the larger expressive picture. The two facets of understanding serve each other. This is related (rather exactly, I think) to the interplay between our hearing of particular words as we listen to speech, and our progressive apprehension of the overall meaning that more and more shines through those words, modifies their identity, and subordinates them to the developing direction of thought. We could not understand speech without hearing individual words, but neither could we understand the individual words in their current meaning without grasping the overall import of what is being said.

(from “Who Are You and Who Am I and Who Are We?”)

February 7, 2022

In the growing embryo literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.

(from “How Biologists Lost Sight of the Meaning of Life”)

January 31, 2022

All science, right down to its most tough-minded, quantitative formulations, remains permeated by qualities wherever its equations and algorithms touch revealingly upon actual physical phenomena — that is, whenever the science gives us understanding of the world. But the reductionist, while relying upon these qualities for the sense of his explanations, refuses to speak about them in any meaningful way.

Some day we will be dumbfounded at the long-sustained pathology whereby the scientist looked out upon a world consisting of nothing but qualities and then claimed to explain it while refusing to say anything substantial about the nature of those qualities.

(from “Recognizing Reality”)

January 24, 2022

Our failure to reckon adequately with the wild Other is as much a feature of human social relations as of our relations with nature, and as much a feature of our treatment of domesticated landscapes as of wilderness areas. In its Otherness, the factory-farmed hog is no less a challenge to our sympathies and understanding than the salmon, the commonplace chickadee no less than the grizzly bear. We do not excel in the art of conversation. If the grizzly is absent from the distant mountains, perhaps it is partly because we have lost sight of, or even denigrated, the wild spirit in the chickadee outside our doors.

If we really believed in the saving grace of wildness, we would not automatically discount habitats bearing the marks of human engagement. We would not look down upon the farmer whose love is the Other he meets in the soil and whose struggle is to draw out, in wisdom, the richness and productive potential of his farm habitat. Nor, thrilling to the discovery of a cougar track in the high Rockies, would we disparage the cultivated European landscape which, at its best, serves a far greater diversity of wild things than the primeval northern forest.

The point is not to pronounce any landscape good or bad, but to ask after the integrity of the conversation it represents. None of us would want to see the entire world reduced to someone’s notion of a garden, but neither would we want to see a world where no humans tended reverently to their surroundings. We should not set the creativity of the true gardener against the creativity at work in our oversight of the Denali wilderness. They are two very different conversations, and both ought to be — can be — worthy expressions of the wild spirit.

(from “A Conversation with Nature”)

January 17, 2022

Nine years ago Richard Conn Henry, an astrophysicist at Johns Hopkins University, published an opinion piece in Nature entitled “The Mental Universe”. He urged the scientific community to repeat Galileo’s achievement in “believing the unbelievable”, and recalled Sir James Jeans’ famous remark that “the Universe begins to look more like a great thought than like a great machine”. We don’t know all that this implies, he continued, “but — the great thing is — it is true. ... The Universe is immaterial — mental and spiritual. Live, and enjoy”.

The most dramatic thing about the article was the lack of drama: it produced no visible controversy. After all, physicists have long been accustomed to receive such assertions peaceably, because the science itself seems tolerant of them.

But suppose Henry had made a narrower and more modest claim — just a small part of what he implied in “The Mental Universe”. Suppose he had written only of “The Mental Cell”. Would the occasion have been equally unremarkable? Most molecular and cellular biologists, I suspect, will readily picture the unseemly consequences likely to follow upon the appearance of words like immaterial, mental, and spiritual in their published papers. It would be as if an unspoken taboo were violated.

(from “Let’s Loosen Up Biological Thinking!)

January 10, 2022

From humans to bacteria, every organism is a cognitive creature, carrying out mind-like functions in every aspect of its life. All biologists know this, even if they are strongly encouraged by the reigning intellectual climate to forget it. Be aware, however, that one might speak of the mind-like aspects of simpler organisms (1) without suggesting that these organisms have minds in anything like the familiar human sense, and (2) while recognizing that the effective wisdom playing through the simplest, one-celled organism — and the cells of our own bodies — far transcends any mental achievements we humans are consciously capable of.

(from “Psyche, Soma, and the Unity of Gesture”, Part 2 of “From Bodily Wisdom to the Knowing Self”)

January 3, 2022

It ought to be a truism among biologists that our understanding of living creatures must be, at its most fundamental (irreducible) level, an understanding of activity. And therefore our knowledge of changes in the organism — for example, evolutionary changes, or the transformations during development — must be, fundamentally, a knowledge of changes in activity, not mere rearrangements of things with predefined functional identities. The experimentalist, in comparing two specimens under different conditions, can note down all the differences in quantities of this or that molecule, or all the differences in morphology of leaf or limb. But each of these changes precipitates, so to speak, out of an altered process.

The organism is always a becoming, and to think about a capacity for becoming is radically different from thinking about a collection of well-defined (which is to say, context-independent) things. If the biologist’s training included even one week where this difference was held up for attention, everything in biology would be colored differently. We can perhaps glimpse the difficulty of the task by asking: How would we characterize a change in directed (forming) activity, as opposed to a change from one finished form to another, or a mere rearrangement of things?

(from “Who Are You and Who Am I and Who Are We?”)

December 27, 2021

Mathematical biologist Joshua Plotkin, referring to the discovery of vast regulative processes bearing on DNA, concludes: “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naïve” ... And referring to the “huge number of potentially regulatory elements in a very crowded nucleus”, University of Massachusetts geneticist Job Dekker wonders “How do cells ensure that genes only respond to the right regulatory elements while ignoring the hundreds of thousands of others”

It’s a good and obvious question. An editor of Science amplifies it this way: “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”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going”.

Of course, there’s not much sense in saying particular molecules “know” where they are going. But the context they find themselves in certainly embodies and gives expression to a kind of wisdom that proves highly effective in coordinating their movements.

(from “How Biologists Lost Sight of the Meaning of Life”)

December 20, 2021

A reader responded to my article, “The Reduction Complex”, by complaining that “Talbott never defines what he means by ‘quality’”. Another reader voiced a similar concern when he asked me for a definition of “the exact method of holism — how it runs as a science and not as poetry”. I respect these requests. This essay is the beginning of a response. But I am afraid my response may not be quite what my correspondents were looking for. The crucial issue, we will find, is whether their insistence upon a definition and an exact method is an insistence upon conformity to the very science we need to reform. After all, we typically try to define a thing by holding it fast, freezing it, nailing it down. We want to say what it is, so that we can point at and delineate it in no uncertain terms. We want to grasp it securely and without ambiguity.

There is, in other words, an aggressive philosophical stance concealed in the seemingly innocent demand for a definition. But what if reality, like water, slips through our clutching fingers? How much good will it do us to pin something down if the reality we are trying to lay hold of is a power of movement and becoming — a living, animating power by which each thing is continually becoming something different? What if the entire business of qualities is to express the moving, pulsing, darting, gliding, ascending and descending, throbbing, living, self-transforming character of the world's phenomena? Can we exactly define that which is continually transforming itself?

If, from the start, we insist that the poet could not possibly be exercising badly needed cognitive faculties neglected by today's dominant science — well, then, we are not asking what sort of new science might arise. Rather, we are insisting that, whatever it is, it must embody the limitations of the science we already have.

(from “Recognizing Reality”)

December 13, 2021

Tolkien once wrote that we create “by the law in which we’re made.” Our own creative speech is one, or potentially one, with the creative speech of nature that first uttered us. (How could it be otherwise?) This suggests that our relation to every wild thing is intimate indeed. We speak from the same source. We cannot know ourselves — cannot acquaint ourselves with the potentials of our own speaking — except by learning how those potentials have already found expression in the stunning diversity of nature.

Every created thing images some aspect of ourselves, an aspect we can discover and vivify only through understanding. The destruction of a habitat and its inhabitants is truly a loss of part of ourselves, a kind of amnesia. Wendell Berry is right to ask, “How much can a mind diminish its culture, its community and its geography — how much topsoil, how many species can it lose — and still be a mind?” As Gary Snyder puts it, “The nature in the mind is being logged and burned off.”

When Thoreau told us, “In wildness is the preservation of the world,” the wildness he referred to was at least in part our wildness. If humankind fails to embrace with its sympathies and understanding — which is to say, within our own being — every wild thing, then both we and the world will to that extent be diminished. This is true even if our refusal goes no further than the withdrawal from conversation.

(from “A Conversation with Nature”)

December 6, 2021

It is not at all clear how a universe of appearing things — things declaring themselves to us and bearing the sources of our language and thought within them — could possibly be alien to our own story. Not only have we drawn our interior life from the world’s meanings, both sublime and awful, but we live in a world whose very nature is to be encompassed within our consciousness — to live within us. Far from finding ourselves strangers in an alien universe, we embrace with our imagination and understanding the most distant galaxies, bearing witness to the significances of their light.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

November 29, 2021

How does the cell divide? How is body temperature maintained? How do signals originate, move through the uncertainties of multicellular environments, get transduced, and ultimately produce their specific effects within individual cells? — such inquiries about sustained narratives commonly provide the questions for molecular biological research projects. But the “explanations” arrived at typically abandon the narrative context of the original inquiry and focus instead on isolated physical causes. For example, how does the structure of this molecule fit together with the structure of that one, or which proteins interact with which others? It may be implied that answers to such questions explain the narrative, but they never do. The physical transactions are simply caught up in the narrative.

The truly biological problems have to do with how countless such interactions are woven together as the threads of an integral and recognizable story, when it would be perfectly lawful, in a physical sense, for every one of the interacting molecules to head off in a direction irrelevant to the storyline and engage in any one of a thousand other transactions. No analysis of physical lawfulness can distinguish the different cases, because physical laws know nothing of the organism’s storyline.

What the typical explanations fail to acknowledge, in other words, is the overall, ongoing, coordinated activity — the appearance of purpose — that prompted the very questions the biologists began investigating. The language of physical causes never gets us to the story of the organism — never traces the organism’s unique and colorful path through its own world. Of course, we do need the usual physical picture, but we get its meaning only when we look through it, rather as we “listen through” the physical sounds of speech in order to discern the thoughts and intentions of the speaker.

(from “The Problematic Effectiveness of Reason in Biology”, Part 1 of “From Bodily Wisdom to the Knowing Self”)

November 22, 2021

The problem of form in the organism — how does a single cell (zygote) reliably develop to maturity “according to its own kind” — has vexed biologists for centuries. But the same mystery plays out in the mature organism, which must continually work to maintain its normal form, as well as restore it when injured. It is difficult to bring oneself fully face to face with the enormity of this accomplishment. Scientists can damage tissues in endlessly creative ways that the organism has never confronted in its evolutionary history. Yet, so far as its resources allow, it mobilizes those resources, sets them in motion, and does what it has never done before, all in the interest of restoring a dynamic form and a functioning that the individual molecules and cells certainly cannot be said to “understand” or “have in view”.

We can frame the problem of identity and context with this question: Where do we find the context and activity that, in whatever sense we choose to use the phrase, does “have in view” this restorative aim? Not an easy question. Yet the achievement is repeatedly carried through; an ever-adaptive intelligence comes into play somehow, and all those molecules and cells are quite capable of participating in and being caught up in the play.

(from “Who Are You and Who Am I and Who Are We?”)

November 15, 2021

Meaning is a fundamental given of the world we live in. If there is anything in the evolutionary literature purporting to explain the origin of speech that does not already assume a capacity for speech, I would like to know about it. As Owen Barfield has succinctly fingered the matter: asking about the origin of language is like asking about the origin of origin. We can speak only because we were first spoken. And before we were spoken, the single cell was spoken, bearing in all the narrative details of its molecular adeptness and harmony the reverberating imprint, the resonance, of the speaking through which it lives.

So, no, we do not require a tortuous philosophical analysis of meaning. We need only wake up to the sea of meaning within which we all swim, and without which we would have no world whatever. We live by grace of meaning; our world is a logos-world. To pretend to refuse this meaning is to attempt a self-effacement (and a world-effacement) we can never fully carry out. It is to refuse to stand awake as human beings.

Meaning never arises from the non-meaningful. The question we should ask ourselves is not whether meaning can arise from what is not meaningful, but whether “not meaningful” makes any sense at all. Which, of course, is to ask whether “meaninglessness” has any meaning. That’s the kind of absurd territory we lose ourselves in when we ask for an informative and truthful science without meaning.

(from “How Biologists Lost Sight of the Meaning of Life”)

November 8, 2021

Nothing here implies that humans possess greater “moral worth” (whatever that might mean) than other living things. What distinguishes us is not our moral worth, but the fact that we bear the burden of moral responsibility. That this burden has risen to consciousness at one particular locus within nature is surely significant for the destiny of nature. When Jack Turner suggested that the last ten thousand years of human history may have been “simply evil,” he ignored the worthy historical gift enabling him to pronounce such a judgment. How can we downplay our special gift of knowledge and responsibility without fatal consequences for the world?

(from “A Conversation with Nature”)

November 1, 2021

We have seen that a great unknown presses in upon us from all sides. Despite our impressive technological successes, the fundamental terms of our science remain seemingly impenetrable mysteries. What one physicist wrote in 1985 is no less true today: “As yet no physicist can tell you what sort of world we happen to live in”. Humbling as it may seem in an era so arrogantly dismissive of the past, our current physical science gives us no basis for belittling the ancient human experience of living in something rather more like a universe of beings than a universe of things.

But we have also seen that an intelligible world is more intimately near to us than most of us have dared to hope. If we understand the world at all — and we are all convinced we do — it can only be because it consists, by nature, of qualitative appearances (“phenomena”) available to experience. It presents itself on the stage of our inner being.

And, finally, by looking at the history of language we have seen that the expressive face of the world appeared to our ancestors as a kind of speech, and it was from this presentation that our own powers of speech derived. Like language, every natural phenomenon was an exterior through which there shone interior significances. The essential elements of nature were not mute, expressionless things, but resonant images symbolizing meanings.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

October 25, 2021

We find some sort of reason and intention (or purpose) at all levels of biological description. No explanation of electrical, mechanical, and chemical interactions in a dividing cell conveys the narrative meaning of cell division. Nearly all the specific interactions, considered singly, could occur under other circumstances, or could occur differently in the present circumstances. Their elaborate and magnificently coordinated “striving toward cell division” — a striving that tries to adapt in a consistently directed way to whatever conditions the environment may throw up — does not lawfully follow from the underlying physical lawfulness. The striving and adjustment to circumstances, rather than being explained by the physical lawfulness, gives direction to it.

In one way or another all biologists acknowledge intention or purpose in this inescapable, practical, and descriptive sense. They recognize that the objects of their study are creatures caught up in a narrative — a narrative that is coming from somewhere and going somewhere in a reasonable, means-end sort of way, and not merely a law-abiding way. Organisms live purposeful lives. Yet, it is this narrative stream that the molecular biological literature assiduously ignores.

(from “The Problematic Effectiveness of Reason in Biology”, Part 1 of “From Bodily Wisdom to the Knowing Self”)

October 18, 2021

Even a superficial acquaintance with the biological literature today makes it clear that the effort to explain the whole organism as a result of self-contained causal parts that do not participate in, and are not sustained by, the life of their larger context is destined to fail. If biologists are going to speak incessantly about the importance of context, then they need to reckon honestly with the problems it raises, rather than immediately change the subject to “controlling factors” — factors that, as the contemporary literature makes so vividly clear, never do control in absolute terms. If all such factors are context-dependent, we ought at least to ask ourselves how this qualification modifies the notion of “control”.

We are, in fact, beset by questions on all sides. What exactly are we referring to when we speak of “context” and “organism”? How can we make these terms, as we are compelled to use them, more than necessary blanks in our descriptive language — blanks about whose necessity we can say nothing? For example, does our actual use of these terms differ much from the way people of an earlier era might have used “archetype” or “entelechy” or “being”?

When biologists speak of the organism’s activity, who exactly do they mean to say is performing that activity? When they acknowledge that something in the organism is context-dependent, what in fact is it dependent upon — what agency, or unified sphere of activity, or principle, or lawfulness, or other reality of any sort are they appealing to? They cannot be pointing merely to a particular collection of objects, because the collection can be endlessly varied or perturbed, and yet the context remains more or less coherent, and the organism more or less maintains its character. What is coherent? What has this character?

(from “Who Are You and Who Am I and Who Are We?”)

October 11, 2021

If we cannot define “meaning”, what are we doing when we ask what someone means? Apparently what we’re asking for is not something neatly packageable or nailed down like a ... — well, I was going to say “like a dictionary definition”. But, of course, dictionary definitions do not nail down anything at all. They define words by using other words, and simply assume that we will be able to dance our way into the midst of the circling words by moving in tune with the meanings we already possess and improvising upon them.

Meaning of any significance is never something we can hand someone definitively, because each word we speak depends upon and participates in all the others. We can never say of any profound meaning, “There! I’ve got it!” Meaning is a journey. We can only track meaning as we might track the blossoming of a flower, getting to know it better and better even as we continually lose its old form and must rediscover its truth newly metamorphosed.

The English philologist, Owen Barfield, reminded us that we can suggest meaning, but cannot convey it as though it were a “bit” of the information biologists are so fond of. This is why, as Barfield demonstrated, our grasp of new meaning is typically mediated by figurative or metaphorical language — language that can only encourage and assist us toward exercising our own powers for intuiting the content at issue. We do not transmit information; we assist at the birth of insight.

(from “How Biologists Lost Sight of the Meaning of Life”)

October 4, 2021

When we consider that an almost unfathomable intelligence is already at work in the zygote — for example, in the very processes through which the future brain will be formed and begin to function — it seems rather rash to regard the conscious intelligence with which we employ our brains as absolutely separate from that earlier, brain-forming intelligence. It’s not clear how we might even speak coherently about the presence of fundamentally disconnected intelligences at play within the unity of an organism.

(from “Toward a Thought-Full Teleology”)

September 27, 2021

The well-intentioned exhortation to replace anthropocentrism with biocentrism, if pushed very far, becomes a curious contradiction. It appeals to the uniquely human — the detachment from our environment that allows us to try to see things from the Other’s point of view — in order to deny any special place for humans within nature. We are asked to make a philosophical and moral principle of the idea that we do not differ decisively from other orders of life — but this formulation of principle is itself surely one decisive thing we cannot ask of those other orders.

There is no disgrace in referring to the “uniquely human.” If we do not seek to understand every organism’s unique way of being in the world, we exclude it from the ecological conversation. To exclude ourselves in this way reduces our words to gibberish, because we do not speak from our own center.

(from “A Conversation with Nature”)

September 20, 2021

So far as the historical record testifies, our evolutionary trajectory has not accorded with the usual assumptions. There is no evidence that we slowly ascended from a crude life of material unmeaning to a humanly contrived realm of meaning, value, culture, and spirituality. Our life today, with its materialistic convictions about the meaninglessness of nature, has required a long descent from the living, ensouled landscape upon which our ancestors were nurtured.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

September 13, 2021

Organisms do things; rocks have things done to them. Even at rest a cat is doing something; rocks do not rest, but are brought to rest. An organism is always engaged in tasks, always going somewhere. Its activity is directed and in some sense intentional and purposeful (“teleological”). Its judgments in responding appropriately to environmental challenges reflect a profound biological wisdom.

From the molecular level on up, organisms mobilize their resources in order to achieve things, whether replicating DNA, splicing RNA, orchestrating cell division, forming embryonic organs, healing wounds, breathing, constructing a nest, securing food, caring for offspring, shedding a skin, maintaining body temperature, hibernating, or anything else we can properly regard as biological activity. Such activity is always part of a life story, and the protagonist in that story is in some sense what every story protagonist must be: a reasoning agent.

But you will already have asked, quite rightly, what is meant by “reasoning agent”? And even if we are driven to use such a phrase, how can we distinguish an aphid’s “reasoning” from that of a nuclear physicist? This is the question I will address here. Until we sort the matter out, the language of the preceding paragraphs (and even much of the standard biological literature) invites horrible misunderstandings. Note that I have already twice said, in some sense. We must be on our guard.

(from “The Problematic Effectiveness of Reason in Biology”, Part 1 of “From Bodily Wisdom to the Knowing Self”)

September 6, 2021

[Regarding the hair follicle niche in mammals and the primacy of context over cellular identity:] Dramatically, the authors [of a technical article] show that “niche stem cells can be dispensable for tissue regeneration, provided that the overall integrity of the niche is maintained”. When the stem cell population in the bulge or hair germ is destroyed by laser ablation, distant epithelial cells flow toward the damaged compartment and go through a transformation of identity enabling them to replace the lost cells. As the authors summarize it, “The overall structure and function of the tissue is maintained because cells are capable of adopting new fates as dictated by their new niche microenvironment”.

It is impossible to reconcile these goings-on in the hair follicle with the picture of an organism being constructed from an available collection of well-defined parts as building blocks. The larger context helps to “decide” what sorts of elements it will have, how they should be transformed, and how they will come into mutual relationship. Nothing could be further from the common picture of the organism or the cell as a product of bottom-up causation, where the sole basis for understanding consists of putting back together in our minds the parts we have previously analyzed out of — and severed from — their life-receiving connection to the whole.

(from “Who Are You and Who Am I and Who Are We?”)

August 30, 2021

[Regarding physicist Steven Weinberg’s remark that “The more the universe seems comprehensible, the more it also seems pointless”:] By “pointless”, Weinberg later explained, he meant “not particularly directed toward human beings” (NPR interview, undated). But what does that mean? Surely we do not need, or want, the universe pointing to us in some selfish sense. But when we comprehend things — when we are joined to them in an act of understanding — they lend themselves to the intimacy of our innermost being; their sensibility becomes our own. A universe that gives itself to us in this way does not seem to have the “chilling, cold impersonal quality” Weinberg finds in it.

Actually, you couldn’t find more anthropomorphic — which is to say, more humanly meaningful — terms than “chilling”, “cold”, and “impersonal”. Weinberg, one happily notes, has not entirely fled his own humanity. And we doubtless do run into things we justly describe with the qualities he discerns, thereby relating them to our inner life and discovering something about their character. It’s just that these are not the only or even the most common qualities human beings find when they gaze, fully informed, into a starry sky or the teeming protoplasm of a living cell.

(from “How Biologists Lost Sight of the Meaning of Life”)

August 23, 2021

When a pianist plays a Beethoven sonata, the infinitely complex movements of her fingers, arms, and whole body must somehow express her intentions. On any particular occasion — say, a funeral or wedding — she may inflect her interpretation so as to yield a slight shift of character and mood. This means she will modify all those complex movements in an almost unthinkably nuanced manner.

The result is an utterly refined physiological realization of her intentions, all the way down to the finest details of gene expression. These must vary, for the sake of the performance, from one cell to the next over trillions of cells.

So tell me: Do we, in this picture, find any break between the pianist’s conscious effort to realize her expressive intentions, and the unconscious expression of those intentions at the molecular level? Is not every cell of her body informed by her thoughts, feelings, and intentions — this despite the fact that no cell thinks, feels, or intends in any way we would want to call “conscious”?

(from a talk titled “Toward a Thought-Full Teleology”)

August 16, 2021

The classicist, Bruno Snell, somewhere remarked that to experience a rock anthropomorphically is also to experience ourselves petromorphically — to discover what is rock-like within ourselves. It is the kind of discovery we have been making, aided by nature and the genius of language, for thousands of years. It is how we have come to know what we are — and what we are is (to use some old language) a microcosm of the macrocosm. Historically, we have drawn our consciousness of ourselves from the surrounding world, which is also to say that this world has awakened, or begun to awaken, within us.

(from “A Conversation with Nature”)

August 9, 2021

Historically, then, nature presented us with exteriors whose inner significances were, so to speak, written on their faces. Phenomena constituted a living language, rather as, still for us today, the sense-perceptible human face can scarcely be distinguished from its expressive eloquence — from the meaning it communicates. Similarly, it was from the evocative countenances of nature that our forebears discovered, in a living unity, the profound potentials of meaning that eventually yielded our current, analytically refined language.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

August 2, 2021

How, precisely, do we define a protein, when its form and function depend on the molecules with which it associates? How do we understand the identity of a cell in the developing embryo, when it can become any one of many different kinds of cell, depending on where it migrates to? And when we find the same plant with a radically different character in different environments, what are we recognizing as the “same”? How, if at all, can we conceive the separate identity of something that is always taking on the character of its larger context?

(from “Who Are You and Who Am I and Who Are We?”)

July 26, 2021

To demand a definition of “meaning” — that is, to ask for the meaning of “meaning” — is actually to run away from it. Meaning is where we start from. We cannot define it because meanings are what we employ in order to define things. Asking what “meaning” means is like trying to prove the validity of the logic we use in proofs. As human beings we must — and do every day — simply wake up to meaning. If we possess cognitive capacities, even as infants, it can only be because these capacities are themselves products of the world’s play of meaning — call it the logos if you wish — through which you and I have come into being.

So asking about the meaning of “meaning” does not send us in a circle. It returns us to our origin and to the immediately given character of the world that produced the deer and bee and us.

(from “How Biologists Lost Sight of the Meaning of Life”)

July 19, 2021

It seems that, while we are free to imagine organisms chock full of machines, information processors, and cybernetic devices — all of which import the human interior into the organism — any actual reckoning with this conscious interior is taboo.

(from a talk titled “Toward a Thought-Full Teleology”)

July 12, 2021

[Regarding the view that humans are incompatible with nature and can only harm it:] We do as much damage by denying our profound responsibilities toward nature as by directly abusing them. If you charge me with anthropocentrism, I accept the label, though on my own terms. If there is one creature that may not healthily scorn anthropocentrism, surely it is ó anthropos. How should we act, if not from our own center and from the deepest truth of our own being? But it is exactly this truth that opens us to the Other. We are the place within nature where willing openness to the Other becomes the necessary foundation of our own life ...

There is no disgrace in referring to the “uniquely human.” If we do not seek to understand every organism’s unique way of being in the world, we exclude it from the ecological conversation. To exclude ourselves in this way reduces our words to gibberish, because we do not speak from our own center.

(from “A Conversation with Nature”)

July 5, 2021

The story of the Greek sun-god “Helios” could hardly have originated as an animistic effort to account for a material sun, given that neither the history of language nor what we know of mythic consciousness affords any evidence that a purely material sun had yet been conceived. The sun’s glory, its light and warmth, were directly and non-reflectively experienced as ensouled realities.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

June 28, 2021

What do we mean when, regarding ourselves, we speak, as so many do, of a psychosomatic unity? Who will specify exactly what is meant by the psychological half of “psychosomatic”? And whatever is meant by it, how and in what sense do psyche and soma become a unity? — a question neither biologists nor cognitive scientists nor philosophers have been able to resolve with any hint of consensus, despite centuries of effort. Looking beyond ourselves, in what sense do we find anything like a psychosomatic unity in chimpanzee, nightingale, cricket, or amoeba? If we cannot answer such a basic question despite our being driven to employ a descriptive language that includes both physical and psychic terminology, then what do we understand?

(from “Who Are You and Who Am I and Who Are We?”)

June 21, 2021

We are nothing but creatures of meaning. We never make a movement that isn’t a meaningful gesture — one that the psychiatrist, physical therapist, student of temperaments, sociologist, stage director, and all the rest of us can read with more or less success. Even an infant, in its own way, finds significance in the most subtle human movements. Any infant who is not raised in a speaking environment fails to develop anything like normal human capacities. And “speaking environment” refers to the meaning implicit in every significant gesture. Before they themselves can speak, infants take an interest in and learn to read gestures — to the point of distinguishing, in silent videos, between speakers of two languages they have never heard before.

Meaning is just there, whether we speak words or not. Every act of ours is a signifying. And we collectively understand each other’s meanings well enough to engender civilizations that are infinitely complex tapestries woven from those meanings ...

Here, then, is my question for the skeptic: Where in the pervasive matrix of meaning I have just characterized do you find an unscientific obscurantism? More particularly, which of the meanings you speak and understand and found your life upon and discover in other creatures is a puzzle to you? I would like to know the precise nature of the disreputable element in these meanings you live by — for example, in all the words you have spoken, understood, and been willing to respond to today. This collection of words, I am sure, goes far beyond the more acceptable technical terms of any particular science. Yet, apart from specially deserving cases, you don’t recoil from such words in disgust.

(from “How Biologists Lost Sight of the Meaning of Life”)

June 14, 2021

[Regarding human manipulation of the natural environment:] There is an alternative to the ideal of prediction and control. It helps, in approaching it, to recognize the common ground beneath scientific managers and those who see all human “intrusion” as pernicious. Both camps regard nature as a world in which the human being cannot meaningfully participate. To the advocate of pristine wilderness untouched by human hands, nature presents itself as an inviolable and largely unknowable Other; to the would-be manager, nature is a collection of objects so disensouled and unrelated to us that we can take them as a mere challenge for our technological inventiveness. Both stances deprive us of any profound engagement with the world that nurtured us.

My own hope for the future lies in a third way. Perhaps we have missed this hope because it is too close to us. Each of us participates in at least one domain where we grant the autonomy and infinite worth of the Other while also acting boldly to affect and sometimes even rearrange the welfare of the Other. I mean the domain of human relations.

We do not view the sovereign individuality and inscrutability of our fellows as a reason to do nothing that affects them. But neither do we view them as mere objects for a technology of control. How do we deal with them? We engage them in conversation.

(from “A Conversation with Nature”)

June 7, 2021

In Odysseus’ day, techne was a conscious resourcefulness that had scarcely begun to project itself into the material apparatus of life. What apparatus existed was an enticement for further creative expression of the nascent human self. While the technology of the Greeks may seem hopelessly primitive to us, it is worth remembering that the balanced awakening heralded by Homer culminated in a flowering of thought and art that many believe has never been surpassed for profundity or beauty anywhere on earth.

Today, that balance seems a thing of the past. The powers of our minds crystallize almost immediately, and before we are aware of them, into gadgetry, without any mediating, self-possessed reflection, so that we live within a kind of crystal palace that is sometimes hard to distinguish from a prison. The question is no longer whether we can use the enticement of clever devices as a means to summon the energies of dawning selfhood; rather, it is whether we can preserve what live energies we once had, in the face of the deadening effect of the now inert cleverness bound into the ubiquitous external machinery of our existence.

(from “The Deceiving Virtues of Technology”, Chapter 1 of In the Belly of the Beast)

May 31, 2021

We have learned, especially since Darwin, that knowledge of the past illuminates the biological present — that, as the mantra of contemporary evolutionary theorists would have it, “Nothing in biology makes sense except in the light of evolution”. The mantra could serve as Barfield’s theme as well, but with this difference: he did not forget to include consciousness in that which evolves. The omission, after all, looks on its face to be disastrous. If we had no hope of fully understanding the biology of organisms before the idea of evolution dawned upon us, how much more must we remain in darkness while ignoring the evolution of the cognitive instruments through which alone we can grasp that idea — that is, while ignoring the evolution of the instruments of our understanding itself.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

May 24, 2021

In biology, the word “mechanism” today often refers merely to “lawful physical interaction”. This habit of expression makes it easier to associate physical lawfulness with machines. But clouds, though physically lawful, are not machines. Nor are rocks and rivers. Nor is cytoplasm.

If only biologists using the word “machine” were required to say what they mean beyond “lawful physical interaction”! The only thing distinguishing a machine from physical objects generally is the human purpose unnaturally imposed on the arrangement of parts. So anyone who feels the need to draw on the idea of a machine rather than lawful objects unmanipulated by human intelligence, is probably invoking human purposes under the table, even if unwittingly.

(from a draft of a talk titled “Toward a Thought-Full Teleology — Beyond the Hollow Organism”. The talk, not yet publicly available, is scheduled to be delivered at a June 28-29, 2021 conference sponsored by The Linnean Society of London. The conference theme is “Evolution ‘On Purpose’: Teleonomy in Living Systems”.)

May 17, 2021

In every sphere of knowledge it’s easy to put out of mind those questions that are so fundamental and yet so seemingly impenetrable that they leave everything we think we understand woefully ungrounded. Biology is no exception.

Who, or what, is the organism, and what guarantees the remarkable unity of character, the distinctive and recognizable way of being, consistently achieved by the developing individuals of a species? Where do we look for collection of parts — an explanation for the integral performance of the whole?

(from “Who Are You and Who Am I and Who Are We?”)

May 10, 2021

Are the meanings we find in the world specifiable? I would answer that we can always make a start at a valid description and, happily, we can never make an end of it. In observing the rose, we may note its color and beauty, its water- and sap-transporting processes, its thorny power of rending, its changing appearance under sunlight, shade, and moonlight, its unique relationship with each insect among its circle of animal companions, the scent of its flowers, its way of reflecting the world in a dewdrop, the distinctive pattern of its root growth, its cellular metabolism from one cell type to another, the sour taste of its fruits, and much, much more. And we may hope to glimpse, running through all these features, the unity that constrains the entire ensemble to perform qualitatively and harmoniously as this kind of plant, and not another.

No human biography or characterization of a plant is ever complete, but neither are we absolutely barred from any understanding we may seek. That is the way with meaning; we can always plumb it more deeply or from different angles. Meaning is never a fixed quantity, but always opens out onto the entire universe of meaning. Text and context are inseparable. And if we know enough to ask a half-way coherent question, then in the very framing of the question we have already found our way toward some of the understanding we seek.

(from “How Biologists Lost Sight of the Meaning of Life”)

May 3, 2021

Why, after all, does Jack Turner agree with his opponents that acceptable “messing” with ecosystems would have to be grounded in successful prediction and control? Once we make this assumption, of course, we are likely either to embrace such calculated control as a natural extension of our technical reach, or else reject it as impossible. And yet, when I sit with the chickadees, messing with their habitat, it does not feel like an exercise in prediction and control. My aim is to get to know the birds, and to understand them. Maybe this makes a difference.

(from “A Conversation with Nature”)

April 26, 2021

[Russian philosopher Vladimir Solovyov remarked that] “The body of the universe is the totality of the real-ideal, the psycho-physical”. Solovyov points out that there can be no such thing as a “material unity” — not, at least, as matter is normally conceived. “Material things”, imagined as empty of thought, just coexist side by side. Any unity must be ideal. After all, even the mathematical laws of physics, which offer one route toward a unified understanding of phenomena, are ideas — but ideas that belong both to our understanding and to the nature of things themselves.

(from “Vladimir Solovyov on Sexual Love and Evolution”)

April 19, 2021

[It would be well to say:] “technology is our hope if we can accept it as our enemy, but as our friend, it will destroy us.” Of course technology threatens us, and of course it calls for a certain resistance on our part, since it expresses our dominant tendencies, our prevailing lameness or one-sidedness. The only way we can become entire, whole, and healthy is to struggle against whatever reinforces our existing imbalance. Our primary task is to discover the potentials within ourselves that are not merely mechanical, not merely automatic, not reducible to computation. And the machine is a gift to us precisely because the peril in its siding with our one-sidedness forces us to strengthen the opposite side — at least it does if we recognize the peril and accept its challenge.

(from “The Deceiving Virtues of Technology”, Chapter 1 of In the Belly of the Beast)

April 12, 2021

According to the evolutionary story that most of us have forcibly absorbed from a young age, humankind somehow raised itself above the beastly, mindless, material substrate of its origin so as to achieve, step by step, the mystifying wonders of language and poetry, music and art, politics and science, and all the other sublimations contributing to high culture. The sea of meaning within which we now swim — without which we would have nothing we could recognize as human life — somehow bubbled up from somewhere, if only as an illusion of the human mind, and cast a kind of spell over the bedrock meaninglessness of brute matter.

“Somehow”, I say, since the meaning at issue, and the question how it could have emerged from an eternal silence of Unmeaning is so great an enigma for conventional thinking that it has received no fundamental elucidation. Nor is it evident that we need to seek an origin of meaning. Perhaps what we will actually discover is a larger, meaning-soaked surround, progressively coming to a focus in human minds.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

April 5, 2021

René Descartes’ cleaving stroke through the heart of reality has been almost universally accepted — perhaps most of all in biology. We live with the violence done to the unity and harmony of the world by that stroke, and merely choose which half of this improbably fractured whole to accept and which half to reject. And so the “material” that materialists accept is dualistic material, just as the mind, or interiority, they reject is dualistic interiority. Instead of searching for a non-Cartesian way forward, we imagine ourselves shut up in suspiciously deceptive minds, looking out at an alien world of mindless extended substance.

(from a draft of a talk tentatively titled “Toward a Thought-Full Teleology — Beyond the Hollow Organism”. The talk, not yet publicly available, is scheduled to be delivered at a June 28-29, 2021 conference sponsored by The Linnean Society of London. The conference theme is “Evolution ‘On Purpose’: Teleonomy in Living Systems”.)

March 29, 2021

Precisely at the point in evolutionary history where the understanding consciousness arises and becomes aware of itself, it begins to deny its own powers. We are those who, by grace of our own evolutionary inheritance, can in one way or another enter into the meaning of the life of every living creature and make it our own. Yet, fearing “anthropocentrism” — which is to say, fearing ourselves — we end up belittling the gift of understanding.

As for the dangers of anthropocentrism: yes, there are such dangers. Projecting ourselves onto other creatures as if they were blank screens is always a temptation. But I would say an equal danger today is quite the opposite. We are òi anthropoi, and it is therefore our obligation to be properly anthropocentric — to exercise our full potentials rather than to project onto ourselves and fellow organisms the character of particular mechanical products of our own activity. Scientists wish to understand life. Wouldn’t it be far better if they brought to bear upon this life the expressive powers of the living, cognizing thought through which we conceive and build machines, rather than constrain their thinking to the deadened terms of the contrived objects?

(from “How Biologists Lost Sight of the Meaning of Life”)

March 22, 2021

If bird feeders are problematic [because of an unnatural crowding of birds], what was I to think of my own habit of sitting outside for long periods and feeding birds from my hands? Especially during the coldest winter weather and heavy snowfalls, I sometimes found myself mobbed by a contentious crowd, which at different times included not only chickadees but also titmice, red- and white-breasted nuthatches, hairy woodpeckers, goldfinches, juncos, blue jays, cardinals, various sparrows, and a red-bellied woodpecker. To my great delight, several of the less wary species would perch on shoulders, shoes, knees, and hat, as well as hands.

But by what right do I encourage tameness in creatures of the wild? The classic issue here has to do with how we should assess our impact upon nature. Two views, if we drive them to schematic extremes for purposes of argument, conveniently frame the debate ...

(from “A Conversation with Nature”)

March 8, 2021

The Russian philosopher Vladimir Solovyov spoke of a two-fold impenetrability of things: they are separated from each other both in time and in space. “That which lies at the basis of our world is being in a state of disintegration, being dismembered into parts and moments which exclude one another”.

Overcoming this disintegration — re-membering ourselves and the world in which we live — is, as Solovyov saw it, a personal and social task with cosmic implications ... He cited — to give but one example of the principle of unity — a simple, profound, and universal physical phenomenon, one that would change a great deal of modern thought if we would only spend some time contemplating it: I mean the phenomenon of two objects gravitationally attracting each other. In Solovyov’s language: here we see that “parts of the material world do not exclude one another, but, on the contrary, aspire mutually to include one another and to mingle with each other”.

We could not retain our commonplace image of separate parts if we truly reckoned with the mutual participation of two objects gravitationally attracted to each other. It is not a matter of one object exerting an external force upon another “from a distance” (as students are often asked to imagine the matter), but of two entities caught up in a single, unified embrace wherein the being — the very substance and activity — of one is inseparable from that of the other. This truth, evident enough to the physicist, suggests that there is something pathological about our routine habits of perception through which we form our picture of a world consisting of separate and disconnected objects.

(from “Vladimir Solovyov on Sexual Love and Evolution”)

March 1, 2021

Early technological man carved out his civilized enclosures as hard-won, vulnerable enclaves, protected places within an enveloping wilderness full of ravening beasts and natural catastrophes. We, by contrast, live within a thoroughly technologized and domesticated landscape where it is the remaining enclaves of wildness that appear painfully delicate and vulnerable. Today, if we would set bounds to the wild and lawless, it is the ravening beast of technology we must restrain. If nature still threatens us, the threat is that it will finally and disastrously succumb to our aggressions.

(from “The Deceiving Virtues of Technology”, Chapter 1 of In the Belly of the Beast)

February 22, 2021

The question, “What sort of world do we live in?” came to be enveloped in darkness precisely at the point where our science was thought to be most fundamental! We have a physics of light and color framed as far as possible in language suitable for those who cannot see, and a science of acoustics that might just as well have been formulated by those who cannot hear.

The dismissal of qualities from science — which is to say, the dismissal of the world of experience — has meant that physicists, when they venture at all beyond their equations and well-designed instruments, lose themselves in a Wild West of speculation, illustrated by the “many worlds” theories so prominently heralded today. This is high-flying conjecture that puts to shame those medieval doctors whose soaring intellectual acrobatics were precisely what the pioneers of the Scientific Revolution so badly wanted to bring down to earth, where ideas could be tested within human experience.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

February 15, 2021

Where do we look for an understanding of life? Where, if anywhere, does life put its own meaning on display most forthrightly and clearly?

There is one high promontory within the sprawling panorama of life on earth that does indeed afford a perspective upon the whole — a place from where the unique processes occurring throughout the kingdoms of life become peculiarly visible, manifesting their significance. There is, we can know without a doubt, one evolutionary achievement that offers not only an unlimited survey of the entire drama of life, but also lends itself to the penetrating insight we need for recognizing and expressing the many meaningful aspects of the drama.

This evolutionary achievement lies in the place we know best — in fact, the only place where the necessary sort of knowing occurs at all. It is where life becomes conscious of itself — where the living creature not only acts out its own significant existence, but is capable of contemplating this existence along with that of all other living things. It is the one outgrowth within the great, age-old tree of life where life’s own power of survey blossoms and reaches its fullest fruition: the understanding consciousness of man.

(from “How Biologists Lost Sight of the Meaning of Life”)

February 8, 2021

What must be realized through individual human striving today can be seen as an expression — a further development and transformation — of the very processes that were at work in simpler, less individuated life forms. When we observe animals of increasing complexity, we notice a progressive internalization of function and an expansion of interior, sentient life, culminating in self-awareness. That which worked on the organism throughout evolutionary history to develop this capacity for self-awareness, now works through the human being in the exercise of this capacity. Is there any reason to doubt that it is the same power in both cases?

All of which suggests that evolution has had a certain mindful character all along — or a more-than-mindful character, inasmuch as the power to engender minds can hardly be alien or inferior to the capacity of the minds it engenders.

(from “Vladimir Solovyov on Sexual Love and Evolution”)

February 1, 2021

I’d like you to think for a moment of the various words we use to designate technological products. You will notice that a number of these words have a curious double aspect: they, or their cognate forms, can refer either to external objects we make, or to certain inner activities of the maker. A “device,” for example, can be an objective, invented thing, but it can also be some sort of scheming or contriving of the mind, as when a defendant uses every device he can think of to escape the charges against him. The word “contrivance” shows the same two-sidedness, embracing both mechanical appliances and the carefully devised plans and schemes we concoct in thought. As for “mechanisms” and “machines,” we produce them as visible objects out there in the world even as we conceal our own machinations within ourselves. Likewise, an “artifice” is a manufactured device, or else it is trickery, ingenuity, or inventiveness. “Craft” can refer to manual dexterity in making things and to a ship or aircraft, but a “crafty” person is adept at deceiving others.

This odd association between technology and deceit occurs not only in our own language, but even more so in Homer’s Greek, where it is much harder to separate the inner and outer meanings, and the deceit often reads like an admired virtue. The Greek techne, from which our own word “technology” derives, meant “craft, skill, cunning, art, or device” — all referring without discrimination to what we would call either an objective construction or a subjective capacity or maneuver. Techne was what enabled the lame craftsman god, Hephaestus, to trap his wife, Aphrodite, in a promiscuous alliance with warlike Ares. He accomplished the feat by draping over his bed a wondrously forged snare whose invisible bonds were finer than a spider’s silken threads. The unsuspecting couple blundered straightway into the trap. As the other gods gathered around the now artless couple so artfully imprisoned, a gale of unquenchable laughter celebrated the guile of Hephaestus. “Lame though he is,” they declared, “he has caught Ares by craft (techne).” Here techne refers indistinguishably to the blacksmith’s sly trickery and his skillful materialization of the trick at his forge.

Likewise, the Greek mechane, the source of our “machine,” “mechanism,” and “machination,” designates with equal ease a machine or engine of war, on the one hand, or a contrivance, trick, or cunning wile, on the other. The celebrated ruse of the Trojan Horse was said to be a mechane, and it was admired at least as much for the devious and unexpected turn of mind behind its invention as for the considerable achievement of its physical construction.

(from “The Deceiving Virtues of Technology”, Chapter 1 of In the Belly of the Beast)

January 18, 2021

If we believe that an empirical (experience-based) science — a science grounded in the conceptual ordering of sensible appearances — really does give us genuine knowledge of the world, then a reasonable conclusion is that this world is, by nature, a realm of conceptually ordered appearances possessing the qualities of sense. It asserts its existence and character in the terms of conscious, thought- and sense-derived experience.

(from “A Physicist, a Philosopher, and the Meaning of Life”)

January 11, 2021

[Regarding the nineteenth-century Russian philosopher Vladimir Solovyov’s treatment of evolution:] Consciousness alone is where the evolutionary process is first fully and explicitly realized. Evolution here “comes into its own” and declares itself in human awareness. That which has gone on from the beginning now operates, at least in part, through the conscious choice of the individual and the quest for universal ideals.

In slightly different words: what must be realized through individual human striving today can be seen as an expression — a further development and transformation — of the very processes that were at work in simpler, less individuated life forms. When we observe animals of increasing complexity, we notice a progressive internalization of function and an expansion of interior, sentient life, culminating in self-awareness. That which worked on the organism throughout evolutionary history to develop this capacity for self-awareness, now works through the human being in the exercise of this capacity. Is there any reason to doubt that it is the same power in both cases?

All of which suggests that evolution has had a certain mindful character all along — or a more-than-mindful character, inasmuch as the power to engender minds can hardly be alien or inferior to the capacity of the minds it engenders.

(from “Vladimir Solovyov on Sexual Love and Evolution”)

January 4, 2021

[Concerning the fairly recent researches into “competing endogenous RNAs”:] They participate in a vast “breathing” process, one of whose primary outcomes is the regulation — the balancing and counterbalancing — of the mRNAs themselves in proper relation to ever-changing conditions in the cell and its environment. The challenge for our understanding is considerable when we realize that all these RNAs are (to revise the metaphor only slightly) “swimming” in a common pool, one whose significant eddies and currents can be intricately distinct even as they continually flow one into the other.

The upshot of it all is that protein-coding RNAs are found to share broadly in the fluid life of the organism, and not to be mere cogs in a deterministic mechanism. In particular, they gain additional, noncoding (regulatory) functions, and the sharp distinction between coding and noncoding regions of DNA begins to look even more artificial than it has already become.

(from “RNA: Dancing with a Thousand Partners”)

December 28, 2020

Surely our technological prowess does reflect a practical knowledge of the world. But the pleasure and wonder of it easily blinds us to the fact that we remain infants in fundamental understanding. How often do we remind ourselves that the nature of matter and energy is a mystery to us, or that, when we speak of “the physical”, it is difficult to indicate even roughly what we mean? When we get down to the submicroscopic specifics, we find nothing there, no thing of any recognizable sort. We identify reliable mathematical relations suggesting particular structure, but we do not know: the structure of what?

(from “A Physicist, a Philologist, and the Meaning of Life”)

December 21, 2020

[Owen Barfield, commenting on nineteenth-century philosopher Vladimir Solovyov’s view of sexual attraction and evolution, writes that Solovyov] opens with a biological survey which easily, and to my mind irresistibly, refutes the age-old assumption … that the teleology of sexual attraction is the preservation of the species by multiplication. On the contrary, it is apparent from the whole tendency of biological evolution that nature’s purpose or goal (or whatever continuity it is that the concept of evolution presupposes) has been the development of more complex and, with that, of more highly individualized and thus more perfect organisms. From the fish to the higher mammals quantity of offspring steadily decreases as subtlety of organic structure increases; reproduction is in inverse proportion to specific quality. On the other hand, the factor of sexual attraction in bringing about reproduction is in direct proportion. On the next or sociological level he has little difficulty in showing that the same is true of the factor of romantic passion in sexual attraction. Both history and literature show that it contributes nothing towards the production of either more or better offspring, and may often, as in the case of Romeo and Juliet, actually frustrate any such production at all.

Why then has nature, or the evolutionary process, taken the trouble to bring about this obtrusively conspicuous ingredient in the make-up of homo sapiens?

(from “Vladimir Solovyov on Sexual Love and Evolution”)

December 14, 2020

One finds that in once-isolated and sharply focused areas of molecular biological investigation, the focus is rapidly becoming less sharp. Boundaries are becoming more permeable, so that it is difficult to separate one topic from another. Every “classical” function of a molecule or structure or pathway is turning out to be just one of many different and often (at first) seemingly unrelated functions. Every niche is interwoven with other niches, and the play of “causes” and “effects” is more like the flow of a stream with its endless, interpenetrating eddies than an interaction of discrete machine parts

That’s why terms such as “network”, “systems approach”, “interconnected”, “combinatorial complexity”, and above all “crosstalk” and “context-dependence” now show up with such striking frequency in technical papers. The take-home message is that we’re witnessing a transformation in the way we must think of organisms.

(from “Dancing with a Thousand Partners”)

December 7, 2020

Can the kind of agency we witness so obviously in the development of an individual organism be at all applicable to evolution — that is, to vast populations of co-evolving organisms?

When we speak, not about physical processes as such, but rather about an underlying biological agency, intention, and purposiveness, then the distinction between an individual animal as a collection of molecules, cells, and tissues, on the one hand, and an entire population as a collection of organisms, on the other, becomes an open question. The whole business of telos-directed biological activity, wherever we have observed it, is to bridge radically different physical processes. That is, it brings diverse and complex physical phenomena — for example, in the brain, heart, liver, intestines, and skin of a developing mammal — into integral unity and harmony, making a larger whole of them. When we have seen this purposeful coordination and harmonization in one organic context involving many distinct physical elements, it is only natural to look for it in other organic contexts.

(from “Teleology and Evolution: Why Can’t We Have ‘Evolution on Purpose’?”)

November 30, 2020

When we speak of agency, we speak of capacities we ourselves routinely exercise. But at the same time we must admit that our experience of our own agency is closely bounded on all sides by mystery. We do not fully understand where our thoughts and actions come from, or how our intentions move our bodies. It would be a mistake to clothe the mystery of biological agency in the imagined form of a grandly sovereign, all-knowing human individual.

And if we cannot be entirely clear about the sources of agency in our own lives, we can hardly be dogmatic about the nature of the agency — or diverse agencies — at work in a single bee colony, a particular species of rodent, or the biosphere as a whole. Nothing, however, prevents our being good observers of living beings, which is also to be observers of the clear manifestations of biological agency. In this way we become familiar with the complex and perhaps many-voiced character — the way of being — of particular organisms.

(from “Teleology and Evolution: Why Can’t We Have ‘Evolution on Purpose’?”)

November 16, 2020

This sort of interpenetrability [characteristic of biological agencies] is exactly what we find in language — that is, in different contexts, and even in different words and phrases. We can put words together in infinitely varying ways. Any two words or ideas or philosophies, no matter how different, can be brought into meaningful relation, thereby modifying each other. A word is given its meaning by the character of the larger thought in which it participates, just as a heart receives its meaning from the larger organism in which it participates. Neither the word nor the heart thereby suffers a loss of identity, but rather gains in the richness of its meanings and its relational potentials.

(from “Teleology and Evolution: Why Can’t We Have ‘Evolution on Purpose’?”)

November 9, 2020

An animal’s development from zygote to maturity is a classic picture of telos-realizing activity. Through its agency and purposiveness, an animal holds its disparate parts in an effective unity, making a single whole of them. This purposiveness informs the parts “downward” from the whole and “outward” from the inner intention, and is invisible to strictly physical analysis of the interaction of one part with another.

(from “Teleology and Evolution: Why Can’t We Have ‘Evolution on Purpose’?”)

October 19, 2020

Technology is our hope if we can accept it as our enemy; as our friend it will destroy us. If we look to technology for the solution to our problems, we will only worsen our existing one-sidedness and invite the destruction of everything worth saving. If, on the other hand, we oppose technology with what is not machine-like in ourselves — with an ability to read the world instead of merely manipulating it and losing sight of it — then we will receive from technology the gift of our highest selves.

(from “Owen Barfield and Technological Society”)

Steve Talbott :: Biology Worthy of Life