{"id":10361,"date":"2011-05-18T00:00:00","date_gmt":"2011-05-18T04:00:00","guid":{"rendered":"http:\/\/localhost\/thenewatlantis.com\/publications\/what-do-organisms-mean"},"modified":"2021-04-06T13:40:31","modified_gmt":"2021-04-06T17:40:31","slug":"what-do-organisms-mean","status":"publish","type":"article","link":"https:\/\/www.thenewatlantis.com\/publications\/what-do-organisms-mean","title":{"rendered":"What Do Organisms Mean?"},"content":{"rendered":"

I<\/span>f a single problem has vexed biologists for the past couple of hundred years, surely it concerns the relation between biology and physics. Many have struggled to show that biology is, in one sense or another, no more than an elaboration of physics, while others have yearned to identify a \u201csomething more\u201d that, as a matter of fundamental principle, differentiates a tiger \u2014 or an amoeba \u2014 from a stone. The former, reductionist aim can easily seem to ignore what is special about living creatures \u2014 and above all to ignore the way meaningful human experience seems to transcend the kind of lawfulness we observe in inanimate physical objects. But, on the other hand, scientists who attempt to articulate a principle differentiating the living from the non-living have all too often posited some kind of special matter or vital force that no one ever seems able to identify.<\/p>\n

We discussed in previous articles how, whatever their belief in these matters, biologists today \u2014 and molecular biologists in particular \u2014 routinely and unavoidably describe<\/i> the organism in terms that go far beyond the language of physics and chemistry. Words like \u201cstimulus,\u201d \u201cresponse,\u201d \u201csignal,\u201d \u201cadapt,\u201d \u201cinherit,\u201d and \u201ccommunicate,\u201d in their biological sense, would never be applied to the strictly physical and chemical processes in a corpse or other inanimate object. But they are always employed in attempts to understand the living organism. The prevalent descriptions portray the whole organism as an active unity, with powers of regulation and coordination intelligently directed toward the achievement of the organism\u2019s own ends. Further, we noted that such descriptions, rooted as they are in the observable character of the organism, show no sign of being reducible to less living terms or to the language of mechanism.<\/p>\n

But this immediately raises a suspicion of vitalism in the minds of many scientists. Who, after all, is this organism? And by what special powers does it \u201cregulate,\u201d \u201cintegrate,\u201d \u201crespond,\u201d and \u201ccommunicate\u201d? Bear in mind, however, that these questions press just as urgently upon the conventional molecular biologist as on the suspected vitalist. After all, the loaded terminology comes straight from the laboratory, where researchers are trying to make sense of what they see.<\/p>\n

A subject possessing a power of agency adequate to regulate or coordinate at the level of the whole organism looks for all the world like what has traditionally been called a being<\/i>. But you will not find biologists speaking of beings. It\u2019s simply not allowed, presumably because it smells too<\/i> explicitly of vitalism, spiritualism, the soul, or some other appeal to an immaterial reality. We will see later what extraordinary confusion bedevils this attitude, but for now let us simply yield to the biologist\u2019s language of choice, provisionally defining a \u201cbeing\u201d as \u201cwhatever makes sense as the subject of all those terms of agency found in every biological research paper.\u201d What, or who, is capable of all the highly directed activity of cell and organism? We will leave aside for now any features of that agency other than ones for which the life scientist has vouched.<\/p>\n

To think of it positively: We are looking for a way to justify the standard language of biological theory and description. After all, a lot of experiment and observation has led to this language; if we start with it, we will surely gain valuable clues about the being of the organism. For example, the language tells us that every organism discriminates in many circumstances between health on the one hand and disease or injury on the other, and acts flexibly and intelligently \u2014 within its own limits and based on the particulars of its disorder (which may involve conditions it has never encountered before) \u2014 to restore health. More generally, it pursues a coherent path of development and self-maintenance, and manages to produce new life from existing life via intricate processes at the molecular, cellular, and behavioral levels.<\/p>\n

The biologist\u2019s \u201cbeing\u201d \u2014 the subject of those verbs of agency \u2014 is also at home with meaning, or information, continually transmitting and receiving it, extracting it from or imposing it upon the environment, interpreting it in light of its own needs, acting on it, distinguishing the relevant from the irrelevant. If the biological literature is to be believed, the organic being in some sense perceives, knows, and responds appropriately to the meanings of diverse stimuli.<\/p>\n

This being is also said to be a self \u2014 whatever the self is that engages wholesale in \u201cself-organization.\u201d It does so in part by sponsoring many partial and subordinate \u201cselves,\u201d as when one speaks of self-organizing neural networks, self-organizing chromosome territories, self-organizing tissues, self-organizing protein structures, and so on. And it may even participate in a superordinate self: ants are sometimes said to be part of a \u201cself-organizing ant colony.\u201d<\/p>\n

Such, at least, is the being we are handed by biologists. Not unanimously in all details, to be sure, and in need of critical assessment without a doubt. But it\u2019s a place to start. Our aim is to locate this being of the organism a little more comfortably within the landscape of an acceptable science \u2014 locate it in a way that remains faithful to observation while sparing biologists any embarrassment at their own language. It will require a considerable journey.<\/p>\n\n

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\r\n\t\tTwo Ways of Explaining\t<\/h5>\r\n<\/div><\/div>\n\n

W<\/span>e commonly explain occurrences by saying one thing happened because of \u2014 due to the cause of \u2014 something else. But we can invoke very different sorts of causes in this way. For example, there is the because<\/i> of physical law (the ball rolled down the hill because<\/i> of gravity) and the because<\/i> of reason (he laughed at me because<\/i> I made a mistake). The former hinges upon the kind of necessity we commonly associate with physical causation; the latter has to do with what makes sense within a context of meaning.<\/b><\/p>\n

Any nuance of meaning coming from any part of the larger context can ground the because<\/i> of reason. \u201cI blushed because I saw a hint of suspicion in his eyes.\u201d But I might not have blushed if his left hand had slightly shifted in its characteristic, reassuring way, or if a rebellious line from a novel I read in college had flashed through my mind, or if a certain painful experience in my childhood had been different. In a meaningful context, there are infinite possible ways for any detail, however remote, to be connected to, colored by, or transformed by any other detail. There is no sure way to wall off any part of the context from all the rest.<\/p>\n

The Canadian cognitive scientist and philosopher, Zenon Pylyshyn, once neatly captured the distinctiveness of the because<\/i> of reason this way:<\/p>\n\n\n

Clearly, the objects of our fears and desires do not cause behavior in the same way that forces and energy cause behavior in the physical realm. When my desire for the pot of gold at the end of the rainbow causes me to go on a search, the (nonexistent) pot of gold is not a causal property of the sort that is involved in natural laws.[1]<\/a><\/sup><\/p><\/blockquote>\n\n\n

The because<\/i> of reason does not refer to mere \u201clogic\u201d or \u201crational intellectuality.\u201d Nor need it imply conscious ratiocination. It is constellated from the entire realm of possible meaning, including such things as our desire for pots of gold or our subconscious urges toward violence. I will therefore refer interchangeably to the because<\/i> of reason and the because<\/i> of meaning, by both of which I refer to all the semantic relations and connotations, all the significances, that weave together and produce the coherent tapestry of a life, or of any other expression of meaning, such as a profound text \u2014 say, Aeschylus\u2019 Agamemnon<\/i> or Lincoln\u2019s Gettysburg Address, or, for that matter, the text of a biological description.<\/p>\n

Meaning is notoriously difficult to define \u2014 and, in fact, meaning lies at the opposite pole from precise definition. Words gain fullness of meaning only when they are removed from the dictionary and placed in a concrete context, where an interplay of qualities, connotations, suggestions, and metaphorical juxtapositions enables the words to interpenetrate and pulsate with many-dimensioned significance. To \u201cnail something down\u201d in a definition is rather like removing all the overtones from what had once been the richly resonant song of a violin string in order to get a precise, definable rate of vibration. Qualities are reduced to number. As semantic historian Owen Barfield has pointed out, every effort at definition, to the degree it achieves the desired endpoint of abstract, decontextualized precision, becomes mere counting.[2]<\/a><\/sup> Water, for example, might be defined in terms of boiling point, melting point, density, transparency (percent transmission of light), and so on.<\/p>\n

But despite the loss of meaning in the very attempt to define it, we all have a certain sense for what meaning is, because we all know what we mean<\/i> when we speak.<\/p>\n

By contrast, the because<\/i> of physical law applies to things that do have more or less precisely defined and delimited relationships, which therefore lack a meaning-driven character. We need not appeal to \u201cwhat makes sense\u201d in a larger, more richly expressive context, because a proposed physical law is either \u201cobeyed\u201d or not, despite any look of the eyes or gesture of the hand. A thrown ball respects the law of gravity even if a strong wind is blowing it this way or that. Whereas each detail of a meaningful text gains its significance from the way many contextual elements color and modify each other, we observe the lawfulness of a physical event by isolating (as far as we can) a precisely defined and invariant relationship. The physicist\u2019s strong preference is for strict mathematical laws.<\/p>\n

Meaning is inseparable from language. But it will prove important to understand that, in distinguishing the because<\/i> of reason from that of physical law, we are not distinguishing the language-like from the non-language-like. Rather, the relation between the two becauses<\/i> is more like the relation between a full-bodied language, on the one hand, and a syntax or reduction of that language, on the other. Mathematics, logic, grammar, algorithmic formalisms \u2014 these are examples of such reductions. They give us a kind of generalized skeleton abstracted away from all the concrete expressive potentials of the language. And while these reductions are severely restricted in their ability to describe or characterize the fullness of the phenomenal world, they serve very well to capture the lawfulness we associate with what are often called the \u201cmechanistic\u201d aspects of the world.<\/p>\n

Here, then, is the point. What distinguishes the language of biology from that of physics is its free and full use of the because<\/i> of reason. Where the inanimate world lends itself in some regards to application of a \u201cdeadened,\u201d skeletal language \u2014 a language that perhaps too easily invites us to think in terms of mechanisms \u2014 the organism requires us to recognize a full and rich drama of meaning.<\/p>\n

And so when we ask whether a protein has folded correctly<\/i>, we\u2019re not suggesting it may have rashly disregarded the laws of physics. Its respect for the syntax of a physical law is not the issue we\u2019re addressing. We want to know something much more plastic \u2014 more plastic in the way that meaning is more plastic than a rigid grammar or mathematical formula. That is, we want to know whether the folding is consistent with \u2014 serves the needs of and is harmonious with \u2014 the coherence and the active, self-expressing identity we recognize in the surrounding context. It\u2019s a context and an identity whose qualities and intents differ greatly from a snake to a lion, from a German shepherd to a golden retriever, or from a lung to a kidney. Likewise, when we inquire into the communication between cells, we are not merely curious about the physical impact of molecular projectiles fired from one cell to another; we are trying to clarify a context of meaning. The one cell is saying something<\/i> to the other, not just pushing against it.<\/p>\n

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:<\/p>\n\n\n

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\u2019s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]<\/a><\/sup><\/p><\/blockquote>\n\n\n

A context of meaning can be thought of in various terms. We can take it, for example, to be the organism\u2019s unified form<\/i> in the fullest sense \u2014 not only its bodily form (as a flexible, dynamic trajectory of development), but also the \u201cshape\u201d of its pattern of activity, its recognizable and irreducibly qualitative way of being, distinct for every species.[4]<\/a><\/sup> Every organic form is a gesturing<\/i>, which is also to say, a kind of speaking<\/i> or an expression of meaning. And we could just as well say that the organism\u2019s gesturing manifests the character<\/i> we recognize in the organism as a whole.<\/p>\n

Gesture, character, significant form, a tapestry of meaning \u2014 these terms all point to the \u201csomething more\u201d that, as we found earlier, makes the language of physics and chemistry inadequate to describe the organism. They also typify our way of thinking about beings, as opposed to things. That is, they require a language of directed intention (respond<\/i>, develop<\/i>, adapt<\/i>, regulate<\/i>, and so on); an aesthetically colored language (everything relating to health<\/i> and disease<\/i>, order<\/i> and disorder<\/i>, rhythm<\/i> and dysrhythmia<\/i>, harmony<\/i> and disharmony<\/i>); and a language of wholeness (unity<\/i>, coordination<\/i>, integration<\/i>, organization<\/i>). In fact, just about all the kinds of meaning we express in our words, thought, and activity find their analogue in our descriptions of organisms. Not surprisingly, then, the biologist directly invokes meaning itself in terms such as message<\/i>, information<\/i>, communication<\/i>, and signal<\/i>.<\/p>\n

The biologist\u2019s reliance upon the because<\/i> of reason \u2014 a because<\/i> that resonates so intimately with the meaning of our own lives \u2014 is no small thing. It is no small thing, that is, to find ourselves living together with all our fellow creatures in a community of meaning<\/i>. For in the realm of meaning, there can be, finally, only one community; a hermetically sealed compartment of meaning wholly disconnected from all other meaning is an impossibility. If this truth of community hasn\u2019t been loudly proclaimed from the research laboratories to the wider public, it is only because biologists have gone on for decades using the language of meaning while remaining content never to reckon<\/i> with it \u2014 and even effectively denying it with a contradictory language of mechanism and control. It is past time for the reckoning.<\/p>\n\n

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\r\n\t\tThe Inwardness of Beings\t<\/h5>\r\n<\/div><\/div>\n\n

M<\/span>eaning \u2014 at least when we are not trying to camouflage it in some narrow mechanical or mathematical notion of information \u2014 derives from and expresses a qualitative inwardness<\/i>. It testifies to mind, feeling, volition, consciousness. And because, in our biological descriptions, we refer meaning to organisms, it appears we are ascribing inwardness to these organisms. And so we are. But there are important distinctions to be made.<\/p>\n

Meaning need not be thought of solely in terms of our own human consciousness. Everyone accepts that neither the bird building a nest nor the embryo \u201cconstructing\u201d a heart is self-consciously realizing its own purposes and meanings. Likewise, the directed nature of cellular processes does not imply conscious, human-like purpose, and, more generally, the meaning I have been referring to need not involve anything like our own conscious awareness.<\/p>\n

This is not to suggest, however, that meaning is no longer meaning. Our knowledge of ourselves informs us that the because<\/i> of reason can play out in less than full consciousness. We know that it weaves throughout the psyche, conscious or otherwise, all the way down through subconscious urge and habit to biologically rooted instinct and even to physical reflex.[5]<\/a><\/sup> It is not so unexpected, then, to discover meaning-governed activities also at the molecular level, where they manifest as regulation, organization, signaling, responsiveness, and all the rest. Organisms, so far as the biologist has been able to determine, are alive and whole and engaged in activity shaped by relations of meaning \u2014 a meaning whose signature is recognizable all the way down.<\/p>\n

What is it, after all, that becomes conscious in the human being? All our growing knowledge of our own complex psychosomatic unity suggests that the inwardness at work in the formation and activity of the body, from the molecular level on up, is akin to \u2014 not radically other than \u2014 what comes to awareness of itself as psyche. The fact that our physical organism so directly and intimately reflects not only our explicit volitional commands but also our inner, meaningful states (\u201cI blushed because I saw a hint of suspicion in his eyes\u201d) \u2014 while, conversely, our inner life is directly affected by our bodily state, as when we are sick or in pain \u2014 leaves little room for a radical separation of psychic meaning from the bodily (molecular) meaning we traced earlier.<\/p>\n

You will recall that we have been trying to identify the being<\/i> assumed (whether explicitly or otherwise) by biologists when they describe the organism. This being pursues its life within a context of meaning, and possesses a kind of inwardness that is not sharply separable from human consciousness. Beginning with a molecular-level analysis of the simplest, single-celled organism extant today and proceeding through all the ever more complex creaturely orders, we see no sudden discontinuity in the play of meaning and inwardness \u2014 a play that progressively comes to a focus in the individuated centers of consciousness we know as our selves.<\/p>\n

If there is an uncomfortable element in all this for many biologists, it arises from the perceived difficulty of reconciling the inwardness of beings with a faith in all the materialist metaphysical baggage that has accumulated around the sciences. This presumably accounts for biologists\u2019 shyness in owning up to their own language. But, leaving aside the oddity that biologists seem much more concerned than physicists to preserve a materialist faith, we will now see that the problem posed by living beings in relation to physical science results solely from misunderstanding.<\/p>\n\n

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\r\n\t\tLaws and Causes\t<\/h5>\r\n<\/div><\/div>\n\n

T<\/span>he physicist wants laws that are as universal as possible, true of all situations and therefore unable to tell us much about any particular situation \u2014 laws, in other words, that are true regardless of meaning and context. So far as a physical law is concerned, once we know it, every subsequent observation merely demonstrates something we already knew: the law will yet again be obeyed. This requires a severe abstraction from the presentational richness of the phenomenal world, which presents us at every moment with something new. Such abstraction shows up in the strong urge toward the mathematization of physical laws.<\/p>\n

While the laws usually considered most fundamental remain (at least ideally) valid regardless of context, we can put them most conveniently on view by establishing carefully contrived closed systems<\/i> \u2014 systems as immune as possible to outside (contextual) interference. That\u2019s because contextual changes tend to obscure the particular law we are after. An apple released from a tree may<\/i> fall straight toward the center of the earth with more or less constant acceleration \u2014 but not if I stretch out my hand and grab it, or a sudden gust of wind arises, or it strikes a bird or insect, or there is a meteoric explosion nearby, and so on. Gravity, of course, will be respected in any case, but sometimes we want to see its role displayed without ambiguity or interference \u2014 see it as a matter of demonstrable cause and effect and easy measurement. And so, perhaps, we may contrive to drop the apple within a vacuum chamber, a relatively closed system that eliminates air resistance and insects, and demonstrates the mathematical lawfulness of gravity as directly as possible.<\/p>\n

This allows us to talk more convincingly about how one thing \u201cmakes\u201d another happen: depressing a button on the outside of the chamber releases a lever, which makes the platform drop suddenly, whereupon the apple, under the effect of the earth\u2019s gravitational field, accelerates downward. There is a predictable sequence of events here, so that we commonly say one thing or event causes<\/i> the next \u2014 or, at least, does so if the release mechanism isn\u2019t corroded, an earthquake doesn\u2019t upset the apparatus at a crucial moment, air hasn\u2019t leaked into the system, there\u2019s been no sublimation of gases from the materials inside the chamber, and so on.<\/p>\n

Clearly, the \u201ccauses\u201d in our demonstration are not laws; they never make things happen with the kind of unvarying certainty we associate with physical law. In fact, a \u201ccause\u201d is nothing anyone has ever managed to define with any adequacy. It\u2019s a rather vague, approximate, and anthropomorphic idea, derived from our own experience in \u201cmaking things happen.\u201d Statistician David Salsburg, author of the 2001 book The Lady Tasting Tea<\/a><\/strong><\/i>, states bluntly that \u201cThere is, in fact, no such thing as cause and effect. It is a popular chimera, a vague notion that will not withstand the batterings of pure reason.\u201d[6]<\/a><\/sup><\/p>\n

I can now clear up a certain ambiguity in my earlier discussion of the because<\/i> of physical law, where I might have been taken to imply that gravity \u201ccauses\u201d a ball to roll downhill. There are, in fact, various occasions when balls roll uphill, whether due to wind or ocean waves on the beach or some other factor. Gravity doesn\u2019t make balls roll downhill, but rather accounts for certain invariant and lawful aspects of their motion, whatever that motion may be. If we want the because<\/i> of physical law to retain the strict, syntactic precision I spoke of, then it should refer only to these invariant, lawful features.<\/p>\n

As for what Salsburg calls the \u201cchimera\u201d of causes, popularly conceived, there is no reason we cannot speak of them, if only roughly, in contexts that are more or less stable and closed. They are the basis for what we might refer to as the \u201ccause-and-effect because<\/i>,\u201d or the \u201cmachine-like because<\/i>,\u201d for we try to make our machines (in their standard working contexts) into just such closed, causal systems. And we typically succeed well enough, until rust or a power glitch or the fist of a disaffected user or normal wear and tear brings an end to the desired causal regularity of the system. Presumably nothing ever goes wrong with the physical laws that were operative in the system, but any given causal relations can always be sabotaged by a contextual change.<\/p>\n

We can see, then, why physicists are more interested in lawfulness than in identifying causes. They know it is impossible to construct an absolutely closed system with absolutely reliable causes. Any local causal arrangement can be invalidated by a different context (the meteoric explosion), and therefore the arrangement doesn\u2019t have the kind of perfectly predictable character that physical laws are often thought to have. The observed \u201ccausal\u201d character is neither unqualified nor intrinsic to the given objects and processes in the way that physical laws seem intrinsic to material phenomena.<\/p>\n

It will be important to keep in mind these distinct aspects of the physical sciences: on the one hand, precise, invariant relationships \u2014 the fundamental laws \u2014 implicit in whatever happens; and, on the other hand, the much less precise, never absolute, never infallible notion of a cause<\/i>, which is supposed to tell how one thing makes another happen, that is, how one event, or set of conditions, brings about another event or set of conditions.<\/p>\n

Many people, when they speak of the world\u2019s \u201ccausal regularity,\u201d are actually referring to its lawfulness. This conflation of law and cause \u2014 this illegitimate bestowal upon physical causes<\/i> of the regularity, predictability, and certainty associated with physical laws<\/i>, as if the causes had the same necessity as the laws \u2014 yields a great deal of mistaken thought. Among other things, it lends to any science guilty of it the illusion of vastly greater explanatory power than it in fact possesses. This helps us to understand why so many biologists see a determinate machine where there is in fact a living being; the physical lawfulness<\/i> discoverable in the organism is unthinkingly equated in their minds with a collection of causal mechanisms<\/i>.<\/p>\n

In sum: laws do not determine any event at all, but only tell us something about how it will happen: certain invariant relations will be respected. Causes, on the other hand, approximate and ill-defined though they be, can give us a contingent sense for what may reasonably be expected within a temporarily limited and more or less closed system.<\/p>\n

Curiously, physicists are much less likely to confuse law and cause than are biologists. I say \u201ccuriously\u201d because at least the physicist can achieve, with machines, an approximation of reliable causes. The biologist, as we will now see, is denied even a reasonable approximation.<\/p>\n\n

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\r\n\t\tBeings in Context\t<\/h5>\r\n<\/div><\/div>\n\n

A<\/span>ll this gives us a further perspective on the animate-inanimate distinction. We have already seen that biology is distinguished from the physical sciences by the free use of the because<\/i> of reason. Now, looking from a slightly different angle, we can consider the issue in terms of law and cause.<\/p>\n

No biologist today will deny that fundamental physical laws continue to apply without exception to organisms. But what about causes? We have just now noted that, by means of carefully designed closed systems more or less immune to contextual interference, it is possible to say one thing \u201ccauses\u201d another, with due caveats. Machines are such systems. But what happens when the biologist attempts to see the organism in the same mechanistic light, making a closed system of it?<\/p>\n

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

Remember that, in a play of meaning, every new element, every new encounter, every new \u201cword\u201d that is expressed may shift the connotation or significance of every other element. The whole purpose of meaningful expression is to add something to what has already been said \u2014 to reshape an existing context in light of a further meaning; otherwise, no speaking, no gesturing, would be necessary. A coherently changing context is the very substance of meaning. 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.<\/p>\n

Or (to focus on the cellular level): 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 context \u2014 and similarly when a cell experiences heat shock, oxygen deprivation, or other stress; when it comes into contact with new neighbors; or when it proceeds along a path of embryonic differentiation. The cellular environment, as an evolving context, is continually being reinterpreted<\/i> and responded<\/i> to \u2014 is itself a reinterpreting and responding.<\/p>\n

Because every local activity of the organism must find its meaningful place within the encompassing activity of a striving, developing, self-transforming whole, there can be no fixed syntax, no mechanical constancy of relations among the parts. Certainly you still can, without self-deception, consider yourself to be identifying causes in the organism. What you are doing is recognizing physical lawfulness in the current context. But it is a context that remains what it was only for a moment. The organism, regarded as a closed system relative to the causes under investigation \u2014 the only kind of system in which stable causes can even be defined \u2014 is forever abandoning its old state and entering a new one. Therefore no cause can reliably be assumed to remain the same cause over a period of time. When a larger, dynamic intention is reflected in the changing significance of each part, the organism as a whole governs the activities of its parts rather in the way the meaning of an unfolding text or play governs its parts.<\/p>\n

Against this backdrop, it\u2019s worth taking a moment to listen to biologists puzzling over questions of cause and effect. To keep the following survey brief, we will focus narrowly on certain issues of gene regulation, especially in relation to the organization of the cell nucleus. All of these examples are from the last decade. (There is no need to worry about the technical details; the general sense of the remarks is all that matters here. One note, however: chromatin is the complex of DNA, protein, RNA, and other molecules that constitute chromosomes.)<\/p>\n\n\n

\u2022    Technological advances are … revealing an unexpectedly extensive network of communication within and between chromosomes. A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it.[7]<\/a><\/sup><\/p>

\u2022    Together, these results further emphasize the role for RNA polymerase in shaping the chromatin landscape of the genome and point toward the difficulty in disentangling cause and effect in the relationship between chromatin and transcription.[8]<\/a><\/sup><\/p>

\u2022    A longstanding question is whether [cell] replication timing dictates the structure of chromatin or vice versa. Mounting evidence supports a model in which replication timing is both cause and consequence of chromatin structure by providing a means to inherit chromatin states that, in turn, regulate replication timing in the subsequent cell cycle.[9]<\/a><\/sup><\/p>

\u2022    Despite the difficulties in proving cause and effect, these examples convincingly illustrate how chromatin crosstalk can functionally increase the adaptive plasticity of the cell exposed to the changing microenvironment.[10]<\/a><\/sup><\/p>

\u2022    A related unresolved question is whether chromatin loops are the cause or the effect of transcriptional regulation.[11]<\/a><\/sup><\/p>

\u2022    Which genes are the \u201ccause\u201d and which are the \u201cconsequence\u201d of plastic development?[12]<\/a><\/sup><\/p>

\u2022    Despite abundant evidence that most kinds of tumor cells carry so-called epigenetic changes, scientists haven\u2019t yet worked out exactly whether such glitches are a cause or a consequence of disease.[13]<\/a><\/sup><\/p>

\u2022    The clarification of the cause-and-effect relationship of nuclear organization and the function of the genome represents one of the most important future challenges. Further experiments are needed to determine whether the spatial organization of the nucleus is a consequence of genome organization, chromatin modifications, and DNA-based processes, or whether nuclear architecture is an important determinant of the function of the genome.[14]<\/a><\/sup><\/p><\/blockquote>\n\n\n

One would think that biologists might pause and consider the possibility that the kind of stable causal relationship they\u2019ve been looking for simply isn\u2019t there \u2014 the possibility that they\u2019ve defined their task in misleading terms. Yet when researchers find, for example, that patterns of nuclear organization are implicated in cancer, an almost automatic exhortation follows: \u201cHowever, it is crucial to determine the extent to which cancer-associated changes in nuclear organization are cause or effect.\u201d[15]<\/a><\/sup> But is it crucial? Are the actual goings-on in the cell in fact proving so clear-cut? Why do we need<\/i> causes as an addition to lawfulness and meaning? After all, we have no difficulty understanding all the relationships in a meaningful text, even though we cannot say that one part of the meaning causes<\/i> another part.<\/p>\n\n

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\r\n\t\tTo Explain or Portray?\t<\/h5>\r\n<\/div><\/div>\n\n

T<\/span>he pursuit of causes in biology is something fierce. There is evidently a visceral feeling that without causal mechanisms we have no explanation, and without explanation, no understanding. It is a prejudice so deeply engrained, so resistant to removal, that it has badly distorted the entire field of biology. The billions of dollars poured into molecular research during these past several decades bespeak more than anything else a single-minded quest for causes \u2014 a quest that has, by many accounts, been severely frustrated.<\/p>\n

It may seem a mere curiosity that over two centuries ago Johann Wolfgang von Goethe, aware that precisely this single-minded desire for causes had already possessed many of his scientific contemporaries, took a stand against it. He declared of his own pioneering morphological research that \u201cits intention is to portray rather than explain.\u201d[16]<\/a><\/sup> A science whose central task is not to explain, but rather to fill out portraits? At a time when naturalists have become a nearly extinct species and geneticists have found an ideal habitat in front of instrument display panels, not many will be prepared to accept such a prescription for the researcher. And yet, Goethe\u2019s stance was extraordinarily prescient.<\/p>\n

How, in fact, do we come to understand any context of meaning \u2014 a dance, a painting, a novel, a human life, the choreography of a developing embryo? Goethe noted the impossibility of capturing an \u201cinner nature\u201d \u2014 say, a person\u2019s character \u2014 in any kind of direct causal or explanatory way. \u201cBut when we draw together his actions, his deeds, a picture of his character will emerge.\u201d That is certainly how we try to understand each other \u2014 and we, too, are organisms. I daresay that, insofar as several decades of expensive cancer research have brought progress, it is not so much because this or that causal mechanism has been discovered (such mechanisms are announced by the dozens every month in scientific journals) as because all the false starts, dead ends, and mutually contradictory \u201cmechanisms\u201d have bit by bit been revealing (to those looking for it) a qualitative picture \u2014 a personality, so to speak \u2014 of the disease.<\/p>\n

Such knowledge is not impotent. If I familiarize myself with the distinctive way of being of a blue jay, I may not be able to predict exactly what it will do or project its flight as a Newtonian trajectory. But my knowledge is nevertheless real. I will, in appropriate circumstances, be able to say, \u201cYes, that is just like a blue jay,\u201d or \u201cNo, that is not at all what one would expect of a blue jay in this situation. There is something wrong, or something missing from the picture.\u201d With such knowledge I can learn to interact meaningfully with the bird even though I cannot mechanistically predict its behavior. In developing a qualitative portrait, we aim less at exact prediction and control than at understanding and the potentials for working with nature.[17]<\/a><\/sup><\/p>\n

The main question about a portrait is how full, how detailed, how multifaceted a picture we gain. The supposed causes, of course \u2014 when properly contextualized and shorn of their strict causal aura \u2014 help us to build this picture. There is neither any end to our picture-building, nor an inherent limit to how far we can carry it. And biologists surely are<\/i> carrying it further, even when they think they are fingering explanatory causes.<\/p>\n

In other words, these remarks point more toward what is the (partly unrecognized) reality of biological research than toward some utterly new strategy. All the meanings we have seen in biological language are, after all, pervasive, testifying eloquently to the efforts to portray health and sickness within an overall organismal context of coordination, regulation, globally directed communication, and so on \u2014 this despite the simultaneous and contradictory appeal to causes neatly isolated from the whole.<\/p>\n

The Ultimate Cause, of course, was supposed to be the genomic sequence, or DNA. But Florida State University biologist David Houle and his colleagues remind us that, for the most part, phenotypes (observable traits \u2014 partial portraits, if you will) \u201ccontinue to be the most powerful predictors of important biological outcomes, such as fitness, disease and mortality. Although analyses of genomic data have been successful at uncovering biological phenomena, they are \u2014 in most cases \u2014 supplementing rather than supplanting phenotypic information.\u201d[18]<\/a><\/sup> And what is true of prediction applies just as well to causal analyses and treatment \u2014 a fact that\u2019s easy to lose sight of amid all the wonders of modern molecular technologies and all the talk of treatable \u201ccauses.\u201d The International HapMap Consortium (a successor to the Human Genome Project) summarizes the situation neatly in the lead sentence of a report in Nature<\/i>: \u201cDespite the ever-accelerating pace of biomedical research, the root causes of common human diseases remain largely unknown, preventative measures are generally inadequate, and available treatments are seldom curative.\u201d[19]<\/a><\/sup> And William Bains, chief scientific officer at Amedis Pharmaceuticals in the United Kingdom, wrote upon the completion of the Human Genome Project:<\/p>\n\n\n

The chances that genome properties can be used to predict organismal ones is remote. Genomics and its daughter technologies are valuable instruments in the analysis of cells and tissues. They provide means of exploring biological processes and phenomena. However … they will not often address most human needs.[20]<\/a><\/sup><\/p><\/blockquote>\n\n\n

Low-level analyses versus portrayal of the whole: it\u2019s not an either-or matter. Because we\u2019re dealing with meaning, the similarity to the understanding of texts is not accidental: analyses of individual words and their possibilities of meaning can be essential; without a knowledge of the words, we can hardly grasp the whole. But at the same time, it is only the meaning of the whole that gives the individual words their full and proper significance. This is the truth that has for so long been ignored within biology.<\/p>\n\n

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\r\n\t\tCan We Explain the Form of Organisms?\t<\/h5>\r\n<\/div><\/div>\n\n

T<\/span>he challenge and opportunity of portrayal deserves concrete illustration. Consider the effort, common nowadays, to explain an organism\u2019s form by referring to genetic switching networks. Developmental biologist Sean Carroll presents beautiful pictures of patterns in the early fly embryo \u2014 patterns that prefigure and map directly to the later arrangement of larval segments. Each element in a pattern corresponds to the distribution of certain molecules (made visible and colorful with special dyes), which in turn can be at least roughly correlated with the activity of a particular collection of genes. He suggests that a complex arrangement of genetic switches explains<\/i> the molecular patterns and therefore also explains the eventual form of the organisms.[21]<\/a><\/sup><\/p>\n

But we now know from the vast literature on gene regulation (oddly, Carroll does not even mention epigenetics in his book) that those supposed switching networks are in fact penetrated and influenced by virtually everything going on in the cell. By the time we get very far in tracing the relevant interactions through the organism, we realize that we\u2019re witnessing, at the molecular level, the playing out of the very form, the patterns, that we hoped to explain, but at another level of description.[22]<\/a><\/sup> If we really did need explanatory mechanisms, then we\u2019d still be left with a version of our original task: to explain what governs, controls, or regulates the complex, interacting molecular patterns that we find as such vivid, directed, perfectly shaped presentiments of the developing morphology.<\/p>\n

Carroll repeatedly talks about how various genes \u201csculpt\u201d a fly\u2019s wings and various anatomical structures of other animals, adding that the action of these genes \u201cin organizing, subdividing, and specifying and sculpting parts of the embryo becomes clear when visualized.\u201d But it\u2019s obvious enough that a section of a DNA molecule does not \u201csculpt\u201d anything. In fact, the research emphasis today is in the reverse direction: how proteins and the overall activity of the cell sculpt the genes and chromosomes. Biologists speak of \u201cDNA-sculpting proteins,\u201d of histone modifications that \u201csculpt\u201d chromatin (the substance of chromosomes), and of the sculpting of DNA into functional domains and loops. In general, studies on the three-dimensional organization of chromosomes in the nucleus are all the rage, and it is widely recognized that this organization reflects how the organism is making use of its genes. In trying to understand gene expression, biologists \u201care looking for answers\u201d by studying how the chromosome \u201cfolds, moves, and communicates.\u201d[23]<\/a><\/sup><\/p>\n

As this last remark indicates, we\u2019re not talking about a static sculpture. In a 2003 article in Nature<\/i> entitled \u201cBeyond the Double Helix,\u201d Helen Pearson interviewed many geneticists in order to assemble the emerging picture of DNA. One research group, she reported, has shown the molecule \u201cto gyrate like a demonic dancer.\u201d Others point out how chromosomes \u201cform fleeting liaisons with proteins, jiggle around impatiently, and shoot out exploratory arms.\u201d Phrases such as \u201cendless acrobatics,\u201d \u201csubcellular waltz,\u201d and \u201ctwirls in time and space\u201d are strewn through the article. \u201cThe word \u2018static\u2019 is disappearing from our vocabulary,\u201d remarks Tom Misteli of the National Cancer Institute.[24]<\/a><\/sup> Countless extra-chromosomal factors contribute to this dynamic performance.<\/p>\n

The activity of individual genes reflects the choreography of chromosomes, which reflects the larger choreography of the nucleus, which reflects the choreography of the cell and organism as a whole. Who, then, is sculpting whom?<\/p>\n

It\u2019s not that identifying a so-called gene \u201cswitch\u201d \u2014 or calculating kinetic energies or measuring mechanical stresses on macromolecules \u2014 gives us no understanding. Of course such insights are important. But they become biological insights, as opposed to physical and chemical ones, only insofar as they find their place within the living, metamorphosing form of the organism. They do not explain the form. If anything, we should say that the form explains the physical interactions \u2014 in the sense that it gives us an understanding of their pattern, their shape, their direction and place within a functional whole, none of which can be deduced from physical transactions as such. We can observe<\/i> the patterns by tracing the physical interactions, but what those patterns will turn out to be can never be arrived at merely by working out the implications of the physical laws and substances.<\/p>\n

This same scenario is playing out in other biological investigations. One of the most dramatic examples centers on the circadian rhythms that figure so prominently in human life. Biologists, of course, set out to identify the \u201cclock mechanism\u201d that was presumed to \u201ccontrol\u201d these rhythms, and, yes, they found a rhythmical feedback loop involving genes and transcription factors in a certain area of the brain that seemed the perfect candidate. However, ongoing research has revealed distinct \u201cclocks\u201d in different mammalian organs and tissues, and indeed in every cell. These \u201cclocks\u201d are interwoven with each other and, it now seems, with virtually all aspects of the organism\u2019s physiology \u2014 metabolism, reproduction, cell growth and differentiation, immune responses, central nervous system functions, and on and on.<\/p>\n

In each of these areas the quest for causes and master controllers leads to the usual perplexity about who\u2019s doing what to whom. For example: \u201cAlthough 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.\u201d[25]<\/a><\/sup> At the molecular level, one research team remarks that the enzymatic function of a certain clock protein \u201cmay be controlled by changing cell energy levels, or conversely, could regulate them.\u201d[26]<\/a><\/sup> In general, \u201cIt seems that connections between the circadian clock and most (if not all) physiological processes are bidirectional.\u201d[27]<\/a><\/sup><\/p>\n

What we\u2019re gaining from all this research is a wonderful portrait of the organism as a rhythmical being \u2014 a being in time. 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 \u2014 perhaps more centrally here and more peripherally there, but altogether in a single, organism-wide harmony. There is no sensible way, as a scientist, to speak of particular mechanisms that explain<\/i> this harmony. Instead, every isolated \u201cmechanism\u201d is found to be a reflection of the harmony, and we thereby gain further, detailed understanding of how the organism functions as a being in time.<\/p>\n

Finally, 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<\/i>, 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 \u2014 who received a 2002 Nobel prize for his work on C. elegans<\/i> \u2014 acknowledged that development \u201cis not a neat, sequential process…. It\u2019s everything going on at the same time.\u201d Even regarding the carefully mapped cell lineages of this \u201csimple\u201d roundworm, \u201cthere is hardly a shorter way of giving a rule for what goes on than just describing what there is.\u201d In other words, the only \u201crule\u201d for the development of this worm is the developmental description of it. When critics suggested he had not really come to an understanding of the worm, but had \u201conly\u201d described it, Brenner responded, \u201cI\u2019m not sure that there necessarily is anything more to understand than what it is.\u201d[28]<\/a><\/sup><\/p>\n

While there is good reason to think that Brenner never took his own words with full seriousness \u2014 and biologists in general still have not gotten the message these many years later \u2014 Goethe would certainly have seen truth in Brenner\u2019s remark. The difficulties of causal explanation encountered by the C. elegans<\/i> researchers were not accidental. You can\u2019t explain an organism of meaning, and you don\u2019t need to. You need only allow it, like any meaningful text, to speak ever more vividly and clearly, in ever greater detail. The separate processes do not make tidy explanations because they are not really separate and are not just doing one thing; they are harmonizing with everything else that is going on in the organism. We gain understanding when we learn to recognize this harmony in every aspect of the organism. Various analyses can play a crucial role in bringing clarity to our understanding. But the full picture takes shape only when the analytical threads are woven back into the larger fabric of meaning.<\/p>\n

We have an increasing appreciation today of the importance of organismal context, and of the organism\u2019s plasticity, and of its dynamism, and of the complexity of its interweaving processes, and of the causal ambiguity of our explanations. For a mindset fixated upon causal mechanisms, all these factors might be viewed as unwelcome complications \u2014 detours on the way toward real<\/i> understanding. But do they really make our descriptions and explanations less<\/i> revelatory of the organism than what we had before, when gene-mechanisms were supposed to provide a \u201cblueprint\u201d or \u201cinstruction set\u201d for the organism as a whole? Shouldn\u2019t we expect that the processes we cannot neatly tie down or capture in mechanisms are precisely what bring the organism alive<\/i> for us?<\/p>\n\n

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\r\n\t\tFear of Vitalism\t<\/h5>\r\n<\/div><\/div>\n\n

T<\/span>he organism, we have seen, is continually expressing the because<\/i> of reason. Possessed of a certain inwardness, it is a maker of meaning, a fact most immediately presented to us in our own lives as self-conscious beings, but further evident all the way down to the eloquent and concerted molecular interactions of every living cell. We recognize meaning in the vocalizations, body language, and gestures of animals; in the qualities that make the oak tree a recognizable presence, consistently expressing its own character<\/i>, distinct from a willow tree; and in the active, directed striving for self-realization in all organisms \u2014 a striving that enables us to speak reasonably of their health and disease, wholeness and injury.<\/p>\n

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

The truth of the matter may simply be so close to us \u2014 so fundamental and so intimately a part of our nature as understanding beings \u2014 that we cannot readily step back and see it. I mean the truth that any understanding of the world, animate or inanimate, must be an understanding<\/i> \u2014 which is to say, it requires a conceptual<\/i> grasp of things. Whatever is incommensurable with thought and idea will never be contemplated in thought and idea, and therefore will never enter into science. The world we know will always and only be a world in whose inwardness we can participate inwardly \u2014 a world whose being can take form as a content of consciousness. Without a truth of things that can at the same time be a truth of word and thought, we could have no scientific conversations or textbooks \u2014 no science at all.<\/p>\n

The physicist has not<\/i>, as so often claimed, succeeded in presenting us with a world of pure objectivity or outwardness \u2014 a \u201cdisenchanted\u201d or \u201cdisensouled\u201d world. He has only tried to restrict the enchantment to the sphere of mathematics. But mathematical relations or concepts are still ideas, not things, and the universe is, if nothing else, startlingly enchanted by these ideas. The question \u201cWho is the enchantress?\u201d may be beyond our ken at this time, but this does not remove the facts that provoke the question. Oddly, physicists seem far ahead of biologists in their occasional and explicit openness to these facts. When an astrophysicist penned an essay in Nature<\/i> entitled \u201cThe Mental Universe,\u201d it produced hardly a murmur of surprise from his peers.[29]<\/a><\/sup><\/p>\n

None of this is to abolish the qualitative distinction between the animate and inanimate worlds. To say that the world is an embodiment of meaning and idea is not to say that all things have the same meaning or that meaning manifests itself in the same way in all things. We saw above that coherently evolving contexts<\/i> of meaning are the very language of the organic realm. Organisms cannot be fully elucidated in terms of the definitive lawfulness so satisfactory to the physicist \u2014 a lawfulness lending itself to the application of mathematics and other reduced \u201cskeletons\u201d of language. This is a great difference. If we live in a thought-soaked world \u2014 one that includes the amoeba as well as the stone, celestial fires as well as earth-bound winds, human beings as well as human-devised machines \u2014 then it is the task of the scientist to find the appropriate sort of language for bringing to light the phenomena of each different realm.<\/p>\n

But this entire discussion of ideas and meaning in the world<\/i> brings us face to face with a haunting specter we need to exorcise once for all: the specter of vitalism. The accusation of vitalism seems inevitably to arise whenever someone points to the being of the organism as a maker of meaning. This is owing to a legacy of dualism that makes it almost impossible for people today to imagine idea, meaning, and thought as anything other than ghostly epiphenomena within human skulls. So the suggestion that ideas and meaning are \u201cout there\u201d in the world of cells and organisms immediately provokes the assumption that one is really talking about some special sort of physical causation rather than about a content of thought intrinsic to organic phenomena. That is, ideas and meanings are taken to imply a vital force or energy or substance somehow distinct from the forces, energies, and substances referenced in our formulations of physical law. Such an entity or power would indeed be a spectral addition to the world \u2014 an addition for which no one has ever managed to identify a physical basis.<\/p>\n

But ideas, meanings, and thoughts are not material things, and they are not forces. Nor need they be to have their place in the world. After all, when we discover ideal mathematical relationships \u201cgoverning\u201d phenomena, we do not worry about how mathematical concepts can knock billiard balls around. If we did, we would have made our equations into occult or vital causes. But instead we simply recognize that, whatever else we might say about them, physical processes exhibit a conceptual or thought-like character. And so, too: the meanings that give expression to the because<\/i> of reason do not knock biomolecules around, but \u2014 like mathematical relations \u2014 are discovered in the patterns we see. The thought-relations we discover in the world, whether in the mathematical demonstrations of the physicist or the various living forms of the biologist, need to be genuinely and faithfully and reproducibly observed, but must not be turned into mystical forces.<\/p>\n

The scientist observes meanings at play in organisms, and necessarily appeals to them in biological explanation. Anyone who construes this appeal as conjuring unacceptable vital forces needs not only to torch almost the entire biological literature, reconstructing it upon some new and as yet unknown basis; he also puts himself in an untenable position regarding the human being. For at least some of what we do, we do because we consciously think and intend it. If invoking this because<\/i> of reason \u2014 this play of meaning and idea \u2014 in the explanation of human behavior is to rely on vital forces, then virtually everyone (in daily life, if not within a cocoon of theory) is a vitalist. If, on the other hand, we grant meaning to the human being without trying to make this meaning an expression of vital forces, then we can hardly voice the charge of \u201cvitalism\u201d when we observe meaningful activity in less conscious forms \u2014 for example, in the activity of cells and lower organisms.<\/p>\n

So, no, we don\u2019t need vital forces. If the organism as an expression of meaning requires us to recognize a different sort of order from that of inanimate nature, science offers no presumption against this. Our knowledge of some thought-relations in the world \u2014 for example, those of mathematized physical law \u2014 does not tell us what other thought-relations we might discover in various domains. The mathematical order, however, does tell us that there must be<\/i> other principles of order. For mathematics alone does not give us any things or phenomena at all; numbers are not things. Whatever the things may be to which our mathematical formulations refer, they either have a qualitative character that we can consciously apprehend in a conceptually ordered way, or they must remain unknown and outside our science. And that qualitative conceptual ordering cannot be predicted from the mathematics. Rather, the qualitative order is the fuller reality that determines whatever we abstract from it, including mathematical relationships.<\/p>\n

Who can tell us in advance what forms of order we may discover in this more-than-numerical world? If, in organisms, we observe principles of coordination through which physical laws are not only fully respected but also caught up in higher-order, integrated, harmonious, and self-assertive forms \u2014 well, then, that\u2019s what we observe. The ideas expressed in that coordination and integration may be more saturated and resonant than the concepts of the physicist, but they are no more our arbitrary invention than is the mathematical harmony of planetary motions.<\/p>\n

We may not yet understand how the coordination comes about \u2014 how living beings bring such meaningful, ideal relations to manifestation in the world \u2014 but this is no obstacle to scientific acknowledgment of the observed relationships. After all, our ignorance about how gravity works or what energy or space or time or matter is<\/i> does not prevent us from teasing out certain observable, lawful relationships. Disciplined observation should be our guide to the various sorts of order displayed in the world. And while observation shows us an uninterrupted continuity of physical law when an organism dies, it also reveals a striking discontinuity, marked by a loss of the overarching coordination and the governing meaning through which a living form had been sustained. The astonishing fact that scientists of life pay very little attention to the significance of this moment of transition in no way detracts from its significance.<\/p>\n

I do not at all wish to dismiss as unimportant the question so many will feel to be urgent: Who, after all, \u201cspeaks\u201d or gives expression to the meaning we find so clearly displayed in an organism\u2019s life? How are we to understand the substantive nature of the beings with whom we share the earth \u2014 if, indeed, \u201csubstantive nature\u201d is the right phrase? But this is a large issue requiring separate treatment. Given the metaphysical commitments so thoroughly distorting biology today, the first task is to make it at least possible for such questions to be asked. Fortunately, this has required only that we look unflinchingly and without the usual prejudice at what biologists themselves have been discovering.<\/p>\n\n

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\r\n\t\tBiology — More Fundamental than Physics?\t<\/h5>\r\n<\/div><\/div>\n\n

A<\/span> final word about the relation between physics and biology. We have seen that, in the organism, the observed thought-relations have a much thicker texture of meaning than in the physical sciences. The mathematically stated laws toward which those sciences so often strive with at least some success represent thought stripped down to the purest abstraction \u2014 to a kind of bare syntax of quantity and logic \u2014 whereas the language we see spoken in the organism is much more like a contextualized natural language, semantically rich and qualitative.<\/p>\n

While there are real differences here, there are also matters of choice. Physicists have chosen to pull back from the actual phenomena they are confronted with, viewing them as far as possible through the lens of a language blind to those qualitative, phenomenal aspects of the world where we could expect to trace any sort of a meaningful because<\/i>. The kind of world they describe reflects in part the restrictions they impose upon their looking.<\/p>\n

So it is that they aim to describe the world of light and color in terms of colorless \u201cwaves\u201d and \u201cparticles,\u201d or mere statistical non-representations \u2014 that is, in a way that makes as much (or as little) sense for someone without sight as for those with eyes to see; and they try to describe a world of sound that is indifferent to the presence of hearing ears. In general, they tell us what the world would be like if it were not like<\/i> anything at all \u2014 certainly not like anything we can know through our senses, and therefore not like anything we can describe or even imagine. It is no wonder that, at its purest, physics tends to depart from the phenomenal world into abstract and statistical formulations, while physicists enter into debates about the nature of reality that might make a medieval metaphysician blush.<\/p>\n

These choices of the physicist are certainly productive so far as our powers of manipulation are concerned. The single-minded focus on general laws we can recognize in the world enables us to assemble the parts of a machine so as to put those laws to work for us in effective \u201ccausal systems.\u201d Indeed, the fact that science works<\/i> in this sense is often taken to be its chief glory. Certainly it has transformed civilization and given us many things we would rather not do without. But an ability to manipulate things does not imply that we have exhausted the potentials for understanding what we are manipulating. Perhaps it is hardly a beginning. Just as you can drive a car without a clue about how the motor works, so, too, you can \u201cknow\u201d how the motor works without a clue about the true nature of forces or energies or even laws.<\/p>\n

Those who would like not only to reengineer but also to understand the world have every right to ask: If the inorganic world readily accessible to our perception and theorizing is a world partly characterizable (unlike the living aspects of the organism) by ideas reduced toward a kind of grammar, what is the fuller \u201cspeech\u201d implied by the presence of this grammar \u2014 the speech of qualitative phenomena from which alone such a grammar could be abstracted? What would we find if we looked where the physicist disdains to look \u2014 if we attempted to penetrate physical phenomena with a profound qualitative awareness of the sort that Galileo had already foresworn and the biologist cannot avoid?<\/p>\n

To suggest that the world may be a bearer of meaning far beyond what the physicist is currently willing to investigate is not to contend that a rock can be placed on the same scale as an amoeba. It is only to point to the profound darkness of substance itself, in both rock and amoeba, and to ask what quickening mystery may be hidden within it, capable of producing the brilliant kaleidoscope of perceptible qualities we call \u201cthe world\u201d \u2014 and, indeed, capable of producing living things. This hidden potential of the world\u2019s substance must be at least as great as the things it brings to realization.<\/p>\n

Alluding to the void left by the physicist\u2019s withdrawal from phenomena into mathematical law, Stephen Hawking once asked: \u201cWhat is it that breathes fire into the equations and makes a universe for them to describe? The usual approach of science … cannot answer.\u201d[30]<\/a><\/sup> Whatever life it is that breathes fire into the equations of the physicist, it has retreated far enough behind the physical phenomena, as we routinely perceive and theorize about them, to leave us substantially in darkness. My own suggestion, unsupported here, is that we will have to gain a qualitative science and penetrate much more deeply into the mystery of the physical world before we will be able to see how mathematically reduced physical laws are the mere syntactic skeletons remaining after we have abstracted away the much more richly expressive meaning profoundly present in all phenomena. Surely our immediate experience of oceans and stars, mountains and rivers says nothing to discourage such a thought. The aesthetic and even moral character of this experience bespeaks a significance no less real for all our concerted ignoring of it as scientists.<\/p>\n

The depths of physical reality are, of course, as hidden from us in the living organism as they are in the rest of the physical world. But in the organism we encounter something further: reason and meaning come to much more \u201cvisible\u201d and insistent manifestation, narrating the stories of living beings \u2014 stories that, evoking as they do the intentional and meaningful patterns of our own lives, are more accessible to us than whatever speaks to us now through the qualities of inorganic substance. It is ironic that the organism has been regarded as a more difficult challenge for science than the world of physics. The truth is that the organism is much closer to us \u2014 we are, after all, organisms ourselves \u2014 and it offers many informed, articulate responses to our inquiries. We can apprehend it with a richness and depth of comprehension far exceeding the admirable mathematical comprehension of the physicist.<\/p>\n

If the world is indeed intelligible \u2014 if it speaks meaningfully, as must be assumed by every scientist who tries to capture that meaning in revelatory words and ideas \u2014 then the place where we find it speaking most fully and explicitly is presumably the place where we will find its fundamental truths most fully declared. And that is in the living organism.<\/p>\n

The \u201cdifficulty\u201d of the organism is really just the difficulty of reducing it to mere physics and chemistry. Yes, very difficult indeed \u2014 but that\u2019s because the organism is alive, as we are alive, and because every biologist instinctively understands this life as offering more than lessons in physics and chemistry. As for the \u201cnonliving\u201d world: we imagine it is simpler to understand only because we are bewitched by the precision and predictability of the physical laws we find implicit in things \u2014 things of whose nature we know almost nothing.<\/p>\n

\n
Notes<\/span><\/div>\n
[1]<\/a>\u2002Zenon W. Pylyshyn, Computation and Cognition: Toward a Foundation for Cognitive Science<\/a><\/i> (Cambridge, MA: MIT Press, 1984), xii.<\/div>\n
[2]<\/a>\u2002Owen Barfield, Poetic Diction: A Study in Meaning<\/a><\/i> (1928; repr., Middletown, CT: Wesleyan University Press, 1973), 185ff.<\/div>\n
[3]<\/a>\u2002Richard C. Lewontin, \u201cThe Corpse in the Elevator,\u201d New York Review of Books<\/i> 29 (January 1983), 34-7.<\/div>\n
[4]<\/a>\u2002Craig Holdrege, \u201cWhat Does It Mean To Be a Sloth?\u201d NetFuture<\/i> 97 (November 1999).<\/div>\n
[5]<\/a>\u2002Kurt Goldstein, The Organism<\/a><\/i> (1934; repr. and trans., New York: Zone Books: 1995).<\/div>\n
[6]<\/a>\u2002David Salsburg, The Lady Tasting Tea: How Statistics Revolutionized Science in the Twentieth Century<\/a><\/i> (New York: Henry Holt, 2001).<\/div>\n
[7]<\/a>\u2002Peter Fraser and Wendy Bickmore, \u201cNuclear Organization of the Genome and the Potential for Gene Regulation,\u201d Nature<\/i> 447 (May 2007): 413-7.<\/div>\n
[8]<\/a>\u2002Assaf Weiner, Amanda Hughes, Moran Yassour, et al.<\/i>, \u201cHigh-Resolution Nucleosome Mapping Reveals Transcription-Dependent Promoter Packaging,\u201d Genome Research<\/i> 20, no. 1 (2010): 90-100.<\/div>\n
[9]<\/a>\u2002David M. Gilbert, \u201cReplication Timing and Transcriptional Control: Beyond Cause and Effect,\u201d Current Opinion in Cell Biology<\/i> 14, no. 3 (2002): 377-83.<\/div>\n
[10]<\/a>\u2002Anita G\u00f6nd\u00f6r and Rolf Ohlsson, \u201cChromosome Crosstalk in Three Dimensions,\u201d Nature <\/i>461 (September 2009): 212-7.<\/div>\n
[11]<\/a>\u2002Wulan Deng and Gerd A. Blobel, \u201cDo Chromatin Loops Provide Epigenetic Gene Expression States?,\u201d Current Opinion in Genetics and Development<\/i> 20, no. 5 (2010): 548-54.<\/div>\n
[12]<\/a>\u2002Nadia Aubin-Horth and Susan C. P. Renn, \u201cGenomic Reaction Norms: Using Integrative Biology to Understand Molecular Mechanisms of Phenotypic Plasticity,\u201d Molecular Biology <\/i>18, no. 18 (2009): 3763-80.<\/div>\n
[13]<\/a>\u2002Jocelyn Kaiser, \u201cGenes Link Epigenetics and Cancer,\u201d Science<\/i> 330, no. 6004 (2010): 577.<\/div>\n
[14]<\/a>\u2002Robert Schneider and Rudolf Grosschedl, \u201cDynamics and Interplay of Nuclear Architecture, Genome Organization, and Gene Expression,\u201d Genes and Development<\/i> 21, no. 23 (2007): 3027-43.<\/div>\n
[15]<\/a>\u2002Sayyed K. Zaidi, Daniel W. Young, Amjad Javed, et al.<\/i>, \u201cNuclear Microenvironments in Biological Control and Cancer,\u201d Nature Reviews Cancer<\/i> 7, no. 6 (2007): 454-63.<\/div>\n
[16]<\/a>\u2002Johann Wolfgang von Goethe, The Collected Works<\/i>, vol. 12, Scientific Studies<\/a><\/i>, ed. Douglas Miller (Princeton: Princeton University Press, 1995).<\/div>\n
[17]<\/a>\u2002See, for example, Steve Talbott, \u201cTo Explain or Portray?,\u201d In Context<\/i> 9 (Spring 2003): 20-4 and \u201cA Conversation with Nature,\u201d The New Atlantis<\/i> 3 (Fall 2003).<\/div>\n
[18]<\/a>\u2002David Houle, Diddahally R. Govindaraju, and Stig Omholt, \u201cPhenomics: The Next Challenge,\u201d Nature Reviews Genetics<\/i> 11 (December 2010): 855-66.<\/div>\n
[19]<\/a>\u2002International HapMap Consortium \u201cA Haplotype Map of the Human Genome,\u201d Nature <\/i>437 (October 2005): 1299-1318.<\/div>\n
[20]<\/a>\u2002William Bains, \u201cThe Parts List of Life,\u201d Nature Biotechnology<\/i> 19 (2001): 401-402.<\/div>\n
[21]<\/a>\u2002Sean B. Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo<\/a><\/i> (New York: W. W. Norton, 2005).<\/div>\n
[22]<\/a>\u2002See, for example, Steve Talbott, \u201cCan the New Science of Evo-Devo Explain the Form of Organisms?,\u201d NetFuture <\/i>171 (December 2007).<\/div>\n
[23]<\/a>\u2002Monya Baker, \u201cGenomes in Three Dimensions,\u201d Nature<\/i> 470, no. 7333 (2011): 289-94.<\/div>\n
[24]<\/a>\u2002Helen Pearson, \u201cDNA: Beyond the Double Helix,\u201d Nature<\/i> 421 (January 2003): 310-312.<\/div>\n
[25]<\/a>\u2002Vivek Kumar and Joseph S. Takahashi, \u201cPARP around the Clock,\u201d Cell<\/i> 142, no. 6 (2010): 841-3.<\/div>\n
[26]<\/a>\u2002Masao Doi, Jun Hirayama, and Paolo Sassone-Corsi, \u201cCircadian Regulator CLOCK Is a Histone Acetyltransferase,\u201d Cell<\/i> 125, no. 3 (2006): 497-508.<\/div>\n
[27]<\/a>\u2002Xiaoyong Yang, \u201cA Wheel of Time: The Circadian Clock, Nuclear Receptors, and Physiology,\u201d Genes and Development<\/i> vol. 24, no. 8 (2010): 741-7.<\/div>\n
[28]<\/a>\u2002Roger Lewin, \u201cWhy is Development So Illogical?\u201d Science<\/i> 224, no. 4655 (1984): 1327-9.<\/div>\n
[29]<\/a>\u2002Richard Conn Henry, \u201cThe Mental Universe,\u201d Nature<\/i> 436 (July 2005): 29.<\/div>\n
[30]<\/a>\u2002Stephen Hawking, A Brief History of Time<\/a><\/i> (New York: Bantam, 1998), 190.<\/div>","protected":false},"excerpt":{"rendered":"

How life speaks at every level<\/p>\n","protected":false},"author":1,"featured_media":18901,"template":"","article_type":[13],"noteworthy_people":[],"topics":[5006,5010,5028],"_links":{"self":[{"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/article\/10361"}],"collection":[{"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/article"}],"about":[{"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/types\/article"}],"author":[{"embeddable":true,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/users\/1"}],"version-history":[{"count":1,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/article\/10361\/revisions"}],"predecessor-version":[{"id":22030,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/article\/10361\/revisions\/22030"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/media\/18901"}],"wp:attachment":[{"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/media?parent=10361"}],"wp:term":[{"taxonomy":"article_type","embeddable":true,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/article_type?post=10361"},{"taxonomy":"noteworthy_people","embeddable":true,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/noteworthy_people?post=10361"},{"taxonomy":"topics","embeddable":true,"href":"https:\/\/www.thenewatlantis.com\/wp-json\/wp\/v2\/topics?post=10361"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}