When someone persistently hallucinates, seeing things that aren’t there, we usually assume a cognitive aberration of some sort, if not a severe mental illness. What, then, to make of those countless biologists who look at organisms and think they are seeing machines? Or who look at organs, cells, organelles, and even molecules, and see machines within machines?
I will leave it for you to judge. However, one thing is certain: an inexcusable mistake has gripped the scientific community for decades, severely perverting biological understanding.
I have previously tried to explain in various places why the analogy between organisms and machines fails utterly. But in reading the biological literature lately, I have found the insistent appeals to machinery so egregious, so viciously destructive of scientific insight, and so contrary to the obvious evidence, that I have myself been driven rather too close to a pathological reaction, or at least to an unhelpful exasperation. And so I have decided to gather my thoughts together in what I hope will be a more concise and effective statement.
A good place to start is with a concrete example.
The heart, of course, is rather like a mechanical pump1. Everyone knows this. It moves the blood through the circulatory system. Of course, there are some technical challenges, beginning with more than six thousand miles2 of blood vessels in the human body. Most of the blood’s passage occurs through microscopically small capillaries, some of them so narrow that red blood cells must be deformed in order to squeeze through.
The system also proves leaky almost beyond imagination. Every day about eighty times the total volume of our blood plasma seeps out of the capillary system and into the surrounding tissues, whereupon it follows a circuitous route back into the cardiovascular system. The circulation of plasma, in other words, is a tidal flow that continuously percolates through much of the body and just as continuously re-gathers itself.
This is already enough to enable an obvious judgment: if everybody “knows” without even thinking about it that the heart works like a pump, something strange is going on. Make a simple test for yourself. Try blowing, not even viscous blood, but just water, through a 100-foot-long rubber tube. Make it easy by choosing a tube with a one-millimeter, rather than a microscopically small, diameter. Or, for a yet easier test, simply try blowing a few lungfuls of air through the tube. You will realize soon enough that if your heart could suddenly exert enough mechanical force to move blood on a complete circuit involving those several thousand miles of invisibly small and leaky channels, your body would explode.
That, however, is barely to begin reciting the problems besetting the usual understanding of the heart. Here I can mention only one or two oddities. For example, when the heart is weakened or failing, the volume and pressure of blood returning to the heart commonly increases. The heart, it seems, cannot keep up with the flow. In general, people with strong hearts may have weak circulation, while people with weak or malfunctioning hearts may have strong circulation.
Then, too, there’s the fact that some two-thirds of the heart’s oxygen consumption generates heat rather than “mechanical” force. So, as just one of its major functions, the heart contributes a great deal to the warming of our bodies. It seems that the old idea of the heart as the “sun” in the center of the body is not altogether inapt. One wonders how scientific research might have proceeded if such non-mechanical imagery had had a share of the researcher’s imagination.
Surely no one yet possesses any full understanding of the heart and circulatory system. But some things seem fair to say. The muscular contraction of the heart’s left ventricle does give impetus to the blood in sending it swirling out through the arterial portion of the cardiovascular system (amounting to about fifteen percent of the whole). But even here other factors are involved. The arteries dilate or contract to accomodate changes in blood volume, and the wavelike contractions of their walls can aid in moving the blood along.
This helps to explain why, when someone is given an artificial heart and has become reasonably adapted to it, an increase in the device’s pumping rate does not yield a sustained increase in blood pressure or cardiac output. The blood vessels respond by dilating, thereby holding the blood flow at a level that the body has found to be optimal. So the mechanical device is “subverted” and not allowed to act as a central controller; the circulatory system as a whole counters it in order to maintain a desirable state.
There is, then, no simple answer to what moves the blood, especially through the “low-pressure” cardiovascular system that constitutes some eighty-five percent of the whole, including the capillaries, veins, right side of the heart, pulmonary (lung) circulation, and left atrium of the heart. Also needing to be accounted for are the the fluids moving outside the blood vessels through the various bodily tissues and making up a volume twice that of the vessel-contained plasma.
A crucial fact is that, while the heart’s output volume is not directly proportional to heartbeat rate or blood pressure, it is proportional to the oxygen consumed in all the body’s tissues. This suggests that the body’s metabolism is a primary driver of the blood. While muscular exertion, lung movement, and suction from the right side of the heart definitely play roles, the tissues themselves must continually replenish the volume of blood. In doing so they perform a major service in driving the blood back to the heart. The heart then acts as a subtle regulator of this flow — even restraining or damming it up to a degree. It thereby lends rhythm (there is a complex forward - backward - pause rhythm in the arterial flow emerging from the heart) while at the same time warming the blood and, in general, sensing and responding to overall conditions in a harmonizing way. Only in sick hearts does this “musical” performance tend to degenerate into a mechanically regular, metronome-like heartbeat.
Whatever the unknowns in all this — and there are plenty — the one thing abundantly clear is that the picture of the heart as a pumping machine is hopelessly inadequate. How many billions of misdirected research dollars and how many lost lives have resulted from a widely accepted “truism” about the heart that is so grossly misleading?
In building a stereo system, I have to assemble the parts. Mine, so to speak, is an alien hand, manipulating those parts and articulating them together according to my own intentions. The parts, in general, remain discrete, separable, well-defined, and — because they do not interpenetrate each other and do not bear within themselves the imprint of the whole — are subject to arbitrary, radical change in character at my discretion. I could substitute a stainless steel knob for a plastic push button, aluminum wiring for copper, vacuum tubes for transistors, a magnetic medium for an optical disk. I could drastically reconfigure the spatial organization of the thing without destroying its intended function.
And with the finished product before me, I would never say that the parts had came together in this particular arrangement because the idea of the arrangement was actively at work in the parts themselves. Rather, it was I who brought them together. The completed device would embody a functional idea, but the idea would be mine, imposed from without. The idea would not be intrinsic to the materials I had chosen. They themselves would show no inherent intention or behavior directed toward the realization or maintenance or reproduction of my idea.
There is not much here that merits serious comparison to an organism. It seems almost embarrassing, even insulting to the reader, to point out (as today’s intellectual environment requires one to point out) that, unlike organisms, neither the machine nor any of its mechanical parts is alive. The previous two paragraphs merely point to a few of the features reflecting this absence of life.
As a fertilized egg (zygote) proceeds through its development, no alien hand reaches in to adjust the form of the cytoskeleton, or the relations between the nucleus and other organelles, or the permeability of the various membranes. There are, in fact, no fixed parts to adjust. A small clump of cells here or there metamorphoses into a forelimb or heart or liver. Actually, this description is still too “thing-like”. Structures result first of all from movement and flows:
The body does not behave like a plumber, first connecting the water pipes in a house and then turning the water on. ... The first blood-like liquid ... simply trickles through gaps in the tissues. ... Preferred channels develop only very gradually as blood cells are deposited along the edges and eventually merge into the beginnings of vessel walls. (Wolfgang Schad in Holdrege 2002, p. 80*)
Similarly, the walls separating the four chambers of our hearts are already “there” before they exist as solid structures. At first they are simply “still water zones” between distinct, looping currents of blood, and only later do the walls materialize, taking their shape from those already structured flows (Holdrege 2002, p. 12*). No artificial heart is built this way.
More generally, in the early embryo we see streams of cells flowing and multiplying in complex patterns as they gesture the organism’s changes of form. Something similar happens during wound healing. In the organism stable form precipitates out of movement, and so long as a structure remains living, it is never absolutely fixed.
Further, the whole organism is there from the “beginning”. During the entire life cycle from zygote to senescence, there is no stage we can single out and say of it, “Only here do we have the complete or true organism”. And because the whole organism is always there, we never see an assembly of parts. During certain stages of life the parts grow as participants in an integral unity, differentiating themselves out of a prior unity, being transformed in a way that depends intimately upon what is happening around them.
If the whole organism is there from the beginning, then in a very real sense it is the whole that makes the parts. The whole is dynamic, a bearer and realizer of unseen potentials. It works upon itself in the process of differentiation, maintaining its unity all along the way and then gathering its dynamic powers, bringing them to a focus in the intensely potentiated gamete, representing both a continuation and a dramatic renewal of life.
Nowhere in all this do we see a functional idea being imposed upon the parts from outside in the way a human engineer might work. Nowhere do we see a relation of parts suggesting mechanical relations. Nowhere do we even see fixed parts as such, in any machine-like sense.
Presumably the tendency to see machines in organisms is also influenced by the fact that, in observing the extraordinary and often (for us) novel wisdom evident in an organism’s lawful performances, we gain inspiration for the construction of machines. Organisms and machines, after all, must exist within the same physical world.
But nothing in any of this exempts us from noticing the particular natures of the things we liken to each other. In calling the parts of an organism “machines”, we require a justification that goes beyond the fact that they, like machines, are part of the physical world and respect physical laws in the way they accomplish things. We need criteria that do not apply equally well to volcanoes and streams.
Actually, the distinctive play of lawfulness and physico-chemical causes in organisms is itself reason for distancing ourselves from the machine metaphor (Talbott 2011*). One rather telling symptom of this distinctiveness — to which I have previously drawn attention — is the frequent unclarity over what is a cause and what is an effect in the organism.
This ambiguity is everywhere3. To take an article that came my way as I was writing this: biologists are now conducting so-called epigenome-wide association studies, designed to find correlations between certain non-genetic molecular features of the organism and various complex traits. The compelling desire among biologists to discover correlations that are also causes is often frustrated in these studies. “Epigenetic alterations vary drastically between cells of the same tissue, and it can be difficult to determine whether an alteration is a cause or consequence of a disease” (Callaway 2014*).
As researchers probe the organism in ever more molecular detail, such ambiguity seems to increase rather than be resolved. Everything proves — to take a frequently used phrase of the current literature — context-dependent. This is just another way of saying what I suggested above: in a very real sense it is the whole that governs the parts. The relations between the parts are continually shifting according to the requirements of the organism. In particular, causal relations typically do not remain fixed over time and across all circumstances — hardly a surprise given that the parts relating to each other do not themselves remain fixed.
This is not the way of, say, a mechanical watch. Move the watch from here to there and you do not expect its functional relations to change — except so far as it ceases to function altogether under damaging conditions4.
If biologists would only recognize that they are not dealing with machines, the causal ambiguity they continually run up against would cease to frustrate them. They would realize that they are — if they would only raise their eyes to take in the larger, qualitative picture — gaining an ever fuller understanding of the way organisms actually live their lives. There are numberless potential causal relations among the molecules, cells, and organs of any given creature; from among these, and acting as a whole in ever-changing, context-dependent ways, this creature weaves the causal threads of its own life. This weaving, not the collection of threads as such, forms the intentional pattern, or tapestry, that in every detail speaks “sloth” (Holdrege 1999*) or “sea star” or “Douglas fir”.
Perhaps most baffling of all is the incomprehensible but wildly popular habit among biologists of referring to “molecular machines”, a habit that continues unrestrained even as researchers daily reveal more and more of the unmachine-like character of biomolecules — continues, for that matter, a hundred years after physicists struggled with the problematic “wave-particle” nature of photons and electrons together with other, still deeper mysteries that reach not only downward but also upward into the domain of chemistry. If there’s one thing we can be sure the physicists are not dealing with, it is molecular machines.
The facts of the matter couldn’t be clearer in the biological realm. What, for example, has become of the neatly stable lock-and-key proteins whose unproblematic “fitting together” was once thought to shape cellular processes? Today there’s a vivid recognition that molecules of a given protein typically occur as an ensemble of dynamically varying conformations — and the dynamics of variation, the balance among subtly or dramatically metamorphosing, plastic forms, is often pivotal for protein function.
There is also a growing recognition of “communal” interactions. The binding of a given protein regulatory factor to a particular location of DNA may depend on how the protein deforms the DNA, or the DNA deforms the protein, or how a neighboring protein deforms either the DNA or the first protein — or, just as likely, how they all mutually affect each other — and so on in ever more subtly interconnected and outward-rippling patterns of interaction.
Moreover, there is today an intense and rapidly developing interest in intrinsically disordered proteins, whose so-called “disorder” is in fact a plastic and well-shaped potential, an effective dynamism, that is vital for their flexible and many-faceted roles in the cell. In general, the old, rigid, building-block protein molecule has given way to “fluid-like” and “surface-molten” forms. (Grant et al. 2010*; Zhou et al. 1999*). These do not sound like machines.
What is a molecule? But the more fundamental thing is to realize what we are looking at — or, rather, what we are not looking at — when we descend to the atomic and molecular scale. When I speak of “form”, as in “form of a protein molecule”, I certainly have no justification for imagining anything like the matter of the familiar world — matter exhibiting the qualities we work with in building machines. Nothing is there in this sense — no thing — and far too little thought has been given to how we can develop a language faithful to the reality of the instrumentally mediated “observational experiences” we manufacture at the level of molecules. To speak of machines, other than the ones we interpose between ourselves and the objects of our interest — is to lunge at a metaphor incongruous beyond all hope of credibility.
What is an “electron cloud”? How does one part of a large molecular electron cloud interact with another? One thing we do know is that chemical reactions produce almost magical transformations. To whatever degree we can explain the “alchemy” that gives us the qualities of water from the explosive reaction of hydrogen and oxygen, it is not by talking about a mechanical rearrangement of particles. And if not that, then what?
There is every variety and degree of atomic and molecular interaction, so that even classifying the types of molecular bonds has proven a perennial vexation for chemists and physicists. In an instructive essay called “Beyond the Bond”, Nature columnist Philip Ball (2011*), mentions how “the behaviour of one electron depends on what all the others are doing”. More than that, “describing the quantum chemical bond remains a matter of taste: all descriptions are, in effect, approximate ways of carving up the electron distributions”. Ball quotes Roald Hoffmann of Cornell University to the effect that “any rigorous definition of a chemical bond is bound to be impoverishing”. According to Ball, “the static picture of molecules with specific shapes and bond strengths” needs replacing, and we must learn to view “bonds as degrees of attraction that wax and wane ...”
The remarkable thing is how little this understanding has colored the rhetoric of biologists when they talk about molecular machines — for example, the RNA polymerase that transcribes DNA into RNA, the spliceosome that pieces together well-chosen snippets of a precursor messenger RNA (mRNA) into a mature form, and the ribosome that translates mRNAs into protein.
It is well to realize that each of these supposed “machines” is a massive complex of continuously changing molecular composition, with the component molecules themselves subject to modifications crucial for their functioning. All these changes represent an unfathomably intricate shifting of chemical and physical bonds — a qualitative refiguring of the balance of forces. This mean that there is an ongoing, even if often subtle, transformation of substances — the kind of transformation that, at one extreme, produces water from hydrogen and oxygen and, at the other, alters the forces and energies within some portion of a macromolecule just enough to shift its biological activity from one pathway to another.
Where is the justification for interpreting these biochemical metamorphoses as machine interactions?
Mysteries of water. It is also emerging that the cellular contents manifest a kaleidoscopically changing pattern of locally distinct phases — liquid, semi-liquid, solid, gel, and so on. Working with flatworms, Hubstenberger et al. (2013*) found that as egg cells mature, many highly viscous, semi-liquid molecular complexes become more dynamic liquid droplets and their constituents become more mobile, which is thought to promote rapid changes in organization of the complexes after fertilization — changes, for example, that facilitate the differentiation of cells in the growing embryo. Again, where is the “machinery” in this?
Then there is water itself, which is a mediator not only of phase changes in the cell, but also of nearly everything that goes on. When structural biologists Mark Gerstein and Michael Levitt tried to develop a computer simulation of DNA, they found the molecule falling apart until they added water to the simulation. 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 protein folding to just about any chemical reaction, you’d be hard put to find any activity in the organism that is not dependent upon, and in one way or another shaped by, the local and infinitely varying collective structure of water molecules.
Reflecting upon this kind of thing, Philip Ball wrote,
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? (Ball 2013*)
In the molecular realm, where we have no observational justification for thinking in terms of anything like familiar substances or matter, the easiest thing, it seems, is simply to reify our theoretical constructs and leave it at that. Having ignored the deepest mysteries of physics over the past century, biologists, it seems, can simply think “machine”, draw cartoon pictures of molecular complexes that look like machines, and — hey presto! — they have molecular machines.
The idea that the organism is an information-processing machine and that DNA contains instructions or program code for making the organism has proven irresistible — almost obsessional — within biology during the past several decades. The idea is often extended almost without thought to anything and everything, so that we have “transcription factor binding codes”, “RNA splicing codes”, “histone modification codes”, and so on without end. In recent years it’s been suggested that, not DNA, but RNA is the “computational engine of the cell” (Mattick 2009*; Mattick et al. 2009*), and again that the epigenome is the equivalent of a computer’s “working memory”, bridging the gap between the “read-only memory” of DNA and the transient, memoryless signaling processes that operate within and between cells (Milosavljevic 2011*).
Putting it summarily: there are no computer-like instructions or programs written in the material of the organism (if you think there are, please point me to them); there is nothing like the reliable computational machinery required for executing such programs; the computer’s essential lockstep, unexceptioned precision — its coordination of precisely defined pathways involving minutely machined and unchanging parts — is altogether lacking in the organism; a computer that grows its own parts is unthinkable; a computer that divides like a cell, thereby differentiating itself into hundreds of radically different sorts of computers with different programs and different hardware for executing those programs, is likewise unthinkable, just as is a computer that heals injuries through the movement and transformation of parts from surrounding regions of the device; and, finally, I’m not sure there have even been any serious attempts at suggesting what might constitute the global program and hardware that coordinates billions of individual cellular-computers, so as to specify the overall form of an organism and its integral, unified functioning.
Non-digital DNA. Worse, that great store of supposedly digital information — DNA — is far from being any such thing. Researchers are now furiously engaged in revealing how all the imagined “bits” of information in DNA are actually employed, and the picture could hardly be less computer-like. Here are a few factors bearing on the meaning of any given “letter” or sequence of the human genome:
This is barely to touch on the fluid reality that shapes the meaning of any given DNA sequence. We could, for example, look at RNA, whose various transformations — RNA editing, RNA modification, and RNA splicing among them — can re-voice in radically altered ways the meanings of particular DNA sequences. This re-voicing occurs within a huge field of potential variation, and shows exquisite sensitivity to the decidedly non-digital state of the cellular context.
A flexible passivity. The digital illusion so many have suffered since the discovery of the double helix has been produced by the fact that there is an iterative regularity in the DNA sequence: four nucleotide bases (often referred to as “letters” of the genetic code) are repeated along each strand of the double helix in patterns that can vary without effective limit. This immediately made biologists think of a computer program’s digital code, and the idea of such a code, as we now see, dies hard even in the face of the kind of subverting evidence I have only fragmentarily gestured toward above.
The real significance of the DNA sequence, however, directly contradicts the digital notion. Yes, as some have pointed out, isolated DNA is just about the deadest, most crystalline molecule in the organism, doing nothing on its own. But in the cell, DNA is never isolated. It lives in the intricately shaping and changing embrace of numerous other chromosomal constituents. And it participates plastically in the larger cellular environment, which orchestrates changes of chromosomal form — physically, chemically, electrically, spatially, choreographically, and in just about any way you can imagine. There is a certain replicable stability of those iterative elements of DNA, considered in isolation, and there is an approximate causal specificity correlating some of the elements with the sequential constituents of proteins, both facts being extremely important. But at the same time DNA yields itself malleably to the surrounding activity of the cell and organism as a whole. Its life and functioning come from its context5.
The decidedly non-digital malleability of DNA is now the central reality biologists are uncovering, and they are doing so in startling detail that would have been hard to imagine even twenty years ago. But set beside all this the recent remark by Ehud Keinan, whose work at the Technion-Israel Institute of Technology is to insert artificial, programmable elements into the organism:
All biological systems, and even entire living organisms, are natural molecular computers. Every one of us is a biomolecular computer, that is, a machine in which all components are molecules “talking” to one another in a logical manner. The hardware and software are complex biological molecules that activate one another to carry out some predetermined chemical tasks. The input is a molecule that undergoes specific, programmed changes, following a specific set of rules (software) and the output of this chemical computation process is another well-defined molecule. (Quoted in Siegel-Itzkovich 2013*; emphasis added)
This is the kind of thing that tempts one either to despair or to venture rash remarks, as I did above, suggesting the possibility of hallucination. The frightening thing is that such hallucinations (or whatever this sort of vision represents) can be clothed in real substance, as Keinan is bent on doing. It will work, in its own way, and this working seems to be what he really has in mind. That is, we can progressively reduce the organism toward machine-like functioning by forcing our own machine-like constructs upon it. The machine we have so long projected upon the organism has always been an image in our own minds, but images we nourish long enough with our desires and energies have a way of realizing themselves outwardly sooner or later, even if not with quite the results we envisioned.
If biologists would do three things, they could banish for good the distortions introduced by machine-talk. The first is to focus on the living activity out of which relatively stable biological structures take form and are sustained, rather than on the structures as such — structures all too easily frozen in the imagination. The second is to move beyond temporally isolated interactions of parts, tracing instead the narrative threads of activity and observing how they weave together to form part of a life story. The third is to become aware of the distinction between an idea impressed upon a collection of parts from without, on the one hand, and, on the other, an idea intrinsic to the organism, an idea in which the parts participate harmoniously without coercion by an alien hand, an idea that does not assemble parts into a “finished” product, but rather lives as a present activity that, among other things, coordinates causal relations, bringing them into the service of the organism’s own expressive intentions6.
Movement precedes structure. The processes of life are narratives. The functional ideas manifested in the organism belong to the intrinsic inwardness of its life, and are not imposed from without by the mind of an engineer. If we would only keep these truths in view, then we could without distortion note the analogies between the functioning of organisms and machines. If we are thinking in broad enough terms, certainly we can usefully note that, say, a human-piloted glider and a flying squirrel do some similar things.
It can be useful in both directions: having remarked the similarity, we can draw on our knowledge of the physics of glider design to begin investigating the performance of the squirrel. Likewise, we can apply unexpected insights from the squirrel to our own design of gliders. But it will be well to realize that, so far as we remain within the domain of physics, we haven’t yet come to the biology of the squirrel. And when we do take up the biology, we will find that the life and development and activity of the squirrel, even in its gliding, carries us to a world far removed from the making of machines.
1. The information in this section is drawn from a larger article, “On Being Wholehearted” (Talbott 2002*). That article (which contains appropriate references) is a review of a book called The Dynamic Heart and Circulation, edited by my colleague, Craig Holdrege (2002*). For an extremely technical treatment of many of these same issues, see Furst 2014*.
2. I am being extremely conservative. A common estimate is 60,000 miles.
3. It’s also been noted for a very long time and by very influential thinkers, although you would hardly know this by reading the literature of molecular biology. About 225 years ago Immanuel Kant wrote in his Critique of Judgment, referring to organisms as “natural purposes”:
For a thing to be a natural purpose in the first place it is requisite that its parts (as regards their presence and their form) are only possible through their reference to the whole. ... then it is requisite secondly that its parts should so combine in the unity of a whole that they are reciprocally cause and effect of each other’s form. (Kant 2000, pp. 276-7*).
See in the Critique of Judgment: Part 2, Div. 1, paras. 65-6, and more generally, the entire Part 2.
4. Machines, of course, are made to change or “adapt” in all sorts of ways, most trivially, perhaps, by responding to power-on or power-off (where power may be supplied by a human foot, flowing water, steam, electricity, or whatever). They are, after all, made to do things, which implies some sort of response to the varying stages of a process. But all of this activity is, at some level of analysis, designed into a set of defining functional relationships, and no such level of analysis exists in the irreducibly whole organism. With reference to the discussion above: does the heart beat in order to move the blood, or does the flow of blood shape the beating of the heart? Both play a role, and do so in complex interaction with countless other factors that vary with the condition and activity of the organism. We may glimpse a dynamic and organic whole through the integrated activity of its parts, but the parts are less an explanation of the whole than an ever-varying expression of it.
6. By “structure” I mean more or less stable material form — or artificially frozen form, exemplified by proteins subjected to the procedures involved in structural studies. By “narrative activity” I mean neither more nor less than the storylines that biologists are always trying to understand: how DNA, gets replicated, how the cell divides, how a warm-blooded animal maintains its normal body temperature, how the digestion of food occurs so as to meet the body’s energy needs, and so on.
By “idea” I do not refer to the abstract ideas so cherished in much of science, but to the kind of dynamic ideational reality manifested as the inner nature of all material phenomena. In this sense — taking the law (idea) of gravity as an example — we recognize that “the very law itself is also the power”. That phrasing is Owen Barfield’s, as he summarizes elements of Samuel Taylor Coleridge’s thinking. He continues:
Where Newton was content to think of, and to quantify, the link that holds the earth to the sun as a vector, the lesser fry ... must fancy their piece of invisible string or something like it. They could never accept, because they could never understand, that the ultimate explanation of phenomena cannot itself be phenomenal. (Barfield 1971*)
Understanding, that is, comes through our grasp of the ideas at work in nature, as every page of every scientific text testifies. Yet seeing this remains alien to the modern mind, not because the seeing requires any particular subtlety, but because it flies directly in the face of long-established and almost immovable habits of thought (Barfield 1965*). In any case, the ideas evident in organisms are of a quality differing substantially from those the physicist deals with. They embody themselves, not, for example, in the planetary movements that Copernicus, Kepler, and Newton investigated, but rather in the interwoven narrative threads referred to above.
Ball, Philip (2011b). “Beyond the Bond”, Nature vol. 469 (Jan. 6), pp. 26-8. doi:10.1038/469026a
Ball, Philip (2013). “Concluding Remarks: Cum Grano Salis”, Faraday Discussions vol. 160, pp. 405–14. doi:10.1039/c2fd20126g
Barfield, Owen (1965). Saving the Appearances. New York: Harcourt, Brace and World. Originally published in 1957.
Barfield, Owen (1971). What Coleridge Thought. Middletown CT: Wesleyan University Press.
Callaway, Ewen (2014a). “Epigenomics Starts to Make Its Mark”, Nature vol. 508 (April 3), p. 22. doi:10.1038/508022a
Furst, Branko (2014). “The Heart and Circulation: An Integrative Model”. New York: Springer.
Grant, Barry J., Alemayehu A. Gorfe and J. Andrew McCammon (2010). “Large Conformational Changes in Proteins: Signaling and Other Functions”, Current Opinion in Structural Biology vol. 20, pp. 142-7. doi:10.1016/j.sbi.2009.12.004
Holdrege, Craig (1999). “What Does It Mean To Be a Sloth?” NetFuture #97 (Nov. 3). Latest version is available at http://natureinstitute.org/nature/sloth.htm.
Holdrege, Craig (1996). Genetics and the Manipulation of Life: The Forgotten Factor of Context. Hudson NY: Lindisfarne.
Holdrege, Craig, editor (2002). The Dynamic Heart and Circulation, translated by Katherine Creeger. Fair Oaks CA: AWSNA.
Hubstenberger, Arnaud, Scott L. Noble, Cristiana Cameron and Thomas C. Evans (2013). “Translation Repressors, an RNA Helicase, And Developmental Cues Control RNP Phase Transitions during Early Development”, Developmental Cell vol. 27 (Oct. 28), pp. 161-73. doi:10.1016/j.devcel.2013.09.024
Siegel-Itzkovich, Judy (2013). “Technion Scientists Create Biological Computer”, Jerusalem Post (April 13). Available at http://www.jpost.com/Health-and-Science/Technion-scientists-create-biological-computer-315871
Kant, Immanuel (2000). Critique of Judgment, translated by J. H. Bernard. Amherst NY: Prometheus Books. Originally published in German in 1790.
Mattick, John S. (2009). “Has Evolution Learnt How to Learn?” EMBO Reports vol. 10, no. 7, p. 665. doi:10.1038/embor.2009.135
Mattick, John S., Ryan J. Taft and Geoffrey J. Faulkner (2009b). “A Global View of Genomic Information: Moving Beyond the Gene and the Master Regulator”, Trends in Genetics vol. 26, no. 1. doi:10.1016/j.tig.2009.11.002
Milosavljevic, Aleksander (2011). “Emerging Patterns of Epigenomic Variation”, Trends in Genetics vol. 27, no. 6 (June), pp. 242-50. doi:10.1016/j.tig.2011.03.001
Talbott, Stephen L. (2002). “On Being Wholehearted: From Mechanical Metaphor to Reality”. Originally published in NetFuture #140 (Dec. 26). Available at here.
Talbott, Stephen L. (2011b). “From Physical Causes to Organisms of Meaning”, The New Atlantis no. 30 (winter), pp. 24-49. Original version published as “What Do Organisms Mean?” in NetFuture #182 (Feb. 22). Latest version and a brief summary are available at http://natureinstitute.org/txt/st/mqual/genome_6.htm
Talbott, Stephen L. (2012). “The Poverty of the Instructed Organism: Are You and Your Cells Programmed?”. Latest version and a brief summary are available at http://natureinstitute.org/txt/st/mqual/genome_9.htm.
Talbott, Stephen L. (2013). “Free Life and Confining Form”. Latest version available at http://natureinstitute.org/txt/st/mqual/genome_10_polar.htm.
Zhou, Yaoqi, Dennis Vitkup and Martin Karplus (1999). “Native Proteins Are Surface-molten Solids: Application of the Lindemann Criterion for the Solid versus Liquid State”, Journal of Molecular Biology vol. 285, pp. 1371-1375. doi:10.1006/jmbi.1998.2374
A somewhat different discussion of the machine-idea is found in the section, “The Organism Is Not a Machine”, in “The Unbearable Wholeness of Beings”.
This document: BiologyWorthyofLife.org/comm/ar/2014/machines_18.htm
Steve Talbott :: Biology’s Shameful Refusal to Disown the Machine-Organism