ANALOGIES BETWEEN A MOLECULE AND AN ORGANISM
Whenever something is a characteristic part of something else, as a molecule is a part of an organism, there will be some interest in seeing whether the mutual analogies they possess intimate the existence of any type, degree, or analog of a- 'fractal' relationship. The reasons for this Interest are at least two: it is now known that such fractal relationships between different "length scales" (size levels), both within and between things, are at least rather common in nature, and are therefore to that extent to be expected in arbitrary situations; and secondly, the ideonomist is preeminently that scientist who expects and seeks universality in, among, and above things, and it is therefore important for him to know whether-or in what measure-some general fractal principle, law, or pattern governs the whole universe or all reality. It is also true that the mean ring of 'fractality' must in part be empirical and dependent for its clarification upon the findings of such investigations as this.
A general ideonomic principle summarizes a common discovery in the history of science: When the range of occurrence or exemplification of some generic property, phenomenon, or relation is in the study of a subject initially assumed but not proven to be bounded above or below, circumscribed, or discontinuous, the restriction is often later shown to have been unfounded, premature, overly general, misdirected, or deleterious. There is another principle that is relevant here: Where two things are at first assumed to be sharply separated or divided from one another, or to be separated by an absolute gap or hiatus or by an interval over which their abundance, strength, or effect is zero-or are assumed to differ from one another absolutely, fundamentally, or dichotomically-it is often subsequently discovered that in reality the things are joined or united by a continuous intergradation or intertransformation, either direct or virtual.
I will return to these matters later, after I have discussed some of the 69 entries on the chart "Molecule-Organism Analogies" (see).
1. A molecule and an organism are alike in that both FORM GRADIENTS. The known and possible ways, senses, and instances in which organisms 'form' gradients' are numberless, but it will be instructive to mention a few. The density distribution of the bionts in the population of a species will contain intricate monotonic and nonmonotonic gradients throughout the range of the species. There will be thousands or millions of gradients for just the simplest polymorphisms. A species population will itself serve as a gradient for other species that compete with, eat, are transported by, coevolve with, or otherwise interact with it. The cumulative spoor of an animal will form a gradient over its territory. Velocity and pressure gradients are formed and followed by winds that forever circulate around the body of an organism. Sounds and smells emitted by an animal form gradients. In an organism's interior-in and as its tissues, major bodily systems, organs, cells, biochemical pathways, etc-there exist 1-, 2-, 3-, and hyperdimensional gradients that number many powers of a million organisms are of course both cause and effect of myriad molecular gradients, including geochemical gradients.
The electromagnetic forces within and between molecules are gradient. Within materials and massive objects there are gradients of different chemical species. The molecular cohesion of a viscous liquid will cause it to form height, velocity, directional, and other gradients as it gravitates away from a spill site.
But what subtler organismal and molecular gradients might be imagined?
Perhaps the great variety of radicals and other chemical species that are generated by the chemical kinetics of a reaction form 1-, 2-, and 3-dimensional : unbranched and branched:,steady state and protean : gradients that, in part, are like natural chromatography, and that may even play an active role in shaping the dynamics or outcome of the reaction, or the structures and materials it may give rise to. Such gradients might be perfected and harnessed by the chemical industry.
What are the ontogenetic gradients that control the cellular differentiation of the human body after the formation of the monadic zygote?
What interwoven hierarchy of gradients exist in the brain as the basis of its mental processes? How is neural information strung along polysynaptic chains of neurons? Are there molecular gradients inside or over the surface of a neuron that contribute to memory? What is the structure of the gradient flows of energy within a neuron?
2. Molecules may be analogous to organisms in that, hypothetically, both CAN BE SELF-REPAIRING. Biological self-repair is well-known, and in fact the-tendency of an organism to correct such internal defects as arise through aging, wear, error, and injury is generally thought of as being one of life's major and basic properties. Although the process of repair is manifestly imperfect, new mechanisms, examples, and effects are continually being found and hypothesized. Nor is it clear what degree of repair might be optimal for life-or excessive. Just as the 'fundamental goals and priorities' of life qua life or qua the bios are unknown and almost impossible to imagine, the reasons-for its self-repair largely remain problems for the future.
What scientists certainly must seek to achieve eventually is some synthesis of all the different bodily, ecological, and evolutionary elements of self-repair, in part.with those elements reduced to some timeless, universal, and necessary form, or generalized to the point that they have ceased to be merely biological and have become ideonomic phenomena, with rich and equally necessary and comprehensive illustrations in the sciences of (supposedly) inanimate things. Life's totality of reparative elements must be redescribed within the system of meta-structures : of hierarchies, networks, series, rings, vergences, etc : that cause, govern, serve, and manifest them.
How, for example, do biological processes of repair rectify one another and repair themselves? How, inevitably, do they interfere with one another? Is bodily repair centralized or distributed? What are its redundant and irredundant features? Are the same or different processes at work at different (spatial, temporal, energetic, etc) scales? How homogeneous and heterogeneous is repair across the set of all species? What starts, supervises, and halts repair? What is the scale of efficiencies for all types of repair?
If biological self-repair is well-accepted, the concept of molecular self-repair is not, and indeed little has been said about the possibility of such repair. Except, of course, in the case of biomolecules, especially ones that play a direct role in the life of the genome. Currently (1988) complete and partial : direct and indirect : 'self-repair' by DNA and RNA molecules is a lively topic in molecular biology.
But might the concept of self-repair deserve extension to abiotic molecules or to physical chemistry?
If so, might the diverse simple and complex mechanisms of self-repair that are known to exist or that might be surmised to operate in the special case of biological molecules, also find some degree and form of illustration in the larger world of chemistry, if perhaps only metaphorically? The connection could actually justify the funding of research into biomolecular self-repair for the sake of the potential spin-off in other fields. The.chemical industry could both exploit the natural processes and develop quite novel artificial ones. Moreover the generalization of molecular self-repair to all of chemistry would make it more probable that such repair is not peculiar to molecules but rather is a general property of natural phenomena. A search for generalized mathematical-or even logical -laws might be warranted.
Of course speculations such as this require us to define more precisely what we mean when we speak of "self repair", and they also require that we delimit or circumscribe the concept.
A minimal example of-so-called self-repair in a nonbiological molecule might be where a transient loss of structure or of a constituent by such a molecule might have a tendency to be very quickly corrected through nothing more 'intrinsic' to the molecule than the regulative effects of other (like or different) molecules in its vicinity, which would presumably 'prefer' the molecule to have a certain form or to be of a certain type (owing to the kinetic equilibria of the total system).
But from here one can proceed to imagine more complex and essential forms of self-repair that might exist, as well as processes that might assist with such repair in a secondary to even tertiary capacity.
Perhaps when any molecule exists in the presence of other molecules it tends to organize its environment or those other molecules in ways that reinforce its peculiar nature or that contribute to the chances of its survival. Or different molecular species, when present together, might compete with one another, and induce in this manner a degree of natural selection of 'fittest' molecules. Smaller or specialized molecules might have a tendency to accumulate in the immediate neighborhood of a 'dominant' species of molecule, and play roles in its maintenance and repair (if only statistically, or from the standpoint of some sufficiently large sample).
Molecules that are directly self-repairing might also be selected for.
The concept of molecular self-repair could simply mean that the flexibility and resilience of a molecule that is subjected to a stress is fundamentally greater than would normally be assumed on the basis of the orthodox picture of molecules as delomorphous, nonself-adjustive entities possessed of meager dynamic equilibrium and 'cybernetics'.
Are the most familiar, stable, or long-lived molecules those that have the greatest self-reparative powers? May existing chemical laws and theories unknowingly subsume self-reparative behavior; and if so, can tests be devised to demonstrate or disprove its existence?
Generalization of molecular self-repair in such ways as this could in turn redound to the advantage of biochemistry. Thus to the extent that self-repair is chemically or physically universal, the prebiotic origin of life is easier to undetstand-or to believe in and model.
3. Molecules and organisms may be alike in that both hypothetically HAVE or involve 'LANGUAGES'. That people have languages is trivial. All of life may be permeated with languages or things analogous to language. We still know almost nothing about animal communication and behavior, save that they are rife with 'linguistic' aspects, and true progress here may await breakthroughs in artificial intelligence, neurology, cognitive science, computer hardware, and even ideonomy. Language is one of the most badly defined, or moronically restricted, terms in all of science (as will be seen from discussions of it elsewhere in this book). Common sense alone would extend it so as to include microkinesics (body language), mathematics, music, diplomatic conduct, human customs, and the genetic code. But it is almost equally evident that the concept should be understood to embrace logic, nosology, all taxology, rules of games, emotional processes and states (or the system thereof), neural codes (defining messages sent by action potentials, used in memory, etc), perceptual codes (vocabularies, grammars, and messages), immunological recognition codes, protein structures, biochemical processes in general, information theory, all molecular interactions, all many-body processes and interactions in physics, crystallographic rules, and a great deal more. (Note that, in several senses, 'molecular language' is included in this list.)
If the postulated molecular languages really do exist, then these might be used-as the basis of new forms of chemical technology-to control the synthesis and manipulation of molecules in fantastically specific, precise, efficient, complex, and arbitrary ways, and to heighten in the same extreme way the perceptual powers of.analytical chemistry.
Since life is fundamentally a chemical process or.is a process that originally arose from and that currently is controlled by molecular interactions-it is perfectly conceivable that it is based throughout upon a single chemical language, or upon some permutation, transformation, evolution, expansion, or condensation of some earliest biotic or prebiotic chemical language, one that might have been either extremely simple or extremely complex. All present-day biological processes and languages may endlessly use and reuse this archetypal language. It may be repeated fractally at every level of an organism. It may offer a primitive key or else a Rosetta stone for deciphering the many 'languages of the body or for lintertransiating the Earth's millions of different species.
So the astonishing possibility exists that molecules and organisms are alike, not simply because they both have languages, but because they make use of or represent expressions of the same language!
4. Molecules and organisms are similar in that hypothetically both CAN HAVE 'INTERNAL CLOCKS'. We know that organisms have such clocks, although we have no idea how many different clocks they have or how diverse their bases may be. Clocks appear in brain waves, circadian rhythms, seasonal phases (as of flowering, fruiting, leaf color change and fall, migration, and hibernation), episodes of bodily development (such as those at human puberty),,senescence and death, and ecological succession. "Protein clocks" are used to time the genomic distance of two species from one another. Almost surely there are kilohertz, megahertz, gigahertz, and terahertz 'clocks' in organisms., since those frequencies.correspond to the characteristic periods of so many chemical reactions and events; and probably petahertz clocks as well, since so many physical phenomena occur on the corresponding temporal scale (of femtoseconds).
How might molecules be clock-like or contain clocks?
I will start with what are least relevant:.entire chemical reactions. It is conceivable that there are certain reactants or combinations of reactants that can give rise to Interactions and reactions characterized by motion or activity-vibrational, rotational, translational, excitational, relaxational, exchange, 'tessellational', 'choreographic', 'spin glass Hamiltonian', progressional, e/vc-that Is extraordinarily: cylic, synchronous, temporally sharp (leptokurtotic or spike-like), organized,- wave-like, time-invariant, simple, universal, holistic, cascade-like, e/vc. But here the 'clock' would really be relational: a result of the interaction of two or more molecules, either of the same species or of different chemical species. Such a collective clock might 'give the time externally' by means of any of various possible emissions or manifestations (or, should it be a passive sort of clock, the time it keeps could still be read by a variety of probes and methods): emitted or transmitted photons, surface phenomena, escaping molecules, atoms, or electrons, postmortem examination, etc.
One could also imagine a collective clock of 'non-relational' nature whose particles would simply all fire off at approximately the same time, either spontaneously or as a result of being primed from without.
More relevant, perhaps, would be individual molecules behaving in a clock-like manne. These might emit or absorb photons or other particles with the kind of regularity and sharpness suggested above; or they might pulsate, rotate, deform, internally permute, circulate (e.g. as fluxional molecules) parts of themselves within themselves, periodically self-excite, incrementally decay, etc with such metronomic precision.
Or one could fantasize other and more complex types of molecular horologes. Particularly legant mathematical (or number-theoretic) relationships might characterize the interactions of the different atoms, electrons, or structures within a molecule, especially if the molecule is of high molecular weight, has intricate structure, or is a biomolecule. The set of dynamic or electromagnetic spectra of the molecule's constituents might have harmonic or other spectroscopic correlations that contribute to clock-like resonances or sequences of behavior.
A molecule might have a structural or massive center or axis that dominates and modulates the energetics of the rest of the molecule, again with r-lock-like effect.
Microstructures that behave micromechanically as twistable or elastic springs, pendulums, rubberbands, flywheels, etc or that behave as electronic microcircuits and microcomponents, might simulate timepieces.
The generic concept of a molecular clock might also be extended to forms of molecular aging or evolution that are especially regular and useful.This clock here might keep either universal time, or time in the sense of counting stimuli or measuring external rates or degrees of change.Its mechanism might be either deterministic or stochastic.
Might a molecule involved in a chemical reaction have the ability to 'clock' temporal characteristics of the molecules it encounters, and reset its' own temporal characteristics so as to favor, oppose, or specialize the reactions that actually occur (or at-least might there be some molecules like this, or that the mind of man could create for special purposes)?
Molecules that are clock-like to the extent that they count things could conceivably do some minimal calculations or otherwise behave in the manner of a computer.
A molecule that ages incrementally and progressively in a clock-like way could reveal the age of the material or object in which it occurs or when it oriIts host was formed. Yet even without such internal aging, a molecule could serve as a clock if its structure or composition simply contained a single element dating a single past event. Micrometeorites, by analogy, have served as both types of clock (via diverse elements).
Organisms may also have computer-like features, and like today's computers may require a clock. The speculative molecular clocks we have been considering might play the role of such a clock, or even be the basis of the computational features.
5. Molecules and organisms are alike in that both may hypothetically., HAVE their 'OWN ATMOSPHERES'. This might be so in both literal and metaphorical senses of "atmosphere".
Organisms certainly possess atmospheres. The human body Is surrounded by an atmosphere of water vapor, odorants, ions, electrons, and warmed ambient air. This atmosphere continually rises, boils, diffuses, blows, trails, sinks, and expands away, and is replenished. All of which is also true of Earth's atmosphere.
And just as with the terrestrial atmosphere, the eponymous atmosphere of an organism penetrates, or has analogs, within the body of the organism. There are the semigaseous chambers of the,alimentary and respiratory tracts and the ear canal, of course. But then there are also the micro-atmospheres of skin pores and of in vivo micro-bubbles analogous to those found everywhere in stones and the sea.
Doubtless there are 'auroras' in bodily atmospheres just as t ere are auroras in our planet's atmosphere. And If one analogically tosses in Earth's magnetosphere, the body's magnetic field might be considered in a parallel way.
Multitudes of organisms of course give rise to a collective atmosphere on a larger scale, and ultimately the Earth's entire atmosphere may be the product of its bios (a biogenic atmosphere).
Turning then to the possibility that even individual molecules may be possessed of discrete, finite, and characteristic 'atmospheres'.
Prima facie the idea seems dubious for several reasons: at such an ultramicroscopic level gravitation is vanquished by electromagnetism, commotion of the molecular vicinity will be disruptively fierce, the exponential surface-to-volume law will make the effective content of a molecule (from which an atmosphere might evolve) insignificant, molecules seemingly do not have internal processes capable of generating an atmosphere, intermolecular distances are too slight, etc.
Yet at the molecular scale an 'atmosphere' could consist of as little as one monatomic molecule, atmospheric molecules would not have to be 'in' the gaseous state (in the usual sense), the atmosphere could comprise a single or fragmented monomolecular layer, different molecules could simply share a common minimal atmosphere, molecules could in some sense themselves be one another's atmosphere, 'atmospherical' molecules could protrude-into or reside within the molecules that would be said to have atmospheres, for brief moments of time pieces of the molecule or of other molecules about it may continually dissociate (fully, partly, or in a sense) and behave as atmospheric particles, the atmosphere of a molecule may resemble a hydrosphere in the sense that the atmospheric particles never really break free of the surface or framework of the molecule but rather roll, slide, bounce, stream, eddy, boil, flap, or undulate about; the constituents of a molecule's atmosphere might not be neutral molecules but rather ions, free radicals, an electron plasma, protons, or various quasiparticies; in-lieu of gravitation, the many chemical forces (electromagnetic subforces) could retain an atmosphere about even the smallest molecule; the vastest molecules may have atmospheres even if lesser molecules do not; should it be thought necessary for a molecular atmosphere to be equipped with some richness of phenomena comparable to the phenomena of Earth's atmosphere in order to truly qualify as an atmosphere. It is easy to imagine molecular analogs of clouds, storm fronts, jet streams, lightning, atmospheric strata, precipitation, winds, occlusions, inversions, circulation cells, Rossby waves, tornadoes, atmospheric tides, and even rainbows; etc.
6. A molecule and an organism are alike in that both HAVE 'ENERGY LEVELS'. Molecules have a variety of different forms of 'energy levels': owing to the effects of environmental temperature, excitation of their individual atoms, dynamic states of the molecule and its atoms, ionization, ambient magnetic fields, interstitial electrons, vicinal molecules, structural and compositional variants of the molecule, etc Some of these energy levels are discrete-valued (quantized or at least saltatory), whereas others are continuous-valued.
Of analogous energy levels of organisms we have some knowledge. The delta, theta, alpha,,and beta rhythms of the mammalian brain are like compresent energy levels, and in different arousal, pathic, and ontogenetic states and stages of the organism one of these cycles can be dominant; moreover, much faster and much slower rhythms are known some evidently corresponding to the special 'energy levels' of special brain regions, circuits cells, or functions.
Fever, sleep, hibernation, coma, epilepsy, orgasm, dreaming (or Rapid Eye Movement sleep), etc are other examples of neural energy levels with distinctive bodily manifestations.
Apart from specifically neural rhythms, scales, and energy levels, other bodily systems are replete with equivalents.
But intuition suggests that there are manifold physiological 'energy levels' that are not yet discovered that, individually and collectively, are of profound importance.
Biochemical pathways and processes must inevitably have, at the very least, millions of different energy levels, internal and interactive resonances , 'phase states and transitions', etc. Biotechnological mastery of these would give man tremendous medical, bioengineering, agricultural, and ecological powers..
Looming over everything, of course, is the question, How are the totality of the body's multifarious 'energy levels' orchestrated to produce the integral phenomenon that is life?
Many organismal energy levels may simply reflect, or may originally have evolved from, molecular energy levels.
Collections of organisms may also have various lenergy levels. Some of these will be cause or effect of the energy levels of bionts that were considered above, but others will be sui generis phenomena irreducible 'to the energetics of bionts qua bionts.
Among the phenomena recognized by sociologists that might qualify as the 'energy levels' characteristic of collections of persons, are war, mass hysteria, the atmospheres (or "resonances") of different neighborhoods, national moods, historical renaissances, a symmetric love affair, or the tone of a workplace.
As for hints of possible diverse 'energy levels' in populations of other species of organisms, one thinks of mass migration, population explosions, seasonal group mating, epidemics, speciation, and perhaps certain mass extinctions (and-surges or maxima of taxonic diversity) over geological time.
Are there discrete or continuous 'energy-level fluctuations' of the global bios-either exogenous (e.g. climatic) or endogenous (biogenic) that occur over great periods of time? If so, are they cyclic or aperiodic? Good or bad (say from an evolutionary perspective)? Maximal or constrained? A single repeating cycle or a spectrum or hierarchy of cycles of different types or orders? At what chance energy level are we at present (e.g. moderate, high, or low)?
Perhaps when catastrophic planetary events occur a sudden and persistent deterioration of climate, say, occasioned by the Earth's collision with an asteroid they raise the energy level of the bios (for a while): possibly thereby causing a radical ecological reorganization of Earth, recasting of food chains, the appearance of novel higher taxa, biogeographic reapportionment, revolutions in the population ratios of all species, chaotic and universal. migrations of organisms, inefficient energy flows, great material waste, disrupted biogeochemical cycles, ecological and demographic wars and a generally enhanced competition of the Earth's organisms, accelerated mutation and evolution, quickened rates of adaptation, more multidimensional ('broadened') variation, and/or the like.
In a more literal way, the percentage of incoming solar energy that is used by the bios, as well as the total power (wattage) of the bios, may fluctuate radically the absolute energy consumption even by an order of magnitude, say-over millions or hundreds-of-millions of years.
7. Molecules and organisms may hypothetically be alike If they both FORM 'COLONIAL' STRUCTURES. First let it be said that the approximate concept of 'colonial structures' should probably be extended in biology to embrace many other, recognized and unrecognized, things that would not normally be described colonially: e.g. consortiums of diverse species and taxa of microorganisms, bacterial populations qua multicellular organisms, tumors or galls as quasi-colonial organisms, cooperating organelles within unicellular organisms, the bios as a single Gaian organism, the human genospecies, bodily organs, a genome, or even a viral population or epidemic!
The metaphorical application of the concept of 'colonial structures' to molecules suggests several arresting ideas.
Do certain molecules of the same chemical species have a tendency to cluster together into simple or complex : homogeneous or heterogeneous clouds, structures, or global textures, either in a pure liquid or in a solution of many or even millions of different chemical species? The imagined clusters might be either static or more in the nature of dynamic systems.
When molecules representing different chemical species are compresent in, say, a liquid solution, do they as a general rule exhibit at least. some tendency to organize themselves into diverse subpopulations separated from one another in space and individually comprised of many or all of the different species? Or, again, into clouds, structures, global textures, or dynamic systems (but of diverse chemistry)? Or as the number of different chemical species that are compresent in the solution rises to thousands or millions?
Do transient examples of such 'colonial structures' appear in the course of a chemical reaction as an unsuspected part of its chemical kinetics?
Simple morphological examples of the imagined 'colonial structures' could be where single molecules of species A, B, C, etc would tend to join up in that or some other order as a chain, ring, tree, or the like. The bonding here, or strength of the structure, might be arbitrarily weak; or even zero, since the configured molecules might simply represent a structured process-in space rather than a connected object.
Do the different molecules or molecular species form 'colonial structures' that constantly change kaleidoscopically, that grow, or that evolve? Is there some semblance of colonial organisms or-of biological processes that unexpectedly appears in this ablotic case?
Such colonial structures and processes in the realm of physical chemistry may be connected with the origin of the complex higher-level or multilevel structure that one sees in minerals or materials in general.
They might also help to explain the prebiotic origin of life, and life
processes themselves (which may be more independent of the genome, or of
purely biological constraints, than currently assumed).
But then there is an even higher value that these exercises can have to the scientific development of ideonomy, involving a higher stage and level of conceptual analysis and synthesis: the isolation of ideonomic principles, including principles that are ever more diverse, universal, fundamental, and powerful. The types and uses of these Principles will be various: heuristic (discovery-aiding), classificatory. ideoqenetic idea-stimulating cognitive (thought-aiding), perceptual perception-aiding; which is not synonymous with heuristic), communicative, didactic, inductive (law-developing), organizational, experimental axiomatizing, reductive, synthetic or generalizing, sophic(wisdom-purveying), differentiative, combinatorial, explanatory (not the same as didactic), predictive, definitional, transdisciplinary or pantological, etc.
The ideonomic division Principles and Axiomology will be advanced in this way.
I will now enumerate and discuss such ldeonomic principles as I can think of that assisted or might have assisted, that were Illustrated in or that are generally relevant to, or that were explicitly or implicitly discovered through those molecule-organism analogies that were : listed, conjectured, defined, explained, judged, permuted, transmuted, developed, generalized, categorized, subdivided, propertied or 'dimensionalized', formalized, exemplified, and applied : above.
My remarks, of course, will be neither exhaustive nor perfect. Rather
they will be what everything else in ideonomy is: a fertile beginning.
(Please consult the organon "Ideonomic Principles.Relevant To Molecule-Organism