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Notes on RK Logan's Presentation: Bioinformatics 2.0

Show + Tell _ January 17, 2008 _ Notes

Robert K. Logan _ Bioinformatics 2.0

Point-form notes include an analysis of each point, building upon the informational content of the presentation with information encountered elsewhere (sources to be included in amended versions.)

• ‘Living Systems are necessarily more complex than human descriptions are able to account for.’

-Descriptions are inadequate because they use linguistic and quantitive forms (names, quantities and formulas) to identify and model the exchange of information and energy in living systems, which are structurally-coupled to their environment and consequently are prone to its influences. The challenge lay in determining the best methods of accounting for these influences.

Within living systems themselves, information is instantiated in processual susbstrates; information for a living system exists only to the extent that a living system is able to effect the use of matter and energy (information) to propagate its organization. There are vast differences between how we as cognizers use information to model a living system, and how a living system itself uses information to propagate its organization. Human knowledge of a living system is sought out in order to render a coherent and complete picture of how a living system is observed to behave. The living system itself continues to behave with or without a human observer to declare that behaviour is occuring. In so doing, it evolves beyond the descriptive parameters human beings are only able to cursorily identify.

Katherine Hayles discusses in "How We Became Post-human: Virtual Bodies in Cybernetics, Literature and Informatics" the bifurcation of viewpoints that arose between Humberto Maturana and Francisco Varela regarding how each tried to accommodate biological evolution in their conjunct approach to a theory of living things, known otherwise as autopoiesis. Varela was reputedly more active in his ventures towards a formulation of autopoiesis that was more integrative, but maintained that the complexity of life could only be accorded the fineness of resolution necessary for an adequately sophisticated definition by utilizing dual systems of explanation. Hayles accounts for this duality saying that the "operational explanation would emphasize the physical concreteness of actual processes; the symbolic or systems-theoretic explanation would emphasize more abstract ideas that help to construct the system at a higher level of generality."
(Hayles 155)

It is worth incorporating into RK Logan's discussion of bioinformatics one of Verala's important, albeit intractable insights into the nature of information as it is thought to be embodied through the metabolic and reproductive processes inherent in the activities of biotic systems.

"...To assume in these fields (i.e. systems biology) that information is some thing that is transmitted, that symbols are things that can be taken at face value, or that purposes and goals made clear by the systems themselves is all, it seems to me, nonsense... Information, sensu strictu, does not exist. Nor do, by the way, the laws of nature."

(Verela. p 45 "Describing the Logic of the Living: The Adequacy and Limitations of the Idea of Autopoiesis" article excerpted from Milan Zelany, "Autopoiesis: A Theory of Living Organization.)

The only way that a human observer could determine with certainty the information content of a living cell or multicellular organism would be to execute a virtual simulation using a sufficiently powerful computing resource, so that every effort might be undertaken to know in totality the inner-workings of a living system, and the simulation would be impoverished of very nearly zero variables. Such a system might track the path of every molecule and atom comprising the cell (or multicellular organism) from before the moment when life first emerged, through to the present. Very nearly every influence acting upon every atom would be accounted for, with very nearly zero interactions remaining unaccounted for, so as to minimize the distortion of the simulation’s results due to errors compounded over evolutionary timescales.

• 'Artificial Life and Artifical Intelligence are neither truly living, nor truly intelligent because they are not autonomous.'

– That a system is autonomous would indicate that it was at some point in its evolutionary past subject to a phase transition in its behaviour, wherefrom autonomy or something analogous to it emerged. Autonomy, in the sense of living systems, is a concept that may be taken to refer to the specific set of features that emerged during the course of its past behaviours, where for whatever reason, it was eventually able to “pull itself up by its bootstraps” and engaged in self-guiding behaviour.

• 'Quality information in, Quality information out.'

• 'Living organisms design themselves through natural selection.'

– The apparent organization of ‘design’ is that which occurs when an organism cognizes its environment; it partakes of apparent selectivity in what niches it selects to occupy, which resources or forms of energy it absorbs, etc.

• 'Nobody has designed a computer that designs itself':

–Based on what we know about things that things that are capable of self-designing behaviours, such a computer would require a growth medium that enables an autopoietic unity to permute all of the possible combinations of molecular structure and function necessary before it were able to effect non-arbitrary operations that conform the requirements necessary for sustained living to the constraints posed by the external environment. Such a computer would have to evolve to express the behaviour of a homeostat– it would develop a reflexive patterning of communication between its internal representations of the external environment, and its nervous system activity. (so that the stimuli perceived by the brain has a direct influence on how the computing organism behaves… if the growth medium in which a self-designing computer were to become too hot, the computer would determine which actions to execute so as to prevent damage or destruction due to excessive heat exposure.)

• 'Communication between organisms is an essential feature of life.'

• 'To what extent is an innovation symbiotic?'

–Innovations are more autonomous when coupled in information exchange processes with other innovations… One device benefits from an adjacent device or service, the latter of which performs a function that the former is unable to perform.

• Biomimicry 2.0:

–More than copying, it is concerned with holistic system modelling, to first simulate, then instantiate in a biomolecular medium, the processes through which autonomy is thought to emerge. The emergence of autonomy isn’t concerned strictly with morphological attributes (i.e. to stimulate the emergence of useful anatomical features, such as hooks or protuberances) that accompany apparently autonomous behaviour, but is concerned with processual attributes of autonomy as well, wherein the biotic system being synthesized for an engineering application yields a synthetic system whose attributes of behaviour are such that they behave in a manner similar to, if not discretely comparable to the biotic system whose behaviour the biomimetic system is modelled upon. This prioritizes the notion that a truly biomimetic system should be structurally-coupled to the ecosystem or living medium in which it operates.

• [3] 'A living system is one that processes information.'

–Its nervous system coordinates actions necessary to direct the options selected for by the organism, to such an extent that benefits obtained through the selection of some options and not others yields a pattern of information usage that is consistent with the living system being able to at minimum, satisfy the metabolic requirements of itself or those of its conspecifics (others like itself.)

• [4] 'A living system is a medium of communication.'
–A living system is one generating appropriate messages for interception by its conspecifics and other organisms…

–human nature: What role does human nature play in efforts to progress towards organized ascendancy of a regime of biomimetic technology?

A more explicit question: How can biomimicry be used to sublimate the destructive impulses of human nature? If it is too difficult to change human nature, is it possible to restructure the relationship between human nature and the environment upon which it has an effect, for better or worse?


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