Dear Sri, Thank you for your note, since I was "unhappy" with the point at which the discussion seemed to end. Your perspective on the structure of living organisms seems quite pertinent to the theme of information processes. It is clearly related to Kaufmann-Logan "biotic" information.
However - however - unless I have missed something, you do not take a position on the core thesis of Conrad's theory, namely (and All please correct me if wrong) the coupling between sub-quantum changes and biological molecules. In your note you refer to, among other things 1) the "vacuum" as a metaphorical expression of changes in molecules; 2) an epistemological view where you explicitly use the term "metaphorical spatial remapping of an historical process"; 3) the "adjacent possible" of "vacua", which vacua, however, refer back to your metaphorical pictures. Now I think "adjacent possible" is wonderful expression for structures, among others in your note, that can be formalized, together with their dynamics, by the dialectics of my Logic in Reality. However, this discussion is about Conrad, not Brenner. As I understand him, Conrad placed the locus of his fluctuations at a level, that of string theory or some equivalent, below that of the thermodynamic processes well described by your approach. Might I please ask you to point out the ontological, physical link, if any, that corresponds to the coupling as described above (between sub-quantum changes and biological molecules)? Please note that it is an extraordinarily deep and for me still unanswered question as to whether the terms "history" and "information" can apply to fluctuations in the quantum vacuum at all. Thank you and best wishes, Joseph ----- Original Message ----- From: "Srinandan Dasmahapatra" <s...@ecs.soton.ac.uk> To: <fis@listas.unizar.es> Sent: Sunday, November 14, 2010 7:14 AM Subject: Re: [Fis] fluctuons Hi, I've been meaning to send a note on Kevin Kirby's brief outline of Conrad's fluction framework, but haven't had the time to compose my thoughts coherently. I realised that I wouldn't really have the time to do so, so I had better send something half-baked along anyway to contribute to the discussion. Kevin concludes his piece with the following remark: <quote>Overall, within fluctuon theory "the interaction between the manifest organism and its unmanifest vacuum sea image abets the evolution, persistence, and maintenance of this unique complexity [of life]". This is a fascinating and rich notion. What can we unfold from this notion now in 2010?</quote> The way I see it, organisms are organisational units, and we tend to view genomic content as informational units. However, genomic identifiers are merely one way of providing information tags. Apart from the presence/absence of sequence, there is also the notion of the multiple/collective (to borrow Alain Badiou's language) -- collections of molecules that bear that signature. It is these collectives that comprise the dynamical state of cells and organisms, and the cardinalities of these sets may often be used as a proxy for snapshots of organismal state. This tells us that organisational units such as tissues may be characterised via such cardinalities -- liver cells and heart cells have different protein number distributions within the same organism yet protein distributions in liver cells are more similar across taxa. Hence the fluctuon concept may be viewed in this concept as the creation and annihilation of molecules following gene expression, or the transition into and out of active or inert molecular state, around the "vacuum" -- the steady state of an open dynamical network. The response characteristics of this proteomic or messenger RNA cloud and the entropy production (as measured in terms of fluctuating numbers around the steady state) offer dynamical proxies of the organism, extending the static snapshot. This becomes conceptually and mathematically accessible to perturbative ideas from quantum field theory, and the recasting of stochastic processes via Doi's 1976 work (Doi M (1976) Second quantized representation for classical many-particle systems. J Phys A: Math Gen 9: 1465–1477) has been used, for example, in Sasai M, Wolynes PG (2003) Stochastic gene expression as a many-body problem Proc Natl Acad Sci U S A 100(5): 2374–2379 to do that. Moreover, neutral evolution offers a landscape of adjacent "vacua" in the design space of possible gene expression clouds and their response characteristics. The protein identity matching test pointed out the significance of non-coding, regulatory sequences (King MC, Wilson AC, "Evolution at Two Levels in Humans and Chimpanzees," Science1975, 188:107-16) indicating the necessity of moving beyond identifiers as (sole) information carriers and to what is now called evo-devo. The "vacua" in the "fluctuon" picture provides a way of characterising the landscape in this metaphorical spatial remapping of a historical process which register the dynamical responses of gene expression clouds of organismal, histological and cytological collectives at multiple-generational evolutionary time scales, with neutrality exploring the "adjacent possible" of these vacua, via alternative cis-regulatory underpinnings of dynamical states. This has been explored in the popular press by Gerhart and Kirschner in The Plausibility of Life -- they reference Conrad in there, to bring it back to where the discussion started. Cheers, Sri Srinandan Dasmahapatra School of Electronics and Computer Science University of Southampton Southampton SO17 1BJ Phone: +44(0)2380594503 s...@ecs.soton.ac.uk _______________________________________________ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis _______________________________________________ fis mailing list fis@listas.unizar.es https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis
