Dear Joseph, Yes, I have deliberately stuck to metaphorical usage.
The vacuum is the ground state of a quantum system, which is a difficult thing to get access to, even theoretically. There are very few cases of studying excitations around such a ground state. Most perturbative methods, including those that reinforce our ideas of elementary particles are around a non-interacting ground state, with renormaization brought in to "dress" up the excitations. Ordinary quantum mechanics builds history into probability amplitudes, of course. I know there was an earlier reference to trapping low-level fluctuations in a hierarchically organized manner, generating turtles upon turtles ... probably by Stan Salthe. I find it hard to get my head around it. I know, for example, that there could be a ratcheting mechanism that uses energy to trap thermal motion to give directed motion as in myosin on actin, or RNA polymerases on DNA. But these are fluctuations in motion that are rectified by an active process. Once you average, you are left with an average. Could the hierarchical averaging be a reference to multiple windows for averaging/integration, each with a different subset of features to interface to? Maybe. After all, averaging in *reactive* systems must be implemented with reference to physical interactions. Examples -- temporal averaging based on lifetimes of the states bearing the output; spatially, by the extent of excursions undertaken by the actors; chemically, by the number of transitions undertaken in response to input fluctuations. Not really a logical hierarchy as what is possible by the limits of the physical interactions that bear the relevant information across. On a related train of associations, I wonder if the anticipatory supplement to purely reactive systems can occur in any other way than by oscillatory dynamics. Cheers, Sri PS: Can you point me to something I should read by way of Logic in Reality? On 14 Nov 2010, at 07:44, Joseph Brenner wrote: > 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: <firstname.lastname@example.org> > 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 > email@example.com > https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis Srinandan Dasmahapatra School of Electronics and Computer Science University of Southampton Highfield, Southampton SO17 1BJ, UK Tel: +44 (0)2380594503 _______________________________________________ fis mailing list firstname.lastname@example.org https://webmail.unizar.es/cgi-bin/mailman/listinfo/fis