Re: [Fis] fluctuons

2010-11-15 Thread Srinandan Dasmahapatra
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: 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: quoteOverall, 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

Re: [Fis] fluctuons

2010-11-13 Thread Srinandan Dasmahapatra
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: quoteOverall, 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


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