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.


Srinandan Dasmahapatra
School of Electronics and Computer Science
University of Southampton
Southampton SO17 1BJ
Phone: +44(0)2380594503

fis mailing list

Reply via email to