From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.info-theory
Subject: Re: The Dualism in info theory
Date: 12 Oct 92 23:53:29 GMT
Organization: Crop Science Dept., NCSU, Raleigh, NC 27695-7620

In article <92286.144401ICEAB@ASUACAD.BITNET> ICEAB@ASUACAD.BITNET writes:
>When I first saw your subject, I thought that perhaps you were going to
>start in on a topic of some interest to bacterial geneticists like myself -
>namely, how do your information theories work if the encoded message is
>actually an overlapping one? Many bacterial viruses show overlaps where one
>gene begins or ends within another one. Sometimes they are in the same reading
>frame and sometimes they are not. Even a full scale cell like Escherichia coli
>displays some overlaps, although usually they are in the same frame and just
>represent truncated forms of the longer gene.

The "criticism" is a valid suggestion for a topic of thought and
exploration.  Harking (yes, harking) back to something I recently posted:

>Newsgroups: bionet.info-theory
>Subject: Re: VSLI Spatial Entropy Measure

In article <1992Oct9.233217.26404@ncsu.edu> samodena@csemail.cropsci.ncsu.edu (S. A. Modena) writes:
>                         Suresh Rajgopal
>             Spatial Entropy- A Unified Attribute to Model
              ^^^^^^^^^^^^^^^
>                Dynamic Communication in VLSI Circuits
                 ^^^^^^^^^^^^^^^^^^^^^
>
>
>Improvement in fabrication and processing technology has raised the level 
>of integration in VLSI circuits to over a million transistors on chip. 

      Well, substitute E. coli's gene "density" or virus' gene "density"
      Then think of PhiX's multi-frame/overlapping gene-function-
      timing interleave/overlap structure

>While scaling device dimensions has yielded smaller and faster transistors 
>and gates, the higher density has made it more difficult to connect these 
>devices.  Moreover, the cost of wiring and interconnect can no longer be 
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>neglected; 
^^^^^^^^^^
            Think of the case: prokaryote ->  eukaryote

i>................. the circuit (area-time and power) performance is being 
^^^^^^^^^^
>increasingly dominated  by the communication between the logic gates  
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      rna processing / migration to the cytoplasm / cytoskeletal 
                                                    regulatory
                                                    effects

>rather than the  gates themselves. This dissertation addresses the problem 
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    i.e., rather than a simple gene model, with simultaneous RNA trans-
     scription and protein translation.....

>of capturing the cost of this communication.
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
And most assuredly there is a communications systems involved.....
and signal synchrony can be intimately bound up in what we call
phase or developmental "regulation."....like DNA replication
clearing bound protein factors to expose "late" T7 gene promoter
and transcription signals on the DNA.

>
>The Computer-Aided-Design tools used by a designer often rely on information  
>provided by various circuit attributes, where the quality of the solutions 
>are frequently dictated by the kind and the amount of information provided 
>by these attributes. For instance a static circuit attribute can capture 
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                                   The stage we are at in modelling 
                                   the genomic processes

>circuit structure, but it fails to capture dynamic usage and its distribution 
                             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                                 Where we have to arrive at to begin to
                                 have a sophisticated vision of the genome
                                 in operation/action

>over the various parts of the circuit.  The contribution of this  research 
>is a new circuit attribute called spatial entropy.  It models the dynamic 
>communication effort in the circuit by unifying the static structure and 
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>the dynamic movement of data in the circuit.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
>The dissertation introduces the concept of spatial entropy to the VLSI CAD 
>domain, in the form of a quantative circuit attribute.  This is used to 
>describe a simple and efficient procedure to compute spatial entropy for 
>primitive gates and for an entire circuit.  We characterize the attribute 
>comprehensively over different  levels of abstraction, and extend our 
>definition to describe spatial  entropy vectors. 

How would one express the equivalent for E. coli or HIV virus?

>............................................Finally, we illustrate 
>applications of spatial entropy in  two problems in CAD - variable ordering 
>for binary decision diagrams (BDD),  and boolean function complexity, to 
>demonstrate its  ability to  capture fundamental  function behavior over 
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>a broad class of implementations.                 ^^^^^^^^^^^^^^^^

Perhaps the fundamental short-coming of Tom's model: failure to
capture fundament function behavior....perhaps a necessay extension
to explain Rs/Rf ratios different than 1.0  (thinking of your latest
posting which restricted itself to just two alternatives to explain
the Rs/Rf contradiction).

Steve

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