[Fis] Fw: "Mechanical Information" in DNA

Stanley N Salthe ssalthe at binghamton.edu
Thu Jun 9 21:40:49 CEST 2016


Regarding your last posting, I agree, and would formulate the following
subsumption hierarchy:

(thermodynamic energy flows {Shannon information theory {Peircean
semiotics}}}

STAN

On Thu, Jun 9, 2016 at 10:31 AM, Mark Johnson <johnsonmwj1 en gmail.com> wrote:

> Dear all,
>
> Is this a question about counting? I'm thinking that Ashby noted that
> Shannon information is basically counting. What do we do when we count
> something?
>
> Analogy is fundamental - how things are seen to be the same may be more
> important than how they are seen to be different.
>
> It seems that this example of DNA is a case where knowledge advances
> because what was once thought to be the same (for example, perceived
> empirical regularities in genetic analysis) is later identified to be
> different in identifiable ways.
>
> Science has tended to assume that by observing regularities, causes can be
> discursively constructed. But maybe another way of looking at it is to say
> what is discursively constructed are the countable analogies between
> events. Determining analogies constrains perception of what is countable,
> and by extension what we can say about nature; new knowledge changes that
> perception.
>
> Information theory (Shannon) demands that analogies are made explicit -
> the indices have to be agreed. What do we count? Why x? Why not y?
> otherwise the measurements make no sense. I think this is an insight that
> Ashby had and why he championed Information Theory as analogous to his Law
> of Requisite Variety (incidentally, Keynes's Treatise on Probability
> contains a similar idea about analogy and knowledge). Is there any reason
> why the "relations of production" in a mechanism shouldn't be counted?
> determining the analogies is the key thing isn't it?
>
> One further point is that determining analogies in theory is different
> from measuring them in practice. Ashby's concept of cybernetics-as-method
> was: "the cyberneticist observes what might have happened but did not".
> There is a point where idealised analogies cannot map onto experience. Then
> we learn something new.
>
> Best wishes,
>
> Mark
> ------------------------------
> From: Loet Leydesdorff <loet en leydesdorff.net>
> Sent: ‎09/‎06/‎2016 12:52
> To: 'John Collier' <Collierj en ukzn.ac.za>; 'Joseph Brenner'
> <joe.brenner en bluewin.ch>; 'fis' <fis en listas.unizar.es>
> Subject: Re: [Fis] Fw:  "Mechanical Information" in DNA
>
> Dear colleagues,
>
>
>
> It seems to me that a definition of information should be compatible with
> the possibility to measure information in bits of information. Bits of
> information are dimensionless and “yet meaningless.” The meaning can be
> provided by the substantive system that is thus measured. For example,
> semantics can be measured using a semantic map; changes in the map can be
> measured as changes in the distributions, for example, of words. One can,
> for example, study whether change in one semantic domain is larger and/or
> faster than in another. The results (expressed in bits, dits or nits of
> information) can be provided with meaning by the substantive theorizing
> about the domain(s) under study. One may wish to call this “meaningful
> information”.
>
>
>
> I am aware that several authors have defined information as a difference
> that makes a difference (McKay, 1969; Bateson, 1973). It seems to me that
> this is “meaningful information”. Information is contained in just a series
> of differences or a distribution. Whether the differences make a difference
> seems to me a matter of statistical testing. Are the differences
> significant or not? If they are significant, they teach us about the
> (substantive!) systems under study, and can thus be provided with meaning
> in the terms of  studying these systems.
>
>
>
> Kauffman *et al*. (2008, at p. 28) define information as “natural
> selection assembling the very constraints on the release of energy that
> then constitutes work and the propagation of organization.” How can one
> measure this information? Can the difference that the differences in it
> make, be tested for their significance?
>
>
>
> Varela (1979, p. 266) argued that since the word “information” is derived
> from “in-formare,” the semantics call for the specification of a system of
> reference to be informed. The system of reference provides the information
> with meaning, but the meaning is not in the information which is “yet
> meaningless”. Otherwise, there are as many “informations” as there are
> systems of reference and the use of the word itself becomes a source of
> confusion.
>
>
>
> In summary, it seems to me that the achievement of defining information
> more abstractly as measurement in bits (*H = -* Σ *p log(p)*) and the
> availability of statistics should not be ignored. From this perspective,
> information theory can be considered as another form of statistics (entropy
> statistics). A substantive definition of information itself is no longer
> meaningful (and perhaps even obscure): the expected information content of
> a distribution or the information contained in the message that an event
> has happened, can be expressed in bits or other measures of information.
>
>
>
> Best,
>
> Loet
>
>
> ------------------------------
>
> Loet Leydesdorff
>
> Professor, University of Amsterdam
> Amsterdam School of Communication Research (ASCoR)
>
> loet en leydesdorff.net ; http://www.leydesdorff.net/
> Associate Faculty, SPRU, <http://www.sussex.ac.uk/spru/>University of
> Sussex;
>
> Guest Professor Zhejiang Univ. <http://www.zju.edu.cn/english/>,
> Hangzhou; Visiting Professor, ISTIC,
> <http://www.istic.ac.cn/Eng/brief_en.html>Beijing;
>
> Visiting Professor, Birkbeck <http://www.bbk.ac.uk/>, University of
> London;
>
> http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en
>
>
>
> *From:* Fis [mailto:fis-bounces en listas.unizar.es] *On Behalf Of *John
> Collier
> *Sent:* Thursday, June 09, 2016 12:04 PM
> *To:* Joseph Brenner; fis
> *Subject:* Re: [Fis] Fw: "Mechanical Information" in DNA
>
>
>
> I am inclined to agree with Joseph. That is why I put “mechanical
> information” in shudder quotes in my Subject line.
>
>
>
> On the other hand, one of the benefits of an information approach is that
> one can add together information (taking care to subtract effects of common
> information – also describable as correlations). So I don’t think that the
> reductionist perspective follows immediately from describing the target
> information in the paper as “mechanical”. “Mechanical”, “mechanism” and
> similar terms can be used (and have been used) to refer to processes that
> are not reducible. “Mechanicism” and “mechanicist” can be used to capture
> reducible dynamics that we get from any conservative system (what I call
> Hamiltonian systems in my papers on the dynamics of emergence – such
> systems don’t show emergent properties except in a trivial sense of being
> unant*i*cipated). I think it is doubtful at best that the mechanical
> information referred to is mechanicist.
>
>
>
> John Collier
>
> Professor Emeritus and Senior Research Associate
>
> University of KwaZulu-Natal
>
> http://web.ncf.ca/collier
>
>
>
> *From:* Fis [mailto:fis-bounces en listas.unizar.es
> <fis-bounces en listas.unizar.es>] *On Behalf Of *Joseph Brenner
> *Sent:* Thursday, 09 June 2016 11:10 AM
> *To:* fis <fis en listas.unizar.es>
> *Subject:* [Fis] Fw: "Mechanical Information" in DNA
>
>
>
> Dear Folks,
>
>
>
> In my humble opinion, "Mechanical Information" is a contradiction in terms
> when applied to biological processes as described, among others, by Bob L.
> and his colleagues. When applied to isolated DNA, it gives at best a
> reductionist perspective. In the reference cited by Hector, the word
> 'mechanical' could be dropped or replaced by spatial without affecting the
> meaning.
>
>
>
> Best,
>
>
>
> Joseph
>
>
>
> ----- Original Message -----
>
> *From:* Bob Logan <logan en physics.utoronto.ca>
>
> *To:* Moisés André Nisenbaum <moises.nisenbaum en ifrj.edu.br>
>
> *Cc:* fis <fis en listas.unizar.es>
>
> *Sent:* Thursday, June 09, 2016 4:04 AM
>
> *Subject:* Re: [Fis] "Mechanical Information" in DNA
>
>
>
> Thanks to Moises for the mention of my paper with Stuart Kauffman. If
> anyone is interested in reading it one can find it at the following Web
> site:
>
>
>
> https://www.academia.edu/7835
> <https://www.academia.edu/783503/Propagating_organization_an_enquiry>
>
> [The entire original message is not included.]
>
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