[Fis] Fw: "Mechanical Information" in DNA

Karl Javorszky karl.javorszky at gmail.com
Fri Jun 10 13:46:34 CEST 2016


Dear FIS,

now there is a voice discussing the concepts and methods of counting. This
is highly encouraging.

Taking together with the overall theme of "Mechanical Information in DNA"
of the discussion, it seems that - at least some of - members of FIS begin
to address the quastions of HOW the transfer of information from a sequence
(the DNA) into an organism (a non-sequenced, commutative multitude) can
take place/does take place.

Some of FIS, who are longer than a few months with this chat group, will
have noticed, that I insist that there exists a very nice and neat
algorithm to connect unidimensional descriptions (like the DNA) with
pluridimensional assemblies (like the organism).

I have made an explanation which includes drawings with red and blue arrows
and makes it impossible not to understand how the transfer of genetic
information takles place.

The treatise has 55 pages and is easy to understand. You can have it thru
the publisher (Morawa, Wien), but it has come out just this week, so I
dispose presently only of the proof copies. These I can send to interested
persons.

Please contact me for details. If you are interested in Information Theory,
this is the work that simplifies the question(s) into interpretations of
a+b=c.

The first 100 buyers of the work will get a personally hand-signed copy.
There is a money-back guarantee: if the treatise you buy is not a
state-of-art exercise in the philosophy of the logical language, opening up
algorithms that connect descriptions of linear sequences with descriptions
of pluridimensional assemblies, with easy examples and easy-to-follow
deictic definitioons, you will be refunded on sending back the copy.

Let me express once again the hope that there are some among the
subscribers to the FIS list, who are interested in how information
processing in biology takes actually place.

Karl





2016-06-09 16:31 GMT+02:00 Mark Johnson <johnsonmwj1 en gmail.com>:

> 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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>
>
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