[Fis] Fw: "Mechanical Information" in DNA

Francesco Rizzo 13francesco.rizzo at gmail.com
Fri Jun 10 16:42:11 CEST 2016


Caro Stan e cari Tutti,
la subsumption hierarchy è il basamento epistemologico e logico della mia
"Nuova economia" da 35
 35 anni: Questa è una bella sincronicità tra l'inter-azione o causalità
reciproca o com-penetrazione
metodologica  di Stan e la mia orto-prassi.
Grazie per la conferma e il conforto che (ne) ricevo.
Francesco

2016-06-10 13:46 GMT+02:00 Karl Javorszky <karl.javorszky en gmail.com>:

> 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.]
>>
>> _______________________________________________
>> Fis mailing list
>> Fis en listas.unizar.es
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>
>>
>
> _______________________________________________
> Fis mailing list
> Fis en listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
------------ pr�xima parte ------------
Se ha borrado un adjunto en formato HTML...
URL: <http://listas.unizar.es/pipermail/fis/attachments/20160610/f6db0e70/attachment-0001.html>


More information about the Fis mailing list