Re: [Fis] Fw: "Mechanical Information" in DNA
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.javors...@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 <johnsonm...@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 <l...@leydesdorff.net> >> Sent: 09/06/2016 12:52 >> To: 'John Collier' <colli...@ukzn.ac.za>; 'Joseph Brenner' >> <joe.bre
Re: [Fis] Fw: "Mechanical Information" in DNA
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 <johnsonm...@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 <l...@leydesdorff.net> > Sent: 09/06/2016 12:52 > To: 'John Collier' <colli...@ukzn.ac.za>; 'Joseph Brenner' > <joe.bren...@bluewin.ch>; 'fis' <fis@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 prov
Re: [Fis] Fw: "Mechanical Information" in DNA
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 <johnsonm...@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 <l...@leydesdorff.net>
> Sent: 09/06/2016 12:52
> To: 'John Collier' <colli...@ukzn.ac.za>; 'Joseph Brenner'
> <joe.bren...@bluewin.ch>; 'fis' <fis@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 informat
Re: [Fis] Fw: "Mechanical Information" in DNA
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 -Original Message- From: "Loet Leydesdorff" <l...@leydesdorff.net> Sent: 09/06/2016 12:52 To: "'John Collier'" <colli...@ukzn.ac.za>; "'Joseph Brenner'" <joe.bren...@bluewin.ch>; "'fis'" <fis@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 Commun
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) <mailto:l...@leydesdorff.net> l...@leydesdorff.net ; <http://www.leydesdorff.net/> http://www.leydesdorff.net/ Associate Faculty, <http://www.sussex.ac.uk/spru/> SPRU, University of Sussex; Guest Professor <http://www.zju.edu.cn/english/> Zhejiang Univ., Hangzhou; Visiting Professor, <http://www.istic.ac.cn/Eng/brief_en.html> ISTIC, Beijing; Visiting Professor, <http://www.bbk.ac.uk/> Birkbeck, University of London; <http://scholar.google.com/citations?user=ych9gNYJ=en> http://scholar.google.com/citations?user=ych9gNYJ=en From: Fis [mailto:fis-boun...@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 unanticipated). 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-boun...@listas.unizar.es] On Behalf Of Joseph Brenner Sent: Thursday, 09 June 2016 11:10 AM To: fis <fis@listas.unizar.es> Subject: [Fis] Fw: "Mechanical Information" in DNA Dear Folks, In my humbl
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 unanticipated). 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-boun...@listas.unizar.es] On Behalf Of Joseph Brenner Sent: Thursday, 09 June 2016 11:10 AM To: fis <fis@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<mailto:lo...@physics.utoronto.ca> To: Moisés André Nisenbaum<mailto:moises.nisenb...@ifrj.edu.br> Cc: fis<mailto:fis@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/783503/Propagating_organization_an_enquiry Here is the abstract: Propagating Organization: An Inquiry. Stuart Kauffman, Robert K. Logan, Robert Este, Randy Goebel, David Hobill and Ilya Smulevich. 2007. Biology and Philosophy 23: 27-45. Abstract Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection – and perhaps self-organization - could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the o
