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<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I am inclined to agree with Joseph. That is why I put “mechanical information” in shudder quotes in my Subject
line.<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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>i</i>cipated). I think it is doubtful at best that the mechanical information referred to is mechanicist.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">John Collier<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Professor Emeritus and Senior Research Associate<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">University of KwaZulu-Natal<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">http://web.ncf.ca/collier<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Fis [mailto:fis-bounces@listas.unizar.es]
<b>On Behalf Of </b>Joseph Brenner<br>
<b>Sent:</b> Thursday, 09 June 2016 11:10 AM<br>
<b>To:</b> fis <fis@listas.unizar.es><br>
<b>Subject:</b> [Fis] Fw: "Mechanical Information" in DNA<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Dear Folks,</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">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.</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Best,</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Joseph</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">----- Original Message -----
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:#E4E4E4"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">From:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">
<a href="mailto:logan@physics.utoronto.ca" title="logan@physics.utoronto.ca">Bob Logan</a>
<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">To:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">
<a href="mailto:moises.nisenbaum@ifrj.edu.br" title="moises.nisenbaum@ifrj.edu.br">
Moisés André Nisenbaum</a> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Cc:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">
<a href="mailto:fis@listas.unizar.es" title="fis@listas.unizar.es">fis</a> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Sent:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif"> Thursday, June 09, 2016 4:04 AM<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Subject:</span></b><span style="font-size:10.0pt;font-family:"Arial",sans-serif"> Re: [Fis] "Mechanical Information" in DNA<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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:
<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://www.academia.edu/783503/Propagating_organization_an_enquiry">https://www.academia.edu/783503/Propagating_organization_an_enquiry</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Here is the abstract:<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Calibri",sans-serif">Propagating Organization: An Inquiry. </span></b><o:p></o:p></p>
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<p class="body"><span style="font-family:"Calibri",sans-serif">Stuart Kauffman, Robert K. Logan, Robert Este, Randy Goebel, David Hobill and Ilya Smulevich. </span><o:p></o:p></p>
<p class="body"><span style="font-family:"Calibri",sans-serif">2007. Biology and Philosophy 23: 27-45.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-family:"Calibri",sans-serif">Abstract
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Calibri",sans-serif">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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Calibri",sans-serif">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
<i>about</i> 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 organization of process in the expected biological work cycles to create the diversity in our observable biosphere.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Calibri",sans-serif">Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which,
in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Calibri",sans-serif;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt">Robert K. Logan</span></span><span class="apple-style-span"><span style="font-family:"Helvetica",sans-serif;color:black">
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black">Prof. Emeritus - Physics - U. of Toronto </span></span><span style="font-family:"Helvetica",sans-serif;color:black">
</span><o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black">Fellow University of St. Michael's College</span></span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black">Chief Scientist - sLab at OCAD</span></span><span class="apple-style-span"><span style="font-family:"Helvetica",sans-serif;color:black">
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black"><a href="http://utoronto.academia.edu/RobertKLogan">http://utoronto.academia.edu/RobertKLogan</a></span></span><span style="font-family:"Helvetica",sans-serif;color:black">
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black"><a href="http://www.physics.utoronto.ca/Members/logan">www.physics.utoronto.ca/Members/logan</a></span></span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-style-span"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:black"><a href="http://www.researchgate.net/profile/Robert_Logan5/publications">www.researchgate.net/profile/Robert_Logan5/publications</a></span></span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Helvetica",sans-serif;color:black"><br>
On Jun 8, 2016, at 4:40 PM, Moisés André Nisenbaum <<a href="mailto:moises.nisenbaum@ifrj.edu.br">moises.nisenbaum@ifrj.edu.br</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi, John. It is amazing!!<o:p></o:p></p>
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<p class="MsoNormal">I would like to highlight the word "constraints" at the caption of the DNA diagram (<a href="http://phys.org/news/2016-06-layer-dna.html">http://phys.org/news/2016-06-layer-dna.html</a>)<o:p></o:p></p>
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<p class="MsoNormal">"The rigid base-pair model is forced, using 28 <b>constraints
</b>(indicated by red spheres), into a lefthanded superhelical path that mimics the DNA conformation in the nucleosome. Credit: Leiden Institute of Physics"<o:p></o:p></p>
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<p class="MsoNormal">The same word is used by Bob Logan and Stuart Kauffman to relate mechanical concepts with 'information' (<a href="http://philpapers.org/rec/KAUPOA">http://philpapers.org/rec/KAUPOA</a>)<o:p></o:p></p>
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<p class="MsoNormal">Could it have any parallel between these two approaches?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Also, you usually think "DNA" associated with Biological Sciences, but this research is made at Leiden Institute of
<b>Physics</b>! Of course, to work current (complex, innovative) science you must have an interdisciplinary approach.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Abraço.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Moisés<o:p></o:p></p>
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<p class="MsoNormal">2016-06-08 16:40 GMT-03:00 John Collier <<a href="mailto:Collierj@ukzn.ac.za" target="_blank">Collierj@ukzn.ac.za</a>>:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">A previously hypothesized “second layer” of information in DNA may have been isolated.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://phys.org/news/2016-06-layer-dna.html" target="_blank">http://phys.org/news/2016-06-layer-dna.html</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">John Collier<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Professor Emeritus and Senior Research Associate<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">University of KwaZulu-Natal<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://web.ncf.ca/collier" target="_blank">http://web.ncf.ca/collier</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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_______________________________________________<br>
Fis mailing list<br>
<a href="mailto:Fis@listas.unizar.es">Fis@listas.unizar.es</a><br>
<a href="http://listas.unizar.es/cgi-bin/mailman/listinfo/fis" target="_blank">http://listas.unizar.es/cgi-bin/mailman/listinfo/fis</a><o:p></o:p></p>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Moisés André Nisenbaum<br>
Doutorando IBICT/UFRJ. Professor. Msc.<br>
Instituto Federal do Rio de Janeiro - IFRJ<br>
Campus Rio de Janeiro<br>
<a href="mailto:moises.nisenbaum@ifrj.edu.br" target="_blank">moises.nisenbaum@ifrj.edu.br</a><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
Fis mailing list<br>
<a href="mailto:Fis@listas.unizar.es">Fis@listas.unizar.es</a><br>
<a href="http://listas.unizar.es/cgi-bin/mailman/listinfo/fis">http://listas.unizar.es/cgi-bin/mailman/listinfo/fis</a><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
Fis mailing list<br>
<a href="mailto:Fis@listas.unizar.es">Fis@listas.unizar.es</a><br>
<a href="http://listas.unizar.es/cgi-bin/mailman/listinfo/fis">http://listas.unizar.es/cgi-bin/mailman/listinfo/fis</a><o:p></o:p></p>
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