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<DIV><FONT face=Arial size=2>Dear Folks,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Best,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Joseph</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV style="FONT: 10pt arial">----- Original Message -----
<DIV style="BACKGROUND: #e4e4e4; font-color: black"><B>From:</B> <A
title=logan@physics.utoronto.ca href="mailto:logan@physics.utoronto.ca">Bob
Logan</A> </DIV>
<DIV><B>To:</B> <A title=moises.nisenbaum@ifrj.edu.br
href="mailto:moises.nisenbaum@ifrj.edu.br">Moisés André Nisenbaum</A> </DIV>
<DIV><B>Cc:</B> <A title=fis@listas.unizar.es
href="mailto:fis@listas.unizar.es">fis</A> </DIV>
<DIV><B>Sent:</B> Thursday, June 09, 2016 4:04 AM</DIV>
<DIV><B>Subject:</B> Re: [Fis] "Mechanical Information" in DNA</DIV></DIV>
<DIV><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><FONT
face=Arial size=2></FONT><BR></DIV>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:
<DIV class=""><FONT face=Arial size=2></FONT><FONT face=Arial
size=2></FONT><FONT face=Arial size=2></FONT><BR class=""></DIV>
<DIV class=""><A class=""
href="https://www.academia.edu/783503/Propagating_organization_an_enquiry">https://www.academia.edu/783503/Propagating_organization_an_enquiry</A></DIV>
<DIV class=""><FONT face=Arial size=2></FONT><FONT face=Arial
size=2></FONT><FONT face=Arial size=2></FONT><BR class=""></DIV>
<DIV class="">Here is the abstract:</DIV>
<DIV class=""><B class=""><SPAN class="" style="FONT-FAMILY: Calibri"><BR
class=""></SPAN></B></DIV>
<DIV class=""><B class=""><SPAN class=""
style="FONT-FAMILY: Calibri">Propagating Organization: An Inquiry.</SPAN><SPAN
class="" style="FONT-FAMILY: Calibri"> </SPAN></B></DIV>
<DIV class="">
<P class=Body><SPAN class=""
style="FONT-FAMILY: Calibri; mso-bidi-font-size: 14.0pt; mso-ascii-theme-font: minor-latin; mso-hansi-theme-font: minor-latin">Stuart
Kauffman, Robert K. Logan, Robert Este, Randy Goebel, David Hobill and Ilya
Smulevich. </SPAN></P>
<P class=Body><SPAN class=""
style="FONT-FAMILY: Calibri; mso-bidi-font-size: 14.0pt; mso-ascii-theme-font: minor-latin; mso-hansi-theme-font: minor-latin">2007.
Biology and Philosophy 23: 27-45.</SPAN><SPAN class=""
style="COLOR: windowtext; FONT-FAMILY: Calibri; mso-ascii-theme-font: minor-latin; mso-hansi-theme-font: minor-latin"><O:P
class=""></O:P></SPAN></P>
<P class=MsoNormal
style="mso-pagination: none; tab-stops: 28.0pt 56.0pt 84.0pt 112.0pt 140.0pt 168.0pt 196.0pt 224.0pt 252.0pt 280.0pt 308.0pt 336.0pt; mso-layout-grid-align: none"><B
class="" style="mso-bidi-font-weight: normal"><SPAN class=""
style="FONT-FAMILY: Calibri; mso-ascii-theme-font: minor-latin; mso-hansi-theme-font: minor-latin">Abstract
<O:P class=""></O:P></SPAN></B></P>
<P class=MsoNormal
style="mso-pagination: none; tab-stops: 28.0pt 56.0pt 84.0pt 112.0pt 140.0pt 168.0pt 196.0pt 224.0pt 252.0pt 280.0pt 308.0pt 336.0pt; mso-layout-grid-align: none"><SPAN
class="" style="FONT-FAMILY: Calibri">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></P>
<P class=MsoNormal
style="mso-pagination: none; tab-stops: 28.0pt 56.0pt 84.0pt 112.0pt 140.0pt 168.0pt 196.0pt 224.0pt 252.0pt 280.0pt 308.0pt 336.0pt; mso-layout-grid-align: none"><SPAN
class="" style="FONT-FAMILY: Calibri">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 </SPAN><I
class="" style="FONT-FAMILY: Calibri">about</I><SPAN class=""
style="FONT-FAMILY: Calibri"> 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></P>
<P class=MsoNormal
style="mso-pagination: none; tab-stops: 28.0pt 56.0pt 84.0pt 112.0pt 140.0pt 168.0pt 196.0pt 224.0pt 252.0pt 280.0pt 308.0pt 336.0pt; mso-layout-grid-align: none"><SPAN
class="" style="FONT-FAMILY: Calibri">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></P>
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<DIV class=""><SPAN class=Apple-style-span
style="FONT-SIZE: 12px">______________________</SPAN></DIV></DIV></DIV></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN></DIV></SPAN><SPAN
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size=2></FONT><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR
class=""></SPAN></DIV>Robert K. Logan</SPAN><SPAN class=Apple-style-span
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Emeritus - Physics - U. of Toronto </SPAN>
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<DIV class=""><SPAN class=Apple-style-span style="FONT-SIZE: 12px"><A class=""
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class="">
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class=Apple-interchange-newline></DIV></SPAN><BR
class=Apple-interchange-newline></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN>On Jun
8, 2016, at 4:40 PM, Moisés André Nisenbaum <<A class=""
href="mailto:moises.nisenbaum@ifrj.edu.br">moises.nisenbaum@ifrj.edu.br</A>>
wrote:</DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV></DIV>
<DIV><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><FONT
face=Arial size=2></FONT><FONT face=Arial size=2></FONT><FONT face=Arial
size=2></FONT><FONT face=Arial size=2></FONT><BR
class=Apple-interchange-newline>
<DIV class="">
<DIV class="" dir=ltr>
<DIV class="">
<DIV class="">Hi, John. It is amazing!!</DIV>
<DIV class="">I would like to highlight the word "constraints" at the caption of
the DNA diagram (<A class=""
href="http://phys.org/news/2016-06-layer-dna.html">http://phys.org/news/2016-06-layer-dna.html</A>)</DIV>
<DIV class="">"The rigid base-pair model is forced, using 28 <B
class="">constraints </B>(indicated by red spheres), into a lefthanded
superhelical path that mimics the DNA conformation in the nucleosome. Credit:
Leiden Institute of Physics"</DIV>
<DIV class="">The same word is used by Bob Logan and Stuart Kauffman to relate
mechanical concepts with 'information' (<A class=""
href="http://philpapers.org/rec/KAUPOA">http://philpapers.org/rec/KAUPOA</A>)</DIV>
<DIV class="">Could it have any parallel between these two approaches?</DIV>
<DIV class=""><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR
class=""></DIV>
<DIV class="">Also, you usually think "DNA" associated with Biological Sciences,
but this research is made at Leiden Institute of <B class="">Physics</B>! Of
course, to work current (complex, innovative) science you must have an
interdisciplinary approach.</DIV>
<DIV class=""><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR
class=""></DIV>
<DIV class="">Abraço.</DIV>
<DIV class=""><FONT face=Arial size=2></FONT><FONT face=Arial size=2></FONT><BR
class=""></DIV>
<DIV class="">Moisés</DIV></DIV></DIV>
<DIV class=gmail_extra><FONT face=Arial size=2></FONT><BR class="">
<DIV class=gmail_quote>2016-06-08 16:40 GMT-03:00 John Collier <SPAN class=""
dir=ltr><<A class="" href="mailto:Collierj@ukzn.ac.za"
target=_blank>Collierj@ukzn.ac.za</A>></SPAN>:<BR class="">
<BLOCKQUOTE class=gmail_quote
style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<DIV class="" lang=EN-CA vlink="#954F72" link="#0563C1">
<DIV class="">
<P class=MsoNormal>A previously hypothesized “second layer” of information in
DNA may have been isolated.<U class=""></U><U class=""></U></P>
<P class=MsoNormal><U class=""></U><U class=""></U> </P>
<P class=MsoNormal><A class=""
href="http://phys.org/news/2016-06-layer-dna.html"
target=_blank>http://phys.org/news/2016-06-layer-dna.html</A><U
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<P class=MsoNormal><SPAN class="">John Collier<U class=""></U><U
class=""></U></SPAN></P>
<P class=MsoNormal><SPAN class="">Professor Emeritus and Senior Research
Associate<U class=""></U><U class=""></U></SPAN></P>
<P class=MsoNormal><SPAN class="">University of KwaZulu-Natal<U
class=""></U><U class=""></U></SPAN></P>
<P class=MsoNormal><SPAN class=""><A class="" href="http://web.ncf.ca/collier"
target=_blank>http://web.ncf.ca/collier</A><U class=""></U><U
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<DIV class="" dir=ltr>Moisés André Nisenbaum<BR class="">Doutorando IBICT/UFRJ.
Professor. Msc.<BR class="">Instituto Federal do Rio de Janeiro - IFRJ<BR
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