Re: [Fis] "Mechanical Information" in DNA

2016-06-08 Thread Bob Logan 
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 
organization of process in the expected biological work cycles to create the 
diversity in our observable biosphere.

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.








__

Robert K. Logan
Prof. Emeritus - Physics - U. of Toronto 
Fellow University of St. Michael's College
Chief Scientist - sLab at OCAD
http://utoronto.academia.edu/RobertKLogan
www.physics.utoronto.ca/Members/logan
www.researchgate.net/profile/Robert_Logan5/publications










On Jun 8, 2016, at 4:40 PM, Moisés André Nisenbaum 
 wrote:

Hi, John. It is amazing!!
I would like to highlight the word "constraints" at the caption of the DNA 
diagram (http://phys.org/news/2016-06-layer-dna.html 
)
"The rigid base-pair model is forced, using 28 constraints (indicated by red 
spheres), into a lefthanded superhelical path that mimics the DNA conformation 
in the nucleosome. Credit: Leiden Institute of Physics"
The same word is used by Bob Logan and Stuart Kauffman to relate mechanical 
concepts with 'information' (http://philpapers.org/rec/KAUPOA 
)
Could it have any parallel between these two approaches?

Also, you usually think "DNA" associated with Biological Sciences, but this 
research is made at Leiden Institute of Physics! Of course, to work current 
(complex, innovative) science you must have an interdisciplinary approach.

Abraço.

Moisés

2016-06-08 16:40 GMT-03:00 John Collier mailto:colli...@ukzn.ac.za>>:
A previously hypothesized “second layer” of information in DNA may have been 
isolated.

 

http://phys.org/news/2016-06-layer-dna.html 

 

John Collier

Professor Emeritus and Senior Research A

Re: [Fis] "Mechanical Information" in DNA

2016-06-08 Thread Hector Zenil 
The original article
(http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0156905)
closes with:
"Analysis of two high resolution nucleosome maps revealed strong
signals that—even though they do not constitute a definite proof—are
at least consistent with such a view."

Physorg opens their popularizing note about the above article with:
"Second layer of information in DNA confirmed"

Interesting.


On Wed, Jun 8, 2016 at 11:10 PM, Hector Zenil  wrote:
>> 2016-06-08 16:40 GMT-03:00 John Collier :
>>>
>>> A previously hypothesized “second layer” of information in DNA may have
>>> been isolated.
>
> This is not exactly new, possibly the reason this paper didn't make it
> to Nature or Science. See
> http://tinyurl.com/3Dgenomics
> http://www.cell.com/trends/genetics/abstract/S0168-9525(15)00063-3
>
>
> On Wed, Jun 8, 2016 at 10:40 PM, Moisés André Nisenbaum
>  wrote:
>> Also, you usually think "DNA" associated with Biological Sciences, but this
>> research is made at Leiden Institute of Physics! Of course, to work current
>> (complex, innovative) science you must have an interdisciplinary approach.
>
> Francis Crick was a physicist at the Physics Cavendish Laboratory in
> Cambridge with Watson, Frederick Sanger was a biochemist, etc.
>
> Best,
>
> - Hector Zenil
> http://www.hectorzenil.net/
>
>>>
>>>
>>>
>>> http://phys.org/news/2016-06-layer-dna.html
>>>
>>>
>>>
>>> John Collier
>>>
>>> Professor Emeritus and Senior Research Associate
>>>
>>> University of KwaZulu-Natal
>>>
>>> http://web.ncf.ca/collier
>>>
>>>
>>>
>>>
>>> ___
>>> Fis mailing list
>>> Fis@listas.unizar.es
>>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>>
>>
>>
>>
>> --
>> Moisés André Nisenbaum
>> Doutorando IBICT/UFRJ. Professor. Msc.
>> Instituto Federal do Rio de Janeiro - IFRJ
>> Campus Rio de Janeiro
>> moises.nisenb...@ifrj.edu.br
>>
>> ___
>> Fis mailing list
>> Fis@listas.unizar.es
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>

___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] "Mechanical Information" in DNA

2016-06-08 Thread Hector Zenil 
> 2016-06-08 16:40 GMT-03:00 John Collier :
>>
>> A previously hypothesized “second layer” of information in DNA may have
>> been isolated.

This is not exactly new, possibly the reason this paper didn't make it
to Nature or Science. See
http://tinyurl.com/3Dgenomics
http://www.cell.com/trends/genetics/abstract/S0168-9525(15)00063-3


On Wed, Jun 8, 2016 at 10:40 PM, Moisés André Nisenbaum
 wrote:
> Also, you usually think "DNA" associated with Biological Sciences, but this
> research is made at Leiden Institute of Physics! Of course, to work current
> (complex, innovative) science you must have an interdisciplinary approach.

Francis Crick was a physicist at the Physics Cavendish Laboratory in
Cambridge with Watson, Frederick Sanger was a biochemist, etc.

Best,

- Hector Zenil
http://www.hectorzenil.net/

>>
>>
>>
>> http://phys.org/news/2016-06-layer-dna.html
>>
>>
>>
>> John Collier
>>
>> Professor Emeritus and Senior Research Associate
>>
>> University of KwaZulu-Natal
>>
>> http://web.ncf.ca/collier
>>
>>
>>
>>
>> ___
>> Fis mailing list
>> Fis@listas.unizar.es
>> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>>
>
>
>
> --
> Moisés André Nisenbaum
> Doutorando IBICT/UFRJ. Professor. Msc.
> Instituto Federal do Rio de Janeiro - IFRJ
> Campus Rio de Janeiro
> moises.nisenb...@ifrj.edu.br
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>

___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

Re: [Fis] "Mechanical Information" in DNA

2016-06-08 Thread Moisés André Nisenbaum 
Hi, John. It is amazing!!
I would like to highlight the word "constraints" at the caption of the DNA
diagram (http://phys.org/news/2016-06-layer-dna.html)
"The rigid base-pair model is forced, using 28 *constraints *(indicated by
red spheres), into a lefthanded superhelical path that mimics the DNA
conformation in the nucleosome. Credit: Leiden Institute of Physics"
The same word is used by Bob Logan and Stuart Kauffman to relate mechanical
concepts with 'information' (http://philpapers.org/rec/KAUPOA)
Could it have any parallel between these two approaches?

Also, you usually think "DNA" associated with Biological Sciences, but this
research is made at Leiden Institute of *Physics*! Of course, to work
current (complex, innovative) science you must have an interdisciplinary
approach.

Abraço.

Moisés

2016-06-08 16:40 GMT-03:00 John Collier :

> A previously hypothesized “second layer” of information in DNA may have
> been isolated.
>
>
>
> http://phys.org/news/2016-06-layer-dna.html
>
>
>
> John Collier
>
> Professor Emeritus and Senior Research Associate
>
> University of KwaZulu-Natal
>
> http://web.ncf.ca/collier
>
>
>
> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>


-- 
Moisés André Nisenbaum
Doutorando IBICT/UFRJ. Professor. Msc.
Instituto Federal do Rio de Janeiro - IFRJ
Campus Rio de Janeiro
moises.nisenb...@ifrj.edu.br
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] "Mechanical Information" in DNA

2016-06-08 Thread John Collier 
A previously hypothesized "second layer" of information in DNA may have been 
isolated.

http://phys.org/news/2016-06-layer-dna.html

John Collier
Professor Emeritus and Senior Research Associate
University of KwaZulu-Natal
http://web.ncf.ca/collier

___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Towards the end of the Med Session and Phenomenology

2016-06-08 Thread Pedro C. Marijuan 

Dear FIS Colleagues,

It is time to conclude a long session on phenomenology, information and 
the life sciences. First of all, we should thank Maxine, Lou, Soeren, 
Alex, and Plamen for their time and dedication in conducting the 
discussion sessions. The contact with phenomenology from the point of 
view of information, with all of its ups and downs, has been a curious 
experience. Even the most reluctant hard-nosed scientists will have to 
accept that in this period of upmost intense transformations of science 
--particularly in biology and medicine-- we are missing something 
important in our collective practice. The endless complexity of life in 
all of its domains seems to defy all our bodies of knowledge, from the 
most philosophical and basic to the most applied, and force them to 
participate in the collective game of Knowledge Recombination. My 
personal question to Plamen (sure he has some further comments to make), 
apart from thanking him all the organization job during these months, is 
whether we should envision a new "phenomenology of information" so as to 
guide us in the KR survival game...


Best wishes to all
--Pedro

-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta X
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-



___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis