[Fis] Info Meta-Science?

[Pedro C. Marijuan]

Dear FISers,

The recent message by Sung (& Karl), and a previous one by John T. make 
me the impression that what they are considering becomes closer to a 
meta-science of information rather than to the nucleus of a possible 
information science discipline. Sung's and John's views are widely 
different but both share a translation of fundamental principles of 
life's organization slanted towards the physical. A detailed critique of 
their contents is beyond the scope of the present message (previously, 
it is a must applauding the very brilliant contents both have developed 
in their respective research).


To the point: imagine we have a computer, a lap top, then--what should 
be the fundamental explanation of its functioning? It depends on the 
audience, of course. In principle, it does not make much sense to relate 
it to solid state physics and electronics unless we are talking to 
engineers working in VLSI design; rather, depending on the subjects' 
user level we will need some basics of programming and computer science 
(von Neumann scheme, Turing machine,  commercial informatics, etc.). 
Imagining now the parallel with the living cell, a sort of 
"reverse-engineering" approach to the informational scheme of the cell 
is needed, but a new one, as present views are still terribly biased by 
classical molecular biology (Crick's "Central Dogma"), shallow systems 
biology, and uninteresting Darwinian tenets. Without systematically 
entering the external "information flow", the inner informational 
architectures, the different codes related to the variety of functions, 
the structure of a life cycle, the molecular "meaning"of exchanged 
signals, etc., and tying good portions of all that stuff in formal 
terms, our explanation will  not be relevant in information terms.


Bioenergetics parties have already done their fundamental work. See for 
instance the arch in between the "energy flow" by Morowitz in the 60's 
and the "scaling" work by Geoffrey West in our times. Bio-information 
parties are far away from constituting a similar explanatory arch. And 
this is in my view the very nucleus of info sci as a consistent 
discipline. Beyond that we can enter many other theoretical tools 
already developed, and ascend in scales of complexity to the emerging 
communicational realms stemming out from Life. That some of the new 
communicational/semiotic/economic/cultural realms become more or less 
independent, at least in the way they are currently conceptualized, 
seems OK. We should not forget, however, that the human life cycle, with 
all its materiality and aspirations, stands at the very heart of 
everything we may exchange, from conversation to goods, to money, to 
artworks.


Otherwise, prematurely going towards a grand narrative connected with 
physics, or with maths, becomes close to a strategic error as we 
overextend a confuse info idea into a meta-science (taking this with a 
pinch of salt, as one never knows how our Gordian knot will be cut). 
Maybe it is better leaving the possible extensions/overextensions into 
the critical hands of information philosophy practitioners.


Best wishes

--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 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] Informatics of DNA

[Xueshan Yan]

Dear Sungchul,

1. I highly appreciate your informational parsing on cell language and the 
comparative study of cell language and human language. By the end of last 
century, the main topics of (Human) Linguistics have been basically completed. 
It is not known whether human language study can get any inspiration from cell 
language study.

2. What kind of information definition and principle(s) have you got from the 
cell language study? To what extent are they applicable to other information 
fields? Exactly, your conclusions are mainly from the analysis of genetic cell. 
Among the biological information, the second major field of information 
application is neural cell. Are they effective in Neuroscience?

3. At the macro level, in your seven (six) steps of information flow scheme, we 
can consider all the content as "cell information / genetic information". But 
on the step 6, what you call it: Cell Functions→Human Behaviors, they transform 
cell information / genetic information into human information. If some 
information can be understood by a cell, it must not be understood by a (human) 
brain, and vice versa. How do you think of it?

4. In your information flow scheme of DNA→pre-mRNA→mRNA→proteins→IDS→Cell 
Functions→Human Behaviors, should the leftmost DNA be molecule? So far, we have 
seen that many researches thought that there are communication between 
molecules. From your research experience, are there any real examples of 
information communication took place between molecules?

5. Before 1952, the concept of "information" was rarely used in the works of 
Genetics. After Molecular Genetics, or after Crick's "central dogma", in 
Genetics research, many places used to use "gene" were replaced by 
"information". Do you think is it feasible to replace all "gene" with 
"information" completely at last?

 

Best wishes,

Xueshan

 

From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On 
Behalf Of Pedro C. Marijuan
Sent: Wednesday, November 29, 2017 9:41 PM
To: 'fis' 
Subject: [Fis] Informatics of DNA (Sungchul Ji)

Hi FISers,

We may have in DNA a golden opportunity to define what information is. 

 (1) We now know that we are different from mice because our DNA sequences 
are different from those of mice [1].  That is, we are different from mice 
because our DNA carries different kinds (both with respect to quality and 
quantity) of INFORMATION from the mouse DNA:

 ”When it comes to protein-encoding genes, mice are 85% similar to humans.  For 
non-coding genes, it's only about 50%. The National Human Genome  Research 
Institute attributes this similarity to a shared ancestor about 80 million 
years ago.”

 
http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5

 (2)  We also know that our properties or behaviors are at least in part 
determined by both DNA sequences (i.e., genetics) and the way they are turned 
on or off  by environment-sensitive cells constituting our body (i.e., 
epigenetics): We are the products of both our genes and our environment.  The 
causal link between DNA and our behaviors can be briefly summarized as follows: 
 

   1   2 3  
 45   6

DNA > pre-mRNA -> mRNA -> proteins ->  IDS -> Cell 
Functions  -> Human Behaviors
  ^ 

|
   |

  |
   |

  |
   |

  |
   
|_|


 7

  Figure A.  The flow of genetic and epigenetic informations between DNA and 
the human behavior.  IDS stands for the Intracellular Dissipative Structures 
(also called the Dissipative Structures of Prigogine) such as ion gradients 
across cell membranes and within the cytoplasm without any membrane barriers.  
According to the Bhopalator, a molecular model of the living cell proposed in 
1985 in a meeting held in Bhopal, India, IDS's are postulated to be the 
immediate or the proximal causes for all cell functions [2].  The seven steps 
in the scheme are  

1 = transcription

2