[Fis] Fw: "Mechanical Information" in DNA

Loet Leydesdorff loet at leydesdorff.net
Thu Jun 9 13:51:03 CEST 2016

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.






Loet Leydesdorff 

Professor, University of Amsterdam
Amsterdam School of Communication Research (ASCoR)

 <mailto:loet en leydesdorff.net> loet en 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=ych9gNYAAAAJ&hl=en> http://scholar.google.com/citations?user=ych9gNYAAAAJ&hl=en


From: Fis [mailto:fis-bounces en 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



From: Fis [mailto:fis-bounces en listas.unizar.es] On Behalf Of Joseph Brenner
Sent: Thursday, 09 June 2016 11:10 AM
To: fis <fis en 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.






----- Original Message ----- 

From: Bob Logan <mailto:logan en physics.utoronto.ca>  

To: Moisés André Nisenbaum <mailto:moises.nisenbaum en ifrj.edu.br>  

Cc: fis <mailto:fis en 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: 




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.


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 





On Jun 8, 2016, at 4:40 PM, Moisés André Nisenbaum <moises.nisenbaum en ifrj.edu.br> 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.






2016-06-08 16:40 GMT-03:00 John Collier <Collierj en ukzn.ac.za>:

A previously hypothesized “second layer” of information in DNA may have been isolated.




John Collier

Professor Emeritus and Senior Research Associate

University of KwaZulu-Natal



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Moisés André Nisenbaum
Doutorando IBICT/UFRJ. Professor. Msc.
Instituto Federal do Rio de Janeiro - IFRJ
Campus Rio de Janeiro
moises.nisenbaum en ifrj.edu.br

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