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Re: Metabolic closure in (M,R)-systems

Athel Cornish-Bowden wrote:
Earlier, Judith said that she disputed "the claim made that Robert
Rosen 'never explained the mathematical context nor gave any
mathematical or biological examples'". OK, one can dispute it, but
to dispute it effectively one needs to point to some examples.

Hi Athel,

I will attempt to do so for you. Before I get started, let me say up front that I generally think this is a good paper and I don't want to give the impression that I'm angered by it. Furthermore, I don't have much of a problem with the different lingo or different point of view. Mind you, I see potential for you to see some of the same confusion in your audience regarding the words you chose that my father is criticized for in his own. It's not as easy as using different words that make more sense to you. I can tell you that from personal experience! You can certainly accuse me of bias, but the new word choices don't make as much sense to me as my father's do. I know what he meant, and the definitions I have in my head for the words chosen to replace his have somewhat different meanings.

In fact, part of the trouble I see in trying to clarify the issue from the quote at the top is that I'm not sure what you would regard as "the mathematical context", although I think I know what you mean by biological examples; both the common living realizations of the model he used math to help create and the biological systems he set out to model in the first place. They happen to be the same, in this case. The mathematical context (by my definition) would refer to the method, in mathematics, by which he generated his pictographic model which he named The "(M,R)-System" Model. So we have three entities here: the biological systems to be modeled, the mathematical process RR used to derive his conclusions about the encoding aspect of creating his model, and the model itself.

My only real quarrel with the paper is that it states as fact certain things that are merely opinion, with regards to more than just the perceived deficiencies of Robert Rosen's own development of the "(M,R)-System" model. Among these opinions is the one stating that this model is purely a model of metabolic networks. My father would argue that there is a great deal more to it than just that-- It is a model of living organization; the sort of complex organization from which life emerges as a collective effect. M stands for metabolism but R stands for Repair. The word "replication" was not Dad's own choice for R. (Although he felt that "replication" was a good word to describe how the process of repair often works, as well as being descriptive of how close to reproduction a process such as this would have to be. In other words, the kind of functional capability required for repair is almost the same required for reproduction). Repair is a capability for maintenance of, and building/rebuilding, aspects of the organization itself. Metabolism cannot exist without repair in a living system and vice versa. Living systems are not alive purely because of the metabolic processes; we can create a metabolic process quite well in machines with current technologies. The internal combustion engine comes to mind. So I would suggest that the first paragraph of the paper be reworded to say something to the effect that "the authors will be focusing on the metabolic aspects of Rosen's "(M,R)-System" model."

Unless you say I'm way off base, I will put my efforts into finding you reference pages from several of my father's books, which give what constitute my definition of mathematical context for the conclusions Robert Rosen came up with in developing his "(M,R)-System" model. All right?

More to come...
Judith




Web address: http://www.rosen-enterprises.com
BioTheory: An electronic journal of general science based on the Relational (Rosennean) Complexity Paradigm
On Sep 7, 2005, at 10:48 AM, Athel Cornish-Bowden wrote:

Tim wrote:

I just found a pre-print of the paper here, at one of the authors' site:

http://bip.cnrs-mrs.fr/bip10/rosen.htm

Glad you found this. In due course (once volume, page and year
are known -- I optimistically put 2005 on the HTML version, but
it's more likely to be 2006, given the backlog) I'll post a PDF
file of the paper in its published form.

When I visited my own pages today I found that all the figures were
missing. I have now fixed this. Sorry about the problem, which
was due to my forgetting that Unix treats capitals and lower-case
letters in filenames differently. (Everything worked fine when I
checked the pages locally, but not once they got on the server.)

Earlier in the same message, Tim wrote:

I think the use of some different phraseology on their part is due
in some part to a need to appeal to the editors of JTB or similar
publications. But I do think that some of the negative remarks
about Rosen's work are needlessly hyperbolic.

For the first part, not really. We changed the terminology for the
reason we gave, that we want to be intelligible to biologists outside
the immediate Rosen circle, and we didn't think we could be that
if we used standard biological words like "replication" with entirely
different meanings from those used in biology, or if we avoided
words like "catalyst" and "enzyme" that virtually everyone uses.

Lack of intelligibility is a problem that needs to be taken by anyone
on this list (or elsewhere) who wants to bring Rosen's ¦uvre to a
wider public. At a meeting in Sheffield (you can see what sort of
meeting it was in the meeting report at
http://bip.cnrs-mrs.fr/bip10/genomebi.htm) in January I spoke a
little about Rosen, and included the rash statement that few biologists
had ever heard of him. This proved to be wrong, as several people
told me afterwards that they had heard of him but that they had
not been able to make sense of what he was saying, and couldn't see
how it related to life as everyone else thought they understood it.
I had a similar experience a couple of months later at a meeting in
France. It appears that plenty of biologists have heard of Robert
Rosen, but hardly anyone is trying to advance his ideas in the
primary biological literature. Olaf Wolkenhauer is certainly one of
the few, and Jannie Hofmeyr is another, though in his case I don't
think he has started publishing his ideas yet.

For the second part, what "negative remarks"? We thought we were
displaying a lot of admiration for Rosen, and we'd be worried if
we thought that anything falling short of calling him "Biology's
Newton" would be taken as needlessly hyperbolic and negative.

Earlier, Judith said that she disputed "the claim made that Robert
Rosen 'never explained the mathematical context nor gave any
mathematical or biological examples'". OK, one can dispute it, but
to dispute it effectively one needs to point to some examples.

athel


--
--
Athel Cornish-Bowden
***
http://bip.cnrs-mrs.fr/bip10/homepage.htm