Re: Markup, an abstraction

[Peter Hunsberger <peter.hunsberger@gmail.com>]

Well, I love abstract generalizations probably more than most, but frankly I don't see much use for non-conventional definitions of mark-up in regards to biological artifacts.  For that matter, I don't see much point in trying to map semantic constructs from the programming world to the internal workings of biological processes.  The fact that RNA has start and stop codons does let us draw analogies to Turing machines but that's about as far as I'd want to go as to finding shared abstractions.  

Now, the day may come when we can interface to synthetic genes via Web Services, but that won't be because of any emergent markup phenomenon that was always inherent in the core of biological processes.  Rather, that would be the result of some standardized interface that would likely send Simon off to live as a hermit in some far off land, weaving his own clothes and building furniture lest such an abomination disturb his renaissance man existence....

Peter Hunsberger

On Wed, Aug 28, 2013 at 1:02 AM, Hans-Juergen Rennau <hrennau@yahoo.de> wrote:

Thanks to everyone who responded to my little thought experiment! Among the responses, one sentence written by Peter Hunsberger struck me as revealing a fundamental mismatch between his and my conception of the word "markup". Peter wrote

"Markup is a semantic term we apply to the way we humans label certain groups of things. The biological processes have no more understanding of the internal arrangement of the genome than the car understands that the brick wall it just ran into was the end of the road."

This expresses a conventional use of the word "markup", whereas I propose an alternative which is a rigorous abstraction, of which the human use of markup is but a particular instance. I realize that my previous posting had failed to make it clear that everything I said was based on such an abstraction, and therefore I now try to clarify. Here comes a very tentative sketch how such an abstraction might look. Take it as indicating the direction of thought, rather than giving a definitive shape.

 

[...]

 

I still think that markup defined in the sense sketched above was invented or published more than four million years ago, that it is written into the very core of biological life and that this fact might kindle an interest in "markup" as a phenomenon existing beyond the limits of the conventional use of the term.

Hans-Jürgen Rennau