>I was interested to read your nomenclature paper, when I finally got it.
>The transfer kept stalling - presumably due to net congestion somewhere.
I have just posted another message about this: try
http://ir2lcb.cnrs-mrs.fr/~athel/mcanom7.ps if it doesn't work from South
Africa.
>>1. I'm happy to abide by these symbols and terms in theoretical papers,
>BUT I have got reservations about a second retrospective change in
>nomenclature for general purpose literature. For example, having
>translated the 'Control of Flux' into 'control coefficient' nomenclature in
>1995, I think it would be sad if we needed yet another translation into a
>new terminology in 1999. This is not likely to aid communication with
>general biochemists who are only aware of the broad outlines of MCA and are
>not mathematically sophisticated (i.e. the 99% of them). Can we agree a
>'dispensation' to use the 1984 terminology in 'popular' literature, perhaps
>with some form of words to indicate that this reflects a traditional usage
>and is not the current technically exact usage?
I have a lot of sympathy with David's point here and I think we need to try
to accommodate it. Apart from anything else, people are certainly going to
continue using the enzyme-based nomenclature whatever happens.
>>I do not think it is difficult for us who are familiar with the theory to
>make these slight adaptations, but I do have a strong feeling that it is
>both wrong and counterproductive to convey to the general public that
>control coefficients are only exactly definable at a very low mechanistic
>level. It may be neat for theoretical treatments, but in a practical sense
>it overlooks the fact that there are very few enzymes for which the exact
>mechanism is agreed beyond any reasonable level of doubt. It was never the
>intention of Henrik Kacser, I am sure, to develop a treatment that could
>only be used when the mechanistic minutiae of a metabolic system were all
>fully known - quite the reverse. We will have a very hard job persuading
>people of the necessity to treat metabolic systems at a system level if our
>theory appears to presuppose a level of molecular detail that they never
>envisaged needing to know.
I agree 100%.
>>Furthermore, changing the amount of enzymically active protein is a
>physically realisable modulation. The parallel and specific change of two
>independent rate constants on the other hand is a purely mathematical
>operation: it cannot be implemented as such. We will have an uphill battle
>persuading the rest of the biochemical community of the relevance of a
>theory that is based on a purely hypothetical definition, however sound we
>know it to be.
>>>2. I think it would be really helpful to address the question of total and
>partial derivatives in a systematic way once and for all. The problem is
>that I am not sure of my ground here, but I'll state my beliefs:
>[snip]
>>Whether I'm right or wrong, I think we should come to a clear statement
>about which of these coefficients should be defined with the differential
>operator, and which with the partial differential operator (bearing in mind
>that the notation of a partial differential can include an explicit
>statement of the dependent variables that are constant).
I think this is very important ("we should come to a clear statement") and
I agree with the details of David's position. However, this is something
where we need to have the explicit guidance of some of the more
mathematically trained members of the community. I'm not sure if any of us
are "real" mathematicians (apart from Christine, who is probably not
following this), but some of us must know some real mathematicians.
Athel
Email: athel at ibsm.cnrs-mrs.fr
Site map: http://ir2lcb.cnrs-mrs.fr/~athel/sitemap.htm
New Beer in an Old Bottle: http://ir2lcb.cnrs-mrs.fr/~athel/buchner.htm
MCA FAQ: http://ir2lcb.cnrs-mrs.fr/~athel/mcafaq.htm
MCA chapter from my book:
http://ir2lcb.cnrs-mrs.fr/~athel/mcai.htm
