In article <5ubptc$d3i at mserv1.dl.ac.uk>, RUMYM at BGEARN.ACAD.BG writes
>I very much suspect that the ideal case in which all concentrations of
>"surrounding" metabolites are constant contradicts heavily the leading
>holistic idea. If we want to find characteristics of a pathway which are
But one *has* to put a boundary somewhere, if not you would have to
analyse the entire Universe. So if one is to put up a boundary then it
might aswell be fixed. I don't see any point at this stage in having
floating boundaries since these would eventually dissipate and the
system ends up in equilibrium, which we(I) are not very much interested
in.
>"global properties of the system", it is quite unsuitable to choose an
>ideal case in which all connections with the rest of metabolism are cut,
Where would you 'cut' the system? At the organisms' membrane? Or a few
kilometers away from the creature?
>i.e. in which all characteristics are internal properties of the pathway
>itself, then to "open" the pathway and claim that the same characteristics
>have now become "global properties of the system", and to refer to their
>modification by the rest of metabolism as an evidence in support of their
>"globality".
I don't think there is too much of a problem, the generalities offered
by MCA hold no matter what the size of your system. If you are worried
about the boundary then one possiblity is to study the properties of the
system and then extend the boundary by one enzyme step or what ever and
reanalyse, if there is not much of a change then your original boundary
was ok etc. In any case, many of the basic structural characteristics of
metabolism, eg straight chains, branches, cycles etc. are reasonably
understood in MCA terms. No only that, since MCA is an analysis based on
linearisation, these properties are on the whole additive. For example,
if you change a straight chain and double it's length, making sure you
don't disturb the concentrations in the original pathway, you will find
that the control coefficients in the original pathway do not change in
ratio but only in scale. In other words the MCA characteristics don't
change as the boundary changes. The real problems occur where the
boundary moves so that signal pathways float, eg feedbacks etc. I'm not
up with the literature but it's an area that probably could be looked
into, however someone may have done this already.
Herbert
--
Herbert M Sauro
email: HSauro at fssc.demon.co.uk
Telephone: 01974 282428
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