"Petr Kuzmic" <pkuzmic at biokin.com> wrote in message
news:399F568A.7D2A0EED at biokin.com...
>>> Herbert M Sauro wrote:
> >
> > MCA Analysis or Theory?
> >
> I would like to ask if anybody remembers the work of David Garfinkel in
> computer simulation of metabolic pathways in the 1960's. This, to me
> anyway, was a very serious attempt at applying computational techniques
> to biochemical metabolic systems. It failed, more or less, because the
> *numerical methods* were not mature enough then. I wonder what other
> contributors to this forum think about the significance of Garfinkel's
> work.
>
>From a personally point of view, Garfinkel's work (and other members of his
group) was very important to me. It was one of his early papers which got me
into this field, and like a curse, the interest has stayed with me ever
since. I think what impressed me was his huge vison, his attempt to simulate
entire systems, he wasn't content to work with models with just three or
four variables but he simulated large numbers of variables. In an important
sense his work did not fail becuase I think it influenced many people, it
made people aware of the idea of using computers to model complex cellular
networks. I guess he failed in the sense that scientifically we look back
and think, he didn't have a chance, insufficult data, computers too slow,
numerical methods imature etc. But then doesn't all science look like that
from the perspective of a later generation. I don't believe he failed, he
was one of the first to try this approach and showed the rest of us what can
and cannot be sensibly done with a compuational approach. One thing his
efforts taught me was that simulation in a vacum of formal theory is almost
useless, unless perhaps you're an engineer in which case you might only be
interested in input and outputs. But as a scientist one needs to understand
what's going on inside and for that one needs some sort of organising
framework, and for me that turned out to be MCA/MCT.
Probably the best messaage we can pass to the 'new-enlightment' is to quote
the famous phrase:
"Those who cannot remember the past are condemned to repeat it."--George
Santayana
> My other question, similar in nature, has to do with this book:
>> -----------------
> @book {Haya85,
> author = "K. Hayashi and N. Sakamoto",
> title = "Dynamic Analysis of Enzyme Systems -- An Introduction",
> publisher = "Springer-Verlag", address = "New York", year = "1985"}
> -----------------
>> Is there anybody reading this who was significantly influenced by this
> book? If I remember correctly (I don't have my copy near me at this
> time), Hayashi and Sakamoto say in the introduction that they worked for
> about five years, from 1979 to 1984, I think, to survey and also further
> develop computational methods for the analysis of complex biochemical
> systems. This research was sponsored by the Japanese government.
> What's your evaluation of this work?
>I have to admit that although I know the book and have read some of its
chapters I know nothing about the authors. As for influence, for me it came
a bit late in the day, although it's probably a book worth having on one's
bookself.
> In my opinion, computer analysis of biochemical metabolic pathways has
> been around continuously since the early 1960's, only the reception of
> this methodology by various Gurus, High Priests, and/or Dictators [;)]
> has varied over time.
>> - Petr
>
True
Talking of influencial books and articles, one review which I keep going
back to is the 1977 review by Heinrich, Rapoport and Rapoport (I think the
order is correct), in Progress in Biophys.... It covers a lot of ground and
includes things you might not find in many other places, eg how to deal with
rapid equibibrium reactions.
Herebrt Sauro
> _____________________________________________________________________
> P e t r K u z m i c, Ph.D. mailto:pkuzmic at biokin.com
