"Petr Kuzmic" <pkuzmic at biokin.com> wrote in message
news:39A588FD.AED743AB at biokin.com...
> By the way, I wish someone with sufficient expertise in MCA (that is,
> sufficient to *evaluate* the relevant literature) would take over where
> Pedro Mendes left off in 1996 ...
>>http://gepasi.dbs.aber.ac.uk/metab/mca_refs.htm>> ... and updated the online bibliography of MCA. This kind of
> bibliography would greatly benefit especially people *outside* the
> BTK/MCA/MCT circle, which, to this observer, seems fairly closed at
> times.
>
Athel seems to have an up to date list of references at
http://ir2lcb.cnrs-mrs.fr/~athel/mcarefs.htm#authors
> When I say 'closed' I mean that a citation analysis of people active in
> MCA *might* reveal that it's a cluster of authors referring to each
> other's work. How else could we encounter that surprising piece of
> correspondence, written by a junior researcher at Karolinska to Athel
> sometime around the beginning of July:
>> >I work with PFK and am doing math models as well as molecular
> >biology with this protein. I know of no argument against
> >PFK as rate limiting step. If you have such an argument,
> >could you please explain. Even better, if this is a sound
> >argument, could I politely suggest publishing your idea in
> >Science or Nature. None of my collegues working in this
> >field are aware of this argument and such an argument
> >could potentially discredit many dozens of publications by
> >dozens of the most prominent biochemists in the world.
>
I was talking to a PhD student yesterday about his interest in modelling and
theoretical aspects of cellular networks (which is what he research is
about), and he'd never heard of MCA or BST, but then he hadn't heard of
Garfinkel either nor any of the past modelling attempts. The modelling
software he was aware of was E-Cell, VCell and the mythical BioSpice, he's
never even heard of Gepasi, this is after a year of research which
presumably included a
literature search. One could argue that the supervisor is to blame but many
of the supervisors who
are thinking of starting projects like this (and it seems there are many)
are also completely in the dark
when it comes to past work and for some reason they don't bother to check
either. If anything, this situation
is only going to get worse now that finally the penny has dropped and people
are wondering what are we going to
do with all these genome sequences?
Perhaps it's not a case of the field being
'closed' but more likely that researchers don't read around their literature
areas any more. MCA is fairly well documented, there are at least three
undergrad text books I know which deal with it fairly extensively, there
are at least three more which have a couple of pages about, there are at
least three research text books which have lengthy chapters on MCA, one of
which is a metabolic engineering text book, there is now even a mainstream
biochemistry text book with a page or two on it. Also Steven Roses' new
edition
of Chemistry of Life (which is a popular science paperback) even has a page
on it where
he amazingly admits he was
wrong about his ideas of metabolic regulation in his first edition (written
back in the 70s). There is at least one conference ever two years dedicated
to the topic plus usually a filler in the years in between (quite apart form
the odd talks at 'main-stream' conferences). there was a couple of years
back a special entire
edition of J. theor biol dedicated to it. Almost all the major software
tools
for modelling metabolism have MCA as one of their analysis tools even though
the majority of the software writers
have never published a paper on MCA (i.e it's not just MCA people that write
this sort of software), plus there are quite
a few web sites with information, software etc.
Now all this be from a small group which cites itself?
So I'm not sure if it is a 'closed' area, it just that people don't read
around their subject areas anymore, Researchers have become very specialised
to the extent that they now even 'reinvent/discover', take for example the
work by Stanislas Leibler et al in Nature, they claimed to have discovered a
new principle in biological systems, namely 'robustness', that is resistance
to perturbations. This 'new principle' has been known to the geneticists
for years.
I would be interested though to find out the citation pattern and whether
citations are confined to within the group, but aren't citation patterns in
most research areas like this?
> Of course, saying "none of my colleagues working in this field are
> aware..." shows a lack of experience of the kind that is to be expected
> from a student, but it does mean that this doctoral "Aspirant" was not
> directed by *either* of his two advisors (at Karolinska and at Boston
> University) to read what he needs to read, namely
>
Exactly, there seems to be a problem here that some/many tenured researches
do not seem to investigate what's already been done before launching into a
new area.
>http://ir2lcb.cnrs-mrs.fr/~athel/howler.htm>http://ir2lcb.cnrs-mrs.fr/~athel/rls.htm>> - Petr
Hebrert
