This discussion seems to have moved a very long way from the original
topic, and hence the reported "Subject", could this be continued as a
new thread please ?
Thanks
Andrew
On 17 Nov 2009, at 11:40, Morten Kjeldgaard wrote:
Tim Gruene wrote:
Yes, but models that can be validated against experimental data.
The
defining characteristics of computational models is that they (A)
are 100% dependent on the algortihm, (B) can't be validated at
all.
Cheers,
Morten
Sorry, they can be validated to some extend using biochemical data!
You are joking, right?
I would say that any prediction that can be derived from a model and
confirmed is a validation of the model and the model remains valid
until
replaced by a better one. The sun was orbiting the earth until
evidence
became too contradictorily for this model. Until then it was a good
model - better than no model at all, be it wrong or not.
Whoa there. Let's move back a few steps. This discussion started
because
someone said that there are "rumblings" that modelbuilding would
soon be a
competitive technique to xray-crystallography.
I objected with the fact that computational models cannot be
validated, a
claim which was countered with "they can be validated using
biochemical data".
I think that is really funny. So, you want to compute a model of a
macromolecule from first principles, and then spend the next 10
years in the
biochemistry lab validating it? Because that is what it will take
until you
can convince anyone that the positions of your loops, your rotamers,
your
co-factors and your metal-binding sites are correct.
I thought this list was for crystallographers, but apparently people
no
longer understand what "validation" means in structural science.
-- Morten
PS: The geocentric model is no less correct than the heliocentric
one. It is
simply a matter of choosing a sensible reference frame for your
mathematical
model, and that depends on application. That the geocentric model
was not
convenient for computing the planetary orbits is not a valid
justification
for saying "a poor molecular model is better than no model at all."
In fact,
the geocentric model is a very good one, and is used daily by
millions of
engineers, navigators and scientists. OTOH, a poor molecular model
may cause
unlimited waste of time and money by other scientists.
