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.
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