[ccp4bb] Fwd: [ccp4bb] structure <-> function

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Detection of DNA in protein complex crystals
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2009-06-23

Next message:
Subject: Phantom Crystals - a recap
From: George DeTitta detitta {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2009-06-23

Subject: Fwd: structure <-> function
From: Richard Gillilan reg8 {- at -} CORNELL {- dot -} EDU
Date: 2009-06-23

Begin forwarded message:

From: Richard Gillilan
Date: June 23, 2009 9:43:20 AM EDT
To: "Nadir T. Mrabet"
Subject: Re: [ccp4bb] structure <-> function

A very interesting question.

Stephan Jay Gould was well known for his argument that evolution is
contingent on all kinds of factors (like meteor impacts etc.). He
argued that if we replayed geologic history with minor tweaks, life
might be totally different or not exist at all. Based on these ideas,
I think a lot of people will say evolution has "no direction." It
meanders aimlessly. This is in contrast to idea that life is somehow
always improving or becoming more complex or more advanced (some kind
of "progress").

But I think anyone who's used evolutionary programming to solve
numerical problems realizes that it can be an optimization process
under some conditions that finds "best" solutions. I think there are
certainly situations in which external contingencies are limited and
so evolution can be viewed as a process that sorts out "best"
solutions to certain physical problems.

If a certain reaction needs to be catalyzed in order for a species to
live and reproduce, there may well be only one, or a few good ways to
do this ... limitations of fundamental physics. The fold and sequence
of the proteins may be different, but they still have to reduce the
activation barrier for the reaction, and that involves binding a
certain fixed intermediate geometry of a species that has donors and
acceptors in fixed locations.

Similarly, there are a fixed number of ways objects can achieve
locomotion. Creatures evolved to move efficiently in their element to
compete for resources have to solve the same basic physical problems.
When those problems are simple and have only a few solutions, you
have convergence.

ps, if you haven't seen some of Karl Sims' evolved virtual creatures
videos, they are really worth watching. Astounding in fact:
www.karlsims.com/evolved-virtual-creatures.html

Richard Gillilan
MacCHESS
>
> On Jun 22, 2009, at 11:16 AM, Nadir T. Mrabet wrote:
>
>> Ok, now we can perhaps debate of another problem.
>> With a multiple choice question that has more than one acceptably
>> good answer,
>> is it "convergent", or rather "independent", evolution?
>>
>> This multiple choice question is open for discussion.
>>
>> Greetings,
>>
>> Nadir
>>
>> Pr. Nadir T. Mrabet
>> Cellular & Molecular Biochemistry
>> INSERM U-954
>> Nancy University, School of Medicine
>> 9, Avenue de la Foret de Haye, BP 184
>> 54505 Vandoeuvre-les-Nancy Cedex
>> France
>> Phone: +33 (0)3.83.68.32.73
>> Fax: +33 (0)3.83.68.32.79
>> E-mail: Nadir.Mrabet@medecine.uhp-nancy.fr
>>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Detection of DNA in protein complex crystals
From: Jacob Keller j-keller2 {- at -} MD {- dot -} NORTHWESTERN {- dot -} EDU
Date: 2009-06-23

Next message:
Subject: Phantom Crystals - a recap
From: George DeTitta detitta {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2009-06-23