From owner-biophys@hgmp.mrc.ac.uk Sun Dec 30 22:59:06 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B9E7517AAE for ; Sun, 30 Dec 2001 22:59:05 +0000 (GMT) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C586717ABA for ; Sun, 30 Dec 2001 22:59:03 +0000 (GMT) Received: from niobium.hgmp.mrc.ac.uk (niobium [193.62.192.41]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id C8FD917AAE for ; Sun, 30 Dec 2001 22:59:02 +0000 (GMT) Received: (from news@localhost) by niobium.hgmp.mrc.ac.uk (8.9.3+Sun/8.8.8) id WAA02741 for biophys-list@hgmp.mrc.ac.uk; Sun, 30 Dec 2001 22:51:34 GMT X-Authentication-Warning: niobium.hgmp.mrc.ac.uk: news set sender to using -f Message-ID: <3C2F99FD.8258F2B@shaw.ca> From: Tim Davies Organization: @Home Network X-Mailer: Mozilla 4.72 [en]C-AtHome0404 (Win98; U) X-Accept-Language: en MIME-Version: 1.0 X-Newsgroups: bionet.biophysics Subject: Re: Help on a BIO-PHYSICS book References: <7cb4qj$ifr$1@diana.bcn.ttd.net> <36e927c8.0@news4.his.com> <36E955A3.2493FAC5@fuerst.de> <3C1A2777.CA658CD8@uno.edu> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Lines: 64 Date: Sun, 30 Dec 2001 22:50:30 GMT X-Complaints-To: abuse@shaw.ca To: biophys@hgmp.mrc.ac.uk Sender: owner-biophys@hgmp.mrc.ac.uk Precedence: bulk hi Paul: You mention the few kcal of energy difference in the folded vs unfolded sate of a protein. I am wondering if there is a set of math that when applied will always give you the structure of a molecule, such as a protein. The complexity shouldn't be a factor, just the knowledge that the folding is understood and that these kcal values are not " sampling errors". I realize it may take years to accurately predict the folding with one single set of equations , but the question is do they exist Tim Davies Paul Hanson wrote: > > Hey folks! > Thank YOU for the sudden input of an interesting idea! I've been doing some > reading and come across an odd idea that I've not fully explored yet. It seems > that, with a few exceptions, that as you move up the food chain to more complex > organisms, there is a 10x difference as you move from prey->predator. Now this > strikes me as really, really weird because why the factor of 10? > Now.... > > "Frank Fürst" wrote: > > > Hi, > > > > Eric Fairfield wrote: > > > > > [...] > > > > > > Across all of these pieces of biology, I can't think of a minimum energy > > > rule that holds up to serious scrutiny. > > > > > > I propose the following hypothesis: > > > > > > Biological systems do not abide by a minimum energy rule. They function so > > > that they produce offspring before they exceed the maximum energy available > > > to their particular environment at a particular time. > > > > > I think the main problem with applying a minimum energy rule to > > biology is that biological systems are biological ones because they > > are far from equilibrium. And in non-equilibrium systems the standard > > rules of thermodynamics no longer hold. > > NOT so! We are generally just outside of equilibrium! The difference between a > folded and > unfolded protein is only a few kcal! No wonder I'm always feeling a bit > frazzled! The point is > that the rules of thermodynamics have to hold for biological systems or we'd be > in big trouble. > > > > > If a system is far enough from equilibrium, there exists no state > > function (i.e. entropy production is not a total differential [hope > > thats the right english word]). This results in the fact that there's > > no unique "way down", and that a macroscopic state can be achieved by > > the system several times in a kinetic experiment: Oszillations (and > > even chaos) occur, and that's just what we see in biological systems. > > We have to be careful - what do we define as our system? The body, the earth, > the solar system? Makes a big difference as to how we approach the problem. > > Excellent way to start the weekend...I'll be checkin in on this discussion. > > Paul .