From owner-biophysics@net.bio.net Sun Nov 02 22:00:00 1997 Path: biosci!agate!howland.erols.net!newsfeed.nacamar.de!newscore.univie.ac.at!Cabal.CESspool!bofh.vszbr.cz!lyra.csx.cam.ac.uk!not-for-mail From: Yu Wai Chen Newsgroups: bionet.molbio.methds-reagnts,bionet.biophysics Subject: Site-directed spin labelling Date: Mon, 03 Nov 1997 10:56:58 +0000 Organization: MRC Centre for Protein Engineering Lines: 15 Message-ID: <345DADFA.BA745970@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: i11.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX64 6.2 IP28) Xref: biosci bionet.molbio.methds-reagnts:62585 bionet.biophysics:3655 Dear All, I am trying to introduce a spin probe by reaction at a site-directed-mutated cysteine residue of a GST-fusion protein. If this protein forms aggregate on cleavage of the GST, does anyone has any experience about how to label it? Shall I label it in its GST-fusion soluble form and then cleave off the GST or shall I cut off the GST first and then label the aggregate? Thanks. -- =================================================================== Yu Wai CHEN, Ph.D. .................. email: ywc@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel: 44-(1223) 402148 MRC Centre, Cambridge CB2 2QH, U.K. fax: 44-(1223) 402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/people/wai.html From owner-biophysics@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!prodigy.com!nntp.earthlink.net!usenet From: prismx@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: This Week's Headlines (7 Nov 97) Date: Thu, 06 Nov 1997 23:56:15 GMT Organization: SCIENCE-WEEK Lines: 25 Message-ID: <63ti34$rr0@ecuador.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.161.191 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20681 bionet.biophysics:3657 bionet.cellbiol:8376 bionet.general:28613 Headlines for the current SCIENCE-WEEK (November 7, 1997) For free Email subscription to complete weekly news reports, send SUB SW to 1. Intimidation of Researchers by Special Interest Groups 2. Identification of Human-Tropic Pig Retroviruses 3. A Review of the Birth and Death of Stars 4. Apparent Observation of a Rare Decay Mode of the K-Meson 5. Construction of a One-Electron Transistor 6. A Method to Produce High-Affinity Ligands for Proteins 7. Retrograde and Anterograde Conduction in Neuron Dendrites 8. A New Protein Involved in Alzheimer's Disease 9. Genetics of Aging 10. Life History of Neurons in the Human Brain 11. The Endocrinology of Aging 12. A Neurological Study of Schizophrenia in Children 13. Lack of Correlation of DDT Levels with Breast Cancer Risk The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Wed Nov 05 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: propdig Newsgroups: bionet.biophysics Subject: National Biotech Register(NatBio) New Service Date: Thu, 06 Nov 1997 09:57:07 -0500 Organization: propdig Lines: 5 Message-ID: <3461DAC3.1208@barryinc.com> Reply-To: propdig@barryinc.com NNTP-Posting-Host: p16.ts2.lowel.ma.tiac.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0C-NSCP (Win95; U) NatBio, http://www.barryinc.com/bio is pleased to introduce a new service on our web site. A Biotech Industry Company profile search. Are you looking for information on a particular company. We probably have it. 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Vakser Assistant Professor of Pharmacology Department of Cell and Molecular Pharmacology Medical University of South Carolina 171 Ashley Avenue Charleston, SC 29425 Email: vakseri@musc.edu, Phone:(803)792-2471, Fax:(803)792-2475 From owner-biophysics@net.bio.net Sat Nov 08 22:00:00 1997 Path: biosci!agate!howland.erols.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news-pen-1.sprintlink.net!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!news.sprintlink.net!Sprint!204.92.55.84!feed.nntp.acc.ca!204.92.54.104.MISMATCH!news.ican.net!not-for-mail From: aaa@no-spam.tutoraid.org (Academic Assistance Access) Newsgroups: bionet.biophysics Subject: Do you academic need help in PHYSICS ? Date: Sun, 09 Nov 1997 05:59:57 GMT Organization: Academic Assistance Access Lines: 12 Message-ID: <3465514f.56164313@news.ican.net> Reply-To: aaa@no-spam.tutoraid.org NNTP-Posting-Host: ppp-195.isdn-1.ssm.ican.net X-Trace: news1.tor.acc.ca 879055344 24448 (None) 206.248.78.195 X-Complaints-To: usenet@news1.tor.acc.ca X-Newsreader: Forte Free Agent 1.1/32.230 Academic Assistance Access is a free tutoring service on the Web designed to offer assistance in PHYSICS for both secondary and post secondary students. If you are looking for answers to your PHYSICS questions, our team of professionals can help you make the grade!!! Please, do not ask questions by replying to this message. For assistance you should first subscribe to the following address: http://www.tutoraid.org/ George Richards Academic Assistance Access Do you academic need help in PHYSICS ? From owner-biophysics@net.bio.net Sun Nov 09 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 10 Nov 1997 22:39:29 GMT Organization: Vollum Institute Lines: 42 Distribution: world Message-ID: <6482f1$ma1$1@fremont.ohsu.edu> References: <647tcn$drs@ds2.acs.ucalgary.ca> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Mon, 10 Nov 1997 22:46:36 GMT In article <647tcn$drs@ds2.acs.ucalgary.ca> Walter L. Ash, ash1@freenet.calgary.ab.ca writes: >He's convinced >that >life reverses the trend by organizing matter and energy whereas I'm >convinced that more organized forms of energy are eventually turned >into the random motion of heat by the chemical processes occuring in >cells... You are absolutely right, and your friend is wrong. In fact, your friend's argument (not that he means it this way) is often used by creationists and like-minded people to support the notion that there must be a God. The creationist argument goes something like this: Life is more ordered than non-life, which is chaotic. Since physics says everything must tend towards disorder, but life doesn't do that, life violates the laws of physics. Anything that violates the laws of physics is a miracle. Miracles come from God. Therefore, the existence of life proves that there is a God. I'm sure God is breathing a big sigh of relief, knowing that creationists have finally proven His/Her existence ;-> But the main flaw in the argument is that physics doesn't say that every "thing" tends towards entropy, it says that the entropy of the whole universe put together can't get any smaller than it is now. Little parts of it can, otherwise ice wouldn't form, we would have no salt for our french fries, nor would we be around to eat them. Another flaw is that life is _not_ more ordered than, for example, rocks, salt, ice, etc, and so has no special claim on divine intervention. You can look this stuff up in _any_ physics book with a chapter on thermodynamics of chemical reactions. You don't need a special biophysics book, because it's the same physics all around. Aristotle (in Metaphysics, I think) actually spent whole chapters on the subject "How is Man different from a rock?". Not a simple question to answer, actually. Cheers, Matt From owner-biophysics@net.bio.net Sun Nov 09 22:00:00 1997 Path: biosci!agate!howland.erols.net!news.maxwell.syr.edu!scanner.worldgate.com!rover.ucs.ualberta.ca!news.ucalgary.ca!srv1.freenet.calgary.ab.ca!ash1 From: "Walter L. Ash" Newsgroups: bionet.biophysics Subject: entropy. Date: Mon, 10 Nov 1997 14:12:44 -0700 Organization: Calgary Free-Net Lines: 18 Message-ID: <647tcn$drs@ds2.acs.ucalgary.ca> NNTP-Posting-Host: ash1@srv1.freenet.calgary.ab.ca Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A friend and I were recently debating whether or not the systems in the universe we call "organisms" decreased the overall entropy of the universe, or increased it. Somewhere I had heard or read that even though in the specific area the system exists entropy is decreased, the overall entropy of the universe is increased by the chemical processes of life within a cell or organism. My overall understanding is that no matter how complex life may become our universe as a whole will still move towards entropy; perhapsthe process is even accelerated by the workings of life. He's convinced that life reverses the trend by organizing matter and energy whereas I'm convinced that more organized forms of energy are eventually turned into the random motion of heat by the chemical processes occuring in cells... I couldn't find my textbooks to look it up so I was wondering if anyone here could offer any insight into entropy and life's effect on it. From owner-biophysics@net.bio.net Sun Nov 09 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!News1.Ottawa.iSTAR.net!News1.Edmonton.iSTAR.net!news.istar.net!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: entropy. Date: Mon, 10 Nov 1997 15:19:57 -0700 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 48 Message-ID: <3467888D.41C6@henri.chem.uleth.ca> References: <647tcn$drs@ds2.acs.ucalgary.ca> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) To: "Walter L. Ash" Walter L. Ash wrote: >A friend and I were recently debating whether or not the systems in the > universe we call "organisms" decreased the overall entropy of the > universe, or increased it. [...] > I couldn't find my textbooks to look it up so I was wondering if > anyone here could offer any insight into entropy and life's effect on > it. As far as we know, the second law of thermodynamics is never violated. However, you have to be careful about how you interpret the second law. Here is the second law in its most general form: The entropy of an adiabatic system never decreases. "Adiabatic" means that the system is perfectly thermally insulated or, in other words, that heat can't enter or escape it. As far as we know, the Universe is an adiabatic system (where would the heat go?) so the entropy of the Universe can't decrease. Living organisms on the other hand are about as far from being adiabatic systems as you can imagine. They're not even closed! (They exchange matter with their surroundings.) Living organisms therefore don't satisfy any naive version of the second law. They do satisfy the second law, but you have to include their effect on the rest of the Universe. Here's a semi-mathematical paraphrase of a version of the second law which does apply to living organisms: (change in entropy of organism) + (change in entropy of rest of Universe due to organism) is a positive quantity. The entropy of the organism and its immediate surroundings can decrease PROVIDED the entropy of the rest of the Universe increases more. The short answer then is that you were right. It's possible to make these ideas a great deal more rigorous through nonequilibrium thermodynamics. (Because they are open systems, living organisms pose a number of challenges to classical thermodynamics which was designed mainly to deal with steam engines and other relatively simple machines.) The version of the second law used there suggests that living organisms must produce entropy, which is essentially what I said above. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!europa.clark.net!192.174.65.44!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 11 Nov 1997 00:48:44 GMT Organization: IIF Lines: 13 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <6482f1$ma1$1@fremont.ohsu.edu> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 10 Nov 1997 22:39:29 GMT, Matt Jones wrote: >But the main flaw in the argument is that physics doesn't say that every >"thing" tends towards entropy, it says that the entropy of the whole >universe put together can't get any smaller than it is now. What physics says is that the entropy of an _isolated system_ won't decrease. Whether the universe is an isolated system can be a matter of debate. It is usually considered as an isolated system by definition, for convenience. However, this is rather speculative. 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Call Computer Physician, Inc. today at (215) 836 - 0293 If you would prefer not to recieve future E-mails, please join our unsubscribe list by E-mailing us at computerphys@hotmail.com Include as the body of your E-Mail - REMOVE your_E-mail_address (c) Copyright 1997 Computer Physician, Inc. All Rights Reserved. From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!senator-bedfellow.mit.edu!usenet From: "David F. Green" Newsgroups: bionet.biophysics Subject: Re: entropy. Date: Mon, 10 Nov 1997 21:32:10 -0500 Organization: Massachusetts Institute of Technology Lines: 20 Message-ID: <3467C3AA.41C6@lms.mit.edu> References: <647tcn$drs@ds2.acs.ucalgary.ca> NNTP-Posting-Host: mycroft.lms.mit.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP22) You are correct that the entropy of the universe always increases. While life is highly organized and thus represents a local region of low entropy, the energy expended by life to maintain this highly ordered state ultimately results in a greater increase in the entropy of its surroundings (i.e. the universe other than the organism). That the entropy of the universe (system plus surroundings) must always increase is one of the fundamental laws of thermodynamics. Thus for any process in which the entropy of a system decreases, the entropy of the surroundings must increase by a greater amount. -- ************************************************ David F. Green Department of Chemistry Massachusetts Institute of Technology Cambridge, MA 02139 E-mail: dfgreen@lms.mit.edu Phone: (617) 228-6229 ************************************************ From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 11 Nov 1997 22:08:46 GMT Organization: Vollum Institute Lines: 28 Distribution: world Message-ID: <64al1e$3la$1@fremont.ohsu.edu> References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Tue, 11 Nov 1997 22:15:53 GMT In article Andras Szilagyi, szia@hanga.enzim.hu writes: >Are you sure? Consider the number of microstates realizing a living >organism versus the number of microstates realizing a rock. I think that >the latter must be a great deal larger. I think that a living organism is >much more farther from equilibrium than a rock is. They can be definitely >distinguished from each other thermodynamically. I'm not sure I follow you. If by "microstates" you "mean degrees of freedom" in the sense used in statistical mechanics (or information theory) then whichever has the largest number of microstates would be the _less_ ordered system. Are you saying that a rock has more degrees of freedom than an organism? Generally, crystals are used as an example of extremely ordered systems. Another thing: Being far from equilibrium is not the only thing important in deciding whether something is more complex or less ordered than something else. The sun is very, very far from equilibrium in a strictly thermodynamic sense. Much farther than any living thing. Is it more complex? Is it more ordered? I'd say it's probably less complex than an amoeba and more ordered than a bacterium, but less ordered than a crystalized virus. One can in fact freeze living cells indefinitely, and then thaw them out and they go on dividing etc, as if nothing had ever happened. Do they stop being alive while they are frozen? Cheers, Matt From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!logbridge.uoregon.edu!newsfeed.ecrc.net!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 11 Nov 1997 21:26:23 GMT Organization: IIF Lines: 18 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <6482f1$ma1$1@fremont.ohsu.edu> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 10 Nov 1997 22:39:29 GMT, Matt Jones wrote: >Another flaw is that life is _not_ more ordered than, for example, rocks, >salt, ice, etc, [...] Are you sure? Consider the number of microstates realizing a living organism versus the number of microstates realizing a rock. I think that the latter must be a great deal larger. I think that a living organism is much more farther from equilibrium than a rock is. They can be definitely distinguished from each other thermodynamically. (This is not to say that divine intervention is necessary to create a living organism. Nonequilibrium thermodynamics can account for the appearence of organized complexity in systems subject to a flow of energy.) Andras Szilagyi From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Beer Theories Date: 11 Nov 1997 20:03:52 GMT Organization: Vollum Institute Lines: 14 Distribution: world Message-ID: <64adn8$2he$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Tue, 11 Nov 1997 20:10:59 GMT Hi all, Here's a subject that comes up between myself and colleagues often enough to warrant some serious thought. Maybe this is more of a chemistry question, but since I usually end up discussing it with biophysicists in the pub, I'll post it here. When you open a bottle of beer, bubbles form. Is this purely a physical reaction (i.e., no covalent bonds being made or broken), or does it involve a chemical transformation? Any takers? Matt From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 11 Nov 1997 19:59:09 GMT Organization: Vollum Institute Lines: 86 Distribution: world Message-ID: <64aded$2ef$1@fremont.ohsu.edu> References: <01IPVPM7X0D000007I@buphyc.bu.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Tue, 11 Nov 1997 20:06:16 GMT In article <01IPVPM7X0D000007I@buphyc.bu.edu> Bernard Chasan, bc@BUPHYC.BU.EDU writes: > In his ardor to remove any need for divine intervention Matt >overstates the case . A living organism differs significantly from a rock >in its ability, produced by evolution, to maintain, at least for a while, >its status as an open system, far from equilibrium. Rocks have not >developed enzymes. Rocks don't have the ability to use the incoming solar >energy flux in highly specialized ways. Rocks don't export entropy into >their surroundings. For that matter, rocks don't replicate . > Matt, and other interested readers, would do well to read Schrodinger's essay, >"What is Life ?" Hi Bernard, Your points are well taken and thank you for suggesting the Scrodinger essay. However, let me clarify: I am not interested in removing the need for divine intervention. My personal belief is that the universe is a product of divine fiat. But that's my own personal belief. As a scientist, I don't like it when people construct arguments about God (or anything else, for that matter) that are so terribly flawed as to be totally nonsensical. I don't think such arguments are useful, and they tend to spread misinformation which doesn't help anybody except the person making the argument, who probably has a social, moral or political agenda rather than a scientific one. Now for some fun (the following is intended in the spirit of playful, half-serious debate): You said: >A living organism differs significantly from a rock >in its ability, produced by evolution, to maintain, at least for a while, >its status as an open system, far from equilibrium. The ocean is an open system far from equilibrium. Is it alive? As for rocks, First, geologists (of which I am not one) commonly use the term "evolution" in refering to the formation of rocks. There are actually a lot of complicated reactions that go into producing your average rock, and these reactions take a long time and are subject to things in the environment like temperature, pressure, the earth's magnetic field, even biological activity which produces atmospheric oxygen etc. There _are_ selective pressures on whether a certain rock's chemistry will be stable or unstable in its environment, and whether it will survive in that form or be chemically changed into a different rock. So rocks evolve. Second, Rocks haven't evolved enzymes, true. But rocks contain structures that can catalyze chemical reactions. You can even get some high school chem lab experiments to work faster by tossing in a few pebbles, which presumably provide a large crenulated surface area that somehow helps the reactants to come together. I think this is also why the bubbles in a beer glass always seem to form on the side of the glass instead of in the middle of the beer (ooh, this could be the start of a whole new thread). These catalytic structures just don't happen to be biological proteins, but that is a minor point. Third, until recently people didn't "have the ability to use the incoming solar energy flux in highly specialized ways" either. Were they therefore not alive? Fourth, after sitting in the sun for a while, rocks absolutely _do_ export entropy into their surroundings during the night. That's why the asphalt steams in the morning after a summer rain. Fifth, rocks don't replicate? Hmm. What's crystallization if not the replication of crystals? One crystal serves as a nucleating center for further crystal outgrowth. You can break off chunks of a crystal and look at one, and find that it contains little tiny replicas of the parent crystal. A chip off the old block, as it were. Sixth, Schrodinger postulated that the structure of DNA was an aperiodic crystal. An aperiodic crystal sounds like a rock to me. So, in conclusion: Why is Man different from a rock? Beats me ;-) Cheers, Matt "You block! You stone! You worse than senseless thing!" -From the Epic of Gilgamesh From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: entropy (Pentcho Valev) Date: 11 Nov 1997 16:20:22 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64a0k6$rgr@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk (This message may appear twice - sorry about that). That, for a spontaneous process, the entropy change of the system plus the environment is always positive, is a tautology - it would be the same to say "A spontaneous process is a spontaneous process". In chemistry and biology this statement about the entropy is transformed into "For a spontaneous process, the free energy change is always negative". So let me prove that this last statement is just a tautology. Let us consider the following spontaneous reaction: A -> B /1/ Spontaneity consists in the fact that Vf > Vr /2/ where Vf and Vr are the velocities of the forward and reverse reaction. Therefore Kf(A) > Kr(B) /3/ where Kf and Kr are the respective rate constants and ( ) is concentration. Further Kf/Kr > (B)/(A) /4/ By taking ln and multiplying by RT we obtain 0 > -RTlnK + RTln((B)/(A)) /5/ where K = Kf/Kr is the equilibrium constant, i.e. we obtain 0 > delta Go + RTln((B)/(A) = delta G /6/ Therefore, /6/ follows from and is tautologous to /2/. This means that /6/ is always correct, even if the second law is not. Pentcho Valev From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!BUPHYC.BU.EDU!bc From: bc@BUPHYC.BU.EDU (Bernard Chasan) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 11 Nov 1997 07:47:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 27 Sender: daemon@net.bio.net Distribution: world Message-ID: <01IPVPM7X0D000007I@buphyc.bu.edu> NNTP-Posting-Host: net.bio.net >You can look this stuff up in _any_ physics book with a chapter on >thermodynamics of chemical reactions. You don't need a special biophysics >book, because it's the same physics all around. Aristotle (in >Metaphysics, I think) actually spent whole chapters on the subject "How >is Man different from a rock?". Not a simple question to answer, actually. > >Cheers, > >Matt In his ardor to remove any need for divine intervention Matt overstates the case . A living organism differs significantly from a rock in its ability, produced by evolution, to maintain, at least for a while, its status as an open system, far from equilibrium. Rocks have not developed enzymes. Rocks don't have the ability to use the incoming solar energy flux in highly specialized ways. Rocks don't export entropy into their surroundings. For that matter, rocks don't replicate . Matt, and other interested readers, would do well to read Schrodinger's essay, "What is Life ?" Professor Bernard Chasan Physics Department, Boston University Boston MA 02215 (617) 353-2608 From owner-biophysics@net.bio.net Mon Nov 10 22:00:00 1997 Path: biosci!agate!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Best kept "secrets" finally exposed Date: 11 Nov 1997 14:30:08 -0000 Lines: 73 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <649q5g$jlq@mserv1.dl.ac.uk> Original-To: computerphys@hotmail.com What computer stores don't want you to know is that a well made, state of the art computer, doesn't have to be expensive. You can have a NEW, powerful, Intel Pentium computer directly FROM US, built with ALL quality components at the lowest possible prices in years. Unbelievable, but true! Imagine, $1098 for a 200 MHz MMX Pentium Computer with MMX Technology! (It's faster than a Pentium 200 MHz). 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We selected this amazingly sharp and clear .28 SVGA monitor as the perfect match for your new Computer. We custom build the best for you - for less. Call Computer Physician, Inc. today at (215) 836 - 0293 If you would prefer not to recieve future E-mails, please join our unsubscribe list by E-mailing us at computerphys@hotmail.com Include as the body of your E-Mail - REMOVE your_E-mail_address (c) Copyright 1997 Computer Physician, Inc. All Rights Reserved. From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: entropy (Pentcho Valev) Date: 12 Nov 1997 10:22:11 -0000 Lines: 40 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64c00j$s75@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk (Again, sorry for writing my name in the subject space). That, for a spontaneous process, the entropy change of the system plus the environment is always positive, is a tautology - it would be the same to say "A spontaneous process is a spontaneous process". In chemistry and biology this statement about the entropy is transformed into "For a spontaneous process, the free energy change is always negative". So let me prove that this last statement is just a tautology. Let us consider the following spontaneous reaction: A -> B /1/ Spontaneity consists in the fact that Vf > Vr /2/ where Vf and Vr are the velocities of the forward and reverse reaction. Therefore Kf(A) > Kr(B) /3/ where Kf and Kr are the respective rate constants and ( ) is concentration. Further Kf/Kr > (B)/(A) /4/ By taking ln and multiplying by RT we obtain 0 > -RTlnK + RTln((B)/(A)) /5/ where K = Kf/Kr is the equilibrium constant, i.e. we obtain 0 > delta Go + RTln((B)/(A) = delta G /6/ Therefore, /6/ follows from and is tautologous to /2/. This means that /6/ is always correct, even if the second law is not. Pentcho Valev From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Message-ID: <34696381.167E@came.sbg.ac.at> Date: Wed, 12 Nov 1997 09:06:25 +0100 From: Walter Koppensteiner Organization: Center for Applied Molecular Engineering X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 Newsgroups: bionet.biophysics Subject: Re: Beer Theories References: <64adn8$2he$1@fremont.ohsu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NNTP-Posting-Host: agnes.came.sbg.ac.at Lines: 29 Path: biosci!agate!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!newscore.univie.ac.at!03-newsfeed.univie.ac.at!news.sbg.ac.at!agnes.came.sbg.ac.at Matt Jones wrote: > When you open a bottle of beer, bubbles form. Is this purely a physical > reaction (i.e., no covalent bonds being made or broken), or does it > involve a chemical transformation? Carbondioxide which is solved in water react with it: _ HCO3 + H+ <---> CO2 + H2O The equilibrium of this reaction lies on the side of CO2 but can be shifted to the left side if the system is under pressure (a consequence of simple chemical thermodynamics). If you open a beer bottle the equilibrium is shifted to the right side and CO2 bubbles form. Hope this helps, Walter -- =============================================================== Walter Koppensteiner University of Salzburg Center of Applied Molecular Engineering Jakob Haringer Strasse 3 Phone: +43-662-8044-5794 A-5020 Salzburg, Austria Fax: +43-662-454889 Email: walter@came.sbg.ac.at =============================================================== From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!bloom-beacon.mit.edu!thetimes.pixel.kodak.com!news.kodak.com!news-pen-16.sprintlink.net!newsfeed.nysernet.net!news.nysernet.net!207.41.200.131!news-pen-1.sprintlink.net!news-east.sprintlink.net!news-dc-26.sprintlink.net!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!199.0.65.142!news-feed1.tiac.net!news-master.tiac.net!news@tiac.net From: jamesl@healthtech.com (James W. Larkin) Newsgroups: bionet.biophysics,bionet.molbio.proteins.fluorescent,sci.chem.electrochem Subject: Call for Papers Advances in MOLECULAR LABELS, SIGNALING & DETECTION Date: 12 Nov 1997 12:51:23 GMT Organization: Cambridge Healthtech Institute Lines: 42 Message-ID: <64c8ob$dh1@news-central.tiac.net> NNTP-Posting-Host: 207.60.238.8 Mime-Version: 1.0 Content-Type: Text/Plain; charset=ISO-8859-1 X-Newsreader: WinVN 0.99.9 Beta 1 (x86 32bit) Xref: biosci bionet.biophysics:3677 bionet.molbio.proteins.fluorescent:1728 First Announcement and Call for Papers Cambridge Healthtech Institute’s Second Annual Advances in MOLECULAR LABELS, SIGNALING & DETECTION: Enhancing Sensitivity, Accuracy and Speed May 4-5, 1998 San Diego Hilton Extending the limits of assay sensitivity and accuracy, at the same time meeting the demand for greater speed, requires the application of innovative techniques and systems. The development of new probes and labels, homogeneous assay designs, and approaches which allow for the direct detection of compounds or specific binding events are having an impact in basic research, diagnostic and drug development segments. Novel fluorescent and luminescent technology are also critical for the implementation of greater speed and automation. These advances are being applied to the detection, quantification and localization of gene sequences, proteins, infectious organisms and a variety of other targets. Researchers are encouraged to submit a proposal for presentation of their own work. Recommendations for other speakers to be considered are also welcomed. Among the topics to be covered are: Novel Probes and Labels New Homogeneous Assays Methods for Direct (Non-amplified) Quantitation Methods for Ultra-Sensitive Detection Novel Fluorescent Assay Systems New Luminescent Approaches Please submit proposal or suggestions by e-mail or fax to: Mary Chitty Conference Director e-mail: mchitty@healthtech.com fax: 617-630-1325 telephone: 617-630-1316 For full consideration and to allow time for followup, please submit proposal or suggestions by December 1, 1997. From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!ais.net!News.Toronto.iSTAR.net!News1.Vancouver.iSTAR.net!News1.Edmonton.iSTAR.net!news.istar.net!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: entropy (Pentcho Valev) Date: Wed, 12 Nov 1997 12:18:46 -0700 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 18 Message-ID: <346A0116.41C6@henri.chem.uleth.ca> References: <64a0k6$rgr@mserv1.dl.ac.uk> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) RUMYM@BGEARN.ACAD.BG wrote: > That, for a spontaneous process, the entropy change of the system plus > the environment is always positive, is a tautology [...] > 0 > delta Go + RTln((B)/(A) = delta G /6/ > > Therefore, /6/ follows from and is tautologous to /2/. This means > that /6/ is always correct, even if the second law is not. Delta G = Delta G0 + RT ln(Q) is not a fact independent of the second law. Furthermore, using Delta G can only be used as a criterion of spontaneity under particular conditions (constant T and P). The second law is much more general than that. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 12 Nov 1997 17:26:36 GMT Organization: Vollum Institute Lines: 33 Distribution: world Message-ID: <64cosc$c8f$1@fremont.ohsu.edu> References: <647tcn$drs@ds2.acs.ucalgary.ca> <64al1e$3la$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Wed, 12 Nov 1997 17:33:42 GMT In article Andras Szilagyi, szia@hanga.enzim.hu writes: >Excuse me if my English is not perfect. It's perfect, as far as I can tell. >Please define what you mean by "orderedness". >What I was speaking about was entropy, which is defined in statistical >mechanics as k*ln(Y) where k is the Boltzmann factor and Y is the number >of microstates that make up the given macrostate." Yeah, that's what I meant too, except . >I think that your notion of orderedness is not directly related to >entropy, what the subject of this thread is. Nonetheless spatial ordering, as in a crystal, and entropy are intimately related concepts. For example, one formulation of the third law is the following (from Molecular Thermodynamics, Dickerson, 1969): "The entropy for all pure, crystalline, perfectly ordered substances at absolute zero is zero." This defines an absolute entropy scale based on the spatial ordering of components. Thus, in a "perfectly ordered" crystal, all "microstates" are indistinguishable. An organism therefore must have a higher entropy than such a crystal. Granted, rocks aren't perfect crystals, but they still have lower entropy than an organism because a lot of the microstates are indistinguishable (due to the semi-periodic arrangement of atoms). Cheers, Matt From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: The second law problem (Pentcho Valev) Date: 12 Nov 1997 14:33:56 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64ceok$f95@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk I must admit that my previous message was somewhat enigmatic - in fact, I do not like this typical thermodynamic approach - formally everything is OK but one feels that the truth has remained hidden. So, although I realize that my claims would never be accepted by experts - the conflict of interest is enormous, I still find it suitable to elaborate on the problem - maybe some non-experts would follow the logical line to the end. In the distant future, this might prove rather useful for science. The basic formulation of the second law is a statement about HEAT and WORK. This means that both heat and work are ALREADY defined, and we are to apply or verify the statement in different contexts. This is exactly the case, for instance, when we deal with the Carnot machine. The work an ideal gas does is defined prior to and independently of the second law, so nobody can doubt any version of the second law in this case. However this is not the case in chemistry. CHEMICAL WORK is not defined prior to and independently of the second law. On the contrary, it is defined AD HOC - the delta G concept in fact says: "Chemical work is what the second law says it is". Here begins the tautologous vicious circle - the second law cannot be violated BY DEFINITION - any work done is, by definition, just as much as needed to satisfy the second law. Fortunately, there are cases in which chemical systems do other types of work - e.g. electrical one. This breaks the vicious circle at places. In galvanic systems, for instance, the work done DOES satisfy the second law (if reversible, it is equal to the negative of delta G). However no generalization should be made - this is macroscopic work and the process is closer to gas expansion than to a genuine chemical reaction. So we urgenly need at least one more verification. Everything else is a hidden tautology - nothing can disprove the second law so far as the basic concept - WORK, is defined so as to make any disproval impossible. Of course, the problem is much more complicated than that - I still hope that hostility will end and the discussion will clarify even the most dark corners of the theory. Best regards, Pentcho From owner-biophysics@net.bio.net Tue Nov 11 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!news-was.dfn.de!news-fra1.dfn.de!news-ge.switch.ch!news.bme.hu!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 12 Nov 1997 12:42:32 GMT Organization: IIF Lines: 43 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> <64al1e$3la$1@fremont.ohsu.edu> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 11 Nov 1997 22:08:46 GMT, Matt Jones wrote: >I'm not sure I follow you. If by "microstates" you "mean degrees of >freedom" in the sense used in statistical mechanics (or information >theory) then whichever has the largest number of microstates would be the >_less_ ordered system. Are you saying that a rock has more degrees of >freedom than an organism? Generally, crystals are used as an example of >extremely ordered systems. Please define what you mean by "orderedness". What I was speaking about was entropy, which is defined in statistical mechanics as k*ln(Y) where k is the Boltzmann factor and Y is the number of microstates that make up the given macrostate. That is, what we should compare is the number of ways you can arrange the atoms of a rock to obtain a rock vs. the number of ways you can arrange the atoms of a living organism to obtain that living organism. I'm saying that the latter is much smaller than the first, therefore the entropy of a living organism is smaller than that of a rock (given they have the same number of atoms). If you throw a number of atoms together in a random arrangement then it is much more probable that you will end up with a rock (or a crystal for that matter) than that you will end up with a living organism. I think your notion of orderedness has more to do with periodicity in space but that does not necessarily mean a state of very low entropy. You can replace any unit cell in a crystal by another unit cell and the crystal will remain the same. Actually you can make up a crystal from its unit cells in an extremely large number of ways. A living organism is different: you can't replace a neuron by a liver cell or the like. Thus, I think that your notion of orderedness is not directly related to entropy, what the subject of this thread is. Complexity, however, seems to be directly related to entropy: the more complex a system is the more information is required to create that system from its components, and, consequently, the less is the entropy of the system (as information is actually negative entropy, as we know from information theory). Excuse me if my English is not perfect. Andras Szilagyi From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!FCINDY5.NCIFCRF.GOV!tmmec From: tmmec@FCINDY5.NCIFCRF.GOV (tmmec) Newsgroups: bionet.biophysics Subject: TMMEC - NEW PAPERS Date: 12 Nov 1997 19:56:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <199711130356.WAA01637@fcindy5.NCIFCRF.GOV> NNTP-Posting-Host: net.bio.net Dear List Administrator. Could you consider the following announcement for distribution in your mail list?. Thank you!. __________________________________________________________________________ The Molecular Modeling electronic Conference (TMMeC) announces that the papers on display for its current number are now open for discussion. TMMeC is accessible at: http://bilbo.edu.uy/tmmec/ Or from any of its mirrors. The complete list of mirrors is available at any of these locations: USA: http://129.43.50.11/tmmec/mirrors.html Uruguay: http://164.73.160.8/tmmec/mirrors.html Spain: http://130.206.128.61/tmmec/mirrors.html Germany: http://192.54.49.102/tmmec/mirrors.html Please select the site with the fastest access from your place. TMMeC is a non-for-profit, educational activity sponsored by the Universidad de la Republica, Montevideo, Uruguay. TMMeC is a freely accessible, indexed (ISSN 0797-9274), peer-reviewed multimedia publication established with the aim of providing a setup for fast and continuous display of current work in Molecular Modeling and Computational Chemistry. __________________________________________________________________________ From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: entropy (Pentcho Valev) Date: 13 Nov 1997 09:27:28 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64eh60$ran@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Marc Roussel wrote: Delta G = Delta G0 + RT ln(Q) is not a fact independent of the second< law. Furthermore, using Delta G can only be used as a criterion of< spontaneity under particular conditions (constant T and P). The second< law is much more general than that.< Marc, I believe I have proved the following two things: 1. If the second law is correct, delta G for a spontaneous reaction, at constant T and P, is negative. 2. If the second law is not correct, delta G for a spontaneous reaction, at constant T and P, is also negative. Please tell me whether you accept these two statements. If not, what in my proof do you find wrong? If yes, would you mind if I describe the implications? They are very interesting. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!132.239.254.208!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Don Bashford Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 13 Nov 1997 00:06:06 -0800 Organization: The Scripps Research Institute, La Jolla, CA, USA Lines: 13 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> <64al1e$3la$1@fremont.ohsu.edu> NNTP-Posting-Host: gage.scripps.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Newsreader: Gnus v5.5/Emacs 20.2 szia@hanga.enzim.hu (Andras Szilagyi) writes: > That is, what we should compare is the number of ways you can arrange the > atoms of a rock to obtain a rock vs. the number of ways you can arrange > the atoms of a living organism to obtain that living organism.... Not fair! You allow the rock's atoms any arrangement the forms "A rock", while the organism's atoms must form "THAT living organism". It's as if you want to compare a one-gram insect with with a gram of some freely morphing "rock" system that is actually an equilibrium ensemble of all possible "rocks" composed of a given number and type of atoms. How about comparing a one-gram insect with a single one-gram crystal? From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!news.sprintisp.com!sprintisp!news-peer.gip.net!news.gsl.net!gip.net!news.idt.net!ais.net!news1.chicago.iagnet.net!iagnet.net!nntp.earthlink.net!usenet From: prismx@earthlink.net (Claire Haller) Newsgroups: bionet.neuroscience,bionet.biophysics,bionet.cellbiol,bionet.general,sci.misc Subject: SCIENCE-WEEK: This Week's Headlines (14 Nov 97) Date: Thu, 13 Nov 1997 18:31:36 GMT Organization: SCIENCE-WEEK Lines: 30 Message-ID: <64fdmq$ect@bolivia.earthlink.net> Reply-To: prismx@earthlink.net NNTP-Posting-Host: 153.36.161.52 X-Newsreader: Forte Free Agent 1.0.82 Xref: biosci bionet.neuroscience:20737 bionet.biophysics:3692 bionet.cellbiol:8400 bionet.general:28673 Headlines for the current SCIENCE-WEEK (November 14, 1997) SCIENCE-WEEK weekly news reports are available free via Email To subscribe, send SUB SW to 1. Intimidation of Researchers by Special Interest Groups 2. Identification of Human-Tropic Pig Retroviruses 3. A Review of the Birth and Death of Stars 4. Apparent Observation of a Rare Decay Mode of the K-Meson 5. Construction of a One-Electron Transistor 6. A Method to Produce High-Affinity Ligands for Proteins 7. Retrograde and Anterograde Conduction in Neuron Dendrites 8. A New Protein Involved in Alzheimer's Disease 9. Genetics of Aging 10. Life History of Neurons in the Human Brain 11. The Endocrinology of Aging 12. A Neurological Study of Schizophrenia in Children 13. Lack of Correlation of DDT Levels with Breast Cancer Risk SCIENCE-WEEK is a free retransmission educational resource, which means this headline notice and each issue of SCIENCE-WEEK itself can be retransmitted if intact by any installation. The Editors SCIENCE-WEEK A Free Weekly Digest of the News of Science prismx@earthlink.net http://members.aol.com/sciweek From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!recycled.news.erols.com!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Boltzmann's and thermodynamic entropy do not coincide (Pentcho) Date: 13 Nov 1997 16:03:25 -0000 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64f8cd$qvn@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to Andras Szilagyi I will base my proof on interesting chemical models called semigrand ensembles (Robert Alberty, Legendre Transforms in Chemical Thermodynamics, Chemical Reviews, 1994, Vol. 94, No 6, p. 1463). Here is one of them: I I I I I I I---------piston-------------I I I Imembrane permeable only to DI I I I A + B = C + D I I----------------------------I One of the walls of the chamber in which the gas reaction A + B = C + D occurs is a membrane permeable only to D, and there is a piston behind the membrane. The reaction is strongly exothermic so that, in a REVERSIBLE ISOTHERMAL expansion of D, heat is released by the system. (In other words, the exothermic heat is greater than the work done as the piston is pushed). It follows directly from the last assumption that, as the reaction proceeds, the thermodynamic entropy of the system DECREASES. (This still does not violate the second law - the entropy of the surroundings increases of course). On the other hand, this course of the reaction (comprising expansion of D) can also be spontaneous, i.e. it is a movement towards a more probable state - Boltzmann's entropy INCREASES. I hope the proof is obvious and satisfactory. Pentcho From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!logbridge.uoregon.edu!newsfeed.ecrc.net!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: rock - living organism comparison (Pentcho Valev) Date: 13 Nov 1997 14:27:55 GMT Organization: IIF Lines: 13 Message-ID: References: <64el5k$369@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 13 Nov 1997 10:35:32 -0000, RUMYM@BGEARN.ACAD.BG wrote: >As you are speaking of the entropy of complex systems, do you mean the >Boltzmann entropy (proportional to the ln of probability), or the >thermodynamic entropy (defined by dQ/T)? The two do not coincide - >there are systems for which one can be shown to increase and the other >to decrease. Please prove that. Andras Szilagyi From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!uninett.no!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 13 Nov 1997 14:25:19 GMT Organization: IIF Lines: 37 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <64al1e$3la$1@fremont.ohsu.edu> <64cosc$c8f$1@fremont.ohsu.edu> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 12 Nov 1997 17:26:36 GMT, Matt Jones wrote: >Nonetheless spatial ordering, as in a crystal, and entropy are intimately >related concepts. For example, one formulation of the third law is the >following (from Molecular Thermodynamics, Dickerson, 1969): > >"The entropy for all pure, crystalline, perfectly ordered substances at >absolute zero is zero." > >This defines an absolute entropy scale based on the spatial ordering of >components. This is true for almost everything, not only crystals but living organisms too (probably they will crystallize at T=0). At T=0, S=0 for all substances, with some interesting exceptions. But what about higher temperatures? That at T=0, S=0 does not say anything about how S increases with T and which substance will have higher entropy at T=300K for example. You did not react to my arguments about the relationship of entropy and complexity (and information). Do you agree that more information is needed to describe a living organism than a crystal? If yes, then the entropy of the crystal will be higher because information is negative entropy. Something is wrong with the reasoning of one of us :-) >Thus, in a "perfectly ordered" crystal, all "microstates" are >indistinguishable. S=0 only if Y=1. (Y is the number of microscopic states.) In that case, there is only one single microstate so you actually can't say "all microstates are indistinguishable". Andras From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!newspump.sol.net!sol.net!mr.net!arclight.uoregon.edu!news.ibm.net.il!ibm.net!news.biu.ac.il!news.huji.ac.il!not-for-mail From: "Jonathan B. Marder" Newsgroups: bionet.biophysics Subject: Re: entropy. Date: Thu, 13 Nov 1997 14:22:27 +0200 Organization: Hebrew University Lines: 34 Message-ID: <64ere5$29i$1@news.huji.ac.il> References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> <64al1e$3la$1@fremont.ohsu.edu> NNTP-Posting-Host: marder.agri.huji.ac.il Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 Don Bashford wrote in message ... >szia@hanga.enzim.hu (Andras Szilagyi) writes: > >> That is, what we should compare is the number of ways you can arrange the >> atoms of a rock to obtain a rock vs. the number of ways you can arrange >> the atoms of a living organism to obtain that living organism.... > >Not fair! You allow the rock's atoms any arrangement the forms "A rock", >while the organism's atoms must form "THAT living organism". It's as >if you want to compare a one-gram insect with with a gram of some >freely morphing "rock" system that is actually an equilibrium ensemble of all >possible "rocks" composed of a given number and type of atoms. > >How about comparing a one-gram insect with a single one-gram crystal? I think this misses the point. The rock is not amorphous, but crystalline i.e. order begins on a microscale. In contrast, much of an organism is totally amorphous. Let's just take those 5 litres of blood in the human body and consider the possible microstates which are still compatible with it remaining blood! I would bet that this is orders of magnitude higher than the possible microstates which can form in an equivalent mass of rock From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!vixen.cso.uiuc.edu!howland.erols.net!rill.news.pipex.net!pipex!join.news.pipex.net!pipex!server1.netnews.ja.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: rock - living organism comparison (Pentcho Valev) Date: 13 Nov 1997 10:35:32 -0000 Lines: 8 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64el5k$369@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk As you are speaking of the entropy of complex systems, do you mean the Boltzmann entropy (proportional to the ln of probability), or the thermodynamic entropy (defined by dQ/T)? The two do not coincide - there are systems for which one can be shown to increase and the other to decrease. Best regards, Pentcho Valev From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: entropy (Pentcho Valev) Date: 13 Nov 1997 09:30:18 -0000 Lines: 21 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64ehba$rgk@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Marc Roussel wrote: Delta G = Delta G0 + RT ln(Q) is not a fact independent of the second< law. Furthermore, using Delta G can only be used as a criterion of< spontaneity under particular conditions (constant T and P). The second< law is much more general than that.< Marc, I believe I have proved the following two things: 1. If the second law is correct, delta G for a spontaneous reaction, at constant T and P, is negative. 2. If the second law is not correct, delta G for a spontaneous reaction, at constant T and P, is also negative. Please tell me whether you accept these two statements. If not, what in my proof do you find wrong? If yes, would you mind if I describe the implications? They are very interesting. Best regards, Pentcho From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.uoregon.edu!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's and thermodynamic entropy do not coincide (Pentcho) Date: 13 Nov 1997 21:23:03 GMT Organization: University of Washington Lines: 59 Distribution: bionet Message-ID: <64fr3n$58u$1@nntp3.u.washington.edu> References: <64f8cd$qvn@mserv1.dl.ac.uk> NNTP-Posting-Host: homer34.u.washington.edu X-Trace: nntp3.u.washington.edu 879456183 5406 (None) 140.142.64.6 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto writes: >In reply to Andras Szilagyi >I will base my proof on >interesting chemical models called semigrand ensembles (Robert >Alberty, Legendre Transforms in Chemical Thermodynamics, Chemical Reviews, >1994, Vol. 94, No 6, p. 1463). Here is one of them: > I I I > I I I > I---------piston-------------I > I I > Imembrane permeable only to DI > I I > I A + B = C + D I > I----------------------------I > One of the walls of the chamber in which the gas reaction A + B = C + D >occurs is a membrane permeable only to D, and there is a piston behind the >membrane. The reaction is strongly exothermic so that, in a REVERSIBLE >ISOTHERMAL expansion of D, heat is released by the system. (In other words, >the exothermic heat is greater than the work done as the piston is pushed). > It follows directly from the last assumption that, as the reaction >proceeds, the thermodynamic entropy of the system DECREASES. (This still >does not violate the second law - the entropy of the surroundings increases >of course). On the other hand, this course of the reaction (comprising >expansion of D) can also be spontaneous, i.e. it is a movement towards >a more probable state - Boltzmann's entropy INCREASES. > I hope the proof is obvious and satisfactory. Pentcho Your initial condition involves some (unstated) initial concentrations of the reactants and products. As the piston behind the membrane is moved back, the reaction proceeds to products, and D leaves the reaction chamber. At the end, the reaction chamber will contain C and only a very small quantity of D. Are you really sure the entropy of the reaction chamber hasn't gone down? The problem is that you haven't given any details. What are A, B, C and D? What are the initial and final concentrations? Just how much heat leaves the reaction chamber? (Are you sure you understand what reversible means in the context of the second law?) One more thing, it is possible to determine the entropy of a system at temperature T if you know the heat capacity at constant pressure as a function of temperature from near 0K to T, and also Delta H for any phase transitions between 0K and T. This isn't known for many systems, but for the few that it is, the calcuation can be down and it agrees to within experimental error with the results of statistical mechanics. Bryant Fujimoto fujimoto@u.washington.edu From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: Beer Theories Date: 13 Nov 1997 18:19:38 GMT Organization: Vollum Institute Lines: 39 Distribution: world Message-ID: <64fgbq$mof$1@fremont.ohsu.edu> References: <64adn8$2he$1@fremont.ohsu.edu> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Thu, 13 Nov 1997 18:26:45 GMT In article <34696381.167E@came.sbg.ac.at> Walter Koppensteiner, walter@came.sbg.ac.at writes: >Carbondioxide which is solved in water react with it: > _ >HCO3 + H+ <---> CO2 + H2O > >The equilibrium of this reaction lies on the side of CO2 but >can be shifted to the left side if the system is under >pressure (a consequence of simple chemical thermodynamics). > >If you open a beer bottle the equilibrium is shifted to >the right side and CO2 bubbles form. > I've gotten several responses to this question so far, by email and through this group. So far, there are two classes of responses: About half of the responses said that carbon dioxide was dissolved in solution and formed bubbles when you relieved the pressure, with no chemical reaction at all. The others said the carbon dioxide is produced in response to a change in pressure. This explanation is concisely stated in the quote above, and seems likely to be most accurate. Now, two accompanying questions (we'll get to the bottom of this pint yet!): 1) Why are there bubbles at all? Why doesn't the CO2 just stay equally distributed throughout the solution? And finally: 2) Why do the bubbles form on the glass surfaces, instead of just spontaneoulsy occuring anywhere in solution (you may need to crack open a frosty one and experiment to prove to yourself that this is actually the case. Go ahaead, I'll wait.)? Cheers, Matt Jones From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!news.ohsu.edu!not-for-mail From: Matt Jones Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 13 Nov 1997 18:09:01 GMT Organization: Vollum Institute Lines: 101 Distribution: world Message-ID: <64ffnt$mlh$1@fremont.ohsu.edu> References: <647tcn$drs@ds2.acs.ucalgary.ca> <64ere5$29i$1@news.huji.ac.il> NNTP-Posting-Host: 137.53.99.48 Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Nuntius 2.0.4_68K X-XXDate: Thu, 13 Nov 1997 18:16:08 GMT In article Andras Szilagyi, szia@hanga.enzim.hu writes: >Something is wrong with the reasoning of one of us :-) It might well be my reasoning that's wrong, but I'm not ready to give up yet ;-) >This is true for almost everything, not only crystals but living >organisms too (probably they will crystallize at T=0). At T=0, S=0 for >all substances, with some interesting exceptions. Respectfully, no. It's a well known problem in biology that not everything crystallizes into a well ordered form. A perfect example is the attempt to derive three-dimensional structures of proteins from x-ray diffraction through protein crystals. This works for a lot of proteins quite well, but there are whole families of proteins for which it doesn't work at all (so far, but that may change). There are no crystal structures known for membrane proteins such as neurotransmitter-gated ion channels because of this very reason. So the exceptions are far more numerous than not. That is why the law has to be formulated to include the phrases "pure" and "perfectly ordered crystalline" etc. >But what about higher temperatures? That at T=0, S=0 does not say >anything about how S increases with T and which substance will have >higher entropy at T=300K for example. That's true. But would you be willing to accept that a liquid has more microstates than a solid of the same number of atoms? If so, then a cell is more liquid than a rock, and therefore has more microstates. Now, of course, it's the probability of achieving a particular set of microstates out of the total possible number that one uses in entropy calculations, so the question boils down to exactly what you talked about earlier: How many different ways are there of arranging all the atoms to get an organism, how many ways are there of getting a rock, and how many total combinations are there all together (let's assume were dealing with exactly the same atoms). I'd say that this is not a perfectly straightforward question because there are _a lot_ of different ways of getting an organism from the same atoms. One can conceivably build either an amoeba or a neuron, for example. Also, if one builds an amoeba, it can wiggle around and change it's shape and all that, so there are clearly _a lot_ (perhaps an infinite) of ways of getting an amoeba from the same atoms. One might say the same thing about a rock, I suppose. So as far as I can tell, it's not clear just from this argument, that one has a higher or lower entropy than the other. >S=0 only if Y=1. (Y is the number of microscopic states.) In that case, >there is only one single microstate so you actually can't say "all >microstates are indistinguishable". Well, this is sort of a philisophical issue. How many electrons are there in the universe? We can't tell two electrons apart from each other (because an electron is 100% defined in terms of it's properties, so they're all the same). There could be a lot of electrons, or there could just be one that runs around really quickly and participates in every atomic orbital in existence (like Santa Claus ;-). Either way, you're right, Y=1. But I say it's because there's no way to distinguish two or more (hypothetically) different versions. Now, the critical point which I didn't respond to last time: >You did not react to my arguments about the relationship of entropy and >complexity (and information). Do you agree that more information is >needed to describe a living organism than a crystal? If yes, then the >entropy of the crystal will be higher because information is negative >entropy. This is a tough one. We are used to thinking of living things as being sooo complex that we can't possibly understand them. Oh, if only we had enough information, then we would understand life! Obviously, this reflects your (quite reasonable) point of view that one needs more "information" to describe an amoeba than table salt. So, information theory would seem the logical choice for trying to quantify biological "information" content, and would use a function very similar to the statistical mechanics definition of entropy, Shannon's information entropy: H(P) = -Sigma_i { P_i log P_i }, where Sigma_i denotes summation over the ith observations. So this says that information is basically the negative of an entropy-like quantity. HOWEVER, it's not exactly the same as -entropy in physics, because this formulation includes some specific assumptions that are not required in physics. For example, Shannon was dealing with transmission of signals through phone lines or something, and so was mainly concerned with the _coding_ and _decoding_ of information. Thus, the Shannon information requires that there be a sender and a receiver, and that both of these parties speak the same language and have access to the same dictionary and vocabulary. Also, the Shannon information is explicitly considering an input-transmission line-output situation. Neither of these conditions are required in calculating the physical entropies of substances. So the Shannon information entropy is very useful in trying to understand how neurons "encode", "transmit" and "decode" a sensory phenomenon, for example, or maybe how morphology is "encoded" in DNA and "decoded" by transcription and translation. But as for establishing an absolute Shannon information content of a rock or an organism per se, I don't think it necessarily applies. But I could be wrong. Cheers Matt From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!agate!hammer.uoregon.edu!news.uoregon.edu!news.u.washington.edu!fujimoto From: fujimoto@u.washington.edu (Bryant Fujimoto) Newsgroups: bionet.biophysics Subject: Re: entropy (Pentcho Valev) Date: 13 Nov 1997 21:35:55 GMT Organization: University of Washington Lines: 31 Distribution: bionet Message-ID: <64frrr$5rv$1@nntp3.u.washington.edu> References: <64ehba$rgk@mserv1.dl.ac.uk> NNTP-Posting-Host: homer34.u.washington.edu X-Trace: nntp3.u.washington.edu 879456955 6015 (None) 140.142.64.7 X-Complaints-To: help@cac.washington.edu NNTP-Posting-User: fujimoto writes: >Marc Roussel wrote: >Delta G = Delta G0 + RT ln(Q) is not a fact independent of the second< >law. Furthermore, using Delta G can only be used as a criterion of< >spontaneity under particular conditions (constant T and P). The second< >law is much more general than that.< >Marc, I believe I have proved the following two things: >1. If the second law is correct, delta G for a spontaneous reaction, at >constant T and P, is negative. >2. If the second law is not correct, delta G for a spontaneous reaction, >at constant T and P, is also negative. >Please tell me whether you accept these two statements. If not, what in >my proof do you find wrong? If yes, would you mind if I describe the >implications? They are very interesting. Pentcho Your second statement is not correct. In your attempt to demonstrate it, you made two substitutions, -RT ln(Keq) = Delta G0 and Delta G0 + RT ln(Q) = Delta G However, these are only true if thermodynamics is correct. Regards Bryant Fujimoto From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!rutgers!uwm.edu!newsfeeds.sol.net!newspump.sol.net!sol.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news-pull.sprintlink.net!news-in-east.sprintlink.net!news.sprintlink.net!Sprint!209.89.75.15!News.Toronto.iSTAR.net!News1.Vancouver.iSTAR.net!News1.Edmonton.iSTAR.net!news.istar.net!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: Beer Theories Date: Thu, 13 Nov 1997 14:15:10 -0700 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 38 Message-ID: <346B6DDE.41C6@henri.chem.uleth.ca> References: <64adn8$2he$1@fremont.ohsu.edu> <64fgbq$mof$1@fremont.ohsu.edu> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) Matt Jones wrote: > 1) Why are there bubbles at all? Why doesn't the CO2 just stay equally > distributed throughout the solution? The CO2 bubbles form because the solution (beer) is out of equilibrium: At atmospheric pressure, you simply can't dissolve as much CO2 in water as is present in beer. I know this sounds a bit trite, but the questions you're asking is analogous to asking why ice melts above 0 degrees Celcius. It's out of equilibrium with its surroundings, and that's about all the answer we can give. > 2) Why do the bubbles form on the glass surfaces, instead of just > spontaneoulsy occuring anywhere in solution (you may need to crack > open a frosty one and experiment to prove to yourself that this is > actually the case. Go ahaead, I'll wait.)? Forming a bubble isn't easy. Surface tension causes the bubble to squeeze in on itself. In fact, really tiny bubbles are normally unstable so it's hard to get a bubble started at all. Bubble formation is normally nucleated: Bubbles form near tiny imperfections in your glass. If you had a perfectly smooth glass, you wouldn't get as many bubbles. We have this kind of problem in Chemistry labs because our glassware is normally highly polished. When we're boiling a liquid, we often throw in boiling chips, which are essentially little porous rocks which facilitate bubble formation. Otherwise, you sometimes get "bumping", a nasty little phenomenon in which your usual smooth boil is replaced by irregular formation of really large bubbles. These tend to throw a lot of hot solvent around when they break the surface, so this is considered undesirable. If you're interested in this stuff, get a copy of Marion and Hornyak's introductory Physics book. They have a really neat section on surface science and bubble physics. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Wed Nov 12 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.algonet.se!4.1.16.34.MISMATCH!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!News1.Ottawa.iSTAR.net!News1.Edmonton.iSTAR.net!news.istar.net!mars.online.uleth.ca!news From: Marc Roussel Newsgroups: bionet.biophysics Subject: Re: entropy (Pentcho Valev) Date: Thu, 13 Nov 1997 15:24:42 -0700 Organization: Department of Chemistry and Biochemistry, University of Lethbridge Lines: 33 Message-ID: <346B7E2A.167E@henri.chem.uleth.ca> References: <64eh60$ran@mserv1.dl.ac.uk> NNTP-Posting-Host: henri.chem.uleth.ca Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01 (X11; I; OSF1 V3.2 alpha) RUMYM@BGEARN.ACAD.BG wrote: > > Marc Roussel wrote: > Delta G = Delta G0 + RT ln(Q) is not a fact independent of the second< > law. Furthermore, using Delta G can only be used as a criterion of< > spontaneity under particular conditions (constant T and P). The > second law is much more general than that.< > > Marc, I believe I have proved the following two things: > > 1. If the second law is correct, delta G for a spontaneous reaction, > at constant T and P, is negative. > > 2. If the second law is not correct, delta G for a spontaneous > reaction, at constant T and P, is also negative. > > Please tell me whether you accept these two statements. I do agree with these statements because, as your derivation shows, they are tautologies. If Delta G, Delta G0, Q and K are given their conventional meanings, then Delta G = Delta G0 + RT ln(Q) < 0 for a spontaneous process necessarily follows. However, thermodynamics goes a good deal farther than that by telling us that G is in fact related to two other state functions, namely H and S. That the state function G = H - TS has the property Delta G < 0 for a spontaneous process is a consequence of the second law of thermodynamics. Your derivation shows that such a function exists. The second law tells us what that function should be. Marc R. Roussel (roussel@uleth.ca) Department of Chemistry and Biochemistry University of Lethbridge From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!MSVAX.MSSM.EDU!SMOLYAR From: SMOLYAR@MSVAX.MSSM.EDU Newsgroups: bionet.biophysics Subject: (none) Date: 13 Nov 1997 16:49:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 1 Sender: daemon@net.bio.net Distribution: world Message-ID: <01IPZ1E1K0SI00704U@msvax.mssm.edu> NNTP-Posting-Host: net.bio.net unsubscribe From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: The delta G problem (Pentcho Valev) Date: 14 Nov 1997 12:30:16 -0000 Lines: 33 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64hg8o$hmi@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk In reply to Marc Roussel and Bryant Fujimoto I would propose a way to solve the delta G problem, but am not sure if it would by found interesting. (Maybe nobody believes that there is a problem at all). The point is to find the physical meaning of -RTlnK + RTln((B)/(A)) /1/ Let us assume that, apart from the original system in which the reaction A -> B occurs, there is another system in which the same reaction is at equilibrium. A reversible conversion of one mole A into B can occur along the following path: 1. One mole A is transported, reversibly, from the original system to the equilibrium system (one should only use Henry's law and the ideal gas law). 2. In the equilibrium system, the mole A is converted into B. 3. One mole B is transported, reversibly, from the equilibrium system to the original system. Calculations show that the work extracted from the whole process is Wt = -(-RTlnK + RTln((B)/(A))) /2/ where the subscript t refers to TRANSPORTATION, i.e. it is work done while the mole is transported, outside both systems. I believe this is a promising starting point, but yet the subsequent analysis is complicated, so I must be sure that people are interested. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.ecrc.net!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 14 Nov 1997 15:26:15 GMT Organization: IIF Lines: 17 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> <64al1e$3la$1@fremont.ohsu.edu> <64ere5$29i$1@news.huji.ac.il> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On Thu, 13 Nov 1997 14:22:27 +0200, Jonathan B. Marder wrote: >Let's just take those 5 litres of blood in the human body and consider >the >possible microstates which are still compatible with it remaining blood! >I would >bet that this is orders of magnitude higher than the possible >microstates >which can form in an equivalent mass of rock Are you sure? A rock can take any shape as well, while remaining a rock (although it's harder to change its shape than that of blood). You can put any molecule in the rock anywhere you want, however, you can't do the same to red blood cells. From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!rutgers!nntp.upenn.edu!dsinc!news.voicenet.com!news-peer.gip.net!news.gsl.net!gip.net!news.maxwell.syr.edu!uninett.no!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's and thermodynamic entropy do not coincide (Pentcho) Date: 14 Nov 1997 15:18:24 GMT Organization: IIF Lines: 44 Message-ID: References: <64f8cd$qvn@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) On 13 Nov 1997 16:03:25 -0000, RUMYM@BGEARN.ACAD.BG wrote: > > I I I > > I I I > > I---------piston-------------I > > I I > > Imembrane permeable only to DI > > I I > > I A + B = C + D I > > I----------------------------I > > One of the walls of the chamber in which the gas reaction A + B = C + D >occurs is a membrane permeable only to D, and there is a piston behind the >membrane. The reaction is strongly exothermic so that, in a REVERSIBLE >ISOTHERMAL expansion of D, heat is released by the system. (In other words, >the exothermic heat is greater than the work done as the piston is pushed). > It follows directly from the last assumption that, as the reaction >proceeds, the thermodynamic entropy of the system DECREASES. (This still >does not violate the second law - the entropy of the surroundings increases >of course). On the other hand, this course of the reaction (comprising >expansion of D) can also be spontaneous, i.e. it is a movement towards >a more probable state - Boltzmann's entropy INCREASES. > I hope the proof is obvious and satisfactory. No, that's not clear to me. In which direction does the piston move? Is it moved from outside or the gas moves it? What is the role of the membrane (what if there is no membrane)? How you calculate the probability? Besides, a reversible process is never spontaneous -- spontaneous means irreversible; so your use of terms is confusing. Please give a more detailed analysis, with calculations and derivations. I don't have the reference you gave. Andras Szilagyi From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Boltzmann's versus thermodynamic entropy (Pentcho Valev) Date: 14 Nov 1997 13:33:47 -0000 Lines: 48 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64hjvr$lf4@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Bryant Fujimoto wrote: Your initial condition involves some (unstated) initial concentrations< of the reactants and products. As the piston behind the membrane is< moved back, the reaction proceeds to products, and D leaves the reaction< chamber. At the end, the reaction chamber will contain C and only a< very small quantity of D. Are you really sure the entropy of the< reaction chamber hasn't gone down?< The problem is that you haven't given any details. What are< A, B, C and D? What are the initial and final concentrations? Just how< much heat leaves the reaction chamber? (Are you sure you understand< what reversible means in the context of the second law?)< Bryant, the system is sufficiently defined. Initially, the reaction is at equilibrium, and, by a small reversible movement of the piston, heat is released (since the exothermic heat is, by definition, greater than the work done). Years ago I had a one year dispute with two referees from J.Phys.Chem. They did not find that the system is not defined. Rather, the argument was about the following. I claimed that the following cycle violates the second law: 1. (Small) reversible ADIABATIC expansion. The temperature of the system increases and the system does work. 2. The contact with the surroundings is restored isochorically. The initial temperature is restored. 3. Reversible ISOTHERMAL compression. Work is done on the system. I claimed that the work in step 1 is greater than that in step 3. The referees objected that I had not proved this. So this is the real problem - maybe unsuitable for discussion here. One more thing, it is possible to determine the entropy of a system< at temperature T if you know the heat capacity at constant pressure as a< function of temperature from near 0K to T, and also Delta H for any< phase transitions between 0K and T. This isn't known for many systems,< but for the few that it is, the calcuation can be down and it agrees to < within experimental error with the results of statistical mechanics.< I am not sure what you are driving at, but I have never rejected anything "in general" - I have always tried to be concrete. I do not even reject the delta G presentation of chemical work "in general" - on the contrary, the most important work done in biosystems - that done by the transmembrane pH gradient, is suitably described by delta G. Best regards, Pentcho From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!rutgers!uwm.edu!www.nntp.primenet.com!globalcenter1!news.primenet.com!nntp.primenet.com!dispose.news.demon.net!demon!nntp.news.xara.net!xara.net!server5.netnews.ja.net!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Boltzmann's versus thermodynamic entropy (Pentcho Valev) Date: 14 Nov 1997 18:29:21 -0000 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64i5a1$ctn@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Lines: 54 Andras Szilagyi wrote: No, that's not clear to me. In which direction does the piston move? Is< it moved from outside or the gas moves it? What is the role of the< membrane (what if there is no membrane)? How you calculate the< probability? Besides, a reversible process is never spontaneous --< spontaneous means irreversible; so your use of terms is confusing.< Please give a more detailed analysis, with calculations and derivations.< I don't have the reference you gave.< Andras, I am the only one who tries to present rigorous analysis, but this possibility is limited, especially in an e-mail discussion. Moreover, the proof in this case does not require "calculations and derivations" - the qualitative picture is enough. Maybe I should only have given the formula Q(released) = Q(produced) - P(delta V) /1/ where Q(released) is the heat released by the system as D has undergone a small isothermal reversible expansion, Q(produced) is the heat produced by the reacting molecules inside the system, P is the pressure of D and delta V is the change of volume of D. I speak of EXPANSION of D, so this determines the direction of the piston. Similarly to CO2 expansion as the beer bottle is open, the expansion of D (reversible in this case) drives the reaction (exothermic in this case) towards the products. In other words, it is the gas D that moves the piston, but a slightly weaker force is applied on the other side of the piston. The role of the membrane is to let only D pass. If there were no membrane, the whole system would expand - there would be no chemical reaction - only a mixture of gases would expand. There is no need to calculate the probability (I am not sure if it is possible at all). There can be no doubt that in any spontaneous process the system moves towards a more probable state. Maybe my use of the terms "spontaneous" and "reversible" is confusing, but still I am using a well established procedure in thermodynamics. We want to determine the entropy change for a spontaneous process - in this case a spontaneous expansion of D (combined with the chemical reaction of course) between two equilibrium states of the system characterised by volumes of D V1 and V2 (V1 < V2). For this purpose, we perform the respective REVERSIBLE transition between the two states. As the reversible version is isothermal, the only thing that matters is whether the system absorbs or releases heat. If it absorbes heat, the entropy of the system INCREASES. If it releases heat, the entropy DECREASES. As in this case a lot of heat is produced inside the system but less work is done, the system as a whole RELEASES heat and its thermodynamic entropy DECREASES. So we essentially analyse the SPONTANEOUS process (the reversible version is used only to determine the thermodynamic entropy). However any spontaneous process is a movement towards a more probable state - this means that Boltzmann's entropy INCREASES. (By the way, it is Boltzmann's entropy that each participant in this discussion has in mind). Best regards, Pentcho From owner-biophysics@net.bio.net Thu Nov 13 22:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!192.174.65.44!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: entropy. Date: 14 Nov 1997 16:07:51 GMT Organization: IIF Lines: 68 Message-ID: References: <647tcn$drs@ds2.acs.ucalgary.ca> <3467C3AA.41C6@lms.mit.edu> <64al1e$3la$1@fremont.ohsu.edu> <64ere5$29i$1@news.huji.ac.il> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) Don Bashford wrote in message ... >szia@hanga.enzim.hu (Andras Szilagyi) writes: > >> That is, what we should compare is the number of ways you can arrange >>the > atoms of a rock to obtain a rock vs. the number of ways you can >>arrange >> the atoms of a living organism to obtain that living organism.... > >Not fair! You allow the rock's atoms any arrangement the forms "A rock", >while the organism's atoms must form "THAT living organism". It's as >if you want to compare a one-gram insect with with a gram of some >freely morphing "rock" system that is actually an equilibrium ensemble of all >possible "rocks" composed of a given number and type of atoms. > >How about comparing a one-gram insect with a single one-gram crystal? Right. The basic question is: what is a macroscopic state? I always felt that "macroscopic state" is somewhat ill-defined in thermodynamics, at least it's not always easy to tell what a macroscopic state is. I think that we should consider macroscopic states as arbitrarily defined sets of microscopic states. Let's take an insect, for example. If we take all possible configurations of the atoms of the insect then it's only a very small region of the configuration space in which the system can be called an insect. But "insect" is not a thermodynamically defined set of microstates, it's only a human concept. But if I want to know the entropy of the insect, I should count those microstates, and should not count all other states that make up e.g. a mouse, a handful of grass, etc., although thermodynamically those all may be equivalent. And it's still valid to speak of the entropy of the insect since an insect is a very stable thing, it's in steady-state; it definitely has an entropy. It's a good question about the rock. What is the set of microstates that comprise a single and same rock? If we take the human concept of "rock" then the shape and the arrangement of the atoms in the rock does not matter until that piece of material remains a rock. But the rock will not necessarily try all those microstates in reality. An insect does not appear to be a very ordered thing at a first glance; a crystal seems to be much more ordered. An insect is a mixture of a great number of various substances after all; one may think that its entropy could be decreased by simply separating all those substances. Pure substances have lower entropies because we have no mixing entropy. But that's a false reasoning. In a real mixture, all molecules of all components are allowed to move freely in the total volume of the system. That is not allowable in an insect, however. If all molecules of it could move freely then it would be a homogeneous mass of organic substance, not an insect. Thus, an insect is definitely not a mixture in the thermodynamic sense of the word; and actually it is a very ordered system. And you can't separate all its components because it's no longer an insect then. By the way, the comparison of the entropy of an insect and a rock is also problematic because an insect is a steady-state system that is very far from equilibrium, producing entropy all the time, while a rock is usually an equilibrium system. A rock (or a crystal) could also be moved away from equilibrium, and its entropy would decrease then. By moving it further away from equilibrium (entropy decreases further), at a point it could become an insect. So my impression is that the insect must have lower entropy than the rock. Any comments are welcome. Andras Szilagyi From owner-biophysics@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!classic.msn.com!rcb5 From: rcb5@classic.msn.com ("Ronald Blue") Newsgroups: bionet.biophysics Subject: RE: application of aromatherapy to sports science. Date: 15 Nov 1997 21:33:06 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Well COP theory at http://www.enticypress.com should interest you. It at least suggest support for your approach. You should find this interesting. In the perfume industry after smelling three perfumes your ability to chose a good perfume for your self or some one else approaches zero. When you mix perfumes together they stink. Coffee odor from a fresh coffee can will reset the sensory registors. I suspect that coffee might help in sports science. Ron Blue ---------- From: Sharon Carlin Sent: Saturday, November 15, 1997 8:14 PM To: biophys@net.bio.net Subject: application of aromatherapy to sports science. I am preparing a dissertation on the application of aromatherapy to sports science. Has anyone any experience of using aromatherapy to aid sports performance or training ?? Any information on people or institutions involved in research in this field would be very much appreciated. please reply by email ( n9560593@wlv.ac.uk ) thank you all Sharon From owner-biophysics@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!agate!usenet.INS.CWRU.Edu!vncnews!HSNX.wco.com!hub.org!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!baron.netcom.net.uk!netcom.net.uk!dispose.news.demon.net!demon!news.demon.co.uk!demon!taci.demon.co.uk!not-for-mail From: n9560593@wlv.ac.uk (Sharon Carlin) Newsgroups: bionet.biophysics Subject: application of aromatherapy to sports science. Date: Sun, 16 Nov 1997 01:14:15 GMT Organization: University of Wolverhampton Message-ID: <346e4303.11679193@news.demon.co.uk> NNTP-Posting-Host: taci.demon.co.uk X-NNTP-Posting-Host: taci.demon.co.uk [194.222.32.20] X-Newsreader: Forte Free Agent 1.1/32.230 Lines: 15 I am preparing a dissertation on the application of aromatherapy to sports science. Has anyone any experience of using aromatherapy to aid sports performance or training ?? Any information on people or institutions involved in research in this field would be very much appreciated. please reply by email ( n9560593@wlv.ac.uk ) thank you all Sharon From owner-biophysics@net.bio.net Sat Nov 15 22:00:00 1997 Path: biosci!daresbury!uninett.no!newscore.univie.ac.at!news.iif.hu!szia From: szia@hanga.enzim.hu (Andras Szilagyi) Newsgroups: bionet.biophysics Subject: Re: Boltzmann's versus thermodynamic entropy (Pentcho Valev) Date: 16 Nov 1997 12:22:31 GMT Organization: IIF Lines: 38 Message-ID: References: <64i5a1$ctn@mserv1.dl.ac.uk> NNTP-Posting-Host: hanga.enzim.hu X-Newsreader: slrn (0.9.4.1 UNIX) Thank you, Pentcho, for the description. I think I understand the problem now. However, I think that you are wrong in your conclusion. The first part of your analysis, regarding thermodynamic entropy, seems to be correct. The thermodynamic entropy of the system decreases during the process. You then say that this process is spontaneous so the probability (and, consequently, the Boltzmann entropy) increases during the process. Now that's where you are wrong in my opinion. As I understand from your description, this process is an isothermal process. The spontaneity criterion for an isothermal process is not deltaS > 0, as you imply, but deltaF < 0 where F=E-TS is the free energy of the system (or, if the pressure is held constant too then the criterion is deltaG < 0 where G=H-TS is the Gibbs free energy). In the process in question, entropy decreases, but the internal energy E decreases too (recall that an exothermic chemical reaction occurs) so that deltaF (or deltaG) will be negative. Therefore, at the end of the process, you have fewer "energy packets" to distribute between the particles/energy levels of the system, and the number of microscopic states (which is equivalent to thermodynamic probability) will be smaller. So the probability will decrease and not increase as you assert, and obviously the same is true for the Boltzmann entropy. Of course, this is compensated for by the increase of the thermodynamic probability of the environment. [S(total)=S(system)+S(environment), and that is equivalent with W(total)=W(system)*W(environment) where W=exp(S/k) is the thermodynamic probability.] So the _total_ probability will increase (that's why the process is spontaneous), but the probability of the system itself will _decrease_ in the process. Are you surprised? I am afraid that you did not manage to overthrow thermodynamics this time. :-) Andras Szilagyi From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!192.232.20.2!malgudi.oar.net!hyperion.wright.edu!alpha.wright.edu!discover.wright.edu!s001ipf From: ISAAC FORQUER Newsgroups: bionet.biophysics Subject: Re: Beer Theories Date: Sun, 16 Nov 1997 23:57:34 -0500 Organization: Wright State University Lines: 28 Message-ID: References: <64adn8$2he$1@fremont.ohsu.edu> <01bcef1a$c7003900$01ffffdf@glass> NNTP-Posting-Host: discgate.wright.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In-Reply-To: <01bcef1a$c7003900$01ffffdf@glass> To the interested beer theorists, My bite: I think the only covalent thing that could be going on is the acid-base chemistry going on between CO2 and the beer. I forget how that works, so don't quote me, but wouldn't the out gassing of the CO2 when you open increase the pH slightly because of the decrease in CO2 concentration??? *********************************************************************** Isaac Forquer Wright State University Dept. of Biological Sciences Dayton, OHIO 45435 Home address: 4954 Woodman Pk. Dr. Apt. 16 Dayton, OH 45429 (937)-258-3329 My take off of the great E. J. Rutherford: "All of biology is photosynthesis, the rest is just stamp collecting" ***You best teach what you most need to learn*** *********************************************************************** From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!daresbury!uninett.no!news.maxwell.syr.edu!cam-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!webtv.net!not-for-mail From: yummyone@webtv.net (Annie Whey) Newsgroups: bionet.biophysics Subject: Re: rock - living organism comparison (Pentcho Valev) Date: Mon, 17 Nov 1997 01:49:49 -0600 Organization: WebTV Subscriber Lines: 3 Message-ID: <64osut$159$1@newsd-112.bryant.webtv.net> References: NNTP-Posting-Host: localhost.webtv.net Mime-Version: 1.0 (WebTV) Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT iptsg.epfl.ch/aps/BAPSGEC97/abs/5900002.html Theophrastus Bomblastus From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!164.67.80.81!nnrp.info.ucla.edu!wlheye.jsei.ucla.edu!lukasz From: lukasz@wlheye.jsei.ucla.edu (Lukasz Salwinski) Newsgroups: bionet.biophysics Subject: Re: Boltzmann versus thermodynamic entropy (Pentcho Valev) Date: 17 Nov 1997 21:35:22 GMT Organization: Jules Stein Eye Institute, UCLA Lines: 30 Distribution: world Message-ID: <64qdaq$rc6@uni.library.ucla.edu> References: <01IQ4EE0UHA800007I@buphyc.bu.edu> Reply-To: lukasz@jsei.ucla.edu NNTP-Posting-Host: wlheye.jsei.ucla.edu -- >>>PROCESS BETWEEN TWO EQUILIBRIUM STATES, THE SYSTEM GOES TOWARDS THE MORE >>>PROBABLE ONE. You can find this >> >> >>beep! wrong! not THE SYSTEM but THE ISOLATED SYSTEM. >> >>if the system is interacting with environment (as is the case of an >>isothermic process) the environment is 'selecting' the states according to >>some criterium. an analogy is tossing a coin but showing it to audience >>only if it's tails. probability of getting tails is 1/2 if the system(=coin) >>do not interact with the environment(=experimentator's 'censorship'). if >>there's interaction the probability of tails can be 1. >> >> >>>But is not this an absurdity? >> >>nothing absurd about that. >> >>lukasz > A spontaneous process between two equilibrium states is an oxymoron if >ever there was one. An equilibrium state is the highest entropy state ok ;o) take away EQUILIBRIUM from Pentcho's statement... lukasz From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!BUPHYC.BU.EDU!bc From: bc@BUPHYC.BU.EDU (Bernard Chasan) Newsgroups: bionet.biophysics Subject: Re: Boltzmann versus thermodynamic entropy (Pentcho Valev) Date: 17 Nov 1997 12:55:47 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <01IQ4EE0UHA800007I@buphyc.bu.edu> NNTP-Posting-Host: net.bio.net >-- > >>(probability) and thermo entropy, we need to define them SEPARATELY. The >>only reliable definition of probability I know of is: IN A SPONTANEOUS >>PROCESS BETWEEN TWO EQUILIBRIUM STATES, THE SYSTEM GOES TOWARDS THE MORE >>PROBABLE ONE. You can find this > > >beep! wrong! not THE SYSTEM but THE ISOLATED SYSTEM. > >if the system is interacting with environment (as is the case of an >isothermic process) the environment is 'selecting' the states according to >some criterium. an analogy is tossing a coin but showing it to audience >only if it's tails. probability of getting tails is 1/2 if the system(=coin) >do not interact with the environment(=experimentator's 'censorship'). if >there's interaction the probability of tails can be 1. > > >>But is not this an absurdity? > >nothing absurd about that. > >lukasz A spontaneous process between two equilibrium states is an oxymoron if ever there was one. An equilibrium state is the highest entropy state consistent with constraints. An example of a constraint is a partition between two halves of a box, where one half contains molecules, the other half does not. Now remove the partition and a new equilibrium is attained after some relaxation time. In that state molecules are uniformly distributed throughout the box, and the number of states accessible to the molecules has gone up astronomically. There are not two choices of equilibrium - just one state with maximum possible entropy. BC Professor Bernard Chasan Physics Department, Boston University Boston MA 02215 (617) 353-2608 From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsfeed.internetmci.com!164.67.42.145!awabi.library.ucla.edu!164.67.80.81!nnrp.info.ucla.edu!wlheye.jsei.ucla.edu!lukasz From: lukasz@wlheye.jsei.ucla.edu (Lukasz Salwinski) Newsgroups: bionet.biophysics Subject: Re: Boltzmann versus thermodynamic entropy (Pentcho Valev) Date: 17 Nov 1997 16:16:18 GMT Organization: Jules Stein Eye Institute, UCLA Lines: 28 Distribution: bionet Message-ID: <64pqki$1tpq@uni.library.ucla.edu> References: <64p3ku$8j6@mserv1.dl.ac.uk> Reply-To: lukasz@jsei.ucla.edu NNTP-Posting-Host: wlheye.jsei.ucla.edu -- >(probability) and thermo entropy, we need to define them SEPARATELY. The >only reliable definition of probability I know of is: IN A SPONTANEOUS >PROCESS BETWEEN TWO EQUILIBRIUM STATES, THE SYSTEM GOES TOWARDS THE MORE >PROBABLE ONE. You can find this beep! wrong! not THE SYSTEM but THE ISOLATED SYSTEM. if the system is interacting with environment (as is the case of an isothermic process) the environment is 'selecting' the states according to some criterium. an analogy is tossing a coin but showing it to audience only if it's tails. probability of getting tails is 1/2 if the system(=coin) do not interact with the environment(=experimentator's 'censorship'). if there's interaction the probability of tails can be 1. >But is not this an absurdity? nothing absurd about that. lukasz From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.biophysics Subject: BIOSCI/bionet miniFAQ & Fundraiser Date: 17 Nov 1997 02:00:08 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 233 Sender: daemon@net.bio.net Distribution: world Message-ID: <199711171000.CAA05684@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 30-JUL-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. If you can not find an answer to your question in this or other documentation, the BIOSCI technical support staff answers e-mail queries sent to biosci-help@net.bio.net We can only answer questions about the use of the newsgroups and mailing lists. We unfortunately do not have the staff to do Internet information searches or answer scientific questions. Please post those to the appropriate BIOSCI/bionet newsgroups. Contents: -------- 0) BIOSCI NEEDS YOUR SUPPORT!! 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 0) BIOSCI NEEDS YOUR SUPPORT!! ------------------------------ BIOSCI's government funding has been expended, and we are now operating solely from advertising revenue that we have raised from our Web site at http://www.bio.net/. We need just a few minutes of your time to help us serve you. You can do two important things which will take very little time for you individually and will immensely help us continue to help you. First, please use our WWW system at http://www.bio.net/ to access the archives. You can post or reply to messages via your Web browser as described in item #1 below. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.biophysics Subject: Boltzmann versus thermodynamic entropy (Pentcho Valev) Date: 17 Nov 1997 09:43:58 -0000 Lines: 47 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <64p3ku$8j6@mserv1.dl.ac.uk> Original-To: biophys@dl.ac.uk Andras Szilagyi wrote: The first part of your analysis, regarding thermodynamic entropy,< seems to be correct. The thermodynamic entropy of the system< decreases during the process.< You then say that this process is spontaneous so the probability< (and, consequently, the Boltzmann entropy) increases during the< process. Now that's where you are wrong in my opinion.< As I understand from your description, this process is an isothermal< process. The spontaneity criterion for an isothermal process is not< deltaS > 0, as you imply, but deltaF < 0 where F=E-TS is the free energy< of the system (or, if the pressure is held constant too then the< criterion is deltaG < 0 where G=H-TS is the Gibbs free energy). In the< process in question, entropy decreases, but the internal energy E< decreases too (recall that an exothermic chemical reaction occurs) so< that deltaF (or deltaG) will be negative. Therefore, at the end of the< process, you have fewer "energy packets" to distribute between the< particles/energy levels of the system, and the number of microscopic< states (which is equivalent to thermodynamic probability) will be< smaller. So the probability will decrease and not increase as you assert,< and obviously the same is true for the Boltzmann entropy. Of course, this< is compensated for by the increase of the thermodynamic probability of< the environment. [S(total)=S(system)+S(environment), and that is< equivalent with W(total)=W(system)*W(environment) where W=exp(S/k) is the< thermodynamic probability.] So the _total_ probability will increase< (that's why the process is spontaneous), but the probability of the< system itself will _decrease_ in the process. Are you surprised?< Yes. You have in fact DEFINED the probability by the thermodynamic entropy, but this cannot solve any problem. In order to compare Boltzmann's entropy (probability) and thermo entropy, we need to define them SEPARATELY. The only reliable definition of probability I know of is: IN A SPONTANEOUS PROCESS BETWEEN TWO EQUILIBRIUM STATES, THE SYSTEM GOES TOWARDS THE MORE PROBABLE ONE. You can find this explicit or implicit in any textbook. If you are right, then the following statement should be placed in textbooks: SOME SYSTEMS SPONTANEOUSLY APPROACH A LESS PROBABLE STATE. But is not this an absurdity? So let us think of an independent definition of probability. I cannot accept your attempt to assess it in terms of "energy packets". If statistical mechanics has given a rigorous way to calculate it, then somebody can tell us about that and we are to adopt the method. If not, you should accept that, among different EQUILIBRIUM states, the system chooses the most probable one. Best regards, Pentcho From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed4.bbnplanet.com!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!su-news-feed4.bbnplanet.com!news.bbnplanet.com!webtv.net!not-for-mail From: yummyone@webtv.net (Annie Whey) Newsgroups: bionet.biophysics Subject: Re: National Biotech Register(NatBio) New Service Date: Mon, 17 Nov 1997 01:55:00 -0600 Organization: WebTV Subscriber Lines: 5 Message-ID: <64ot8k$164$1@newsd-112.bryant.webtv.net> References: <3461DAC3.1208@barryinc.com> NNTP-Posting-Host: localhost.webtv.net Mime-Version: 1.0 (WebTV) Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Arcturus.mit.edu/cosmics/doc-html/cosmics.htm l Theophrastus Bomblastus From owner-biophysics@net.bio.net Sun Nov 16 22:00:00 1997 Path: biosci!webtv.net!not-for-mail From: yummyone@webtv.net (Annie Whey) Newsgroups: bionet.biophysics Subject: Re: Best kept "secrets" finally exposed Date: Mon, 17 Nov 1997 01:52:33 -0600 Organization: WebTV Subscriber Lines: 6 Message-ID: <64ot41$15q$1@newsd-112.bryant.webtv.net> References: <649q5g$jlq@mserv1.dl.ac.uk> NNTP-Posting-Host: localhost.webtv.net Mime-Version: 1.0 (WebTV) Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Who is? Camayoc, NEXoh Ltd, Great Britain Ex. x500.ksc.nasa.gov:8888/lcn%3dElectric%20 Eel Theophrastus Bomblastus