From owner-evolution@net.bio.net Tue Apr 01 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!swrinde!howland.erols.net!newsserver.jvnc.net!paperboy.uconn.edu!usenet From: kent@darwin.eeb.uconn.edu (Kent E. Holsinger) Newsgroups: bionet.molbio.evolution Subject: Call for Symposia -- 1998 Annual Meetings SSB/SSE Date: 02 Apr 1997 07:39:35 -0500 Organization: Dept. of Ecology & Evolutionary Biology, University of Connecticut Lines: 92 Sender: kent@WALLACE Message-ID: NNTP-Posting-Host: wallace.eeb.uconn.edu X-Newsreader: Gnus v5.3/Emacs 19.33 *********************************************************************** Call for Symposia SSB/SSE 1998 Annual Meeting The 1998 annual meetings of the Society of Systematic Biologists and the Society for the Study of Evolution will be held in Vancouver, British Columbia, Canada, 20-24 June. The Councils of SSB and SSE invite proposals for symposia to be held in conjunction with those meetings. Detailed requirements for symposium proposals for each society follow. Please note that symposium proposals for SSB and SSE have different requirements and are to be sent to different addresses. Society of Systematic Biologists Symposium proposals for SSB should include: 1) a descriptive title; 2) one or two paragraphs explaining the purpose of the symposium and its relevance to systematics; 3) a list of the presentations, including proposed speakers, their affiliations/institutions, and titles; 4) an indication of whether the speakers have been invited and whether they have agreed to participate; 5) the length of each talk. The Society is particularly interested in symposia whose topics do not overlap those from previous meetings, that introduce new ideas or synthesize important concepts, or that are particularly good examples of the analysis of empirical data. Proposals that unite systematics with other fields are also desirable. We encourage participation from young investigators and others typically underrepresented in symposia. Symposia are restricted to half-day sessions. Limited partial funding is available. Two proposals will be selected at the 1997 Council meeting. The target date for receipt of proposals is 1 May 1997. E-mail or mail proposals to: Dr. Chris Simon, Program Director Society of Systematic Biologists Department of Ecology & Evolutionary Biology, U-43 University of Connecticut Storrs, CT 06269-3043 USA e-mail: CSimon@UConnVM.UConn.Edu (Please send as non-coded ASCII text files.) Society for the Study of Evolution Symposium proposals for SSE should include: 1) a synopsis of the symposium theme; 2) a tentative list of speakers and topics; 3) a rationale for the symposium explaining why this topic and this set of speakers are particularly appropriate for a Society-sponsored symposium. In evaluating symposium proposals the Council will favor those proposals whose topics concern newly emerging fields, fields ripe for synthesis, and fields different from those that have been included in recent Society symposia. The Council particularly encourages proposals that include speakers from groups traditionally underrepresented in Society symposia, e.g., postdoctoral research associates and new assistant professors, investigators from outside North America, women, and members of racial or ethnic minorities. The Council expects to select only two proposals for half-day symposia at its meeting in June 1997. All proposers will be notified of the Council's decision in early July. The Society will provide partial travel support for organizers and participants in sponsored symposia. Details are available on request. To be assured of full consideration proposals must be received at the following address by 5 May 1997: Dr. Kent E. Holsinger, Executive Vice President Society for the Study of Evolution Department of Ecology & Evolutionary Biology, U-43 University of Connecticut Storrs, CT 06269-3043 USA e-mail: Kent@Darwin.EEB.UConn.Edu (Please send as plain ASCII text. Wordprocessor files may be sent as MIME or UUencoded documents. Please do not send as BinHexed documents.) -- Kent Holsinger, Executive Vice President Society for the Study of Evolution -- Chris Simon, Program Director Society of Systematic Biologists From owner-evolution@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!RESULB.ULB.AC.BE!mcmilink From: mcmilink@RESULB.ULB.AC.BE (Michel C. Milinkovitch) Newsgroups: bionet.molbio.evolution Subject: last announcement Date: 3 Apr 1997 04:57:57 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Last announcement: We received many applications (for the workshop/course advertised below) from Belgium, Germany, The Netherlands, and the UK. Because we would like to have as balanced a representation of European countries as possible, we recommend people from East-European and South-European countries to apply, and we changed the deadline for application to ****April 30, 1997****. Of course, residents of West-European countries can still apply given that balanced representation of European countries is not the only criterion used for the selection of applicants. Dear all, Right after the congress organized by the European Society for Evolutionary Biology (ESEB) in Arnhem (The Netherlands, 24-28 August 1997), The International Society for Biochemical Systematics (ISBS) will organize a one-week European workshop on molecular phylogeny and systematics (Antwerpen, Belgium, August 28 - September 5, 1997). The courses will be taught by American and European phylogeneticists (John C. Avise, Lutz Bachmann, Michel C. Milinkovitch, Fred Opperdoes, Rory Post, Arndt von Haeseler, Yves Van de Peer, Marc Van Ranst,... among others). John C. Avise will also give an evening conference. Applicants should submit a brief CV, a brief statement on their interest to attend the workshop, and a list of publications (if available). The workshop is limited to 30 participants, and the application deadline is April 15, 1997. Participants with no experience in molecular phylogenetics are advised to start on August 28, while people with some may start on September 1st. Please, refer to the web site of the ISBS for details on the program (http://isbs-www.uia.ac.be/isbs/). The ISBS is an international society for the general advancement and promotion of research and communication in the study of molecular aspects of evolutionary systematics. The Society takes the broadest possible coverage to include micromolecules [e.g., secondary metabolites] as well as macromolecules [e.g., DNA and Proteins]. All living organisms are included and systematics is taken to mean phylogeny reconstruction and population genetics but also identification and descriptive taxonomy. Additional information on the ISBS and/or the workshop can also be obtained from Yves Van de Peer (yvdp@uia.ua.ac.be) or myself (mcmilink@resulb.ulb.ac.be). -------------------------------------------------- Michel C. Milinkovitch, Assistant Professor, Laboratory of Evolutionary genetics, Dpt of Biology, Free University of Brussels (ULB), cp 244, Bd du Triomphe, B-1050 Brussels, Belgium. Tel: +32-2-650-5412; Fax: +32-2-650-5421; e-mail: mcmilink@resulb.ulb.ac.be -------------------------------------------------- -------------------------------------------------- From owner-evolution@net.bio.net Wed Apr 02 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!cyclic.gsl.net!news.gsl.net!news.maxwell.syr.edu!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 3 Apr 1997 23:29:55 GMT Organization: AT&T WorldNet Services Lines: 65 Message-ID: <01bc3fbd$8f8ecac0$a94892cf@mycomputer> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> NNTP-Posting-Host: 207.146.72.169 X-Newsreader: Microsoft Internet News 4.70.1155 Richard M Kliman wrote in article <5hofnd$l3e@ruacad.runet.edu>... > In article <01bc3976$50366ec0$0a4892cf@mycomputer>, > Joe Potter wrote: > > The idea that you posit here assumes that the organism can see-ahead and > >determine what is best in the long run. This is a no-no, is it not? > > It is a no-no. > > > Dr. Eldredge wrote, " Selection can not be for the 'good of the species.' > >It can only be a measure of what works best for the individual organisms in > >their struggle for existence. ..." > > Careful with the appeals to authority. I doubt Eldredge would deny that > species sometimes compete for resources. The presence of one species > changes the environment faced by another species. And I seriously doubt > that Eldredge would claim that environments, in general, remain constant. > Individuals of a sexually reproducing species may have greater reproductive > success in a given environment than individuals of an asexually reproducing > species. Selection is still acting at the individual level; nature does not > provide a guarantee to that at least one member of a species will always be > allowed to produce offspring. > > > In other words, why sex?????? > > Why *not* sex? You've made the point that sexually reproducing > individuals only pass on 50% of their genes. Assuming that a population > consists of some sexually reproducing and some asexually reproducing > individuals, sexual reproduction is not expected to be fixed unless the > sexually reproducing individuals have substantially greater reproductive > success. Why is this not conceivable? > > The fact is this: sex is *not* a problem for evolutionary biology. > Theories regarding why sex persists (a separate question from how sex > arose - which is also not a problem) are covered by any decent college-level > evolution text. > > Rich Kliman > Dept. of Biology > Radford University > *standard disclaimer* > Any "decent college-level text" would address the point that Dr. Eldredge makes and not talk around it. His point is that if the ultra-Darwinist (his term) view is correct, then sex is a paradox. The view that he is attacking (if this is the correct term) is that evolution is not simply the struggle to leave as many copies of one's genes to the next generation as possible --- as biologists seem to think. Have you read "Reinventing Darwin ?" Regards, Joe From owner-evolution@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!daresbury!uninett.no!news-feed.inet.tele.dk!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!newsxfer3.itd.umich.edu!portc01.blue.aol.com!newsstand.cit.cornell.edu!news.acsu.buffalo.edu!acsu.buffalo.edu!destrier.acsu.buffalo.edu!wjc From: wjc@acsu.buffalo.edu Newsgroups: bionet.molbio.evolution Subject: About DNA Parsimony Date: Fri, 4 Apr 1997 18:02:16 -0500 Organization: University at Buffalo Lines: 10 Message-ID: NNTP-Posting-Host: destrier.acsu.buffalo.edu Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: wjc Hi friends, Recently I got some DNA sequence comparing data generated from DNA Parsimony program. I have no idea about this program and the theory behind it. I wonder if there is any easy book or article can give me a good introduction to this theory. Thanks Warren From owner-evolution@net.bio.net Thu Apr 03 23:00:00 1997 Path: biosci!mail.only!postal From: postal@mail.only Newsgroups: bionet.molbio.evolution Subject: Search Engine Secrets Date: 3 Apr 1997 23:04:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 120 Sender: daemon@net.bio.net Distribution: world Message-ID: <199704040642.WAA05950@global1.global.net> NNTP-Posting-Host: net.bio.net Dear Friend and Fellow Entrepreneur, DISCOVER The Most Powerful & PROVEN Strategies that Really Work To Place You At The Top of the Search Engines! If you have a web page, or site, that can't be found at the top of the search engines then this will be the most important information you will ever read. Everyone know that the key to success on the web is positioning. 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Download your free copy today! ******************************************************************* From owner-evolution@net.bio.net Sat Apr 05 23:00:00 1997 Path: biosci!agate!howland.erols.net!cam-news-hub1.bbnplanet.com!cpk-news-feed1.bbnplanet.com!news.bbnplanet.com!nih.gov!cbmh37.cber.fda.gov!bernsteinr From: bernsteinr@cber.cber.fda.gov (R M Bernstein) Newsgroups: bionet.molbio.evolution Subject: mac vector file format. Followup-To: bionet.molbio.evolution Date: Sun, 6 Apr 97 03:28:48 GMT Organization: FDA/CBER Lines: 26 Message-ID: NNTP-Posting-Host: cbmh37.cber.fda.gov X-Newsreader: VersaTerm Link v1.1.5 Hi all, programmers espec, I'm currently writing a small Mac based utility to work along w/ ClustalW, i.e., a TOPIR executable that could be used to assemble several files [so far i'm going to use gcg and macvector] and place them into 1 TOPIR format file. Currently, to do this, a Mac based ClustalW user must one of several command line format programs. The program I envision would be "desktop" look and feel based. I have the gcg format, but the Mac Vector format/parser has eluded me. Does anyone know the format/parsing, etc that the Mac Vector program now follows? Thanks for your time, Ralph Bernstein, R.M. FDA/CBER/HFM-541 Bld.29A R.M.2b09 29 Lincoln St. Bethesda MD bernsteinr@cber.cber.fda.gov 3018271814 From owner-evolution@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!howland.erols.net!vixen.cso.uiuc.edu!robertson2.life.uiuc.edu!user From: f-soto@uiuc.edu (Felipe N. Soto) Newsgroups: bionet.molbio.evolution Subject: Selection Followup-To: bionet.molbio.evolution Date: Mon, 07 Apr 1997 15:03:43 -0600 Organization: U of Illinois Lines: 19 Message-ID: NNTP-Posting-Host: robertson2.life.uiuc.edu I am studying the evolution of transposable elements in insect and as part of the study I would like to look at the possible presence of selection between different elements of the same family. I have used the M-K test for neutrality, which requires the itemization of fixed, polymorphic, synonymous and replacement subtitutions. The contingency table is easy to deal with, but determining the status of each subtitution can take forever, specially if there are many subtitutions (about 300 for each one of 10 or so pairs). Does any one know of a little program for Mac's that would do the trick? Alternatively, would it be valid to "estimate" the cell placement of a substitution by considering all 1 and 2 positions to be replacements, and all 3 positions synonymous? Thanks for the putative advice -- Felipe N. Soto Department of Entomology University of Illinois f-soto@uiuc.edu From owner-evolution@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!VAXA.CIS.UWOSH.EDU!bentiven From: bentiven@VAXA.CIS.UWOSH.EDU ("Stephen P. Bentivenga") Newsgroups: bionet.molbio.evolution Subject: Position Announcement Date: 7 Apr 1997 06:51:02 -0700 Organization: University of Wisconsin Oshkosh Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <3348FA2B.180C@vaxa.cis.uwosh.edu> NNTP-Posting-Host: net.bio.net The Department of Biology and Microbiology, University of Wisconsin Oshkosh, seeks applicants for two temporary academic staff positions for one academic year only starting Fall 1997. One position will be in the area of microbiology to teach a course in Microbial Genetics lecture and laboratory for the Fall Semester and Biotechnology lecture and laboratory during Spring Semester and help out with teaching beginning courses in microbiology/biology. The second position is in the area of zoology, to teach beginning biology courses during the Fall and Spring Semesters and Parasitology during the Spring Semester. A Ph.D. degree with appropriate specialization is preferred for each of the positions. Send letter of application, CV, 3 letters of recommendation and official transcripts to: M. A. Rouf, Chair, Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI 54901, by April 15, 1997. The University of Wisconsin Oshkosh is an affirmative action/equal opportunity employer. From owner-evolution@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!news.maxwell.syr.edu!news-out.communique.net!communique!uunet!in1.uu.net!204.74.114.90!news.genuity.net!news.annex.com!204.74.67.103 From: "Karl" Newsgroups: bionet.molbio.evolution Subject: Re: evolutionary advantages of homosexual inclinations Date: 7 Apr 97 03:06:07 GMT Organization: Genuity Inc. Phoenix, AZ Lines: 31 Message-ID: <01bc4301$413d5ca0$67434acc@karl.annex.com> References: <331FFDF0.27AE@xs4all.nl> <33231961.1330568@rwja.umdnj.edu> NNTP-Posting-Host: news.annex.com X-Newsreader: Microsoft Internet News 4.70.1155 Keith Christoffers wrote in article <33231961.1330568@rwja.umdnj.edu>... > On Fri, 07 Mar 1997 12:37:20 +0100, michael wrote: > > >Are there scientific or theorethical arguments that homosexual > >inclinations are a benefit for species? > > > >Appreciate advice. > >Alexander Wichmoon > > Is there any species that you know of in which such a phenomenon is > present. Do you see homosexual apes aiding in the copulation of > heterosexual apes? I don't know, it's not a loaded question. > > Keith Christoffers I've become rather a neutralist on the subject myself. My current working hypothesis is that sometimes the mechanisms that enforce sexual preference break down. The reason it happens as often as it does is that it's simply not worth the cost in resources to fix. This was prompted by an article on the egg mimicry in cuckoos. In species whose nests have been parasitized for a long time, the target birds have "installed" elaborate "pattern recognition software" to allow them to reject the eggs of other species. Target birds that have not been subject to such parasitization do not have such "software", and will nest on almost anything. ......Karl From owner-evolution@net.bio.net Sun Apr 06 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!paladin.american.edu!news.jhu.edu!news From: Robert Georgantas Newsgroups: bionet.molbio.evolution Subject: BioScience information Date: Mon, 07 Apr 1997 16:44:19 +0000 Organization: Johns Hopkins University Lines: 65 Message-ID: <33492457.47A@welchlink.welch.jhu.edu> Reply-To: rgeorgan@welchlink.welch.jhu.edu NNTP-Posting-Host: 162.129.38.137 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Mailer: Mozilla 3.01Gold (Macintosh; I; PPC) Announcing the SCIENCE GUIDE. http://www.scienceguide.com A New Internet Directory and Information Service run by Scientists and Physicians for Scientists and Physicians. After visiting the Guide, If you have any suggestion for making the Guide better please let us know. (webmaster@scienceguide.com) The Science Guide consists of a number of different sections designed to help the scientist and physician find information on the internet and to sponsor communication between those interested in science: NEWS SECTION Every day the Science Guide compiles medical and research news from national news sources around the net. Most of the news articles are concerned with medicine, bioscience, and physics, but all other sciences from agriculture to zoology are commonly included. News sources currently listed include: CNN, EurekAlert, HMS Beagle, MSNBC Sci-Tech, Science Magazine’s ScienceNow, CBS Space News, USA Today, The Albuquerque Journal, Scientific American Web Weekly, The Why Files, Discover Magazine, Scientific American, Smithsonian Magazine, and the Technology Review. The news pages also list links to news sources not compiled within the News site. We are currently working on adding a number of other sources to the site to make it even more useful. To make getting science news even easier, we send out a DAILY NEWS EMAILER listing the articles which have been compiled on our site. Anyone can subscribe to the Emailer by sending an email to news@scienceguide.com with the message “Subscribe” DIRECTORY OF USENET NEWS GROUPS and DISCUSSION LISTS The Directory of Usenet and Discussion Groups is compiled quarterly from different sources around the net to provide the scientist and those interested in science easy access to these invaluable sources of discourse and information. We are currently working on finding the proper subscription method for each of the discussion lists. This is taking a bit longer that we thought so please pardon our dust. The Usenet portions of this section are complete. ON-LINE JOURNAL HYPERLINK SECTION The Journals Section contains links to peer reviewed scientific journals on the Internet. Each listing clearly indicates whether the journal provides only the table of contents, TOC with abstracts, or the full text of the journal EMPLOYMENT SECTION The Jobs and Positions Section contains hyperlinks to the best Scientific Employment Databases and Classifieds on the net. GRANTS and FUNDING SECTION The funding section contains links to the best funding and grant databases on the Internet, making it very easy for scientists to quickly find funding opportunities. The featured site of the section is “The Community of Science,” a Johns Hopkins service designed to help scientists find and continue funding. From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 8 Apr 1997 23:47:56 GMT Organization: AT&T WorldNet Services Lines: 61 Message-ID: <01bc43ad$df94b7c0$a84992cf@mycomputer> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> NNTP-Posting-Host: 207.146.73.168 X-Newsreader: Microsoft Internet News 4.70.1155 Mike Koller wrote in article <01bc43c1$209adb60$864da1ce@koller.erols.com>... > > > The fact is this: sex is *not* a problem for evolutionary biology. > > > Theories regarding why sex persists (a separate question from how sex > > > arose - which is also not a problem) are covered by any decent > > college-level > > > evolution text. > > > > > > Rich Kliman > > > Dept. of Biology > > > Radford University > > > *standard disclaimer* > > > > > Yup. I'm taking biology 1 and it's right there in plain english. Not hard > to grasp or understand. It makes a whole lotta sense, scientifcally > speaking of course. > > Some tidbits: > > "Darwin's first point - that evolution occurs - can stand on its own, > whether or not natural selection is the cause". > (What vs. How) > > "Natural selection involves interactions between individual organisms and > their environment, but individuals do not evolve. Evolution can be > measured only as changes in relative proportions of variations in a > population over a succession of generations." > > Why sex is better than no sex (regarding survivability): > > "On average, those individuals best suited to the local environment leave > the most offspring, transmitting their genese in the process. This natural > selection results in adaptation, the accumulation of those genetic > variations that are favored by the enironment. As the environment changes > or a population moves, the population may survive if in each generation, at > least some of its members can cope effectively with the new conditions. > Different genetic variations may work better than those that prevailed in > the old time or place. SEX and mutations are the two sources of this > variation." > > All quotes from "Biology (4th ed.) by Campbell (Benjamin/Cummins Publ.) > > Mike, you seemed to have missed the point. I did not write that sex makes no sense (even after 25 years of marriage it does :-) ), I wrote that Dr. Eldredge (1995 book) wrote that sex is a paradox from the ultra-Darwinist (as in Dr. Dawkins) point of view. Read his book, it will serve you well in your studies. (Eldredge is a major player, if you did not know) Regards, Joe From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeed.nacamar.de!fu-berlin.de!informatik.tu-muenchen.de!lrz-muenchen.de!wap18.zi.biologie.uni-muenchen.de!strimmer From: Korbinian Strimmer Newsgroups: bionet.molbio.evolution Subject: Version 3.1 of PUZZLE available Date: Tue, 8 Apr 1997 10:36:08 +0200 Organization: [posted via] Leibniz-Rechenzentrum, Muenchen (Germany) Lines: 52 Distribution: world Message-ID: NNTP-Posting-Host: wap18.zi.biologie.uni-muenchen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII P U Z Z L E Maximum likelihood analysis for nucleotide and amino acid alignments Version 3.1 April 1997 Copyright 1995-97 by Korbinian Strimmer and Arndt von Haeseler Zoologisches Institut, Universitaet Muenchen, Muenchen, Germany What's new in PUZZLE 3.1: * Much improved user interface to rate heterogeneity (less confusing menu, rearranged outfile, additional out-of-range check). * Possibility to read rooted input trees (automatic removal of basal bifurcation). * Computation of average distance between all pairs of sequences. * Fix of a bug that caused PUZZLE 3.0 to crash on some systems (DEC Alpha). * Cosmetic changes in program and documentation. PUZZLE is an application to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm (quartet puzzling) that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Rate heterogeneity (invariable sites plus Gamma distributed rates) is incorporated in all models of substitution available (nucleotides: TN, HKY, F84, and submodels; amino acids: Dayhoff, JTT, mtREV24). All model parameters including rate heterogeneity can be estimated from the data by maximum likelihood. PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. In addition, PUZZLE offers a novel method, likelihood mapping, to investigate the support of internal branches without computing an overall tree. PUZZLE is available free of charge from http://www.zi.biologie.uni-muenchen.de/~strimmer/puzzle.html (PUZZLE home page) ftp://ftp.ebi.ac.uk/pub/software (European Bioinformatics Institute) ftp://ftp.pasteur.fr/pub/GenSoft (Institut Pasteur) PUZZLE is written as an ANSI C program. This means that it will run on most personal computers and workstations if compiled by an appropriate C compiler. Precompiled executables are available for MacOS and MS-DOS. UNIX and VMS makefiles are also provided. From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!uunet!in2.uu.net!130.235.20.4!news.lth.se!merkurius.lu.se!not-for-mail From: David Hagerberg Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: Tue, 08 Apr 1997 08:09:58 -0600 Organization: Dep Microbial Ecology Lines: 50 Message-ID: <334A51B6.17E5@luecology.ecol.lu.se> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> NNTP-Posting-Host: pc2.ekol.lu.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0Gold (Win95; I) Mike Koller wrote: > > > > The fact is this: sex is *not* a problem for evolutionary biology. > > > Theories regarding why sex persists (a separate question from how sex > > > arose - which is also not a problem) are covered by any decent > > college-level > > > evolution text. > > > > > > Rich Kliman > > > Dept. of Biology > > > Radford University > > > *standard disclaimer* > > > > > Yup. I'm taking biology 1 and it's right there in plain english. Not hard > to grasp or understand. It makes a whole lotta sense, scientifcally > speaking of course. > > Some tidbits: > > "Darwin's first point - that evolution occurs - can stand on its own, > whether or not natural selection is the cause". > (What vs. How) > > "Natural selection involves interactions between individual organisms and > their environment, but individuals do not evolve. Evolution can be > measured only as changes in relative proportions of variations in a > population over a succession of generations." > > Why sex is better than no sex (regarding survivability): > > "On average, those individuals best suited to the local environment leave > the most offspring, transmitting their genese in the process. This natural > selection results in adaptation, the accumulation of those genetic > variations that are favored by the enironment. As the environment changes > or a population moves, the population may survive if in each generation, at > least some of its members can cope effectively with the new conditions. > Different genetic variations may work better than those that prevailed in > the old time or place. SEX and mutations are the two sources of this > variation." > > All quotes from "Biology (4th ed.) by Campbell (Benjamin/Cummins Publ.) In the same time sex is an ensurement of smilarity. A recessive mutant can be hidden by the normal alleles. Thus sex provides both similarity and a library of variation if an organism needa it. Best regards David Hagerberg From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!news From: "Mike Koller" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 8 Apr 1997 02:10:28 GMT Organization: Erol's Internet Services Lines: 41 Message-ID: <01bc43c1$209adb60$864da1ce@koller.erols.com> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> NNTP-Posting-Host: koller.erols.com X-Received-On: 8 Apr 1997 02:10:28 GMT X-Newsreader: Microsoft Internet News 4.70.1155 > > The fact is this: sex is *not* a problem for evolutionary biology. > > Theories regarding why sex persists (a separate question from how sex > > arose - which is also not a problem) are covered by any decent > college-level > > evolution text. > > > > Rich Kliman > > Dept. of Biology > > Radford University > > *standard disclaimer* > > Yup. I'm taking biology 1 and it's right there in plain english. Not hard to grasp or understand. It makes a whole lotta sense, scientifcally speaking of course. Some tidbits: "Darwin's first point - that evolution occurs - can stand on its own, whether or not natural selection is the cause". (What vs. How) "Natural selection involves interactions between individual organisms and their environment, but individuals do not evolve. Evolution can be measured only as changes in relative proportions of variations in a population over a succession of generations." Why sex is better than no sex (regarding survivability): "On average, those individuals best suited to the local environment leave the most offspring, transmitting their genese in the process. This natural selection results in adaptation, the accumulation of those genetic variations that are favored by the enironment. As the environment changes or a population moves, the population may survive if in each generation, at least some of its members can cope effectively with the new conditions. Different genetic variations may work better than those that prevailed in the old time or place. SEX and mutations are the two sources of this variation." All quotes from "Biology (4th ed.) by Campbell (Benjamin/Cummins Publ.) From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!MOLBIOL.UCT.AC.ZA!ed From: ed@MOLBIOL.UCT.AC.ZA ("Ed Rybicki") Newsgroups: bionet.molbio.evolution Subject: Re: Calveria Tree disproves Evolution Date: 8 Apr 1997 00:23:51 -0700 Organization: Dept Microbiology, UCT Lines: 45 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: ed@molbiol.uct.ac.za NNTP-Posting-Host: net.bio.net > From: foster@skink.cs.uidaho.edu (James Foster) > Subject: Re: Calveria Tree disproves Evolution > > Puck, - I find it disturbing that I am considered a "fundies". In my > > small, narrow minded brain I suppose that means = fundamental? > > > It does not make me stupid. It does no make me less educated. I respect > > your passion and knowledge so why are my views and theories considered > > non-science. It is actually all theory - since neither of us were there > > when it happened. I am not miserable. I don't want to convert you. Who > > are you to be so pious? - Who are you to lump me in a single word - > > "fundies"? - I am so much more, do you care to dig deeper? I thirst for > > the truth....do you? > > Yes, your views and theories (by which you mean untested hunches) are > non-science. That's the hallmark of the willfully ignorant fundie. > You don't realize that all "theories" are NOT the same. In > particular, you are unwilling to admit the overwhelming evidence for > the "theory" (which does NOT mean hunch) of evolution. You are even > unwilling to admit that your "evidence" for creation is false, > spurious, or irrelevant. You are interested in confirming your > preconceived notion of what happened and when...not in the "truth". > You are in a conversation with people who make their living pursing > truth, and you are ignoring what they have to tell you. Hear, hear...BUT maybe this should have been directed more generally; this one may be less of a rabid-dog fundamentalist than many B-) > PS to the world...I apologize for posting this, but I have learned > that if you ignore the fundies they get louder, they do *not* go > away. The post to which I am responding should never have appeared on > a moderated newsgroup. This is NOT a moderated newsgroup - but as I have pointed out a number of times (sorry), it SHOULD be. If only to get rid of creationist garbage. Ed Rybicki, PhD Dept Microbiology | ed@molbiol.uct.ac.za University of Cape Town | rybicki@uctvms.uct.ac.za Private Bag, Rondebosch | phone: x27-21-650-3265 7700, South Africa | fax: x27-21-689 7573 WWW URL: http://www.uct.ac.za/microbiology/ed.html "Out here on the perimeter, there are no stars..." From owner-evolution@net.bio.net Mon Apr 07 23:00:00 1997 Path: biosci!agate!spool.mu.edu!uwm.edu!newsfeeds.sol.net!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 8 Apr 1997 23:50:58 GMT Organization: AT&T WorldNet Services Lines: 69 Message-ID: <01bc43ae$4b8c7d00$a84992cf@mycomputer> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> <334A51B6.17E5@luecology.ecol.lu.se> NNTP-Posting-Host: 207.146.73.168 X-Newsreader: Microsoft Internet News 4.70.1155 David Hagerberg wrote in article <334A51B6.17E5@luecology.ecol.lu.se>... > Mike Koller wrote: > > > > > > The fact is this: sex is *not* a problem for evolutionary biology. > > > > Theories regarding why sex persists (a separate question from how sex > > > > arose - which is also not a problem) are covered by any decent > > > college-level > > > > evolution text. > > > > > > > > Rich Kliman > > > > Dept. of Biology > > > > Radford University > > > > *standard disclaimer* > > > > > > > > Yup. I'm taking biology 1 and it's right there in plain english. Not hard > > to grasp or understand. It makes a whole lotta sense, scientifcally > > speaking of course. > > > > Some tidbits: > > > > "Darwin's first point - that evolution occurs - can stand on its own, > > whether or not natural selection is the cause". > > (What vs. How) > > > > "Natural selection involves interactions between individual organisms and > > their environment, but individuals do not evolve. Evolution can be > > measured only as changes in relative proportions of variations in a > > population over a succession of generations." > > > > Why sex is better than no sex (regarding survivability): > > > > "On average, those individuals best suited to the local environment leave > > the most offspring, transmitting their genese in the process. This natural > > selection results in adaptation, the accumulation of those genetic > > variations that are favored by the enironment. As the environment changes > > or a population moves, the population may survive if in each generation, at > > least some of its members can cope effectively with the new conditions. > > Different genetic variations may work better than those that prevailed in > > the old time or place. SEX and mutations are the two sources of this > > variation." > > > > All quotes from "Biology (4th ed.) by Campbell (Benjamin/Cummins Publ.) > > In the same time sex is an ensurement of smilarity. A recessive mutant > can be hidden by the normal alleles. Thus sex provides both similarity > and a library of variation if an organism needa it. > > Best regards > > David Hagerberg > And more to the point, why sex (mixing your genes 50/50) if the whole point of evolution revolves around a struggle to leave as many copies of you genes as possible. Heck, you do not leave even one!!! Regards, Joe From owner-evolution@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!daresbury!is.bbsrc.ac.uk!news From: Mazda Hewitt Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: Wed, 09 Apr 1997 10:53:03 +0100 Organization: John Innes Centre Lines: 18 Message-ID: <334B66FF.167E@bbsrc.ac.uk> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> NNTP-Posting-Host: jiio10.jic.bbsrc.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) Mike Koller wrote: > SEX and mutations are the two sources of this > variation." > > All quotes from "Biology (4th ed.) by Campbell (Benjamin/Cummins Publ.) Another reason for sex is to aliminate muatations which are deleterious, part of the sexulal mechanism (at the molecular level) removes mutations from the other set of chromosomes. Further without sex it would not be possible to combine seperate advantagious mutations happening indiendantly. The second muaution would have to happen to an offspring of the first, this is fine if you are a very fast reproducing organism like a bacterium, but not so good if your generations last 20 years!. Mazda Hewitt From owner-evolution@net.bio.net Tue Apr 08 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!newsxfer3.itd.umich.edu!newsxfer.itd.umich.edu!yale!oitnews.harvard.edu!purdue!mozo.cc.purdue.edu!cwen From: cwen@aux.btny.purdue.edu (Chi-Kuang Wen) Newsgroups: bionet.molbio.evolution Subject: MEETING ANNOUNCEMENT Date: Wed, 09 Apr 97 03:22:23 GMT Organization: Purdue University Lines: 212 Message-ID: <5if238$1sr@mozo.cc.purdue.edu> NNTP-Posting-Host: dial6.acn.ces.purdue.edu X-Newsreader: News Xpress 2.0 Beta #0 Keyword: FERN/DEVELOPMENT/EVOLUTION 1st announcement FERN DEVELOPMENT AND EVOLUTION A SPECIAL MEETING JULY 28-31, 1997 PURDUE UNIVERSITY,WEST LAFAYETTE, IN PURPOSE OF MEETING Ferns have historically played an important role in understanding plant development and evolution. The purpose of this meeting is to explore the diversity of questions in plant development and evolution that have been and can be addressed most effectively using ferns as model systems. This will be accomplished by a series of presentations by fern biologists (listed on the following page). Several workshops will also be held on the genetic, biochemical and molecular tools that must be developed and implemented in order to understand these questions at the cellular, molecular and mechanistic level. SPONSORS National Science Foundation Japanese Society for the Promotion of Science Purdue University CO-ORGANIZERS Akeo Kadota (Tokyo Metropolitan University; kadota@comp.metro-u.ac.jp) and Jody Banks (Purdue University; banks@btny.purdue.edu) INVITIED SPEAKERS: Masamitsu Wada (Tokyo Metropolitan University) "Adiantum as a model system for studying plant development" Les Hickok (University of Tennessee); "Ceratopteris as a model system for studying plant development". Michizo Sugai (Toyama University) "Photocontrol of fern spore germination" Takeshi Kanegae (Tokyo Metropolitan University) "Photoreceptor genes of the fern Adiantum". Takatoshi Kagawa (RIKEN Institute); photobiology of Adiantum.. Akeo Kadota (Tokyo Metropolitan University) "Red light aphototropic (rap) mutants of Adiantum" Takashi Murata (University of Tokyo) "Organization of cortical microtubules in Ceratopteris prothalli". Gar Rothwell (Ohio University) "Land plant phylogeny, homology, and the evolution of ferns" Kathleen Pryer (Field Museum) "Heterospory in ferns". Yasuyuki Watano (Kanazawa University) "Screening of cpDNA variation by PCR-SSCP and its application to the biosystematics of pteridophytes" Shigeo Masuyama (Tokyo Women's Christian University) "The use of allozyme markers to study cryptic species" Mitsuyasu Hasebe (University of Tokyo) "Molecular evolutionary morphology based on MADS box and homeobox gene expression in Ceratopteris" Stan Roux (University of Texas) "Influence of gravity and light on developmental polarity of single gametophytic cells of Ceratopteris richardii". Todd Cooke (University of Maryland) "Genetic basis of pattern formation in the Ceratopteris gametophyte". Jeff Hill (Idaho State University) "Developmental and genetic studies of the sporophyte in Ceratopteris.". Tom Warne (University of Tennessee) "High salinity tolerance and pleiotropy in the stl2 mutation of Ceratopteris-- Analysis of a physiologically complex phenotype" Jody Banks (Purdue University) "The genetic basis of sex determination in Ceratopteris" Chi-Kuang Wen (Purdue University) "Molecular biology of sex determination in Ceratopteris" Cristina Juarez (Purdue University) "Meristem development of the Ceratopteris gametophyte" Keith C. Cheng (Penn State College of Medicine) "Genetic Dissection of genomic instability and cell differentiation in zebrafish (Danio rerio) GENERAL INFORMATION Registration: Attendees must complete the attached registration form plus registration fee ($120.00) and mail by June 1, 1997 to : Ms. Nancy Burget Fern Meeting Department of Botany and Plant Pathology Agricultural Research Building Purdue University West Layafette, IN 47906 (burget@btny.purdue.edu) How to get there: Purdue Univesity is about 60 miles north of Indianapolis. There is a limousine service that runs between the Indianapolis International Airport and the Purdue campus every two hours ($18.00 one-way and $31.00 round-trip). Purdue Unversity also has its own airport, so arrangements to fly directly to Lafayette Airport can also be made. If you wish to take the limo or need transportation from the Purdue University airport, please let us know by contacting Ms. Nancy Burget (email: burget@btny.purdue.edu). Please include arrival and departure flight information. Where to stay: Hotel rooms are available at the Purdue Union Memorial Club. The rates (per number of occupants) are as follows: Deluxe double $78.00 (1) $88.00 (2) $93.00 (3) $100.00 (4) Double and twin 62.00 (1) 68.00 (2) 75.00 (3) - There is no charge for child or children in the same room with parents. Air conditioned dormitory rooms are also available at a rate of $30.80 per night for a single room, or $22.00 per person if you wish to share a room. Please indicate your preference for housing on the registration form. Food: There are many inexpensive eating establishments on and near the Purdue campus. Registration fee: Will include the cost of one evening meal. REGISTRATION FORM FERN DEVELOPMENT AND EVOLUTION JULY 28-31, 1997, PURDUE UNIVERSITY REGISTRATION DEADLINE: 1 JUNE 1997 Name: ______________________________________ Address: ______________________________________ ______________________________________ ______________________________________ ______________________________________ Phone: ______________________________________ Fax: ______________________________________ email: ______________________________________ Are you interested in presenting a poster? If you wish to stay in a dorm, please check here ______. If you wish to stay at the Purdue Memorial Union, please indicate your preference: Two double beds-deluxe _____; no. of persons_____ Double bed and twin bed ______; no. of persons_____ Arrival date: _________ (room reservations are canceled at 6 p.m. unless guaranteed or held by advance deposit; in this case, please give us your American Express, VISA, MasterCard or Discover number and expiration date (___________________) Departure date:_________ (1:00 p.m. check out hour) Please complete this form and a check for $120.00 (Payable to Purdue University) to: Ms. Nancy Burget Department of Botany and Plant Pathology Agriculture Research Building Purdue University West Lafayette, IN 47907 Chi-Kuang Wen Botany & Plant Pathology Purdue University West Lafayette, IN 47907 USA fax(work): (317)494-5896 phone(work):(317)494-0661 ¤å±Ò¥ú ´¶«×¤j¾Ç ´Óª«/´Ó¯f¨t¬ã¨s©Ò USA ¶Ç¯u: (317)494-5896 ¹q¸Ü: (317)494-0661 From owner-evolution@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!csn!nntp-xfer-1.csn.net!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!sprint!EU.net!Norway.EU.net!uninett.no!news.uni-c.dk!news-inn.uni-c.dk!news.uni-c.dk!balder.adm.ku.dk!not-for-mail From: Søren Schandorff Newsgroups: bionet.molbio.evolution Subject: paper on intron alignment Date: Mon, 07 Apr 1997 11:59:07 +0200 Organization: Zoological Institute Lines: 10 Message-ID: <3348C56B.6E9F@aki.ku.dk> Reply-To: SSchandorf@aki.ku.dk NNTP-Posting-Host: pc197.zi.ku.dk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01Gold (WinNT; I) Hi, I was told that somebody (presumably from NCBI) has done a study to determine which and how many introns (in GenBank) that can be aligned. If somebody know who did this study or know a reference I would very much like to know. Thanks, Soeren Schandorff University of Copenhagen E-mail: sschandorf@aki.ku.dk From owner-evolution@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!news-peer.sprintlink.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in2.uu.net!130.235.20.4!news.lth.se!merkurius.lu.se!not-for-mail From: David Hagerberg Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: Thu, 10 Apr 1997 08:24:52 -0700 Organization: Dep Microbial Ecology Lines: 35 Message-ID: <334D0644.5C92@luecology.ecol.lu.sexx> References: <01bc36f8$ee588820$784992cf@mycomputer> <3335BD3A.3288@phylo.zo.utexas.edu> <01bc3976$50366ec0$0a4892cf@mycomputer> <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> <334A51B6.17E5@luecology.ecol.lu.se> <01bc43ae$4b8c7d00$a84992cf@mycomputer> NNTP-Posting-Host: mbio1.ekol.lu.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Joe Potter wrote: > > David Hagerberg wrote in article > <334A51B6.17E5@luecology.ecol.lu.se>... > > > > In the same time sex is an ensurement of smilarity. A recessive mutant > > can be hidden by the normal alleles. Thus sex provides both similarity > > and a library of variation if an organism needa it. > > > > Best regards > > > > David Hagerberg > > > > And more to the point, why sex (mixing your genes 50/50) if the whole > point of evolution revolves around a struggle to leave as many copies of > you genes as possible. Heck, you do not leave even one!!! > > Regards, Joe I think the sex genes are incredible successfull, leaving a copy to every off-spring. Though sex isn't always mixing genes 50/50 and some organisms could reproduce both sexual and asexual, some even have more than two sexes. I think there is actual a struggle between the process of leaving as much copies of the own gene and the process of making a functional organism together with the other genes of the organism. I think Dawkin has described that in "The selfish gene". I suggest you read it and judged it out off what he says there. Best regards Dave From owner-evolution@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!sprint!howland.erols.net!vixen.cso.uiuc.edu!news.uoregon.edu!newsfeed.orst.edu!news.uidaho.edu!not-for-mail From: foster@skink.cs.uidaho.edu (James Foster) Newsgroups: bionet.molbio.evolution Subject: Re: Calveria Tree disproves Evolution Date: 09 Apr 1997 10:28:24 -0700 Organization: Dept of Computer Science, Univ of Idaho. Lines: 32 Distribution: bionet Message-ID: References: NNTP-Posting-Host: 129.101.55.85 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit In-reply-to: ed@MOLBIOL.UCT.AC.ZA's message of 8 Apr 1997 00:23:51 -0700 X-Newsreader: Gnus v5.1 In article ed@MOLBIOL.UCT.AC.ZA ("Ed Rybicki") writes: From: ed@MOLBIOL.UCT.AC.ZA ("Ed Rybicki") Newsgroups: bionet.molbio.evolution Date: 8 Apr 1997 00:23:51 -0700 Organization: Dept Microbiology, UCT Reply-To: ed@molbiol.uct.ac.za Path: news.uidaho.edu!netnews1.nwnet.net!netnews.nwnet.net!arclight.uoregon.edu!rill.news.pipex.net!pipex!uunet!in2.uu.net!204.31.212.2!biosci!MOLBIOL.UCT.AC.ZA!ed Lines: 45 Sender: daemon@net.bio.net Distribution: world NNTP-Posting-Host: net.bio.net Xref: news.uidaho.edu bionet.molbio.evolution:3875 Hear, hear...BUT maybe this should have been directed more generally; this one may be less of a rabid-dog fundamentalist than many B-) I do hate to appear to be attacking any individual fundie. I know (and am related) to several and, frankly, they're a pretty OK bunch socially. But they all have this chip on their shoulder about being attacked when someone disagrees with them. And they all think they are always right...hell, they have a direct line to God! This is not, and will never be, a "scientific" attitude. A fundie doesn't have to be rabid to be wrong. The fellow in this group may not be rabid, but he *is wrong*. -- James A. Foster email: foster@cs.uidaho.edu Laboratory for Applied Logic Dept. of Computer Science University of Idaho www: http://www.cs.uidaho.edu/~foster pgp key available at: ftp://ftp.cs.uidaho.edu/pub/foster/pgp-key.asc From owner-evolution@net.bio.net Wed Apr 09 23:00:00 1997 Path: biosci!PLANTPATH.PP.KSU.EDU!kzeller From: kzeller@PLANTPATH.PP.KSU.EDU ("Kurt Zeller") Newsgroups: bionet.molbio.evolution Subject: Re: Calveria Tree disproves Evolution Date: 10 Apr 1997 10:47:31 -0700 Organization: K.S.U. Plant Pathology Lines: 88 Sender: daemon@net.bio.net Distribution: world Message-ID: <11547A47D08@plantpath.pp.ksu.edu> References: <334D2C4E.B1F60B0E@home.com> NNTP-Posting-Host: net.bio.net > John Caballero wrote: > > > > In article <334d4782.2988928@netnews.worldnet.att.net> S. O. Teryk, > > alien.spydr@worldnet.att.net.nospam writes: > > >For the Fundie, a theroy is a hunch. For the anti-theists then, it > > > is not a hunch. That means that a Theory is a fact. By your reasoning > > > then, Evolution al facts, as reported in the last 35 years, have somehow > > > muted into a different form of facts. > > > > What an interesting and unique straw man. Theories are not facts. > > Theories attempt to explain actual phenomena. Gravitational theory is not > > a fact - it's a working model, if you will, of how gravity works. > > This is a very odd statement. I have always thought that the theory of > gravity was simply an attempt to explain certain motions of objects. > Your statement implies that gravity is first assumed to be an existing > entity, and then the theory is derived to explain how the entity works. At the risk of getting involved in a protracted battle of words & ideas,..... Nope, I don't think his statement implies that at all. The previous facts remain, it is the interpretation and explatations for them that change (generally subtly) over time. Actually the way it (the scientific process) is supposed to work follows this simplified sequence: 1) (an observation or fact) Things tend to fall to earth when you let them go 2) (form a basic hypothesis) Things fall because a force acts on objects & draws them toward the earth. 3) (hypothesis testing) Experiments are conducted to support/refute this hypothesis, and further observations (facts) are collected. 4) (revising/refining the previous hypothesis) Do the experimental results fit the hypothesis? -- if so then you might have the right idea, if not then The previous hypothesis must be revised to fit the new data, or abandoned in favor of a more explanitory idea/theory. ---Repeat as necessary--- Exceptions to expected observations should, and must, be taken into account. These are the observations that (gradually) let us get a better working hypothesis (or hypotheses) as a basis for our theories. Some theories have been around a very long time, and have been generally supported (but continuously & subtly modified). Other times "we" have realized that we were wrong, and completely new theories have had to be developed. That is the whole point of the scientific process. The exceptions to the general theories can be, at least at times, the most interesting part of doing science. They let us know what it is that we haven't quite gotten right as yet. Any Theory that cannot be tested in this manner is not science, and should not be debated as such. > > Evolutionary theory, is not a fact - it's a working model of how > > evolution works. Just as gravitational theory has to be modified when new > > discoveries about gravity are made, so does the evolutionary theory have > > to be modified when new discoveries about evolution are made. > > Same reasoning. And for the above reasons, his reasoning is still correct. Stress the point "Working Model" > > You need to check your premises. > > You may have to check yours s well. > Let's all go back and check our premises. And by the way, hasn't this thread gone on more than long enough already? Kurt ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Kurt Zeller Throckmorton Hall Dept. of Plant Pathology Kansas State University Manhattan, KS 66506 "Mock not the procrastinators,... for they will be the last to die!" From owner-evolution@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!sprint!news.maxwell.syr.edu!uknet!usenet1.news.uk.psi.net!uknet!uknet!newsfeed.ed.ac.uk!singer.cent.gla.ac.uk!usenet From: "Roderic D. M. Page" Newsgroups: bionet.molbio.evolution Subject: Postdoc in molecular systematics and cospeciation Date: Fri, 11 Apr 1997 10:00:57 +0100 Organization: University of Glasgow Lines: 39 Message-ID: <334DFDC9.6FAF@bio.gla.ac.uk> NNTP-Posting-Host: r-page.zoology.gla.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.02 (Win95; I) POSTDOC IN MOLECULAR SYSTEMATICS AND COSPECIATION PIs: R Page, R Griffiths, and R Furness A 3 year NERC funded post doc position is available in the Division of Environmental and Evolutionary Biology, University of Glasgow, Scotland, from June 1, 1997. The project will compare relative rates of molecular evolution in birds and their parasitic lice, concentrating on bird-louse assemblages that are likely to have cospeciated, such as seabirds, swifts and their lice. Both mitochondrial and nuclear genes will be sequenced. The specific aims are to test whether these birds and their lice have cospeciatied, and to determine the relative rates of evolution of homologous genes in the hosts and their parasites. More detailed information on this project an related work at Glasgow can be obtained by visiting http://taxonomy.zoology.gla.ac.uk/Jobs/NERC/postdoc.html. Applicants should be well versed in PCR, cloning, primer design, DNA sequencing and analysis. Experience working with insects is desirable, but not essential. Applications, comprising a C.V., names and addresses (including email address if possible) of two referees, and a statement of research interests, can be sent to Dr Roderic Page at the address below: -- =================================================== Dr Roderic D M Page Lecturer in Taxonomy Division of Environmental & Evolutionary Biology, IBLS University of Glasgow Glasgow G12 8QQ Scotland, U.K. Tel: (0141) 330 4778 Fax: (0141) 330 5971 email:r.page@bio.gla.ac.uk home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html =================================================== From owner-evolution@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!news-relay.ncren.net!hearst.acc.Virginia.EDU!newslink.runet.edu!newslink.runet.edu!news From: rkliman@runet.edu (Richard M Kliman) Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 11 Apr 1997 10:15:16 -0400 Organization: Radford University Lines: 20 Message-ID: <5ilh1k$c5r@ruacad.runet.edu> References: <01bc43c1$209adb60$864da1ce@koller.erols.com> <334A51B6.17E5@luecology.ecol.lu.se> <01bc43ae$4b8c7d00$a84992cf@mycomputer> NNTP-Posting-Host: ruacad-gw.runet.edu In article <01bc43ae$4b8c7d00$a84992cf@mycomputer>, Joe Potter wrote: > And more to the point, why sex (mixing your genes 50/50) if the whole >point of evolution revolves around a struggle to leave as many copies of >you genes as possible. Heck, you do not leave even one!!! Who said there's a point to evolution? You seem to be asking how sex can provide for one leaving more copies of one's genes (actually, a disproportionate amount of one's genes) than clonal reproduction. Passing on many copies of one's genes does not guarantee that one will disproportionately influence future gene pools. The carriers of one's genes must also be disproportionately successful offspring producers. Again, I any decent college-level evolution text explains why sexual reproduction is expected to be favored in certain contexts. Rich Kliman Dept. of Biology Radford University From owner-evolution@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!news.Stanford.EDU!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 11 Apr 1997 10:59:41 GMT Organization: AT&T WorldNet Services Lines: 59 Message-ID: <01bc459e$082011c0$b64792cf@mycomputer> References: <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> <5ikrmc$mhp@nntp3.u.washington.edu> NNTP-Posting-Host: 207.146.71.182 X-Newsreader: Microsoft Internet News 4.70.1155 Joe Felsenstein wrote in article <5ikrmc$mhp@nntp3.u.washington.edu>... > In article , > L.A. Moran wrote: > > [in response to postings about how easy it was to explain "sex"] > > >"It is worth noting that Maynard Smith's argument invalidates the earliest > >genetic argument for the evolution of recombination, that advanced by East > >(1918). That argument is also the one commonly found in textbooks, which > >tend to be a bit out of date (in this case, by over 50 years)." > > > >J. Felsenstein, "Sex and the Evolution of Recombination" in THE EVOLUTION > >OF SEX, R.E. Michod and B.R. Levins eds. Sinauer Associates 1988 (p.78) > > > >"We have the anomolous situation that a detailed population genetic analysis > > reveals not only that the standard explanation for the evolution of > > recombination will not work, but also that there is a good evolutionary > > reason for believing that modifiers will be selected to eliminate > > recombination." (ibid, p.79) > > > >Sex is very definitely a problem for evolutionary biology in spite of what > >the introductory biology textbooks say. > > Whoa. Cited that way, it sounds like my paper of 1988 concludes that > there is no decent explanation for "sex" (actually the argument is about > outcrossing-plus-recombination but it is conventional to call it "sex" so > as to attract more excitement). A more careful reading will disclose > that my position is that we have a whole bunch of explanations of "sex" > and that the problem for evolutionary biology is not to come up with an > explanation of "sex", but to distinguish between different possible ones. > > The passages cited are building up to mentioning a bunch of different > explanations people have advanced. > > -- > Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) > Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA > I took the words of Mr. Moran to be on the original topic that started all of this --- that Dr. Eldgrede has pointed out in his 1995 book that sex is a paradox from the "ultra-Darwinist" point of view. Your words seems to support that. What is your position on Eldredge's claim that sex represents a problem for those like Dawkins who see game as simply the contest to leave as many copies of one's own genes? Regards , Joe Potter From owner-evolution@net.bio.net Thu Apr 10 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in3.uu.net!140.142.64.3!news.u.washington.edu!evolution.genetics.washington.edu!joe From: joe@evolution.genetics.washington.edu (Joe Felsenstein) Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 11 Apr 1997 08:10:52 GMT Organization: University of Washington Genetics Lines: 36 Message-ID: <5ikrmc$mhp@nntp3.u.washington.edu> References: <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Recombination is sort of a problem, sort of not Keywords: evolution, sex, recombination In article , L.A. Moran wrote: [in response to postings about how easy it was to explain "sex"] >"It is worth noting that Maynard Smith's argument invalidates the earliest >genetic argument for the evolution of recombination, that advanced by East >(1918). That argument is also the one commonly found in textbooks, which >tend to be a bit out of date (in this case, by over 50 years)." > >J. Felsenstein, "Sex and the Evolution of Recombination" in THE EVOLUTION >OF SEX, R.E. Michod and B.R. Levins eds. Sinauer Associates 1988 (p.78) > >"We have the anomolous situation that a detailed population genetic analysis > reveals not only that the standard explanation for the evolution of > recombination will not work, but also that there is a good evolutionary > reason for believing that modifiers will be selected to eliminate > recombination." (ibid, p.79) > >Sex is very definitely a problem for evolutionary biology in spite of what >the introductory biology textbooks say. Whoa. Cited that way, it sounds like my paper of 1988 concludes that there is no decent explanation for "sex" (actually the argument is about outcrossing-plus-recombination but it is conventional to call it "sex" so as to attract more excitement). A more careful reading will disclose that my position is that we have a whole bunch of explanations of "sex" and that the problem for evolutionary biology is not to come up with an explanation of "sex", but to distinguish between different possible ones. The passages cited are building up to mentioning a bunch of different explanations people have advanced. -- Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41) Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA From owner-evolution@net.bio.net Thu Apr 10 23:00:00 1997 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in2.uu.net!128.100.1.3!utcsri!utgpu!lamoran From: lamoran@gpu.utcc.utoronto.ca (L.A. Moran) Subject: Re: Evolution or Creation? You Decide :) Message-ID: Organization: UTCNS Public Access References: <5hofnd$l3e@ruacad.runet.edu> <01bc3fbd$8f8ecac0$a94892cf@mycomputer> <01bc43c1$209adb60$864da1ce@koller.erols.com> Date: Thu, 10 Apr 1997 19:47:07 GMT Lines: 40 In article <01bc43c1$209adb60$864da1ce@koller.erols.com>, Mike Koller wrote: >> > The fact is this: sex is *not* a problem for evolutionary biology. >> > Theories regarding why sex persists (a separate question from how sex >> > arose - which is also not a problem) are covered by any decent >> > college-level >> > evolution text. >> > >> > Rich Kliman >> > Dept. of Biology >> > Radford University >> > *standard disclaimer* >Yup. I'm taking biology 1 and it's right there in plain english. Not hard >to grasp or understand. It makes a whole lotta sense, scientifcally >speaking of course. "It is worth noting that Maynard Smith's argument invalidates the earliest genetic argument for the evolution of recombination, that advanced by East (1918). That argument is also the one commonly found in textbooks, which tend to be a bit out of date (in this case, by over 50 years)." J. Felsenstein, "Sex and the Evolution of Recombination" in THE EVOLUTION OF SEX, R.E. Michod and B.R. Levins eds. Sinauer Associates 1988 (p.78) "We have the anomolous situation that a detailed population genetic analysis reveals not only that the standard explanation for the evolution of recombination will not work, but also that there is a good evolutionary reason for believing that modifiers will be selected to eliminate recombination." (ibid, p.79) Sex is very definitely a problem for evolutionary biology in spite of what the introductory biology textbooks say. Larry Moran From owner-evolution@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news.maxwell.syr.edu!news.bc.net!rover.ucs.ualberta.ca!news!wblank From: wblank@gpu.srv.ualberta.ca (Panhead McNipper) Newsgroups: bionet.molbio.evolution Subject: Re: Calveria Tree disproves Evolution Date: Fri, 11 Apr 97 19:43:55 GMT Organization: University of Alberta Biological Sciences Lines: 30 Message-ID: References: <19970411173200.NAA02734@ladder01.news.aol.com> NNTP-Posting-Host: gmslab.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.1 In Article <19970411173200.NAA02734@ladder01.news.aol.com>, cwilson379@aol.com (CWilson379) wrote: >Is anyone else in this newsgroup interested in abandoning this inane >ping-pong match in favor of an intelligent analysis of the supposed >contradictions between scientific models of evolution and biblical >explanations of creation? How about taking it out of bionet.molbio.evolution altogether? From the BIOSCI/bionet homepage: "BIOSCI promotes communication between professionals in the biological sciences. All postings to the newsgroups should be made in that spirit. While the general public may "listen in" to the discussions, these newsgroups are intended primarily for communications between researchers. There are other forums on Usenet such as sci.bio.misc for the asking and answering of biological questions from lay persons. " _That_ is what the sponsors of the bionet newsgroups (bless them) are paying for. Crap like _this_ thread belongs in talk.origins. Wally -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- "Provided it lives with a normally constituted social group, a monkey raised in a restricted laboratory environment differs from a feral animal only in quantitative ways, such as the time required to achieve normal sexual behavior." -- E.O. Wilson, _Sociobiology_ It's all much appreciated. Out! From owner-evolution@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!worldnet.att.net!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!uunet!in3.uu.net!152.163.170.17!newstf01.news.aol.com!audrey01.news.aol.com!not-for-mail From: cwilson379@aol.com (CWilson379) Newsgroups: bionet.molbio.evolution Subject: Re: Calveria Tree disproves Evolution Date: 11 Apr 1997 17:32:05 GMT Organization: AOL http://www.aol.com Lines: 18 Message-ID: <19970411173200.NAA02734@ladder01.news.aol.com> References: NNTP-Posting-Host: ladder01.news.aol.com X-Admin: news@aol.com Is anyone else in this newsgroup interested in abandoning this inane ping-pong match in favor of an intelligent analysis of the supposed contradictions between scientific models of evolution and biblical explanations of creation? I see no contradictions, other than those created by the bickering of underdeveloped minds. I consider myself a Christian and an avid lay researcher in many scientific fields. Knowledge of scientific models, and improvements thereon abetted by more recent discoveries, adds to my understanding of and faith in my spiritual beliefs. Study of scripture and related materials helps me to appreciate the divine aspect of knowledge. Anyone else interested in taking up the possibility of peaceful (not to mention necessary) co-existence between religion and science, please e-mail me. P. S. I do not think of myself as a "fundie" and I do not accept the validity of criticism or ostracism from believers of any persuasion who claim the credential of ignorance in derogation of honest inquiry. From owner-evolution@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 12 Apr 1997 14:57:10 GMT Organization: AT&T WorldNet Services Lines: 30 Message-ID: <01bc45ff$2e46cc20$334892cf@mycomputer> References: NNTP-Posting-Host: 207.146.64.251 X-Newsreader: Microsoft Internet News 4.70.1155 "Ed Rybicki" wrote in article ... > > From: "Joe Potter" > > Subject: Re: Evolution or Creation? You Decide :) > .... > > the object is self-replication as "Ultra-Darwinists" claim. (his term, not > > "Ultra-Darwinists"...hmm: that makes me a Libertarian Dawkinist, > perhaps? Or maybe a Liberal Eldredgite. Or even a Neo-Reformed > Darwinite? Actually, I prefer Punctuated Non-Equilibriumist. > > Ed Rybicki, PhD > Dept Microbiology | ed@molbiol.uct.ac.za > University of Cape Town | rybicki@uctvms.uct.ac.za > Private Bag, Rondebosch | phone: x27-21-650-3265 > 7700, South Africa | fax: x27-21-689 7573 > WWW URL: http://www.uct.ac.za/microbiology/ed.html > > "Out here on the perimeter, there are no stars..." > Ed, I speculate you know that "ultra-Darwinist" is Dr. Eldredge's term for those like Dr. Dawkins. Maybe you should send him your little joke. Regards, Joe From owner-evolution@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!news.maxwell.syr.edu!news-xfer.netaxs.com!netaxs.com!myers From: myers@netaxs.com (PZ Myers) Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Followup-To: talk.origins Date: Sat, 12 Apr 1997 10:13:24 -0400 Organization: Net Access - Philadelphia's Original ISP Lines: 54 Message-ID: References: <01bc43c1$209adb60$864da1ce@koller.erols.com> <334A51B6.17E5@luecology.ecol.lu.se> <01bc43ae$4b8c7d00$a84992cf@mycomputer> <5ilh1k$c5r@ruacad.runet.edu> <01bc4662$fe880e40$294192cf@mycomputer> NNTP-Posting-Host: chestnut1-7.slip.netaxs.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Newsreader: Yet Another NewsWatcher 2.4.0 In article <01bc4662$fe880e40$294192cf@mycomputer>, "Joe Potter" wrote: > Richard M Kliman wrote in article > <5ilh1k$c5r@ruacad.runet.edu>... > > In article <01bc43ae$4b8c7d00$a84992cf@mycomputer>, > > Joe Potter wrote: > > > And more to the point, why sex (mixing your genes 50/50) if the whole > > >point of evolution revolves around a struggle to leave as many copies of > > >you genes as possible. Heck, you do not leave even one!!! > > > > Who said there's a point to evolution? > > > > You seem to be asking how sex can provide for one leaving more copies of > > one's genes (actually, a disproportionate amount of one's genes) than > > clonal reproduction. Passing on many copies of one's genes does not > > guarantee that one will disproportionately influence future gene pools. > > The carriers of one's genes must also be disproportionately successful > > offspring producers. Again, I any decent college-level evolution text > > explains why sexual reproduction is expected to be favored in certain > > contexts. > > > > Rich Kliman > > Dept. of Biology > > Radford University > > > > Rich, you seem to have missed some part of the thread. I pointed out > (earlier) that Dr. Eldrege called sex a paradox from the ultra-Darwinist > (his words, not mine) point of view. > > He is saying that sex makes no sense if Dawkins position is correct that > evolution is simply the struggle to leave more copies of one's own genes. > This is from his 1995 book, last chapter. And he's right -- it doesn't make sense if Dawkins is correct. The proper resolution of the problem, of course, is to assume that Dawkins (or at least, this interpretation of Dawkins) is wrong. The kind of selection you are talking about here does not operate at the level of the genes, but upon individuals. If making sloppy copies of my genes allows me to produce more fit progeny than the individual who demands flawless reproduction, then natural selection will fill up the world with my descendants, not his, and low- fidelity copies of me will rule! As you might guess from the name, ultra-darwinism is an extremist caricature. It's a school of thought that is far out on one end of a continuum, and if you want to argue against it, you will find lots of competent biologists who will argue on your side. Of course, if you think that refuting an extreme interpretation means you've refuted all of evolutionary thought, you might get some argument _against_ you from those same biologists. May I ask why this discussion is going on in bionet.molbio.evolution? It really doesn't belong here, so I've redirected follow-ups to talk.origins. From owner-evolution@net.bio.net Fri Apr 11 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!arclight.uoregon.edu!newsfeed.dacom.co.kr!xfer.kren.nm.kr!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!worldnet.att.net!newsadm From: "Joe Potter" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 12 Apr 1997 10:29:39 GMT Organization: AT&T WorldNet Services Lines: 35 Message-ID: <01bc4662$fe880e40$294192cf@mycomputer> References: <01bc43c1$209adb60$864da1ce@koller.erols.com> <334A51B6.17E5@luecology.ecol.lu.se> <01bc43ae$4b8c7d00$a84992cf@mycomputer> <5ilh1k$c5r@ruacad.runet.edu> NNTP-Posting-Host: 207.146.65.41 X-Newsreader: Microsoft Internet News 4.70.1155 Richard M Kliman wrote in article <5ilh1k$c5r@ruacad.runet.edu>... > In article <01bc43ae$4b8c7d00$a84992cf@mycomputer>, > Joe Potter wrote: > > And more to the point, why sex (mixing your genes 50/50) if the whole > >point of evolution revolves around a struggle to leave as many copies of > >you genes as possible. Heck, you do not leave even one!!! > > Who said there's a point to evolution? > > You seem to be asking how sex can provide for one leaving more copies of > one's genes (actually, a disproportionate amount of one's genes) than > clonal reproduction. Passing on many copies of one's genes does not > guarantee that one will disproportionately influence future gene pools. > The carriers of one's genes must also be disproportionately successful > offspring producers. Again, I any decent college-level evolution text > explains why sexual reproduction is expected to be favored in certain > contexts. > > Rich Kliman > Dept. of Biology > Radford University > Rich, you seem to have missed some part of the thread. I pointed out (earlier) that Dr. Eldrege called sex a paradox from the ultra-Darwinist (his words, not mine) point of view. He is saying that sex makes no sense if Dawkins position is correct that evolution is simply the struggle to leave more copies of one's own genes. This is from his 1995 book, last chapter. Regards, Joe From owner-evolution@net.bio.net Sat Apr 12 23:00:00 1997 Newsgroups: bionet.molbio.evolution Path: biosci!rutgers.rutgers.edu!csn!nntp-xfer-1.csn.net!su-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!howland.erols.net!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in3.uu.net!128.100.1.3!utcsri!utgpu!lamoran From: lamoran@gpu.utcc.utoronto.ca (L.A. Moran) Subject: Re: Evolution or Creation? You Decide :) Message-ID: Keywords: evolution, sex, recombination Organization: UTCNS Public Access References: <01bc43c1$209adb60$864da1ce@koller.erols.com> <5ikrmc$mhp@nntp3.u.washington.edu> Date: Sun, 13 Apr 1997 18:21:34 GMT Lines: 45 In article <5ikrmc$mhp@nntp3.u.washington.edu>, Joe Felsenstein wrote: >In article , >L.A. Moran wrote: >[in response to postings about how easy it was to explain "sex"] [quotations from a Felsenstein paper pointing out that the simple explanations of the evolution of sex are inadequate and that sex is a difficult problem for evolutionists] >Whoa. Cited that way, it sounds like my paper of 1988 concludes that >there is no decent explanation for "sex" (actually the argument is about >outcrossing-plus-recombination but it is conventional to call it "sex" so >as to attract more excitement). A more careful reading will disclose >that my position is that we have a whole bunch of explanations of "sex" >and that the problem for evolutionary biology is not to come up with an >explanation of "sex", but to distinguish between different possible ones. Sorry, I didn't mean to imply that you (and others) don't have educated guesses concerning the orign of sex. (Perhaps hypotheses would be a better term?) The problem is to determine which, if any, of these hypotheses is correct. However, the main point that you make is that the question is far from solved and you mentioned that the simple textbook explanations are not likely to be correct. I wanted to post your comments because it directly refuted the claim that the explanation of sex was easy and could be found in any textbook. I didn't think that you would respond to the original article. I was trying to indicate that some very smart people have concluded that sex is a problem. BTW, this compliment doesn't imply that I agree with all of your hypotheses .... (-: >The passages cited are building up to mentioning a bunch of different >explanations people have advanced. Yep, .... and some of them are interesting while others are very likely to be wrong. Hence, we have a problem with sex. Larry Moran From owner-evolution@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "David Pollock" Newsgroups: bionet.molbio.evolution Subject: Re: Evolution of sex Date: 14 Apr 1997 17:50:47 +0100 Lines: 38 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5itn97$d8r@mserv1.dl.ac.uk> References: <9741405516.~INN-MFDa00253.bionet-news@dl.ac.uk> Original-To: mol-evol@dl.ac.uk In response to Felsenstein/Moran: This thread is getting interesting. Let's ignore earlier attacks on verbal arguments by Eldredge and Dawkins, which are bound to (and do) fall apart under close scrutiny. Also, Felsenstein's specificity about sex as "outcrossing-plus-recombination" (as opposed to concerns over ploidy and two sexes) is useful. Precise work with two-locus recombination modifier models has led to Felsenstein's quote that "modifiers will be selected to eliminate recombination". However, my interpretation of recent work by Charlesworth, Hudson, and others on models to explain why variation is low in regions of low recombination is that these (many-locus) models will in the end offer a very good explanation for outcrossing-plus-recombination. That is, the lower the recombination, the larger the regions of the chromosome which behave as non-recombining units, and the more these units have a lower localized effective population size and tend to suffer from Muller's ratchet effects. Any comments by someone working with these models? David Pollock Laboratory of Mathematical Biology National Institute for Medical Research The Ridgeway, Mill Hill, London, NW7 1AA U.K. d-polloc@nimr.mrc.ac.uk -- David D. Pollock Laboratory of Mathematical Biology National Institute for Medical Research The Ridgeway, Mill Hill, London, NW7 1AA U.K. d-polloc@nimr.mrc.ac.uk 0181-959-3666 ext. 2396 (+44-181-959-3666) Fax: 0181-913-8545 From owner-evolution@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!agate!ihnp4.ucsd.edu!gondor!newshub.sdsu.edu!news.sgi.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!ais.net!uunet!in3.uu.net!192.35.48.11!hearst.acc.Virginia.EDU!newslink.runet.edu!newslink.runet.edu!news From: rkliman@runet.edu (Richard M Kliman) Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 14 Apr 1997 09:43:09 -0400 Organization: Radford University Lines: 49 Message-ID: <5itc9d$8u6@ruacad.runet.edu> References: <01bc43ae$4b8c7d00$a84992cf@mycomputer> <5ilh1k$c5r@ruacad.runet.edu> <01bc4662$fe880e40$294192cf@mycomputer> NNTP-Posting-Host: ruacad-gw.runet.edu In article <01bc4662$fe880e40$294192cf@mycomputer>, Joe Potter wrote: > > >Richard M Kliman wrote in article ><5ilh1k$c5r@ruacad.runet.edu>... >> In article <01bc43ae$4b8c7d00$a84992cf@mycomputer>, >> Joe Potter wrote: >> > And more to the point, why sex (mixing your genes 50/50) if the whole >> >point of evolution revolves around a struggle to leave as many copies of >> >you genes as possible. Heck, you do not leave even one!!! >> >> Who said there's a point to evolution? >> >> You seem to be asking how sex can provide for one leaving more copies of >> one's genes (actually, a disproportionate amount of one's genes) than >> clonal reproduction. Passing on many copies of one's genes does not >> guarantee that one will disproportionately influence future gene pools. >> The carriers of one's genes must also be disproportionately successful >> offspring producers. Again, I any decent college-level evolution text >> explains why sexual reproduction is expected to be favored in certain >> contexts. > Rich, you seem to have missed some part of the thread. I pointed out >(earlier) that Dr. Eldrege called sex a paradox from the ultra-Darwinist >(his words, not mine) point of view. > > He is saying that sex makes no sense if Dawkins position is correct that >evolution is simply the struggle to leave more copies of one's own genes. >This is from his 1995 book, last chapter. I'm confused. I thought the point of this thread was to discuss possible explanantions for the persistence of sexual reproduction in the face a presumed cost to the female. If the point of this thread is to argue the merits of Eldredge's book or Dawkins' "ultra-Darwinist" viewpoint, then fine. If Eldredge argues that sex makes no sense in the context of Dawkins' argument, then either (1) Eldrege is wrong - sex is compatible with Dawkins - or (2) Dawkins is wrong. Either way, this has little to do with the origin and maintenance of sex - i.e., the actual study of evolution. Neither Eldredge nor Dawkins - regardless of their collective contributions to evolutionary biology - should serve as a focus for discussions on the evolution of sex. So what *is* the point to this thread? Rich Kliman Dept. of Biology Radford University From owner-evolution@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!daresbury!uninett.no!hermod.uio.no!nntp.uio.no!newsfeeds.sol.net!news.webspan.net!usenet From: "French A. Lewis" Newsgroups: bionet.molbio.evolution Subject: model organisms Date: 14 Apr 1997 16:44:41 EDT Organization: WebSpan Inc., New Jersey Lines: 13 Message-ID: NNTP-Posting-Host: orion.webspan.net Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Sender: falewis@orion.webspan.net Does any one know of any invertebrate organisms that are less primitive than C. elegans, and more primitive than Drosophila that are currently being studied for neurobiology? We are attempting to clone a C. elegans homologue of a human gene, and are looking for an intermediate organism to jump to. Any information would be appreciated. Thanks in advance, French Lewis CSI/IBR Center for Developmental Neuroscience From owner-evolution@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!fcs280s.ncifcrf.gov!cpk-news-feed1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!disgorge.news.demon.net!demon!dispatch.news.demon.net!demon!uknet!usenet1.news.uk.psi.net!uknet!uknet!yama.mcc.ac.uk!news.york.ac.uk!not-for-mail From: Peter Ashton Newsgroups: bionet.molbio.evolution Subject: Re: model organisms Date: Tue, 15 Apr 1997 17:17:26 +0100 Organization: University of York, UK Sender: pda100@york.ac.uk Message-ID: <3353AA16.10D9@york.ac.uk> References: Reply-To: pda100@york.ac.uk NNTP-Posting-Host: ppp10.york.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.0b2 (Win95; I) X-Priority: 3 (Normal) Lines: 22 French A. Lewis wrote: > > Does any one know of any invertebrate organisms that are less primitive > than C. elegans, and more primitive than Drosophila that are currently > being studied for neurobiology? > > We are attempting to clone a C. elegans homologue of a human gene, and are > looking for an intermediate organism to jump to. Any information would > be appreciated. > > Thanks in advance, > French Lewis > CSI/IBR Center for Developmental Neuroscience Isn't Schistosoma mansoni a model organism as well? It might be just what you need :-) There is quite a lot about the neurobiology of S. mansoni, but I don't have any references to hand...but Rollinson and Simpson, The biology of Schistosomes might be a good place to start.... Pete From owner-evolution@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!gatech!news-relay.ncren.net!hearst.acc.Virginia.EDU!newslink.runet.edu!newslink.runet.edu!news From: rkliman@runet.edu (Richard M Kliman) Newsgroups: bionet.molbio.evolution Subject: Re: Evolution or Creation? You Decide :) Date: 15 Apr 1997 16:08:56 -0400 Organization: Radford University Lines: 28 Message-ID: <5j0n8o$j38@ruacad.runet.edu> References: <5ikrmc$mhp@nntp3.u.washington.edu> <01bc459e$082011c0$b64792cf@mycomputer> NNTP-Posting-Host: ruacad-gw.runet.edu In article <01bc459e$082011c0$b64792cf@mycomputer>, Joe Potter wrote: > I took the words of Mr. Moran to be on the original topic that started all >of this --- that Dr. Eldgrede has pointed out in his 1995 book that sex is >a paradox from the "ultra-Darwinist" point of view. Your words seems to >support that. > > What is your position on Eldredge's claim that sex represents a problem >for those like Dawkins who see game as simply the contest to leave as many >copies of one's own genes? I realize this is addressed to Joe, but may I butt in? Is it *really* Dawkins' view that the "game" is to leave as many copies of ones genes? I find it difficult to believe that Dawkins, of all people, would resort to such a goal-oriented model of evolution. Except in rare cases, the future of a gene depends on it's carrier - i.e., on the ability of individuals carrying it to survive and reproduce relative to those not carrying it. I don't think Dawkins would say otherwise (though I obviously don't speak for Dawkins), and it seems to me that you are presenting a strawman argument. And I still don't understand the fixation on Eldredge's opinions. Do you want to discuss evolution of sex or a particular individual's views on what he perceives to be someone else's model of gene evolution? Rich Kliman Dept. of Biology Radford University From owner-evolution@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!munnari.OZ.AU!news.ecn.uoknor.edu!feed1.news.erols.com!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!susx.ac.uk!mattst From: mattst@cogs.susx.ac.uk (Matthew Stanfield) Newsgroups: bionet.molbio.evolution,bionet.molbio.gene-linkage Subject: DNA - is it alive? Date: 15 Apr 1997 12:52:37 GMT Organization: University of Sussex Lines: 18 Message-ID: <5ivtml$68p@infa.central.susx.ac.uk> NNTP-Posting-Host: tsunx.ctn.cogs.susx.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.evolution:5880 bionet.molbio.gene-linkage:1374 Hi I'm writing a university essay on artificial life. What I would like to know is if DNA could under any circumstances be considered alive? What about proteins? Bacteria, presumably, are considered alive as are viruses. At what point do 'simple things' cease to be alive and become, say, just a chemical reaction? Thanks in advance. (Answers by email would be preferred.) Thanks, Matthew \\\// J Matthew Stanfield (O O) ------------------------oOO----(_)----OOo----------------------------- School of Cognitive and Computing Sciences, University of Sussex, UK Email: mattst@cogs.susx.ac.uk Phone: UK (+44) 0831 542806 Or: matthew.stanfield@bigfoot.com Fax : UK (+44) 01865 514494 ---------------------------------------------------------------------- From owner-evolution@net.bio.net Mon Apr 14 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in3.uu.net!192.220.251.22!netnews.nwnet.net!news-hub.interserv.net!news.sprynet.com!not-for-mail From: jmhoward@sprynet.com (James Howard) Newsgroups: bionet.molbio.evolution Subject: A Theory of the Evolution of Eukaryotes, Crossing Over and Sex Date: Wed, 16 Apr 1997 20:03:36 GMT Organization: Sprynet News Service Lines: 178 Message-ID: <33553012.740891@news.sprynet.com> NNTP-Posting-Host: ad30-129.compuserve.com X-Newsreader: Forte Free Agent 1.1/32.230 A Theory of the Evolution of Eukaryotes, Crossing Over and Sex James Howard (http://www.naples.net/~nfn03605) Steroids, histones, and mitochondria appear in relatively close proximity in the evolution of eukaryotes. It is my theory that the hormone, dehydroepiandrosterone (DHEA), may be the reason that mitochondrial-like organisms (MLOs) successfully invaded "host cells," the combination, of which, eventually produced eukaryotic organisms. My principal hypothesis of my theory is that DHEA is directly involved in the opening of the DNA helix, during transcription and replication. Based on this hypothesis, the host cell produced DHEA for transcription and replication of its own DNA. When MLOs were included into the milieu of the host cells, the DNA of the MLOs benefited from the DHEA. In the following quotation, note that not only is mitochondrial respiration stimulated by DHEA, but protrein synthesis is also stimulated. This is an indication that DHEA positively affects transcription of the mitochondrial DNA. "These findings indicate that mitochondrial respiration is the earliest factor affected by DHEA and may be associated with protein synthesis." Journal of Nutrition 1991; 121: 240 The entry of MLO DNA into the host cell would create a competition for DHEA between the two genomes. This would produce a selection pressure that would affect DNA and DHEA. (Over time, I suggest, this would stimulate an increase in endothermic organisms, as it would also increase the numbers of mitochondria in the organisms.) My theory suggests that DHEA exerts its effect on DNA by hydrogen bonding between thymine and adenine bases in DNA. Therefore, the effect of competition for DHEA in the host cell genome would be an increase in thymine-adenine bases. An increase in T-A bases would increase the effects of DHEA in the host genome. I suggest this is the reason that E. coli has approximately 25% of each of the nitrogenous bases, while humans and other mammals have about 21% cytosine and quanine and 29% thymine and adenine. It may be that this increase in thymine and adenine was accomplished by development of multiple sites for DNA replication in the nuclei of eukaryotes. Replication sites should exhibit increased areas of T-A bases. Increased replication sites should, therefore, increase competition for DHEA by nuclear DNA. It is known that certain levels of nuclear DNA and mitochondria must exist before eukaryotic cells can divide. It is my theory this occurs, because of the competition between the two DNAs for DHEA, i.e., not enough DHEA is produced for nuclear DNA replication during the time of mitochondrial growth, and vice versa. That is, nuclear and mitochondrial DNA compete for a limited supply of DHEA. One waits on the other, i.e., a time lag in mitochondrial growth and nuclear DNA replication would develop. Eukaryotes would accommodate this lag in DHEA availability by developing a mechanism which would inhibit nuclear DNA replication until mitochondrial replication has finished. Following mitochondrial use of DHEA, DHEA and mitochondrial energy could then be used for mitosis. I suggest the mechanisms that evolved for separating the use of DHEA, by the two genomes, are H1 histones and the nuclear envelope, hallmarks of the eukaryotes. H1 histones, according to my theory, developed to repress nuclear DNA replication. That is, these histones are a mechanism to shut down DNA opening by DHEA, therefore, freeing up DHEA for mitochondrial use. Mitochondria do not produce histones. Since a nuclear envelope is also characteristic of eukaryotes, the nuclear envelope may have evolved to sequester H1 histone gene translation in the nuclear envelope, so H1s could not turn off mitochondrial DNA, and, therefore, mitochondrial energy. H1s are, indeed, synthesized directly in the nuclear milieu. (In 1979, work on H1s had established that H1s could repress transcription. Also, in 11979, I developed a detailed explanation of how the H1s can be affected by phosphorylation and nonhistone chromosomal proteins to open DNA for transcription. For sake of brevity, at this time, I will post it at another time.) Crossing Over In 1992, I had the occasion to respond to an author of the Journal of Reproduction and Fertility 1991; 93: 467, about the "fluctuation of histone H1 kinase activity during meiotic maturation in porcine oocyes." I wrote to explain how my model of transcription control by H1s may fit their findings in meiosis. (That letter included my mechanism of H1 control of transcription, in detail) One of my important hypotheses, generated by my letter to them, was a new explanation of crossing over. For this part of my theory, you need to know that phosphorylation of H1s removes H1s from chromatin. This phosphorylation of H1s, according to my theory, is necessary before DNA synthesis in mitosis and meiosis. In the same manner as my transcription theory suggests, H1s must be removed before replication may occur. (H1 kinase phosphorlyates H1s.) Naito and Toyoda contains a diagram of H1 kinase activity, Fig 3, page 471, that shows that H1 kinase activity is low in the germinal vesicle, rises in prometaphase I, and reaches a maximum in metaphase I. The activity then declines to just above that of the germinal vesicle at anaphase and telophase I. It then increases, again, at metaphase II, essentially as high as that of metaphase I. As I reread some textbooks about meiosis in preparation for writing Naito, it occurred to me that crossing over of pachytene during meiotic prophase may result from relatively incomplete phosphorylation of H1 histones at this time. That is, as H1 histones are removed by phosphorylation, detached unphosphorylated H1 histones may actually recombine with core histones of other stands of DNA and cause crossing over. (It is established that H1s are attached at one end to the core histones and at the other end in the "linker region of DNA" between core histones.) During pachytene the levels of H1 kinase, according to my theory of crossing over, is not so high; this would explain why crossing over occurs at pachytene and not later in meiosis, when H1 kinase activity is so high. If my idea is correct, not only will this explain crossing over, but will provide a powerful evolutionary selection pressure for development of H1 histone formation in evolution of eukaryotes. That is, the core histones probably evolved first to act as support structures for DNA replication and condensation in eukaryotes, somewhat advanced beyond yeasts. (Yeasts do not produce H1 histones.) This extremely useful function of crossing over would evolve along with sex and the true eukaryotes. The idea is that if only a small fraction of H1 histones are not phosphorylated on time, crossing over occurs. If the vast majority are not phosphorylated, then nondisjunction occurs; the chromosomes are literally glued together by the histones. This is a general mechanism, supported by the following quotation. "(1) Nondisjunction of the sex chromosomes is largely confined to the first meiotic division; (2) nondisjunction involves chromosomes 2 and 3 as well as the sex chromosomes; this argues against a specific geometrical problem with sex chromosomes pairing and segregation and in favor of a more general physiological effect on the control of meiosis; ...""Genetics 1984; 107: 609 If I am correct, this effect should be relatively global, i.e., it should not be isolated to one particular chromosome. Also, it should occur during the first meiotic division. The Evolution of Sex I suggest that protein kinase evolved to remove H1 histones totally from DNA for replication. Since cell division would benefit from this, it seems appropriate to assume that the activity had selection value. That is, cells that were better at it, divided more. My theory of the interaction of H1s and DHEA also explains multicelluarity. That is, specialization in the manipulation of H1 removal probably occurred over time in different cells. Differential removal of H1s could produce differences in transcription in different cells. Eventually, the non-histone chromosomal proteins, that I utilize to explain differential transcription, would arise. Differential transcription, at some point, must have produced problems for cell division, within multicellular clumps of cells. In cells in which the chromatin exhibited very little transcription, cell division would be a problem. I suggest the protein kinase evolved to over come this division problem. That is, some of these cells over-expressed, or perhaps produced a more powerful protein kinase for allowing cell division. Since these cells would be characterized by highly repressed DNA, the DHEA would be more readily available for the mitochondria. This would increase the energy and cytoplasm available for cytoplasmic division, while the nuclear DNA remained repressed. A single event, or a single cascade of events, involving protein kinase could have evolved that resulted in a rapid DNA replication in cells that have increased tremendously in size, due to increased mitochondrial function and reproduction. This scenario could eventually produce a large cell with a haploid genome, due to a rapid division. Since these cells would be nutrient enriched, fusion of two of them could rapidly produce a diploid cell. This fused cell would exhibit rapid cell divisions, because of extra mitochondrial energy and mass. The daughter cells could produce "normal" multicellularity as the mitochondrial and nuclear genome reestablish a normal ratio of nuclear and mitochondrial DNA to DHEA. Eventually, the formation of the severely repressed cells would occur, and the mechanism would repeat itself. All that would be necessary for "sex" to evolve are mechanisms that would enhance the process. Such things as chromosomal part deletions, crossing over, etc. may enhance the repression in these cells, the size of the cytoplasm, etc. These could produce the large egg and small sperm that we see today. Of course nature is full of the variations leading from simple cell division, to fusion of two similar, haploid cells, to the formation of the egg and sperm that would increase the favorable aspect of fusion of two large haploid cells from two different organisms. James Howard From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!ihnp4.ucsd.edu!news.scripps.edu!not-for-mail From: Rolf Marteijn Newsgroups: bionet.molbio.evolution,bionet.molbio.gene-linkage Subject: Re: DNA - is it alive? Date: Tue, 15 Apr 1997 17:59:04 -0700 Organization: The Scripps Research Institute Lines: 21 Message-ID: <33542458.46A4@lx.student.wau.nl> References: <5ivtml$68p@infa.central.susx.ac.uk> NNTP-Posting-Host: 192.26.254.53 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.01 (Macintosh; I; PPC) Xref: biosci bionet.molbio.evolution:5885 bionet.molbio.gene-linkage:1375 Matthew Stanfield wrote: > Hi I'm writing a university essay on artificial life. What I would like to > know is if DNA could under any circumstances be considered alive? What about DNA is just a (very large) molecule, like proteins, RNA, sugars, starch etc. Definitly not alive (in my not so very humble opinion). > proteins? Bacteria, presumably, are considered alive as are viruses. At what Bacteria are generally considered alive. However viruses are somewere in the twilight zone between live and dead. They can't replicate with their own system alone. The discussion will never end, but I favor the 'dead' option. > point do 'simple things' cease to be alive and become, say, just a chemical > reaction? IMHO: -should be an organised system (of molecules) that can self replicate without outside interference and able to adopt a bit to the environment. This is crude and probably not complete, but it's just my humble opinion. Cheers, Rolv From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!europa.clark.net!news.maxwell.syr.edu!news-peer.sprintlink.net!news.sprintlink.net!sprint!uunet!in2.uu.net!130.235.20.4!news.lth.se!merkurius.lu.se!not-for-mail From: David Hagerberg Newsgroups: bionet.molbio.evolution,bionet.molbio.gene-linkage Subject: Re: DNA - is it alive? Date: Wed, 16 Apr 1997 07:58:34 -0700 Organization: Dep Microbial Ecology Lines: 37 Message-ID: <3354E91A.4B82@luecology.ecol.lu.sexx> References: <5ivtml$68p@infa.central.susx.ac.uk> NNTP-Posting-Host: mbio1.ekol.lu.se Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 2.0 (Win16; I) Xref: biosci bionet.molbio.evolution:5886 bionet.molbio.gene-linkage:1376 Matthew Stanfield wrote: > > Hi I'm writing a university essay on artificial life. What I would like to > know is if DNA could under any circumstances be considered alive? What about > proteins? Bacteria, presumably, are considered alive as are viruses. At what > point do 'simple things' cease to be alive and become, say, just a chemical > reaction? > > Thanks in advance. (Answers by email would be preferred.) > > Thanks, > Matthew > > \\\// > J Matthew Stanfield (O O) > ------------------------oOO----(_)----OOo----------------------------- > School of Cognitive and Computing Sciences, University of Sussex, UK > Email: mattst@cogs.susx.ac.uk Phone: UK (+44) 0831 542806 > Or: matthew.stanfield@bigfoot.com Fax : UK (+44) 01865 514494 > ---------------------------------------------------------------------- The difference between living organisms and vials with chemical reactions and gradients, is that living organisms maintain their state of high order. They could do because they eat and get energy. A chemical reaction will cease when it has reached its equilibrium, but a living orgism will never reach the equilibrium of its metabolic reactions until it dies. DNA is not alive. It has to have a cell which is compatible with DNA. When the whole cell can be considered alive. Viruses are not alive until they enter their host cells and interfere. And, HEY, bacteria is not - I repeat - not just simple things at the border of livings. They are elegantly simple. Best Regards David From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!bcm.tmc.edu!cs.utexas.edu!news.maxwell.syr.edu!news-feed.inet.tele.dk!newsfeed.nacamar.de!news-kar1.dfn.de!news-fra1.dfn.de!news-koe1.dfn.de!news-han1.dfn.de!news.rz.tu-clausthal.de!bibliothek.ankh-morpork.sw!news From: inrkl@bibliothek.ankh-morpork.sw (Rainer Klaffehn) Newsgroups: bionet.molbio.evolution,comp.ai.genetic Subject: Re: A possible definition of life. Followup-To: comp.ai.genetic Date: Wed, 16 Apr 1997 16:31:00 GMT Organization: S.u.S.E GmbH Lines: 14 Message-ID: References: <5j2io1$an6@infa.central.susx.ac.uk> Reply-To: Rainer.Klaffehn@tu-clausthal.de NNTP-Posting-Host: modem6.slip.tu-clausthal.de X-Newsreader: Gnus v5.1 Cc: mattst@cogs.susx.ac.uk In-Reply-To: mattst@cogs.susx.ac.uk's message of 16 Apr 1997 13:04:01 GMT X-Nntp-Posting-Host: localhost Xref: biosci bionet.molbio.evolution:5894 comp.ai.genetic:10918 In article <5j2io1$an6@infa.central.susx.ac.uk> mattst@cogs.susx.ac.uk (Matthew Stanfield) writes: > [some text deleted] > "Life (on Earth) consists of all things built by DNA." Since a virus is build by DNA too, it would be living thing, which is, in my opinion, very doubtful. I think, interaction with the environment is a criterion of life, too. Rainer -- Rainer Klaffehn | Tel: +49 +5323 5613 Buntenboecker Str. 42 | eMail: 38678 Clausthal-Zellerfeld | Rainer.Klaffehn@tu-clausthal.de Germany | Rainer.Klaffehn@informatik.tu-clausthal.de From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!MOLBIOL.UCT.AC.ZA!ed From: ed@MOLBIOL.UCT.AC.ZA ("Ed Rybicki") Newsgroups: bionet.molbio.evolution Subject: Re: A possible definition of life. Date: 16 Apr 1997 08:58:36 -0700 Organization: Dept Microbiology, UCT Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: ed@molbiol.uct.ac.za NNTP-Posting-Host: net.bio.net > To: mol-evol@net.bio.net > From: campbejr@phu989.mms.sbphrd.com (John R. Campbell) > Subject: Re: A possible definition of life. > On 16 Apr 1997 06:37:22 -0700, "Ed Rybicki" wrote: > >By: mattst@cogs.susx.ac.uk (Matthew Stanfield) > >> ... [snip] > >> > >> "Life (on Earth) consists of all things built by DNA." > > > >Because, Matthew, there are those of us who think viruses - at least > >when in their hosts - display the attributes of living things. And > >many viruses have RNA genomes. > > Yes, but in order to be replicated these puppies have gotta > be fed through reverse transcriptase (sp?) to generate the > DNA which can *then* be replicated to make the shell, RNA > strands and more reverse transcriptase. Only if they're a retrovirus - and most RNA viruses replicate RNA<----->RNA, NOT RNA----->DNA------>RNA!!! Ed Rybicki, PhD Dept Microbiology | ed@molbiol.uct.ac.za University of Cape Town | rybicki@uctvms.uct.ac.za Private Bag, Rondebosch | phone: x27-21-650-3265 7700, South Africa | fax: x27-21-689 7573 WWW URL: http://www.uct.ac.za/microbiology/ed.html "Out here on the perimeter, there are no stars..." From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!rutgers.rutgers.edu!gatech!csulb.edu!hammer.uoregon.edu!news-peer.gsl.net!howland.erols.net!news2.digex.net!digex.net!not-for-mail From: jnihr@access5.digex.net (The Journal of NIH Research) Newsgroups: bionet.molbio.evolution Subject: Re: A possible definition of life. Date: 16 Apr 1997 11:25:55 -0400 Organization: Express Access Online Communications, Greenbelt, MD USA Lines: 39 Message-ID: <5j2r23$rpg@access5.digex.net> References: NNTP-Posting-Host: access5.digex.net To make things more confusing, some RNA viruses can "metabolise" outside of cells, given the proper conditions. The phenomenon of natural endogenous reverse transcription (NERT)--in which cell-free RNA viruses synthesize DNA--has been described in several viruses, including HIV-1, where it may play a role in heterosexual transmission because of the abundance of nucleoside triphosphates in uterine environment. David Lewin Writer The Journal of NIH Research In article , Ed Rybicki wrote: >> From: mattst@cogs.susx.ac.uk (Matthew Stanfield) >> Subject: A possible definition of life. > >> I have, what I consider, a possible definition of life. >> >> I have been reading about Artificial Life (studying for college) and have hit >... Please could someone explain to me why the age-old problem of >> defining life is not solved by: >> >> "Life (on Earth) consists of all things built by DNA." > >Because, Matthew, there are those of us who think viruses - at least >when in their hosts - display the attributes of living things. And >many viruses have RNA genomes. This is not to mention the >possibility that computer viruses are, given a brand new niche of >electronic labyrinths in which to electronicaly multiply, also alive >(who are we to argue with Stephen Hawking?). Or memes (thought >viruses - like the tune of "The Macarena"). > >No, Matthew: I prefer: > > "Life (anywhere) is the phenomenon associated with th replciaiton of >self-coding informational systems". > [SNIP] From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!AVIRON.COM!dstec From: dstec@AVIRON.COM (David Stec) Newsgroups: bionet.molbio.evolution Subject: mol-evol@net.bio.net Date: 16 Apr 1997 12:20:43 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 4 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <5j33i6$qrq@mserv1.dl.ac.uk> NNTP-Posting-Host: net.bio.net unsubscribe David Stec end From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Rohan H. Wickramasinghe" Newsgroups: bionet.molbio.evolution Subject: Cytochrome P450 book Date: 16 Apr 1997 18:51:56 +0100 Organization: Institute for Tropical Environmental Studies Lines: 34 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5j33js$r0i@mserv1.dl.ac.uk> Original-To: toxicol@dl.ac.uk, ppg@dl.ac.uk, p450@dl.ac.uk, biophys@dl.ac.uk, cellbiol@dl.ac.uk, neur-sci@dl.ac.uk, mol-evol@dl.ac.uk, peptides@dl.ac.uk, neur-sci@dl.ac.lk, mol-evol@dl.ac.uk, cellbiol@dl.ac.uk Hello, * THE CYTOCHROME P-450 PROTEINS: ENVIRONMENTAL AND GENERAL ASPECTS * by ROHAN H. WICKRAMASINGHE , B.A.(Hons)Cantab., M.A.Cantab., PH.D.(Edinburgh), FNASSL The Cytochrome P-450 proteins play most important roles in living organisms. The above book (ISBN 955-552-029-9) provides an introduction to the field and includes an extensive bibliography of references to the publications which had appeared up to the time the book was prepared. The author has performed research on cytochrome P-450 and associated enzymatic reactions at a number of leading universities in Europe and the United States, viz. Edinburgh University, University of Texas at Galveston, Harvard University and the University of Muenster in Germany. (He has also performed research in other areas at other institutions such as at the College de France in Paris and at the University of Maryland at College Park.) Copies of the above book are available for purchase. Further information could be obtained from the following address: Dr. Rohan H.Wickramasinghe, FNASSL, Institute for Tropical Environmental Studies, 41 Flower Road, Colombo 7, Sri Lanka (e-mail: rohan@ites.ac.lk) From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: "Rohan H. Wickramasinghe" Newsgroups: bionet.molbio.evolution Subject: Cytochrome P450/bacteriorhodopsin Date: 16 Apr 1997 18:51:02 +0100 Organization: Institute for Tropical Environmental Studies Lines: 49 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5j33i6$qrq@mserv1.dl.ac.uk> Original-To: mol-evol@dl.ac.uk Hello, Some time ago we published some papers relating to 1) Cytochrome P450 proteins and their activities and 2) bacteriorhodopsin. We would be very grateful for any information as to whether any of this work has been followed up and for relevant references (esp. in conference proceedings, books etc.) We would be particularly interested to learn whether any other enzymatic activities have evolved which may be sensitive to small changes in the dielectric constant. The publications concerned were: 1) R.H.Wickramasinghe, " Regulation of corticosteroid hydroxylations: the intramitochondrial dielectric constant and proteolipids of adrenodoxin and cytochrome P450 ", CYTOBIOS (Cambridge, England) 8(1973)81-94, 2) R.H.Wickramasinghe, " The regulation of corticosteroid hydroxylations. 1. An effect of inorganic ions in regulating iron- sulphur protein-dependent electron transport " , JOURNAL OF BIOENERGETICS 5(1973)151-161, 3) R.H.Wickramasinghe and C.A.Villee, " Early role during chemical evolution for cytochrome P450 in oxygen detoxification ", NATURE 256(1975)509-511, 4) R.H.Wickramasinghe and C.A.Villee, " Possible origin of cytochrome P450 in the Early Precambrian " , Abstracts, Second College Park Colloquium on Chemical Evolution, University of Maryland, 29 October - 1 November 1975, p.41, 5) R.H.Wickramasinghe and C.A.Villee, " Possible similar role of cytochrome P450 in primordial evolution of species and in chemical carcinogenesis " , PERSPECTIVES IN BIOLOGY AND MEDICINE 19(1976)473-475, 6) R.H.Wickramasinghe, " Model role for bacteriorhodopsin for solar energy utilization by primordial organisms ", CYTOBIOS (Cambridge, England) 17(1976)31-33. Thank you very much for taking the time to read this and in advance for any help you can give. Regards, Rohan H. Wickramasinghe (e-mail: rohan@ites.ac.lk) From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!daresbury!uninett.no!nntp.uio.no!newsfeeds.sol.net!news.maxwell.syr.edu!cpk-news-hub1.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.bbnplanet.com!uunet!in3.uu.net!208.198.64.1!netnews.sbphrd.com!campbejr From: campbejr@phu989.mms.sbphrd.com (John R. Campbell) Newsgroups: bionet.molbio.evolution Subject: Re: A possible definition of life. Date: 16 Apr 1997 13:59:16 GMT Organization: SmithKline Beecham Pharmaceuticals Research & Development Lines: 47 Message-ID: References: Reply-To: soup@jtan.com NNTP-Posting-Host: phu989.sbphrd.com X-Newsreader: slrn (0.8.5) On 16 Apr 1997 06:37:22 -0700, "Ed Rybicki" wrote: >By: mattst@cogs.susx.ac.uk (Matthew Stanfield) >> ... [snip] >> >> "Life (on Earth) consists of all things built by DNA." > >Because, Matthew, there are those of us who think viruses - at least >when in their hosts - display the attributes of living things. And >many viruses have RNA genomes. Yes, but in order to be replicated these puppies have gotta be fed through reverse transcriptase (sp?) to generate the DNA which can *then* be replicated to make the shell, RNA strands and more reverse transcriptase. Well, Matt was trying to focus on the feature that DNA *is* a central point for carbon chauvinistic definitions of life. > This is not to mention the >possibility that computer viruses are, given a brand new niche of >electronic labyrinths in which to electronicaly multiply, also alive >(who are we to argue with Stephen Hawking?). Or memes (thought >viruses - like the tune of "The Macarena"). Of course, that's trying to tie in "virtual" life (though can anybody prove that what I'm going through these past 43 years is a "real" life?). >No, Matthew: I prefer: > > "Life (anywhere) is the phenomenon associated with th replciaiton of >self-coding informational systems". Not entiruely unreasonable and allows nanotech constructs (capable of self-replication) an aspect of life. Actually, what _is_ a cell but a nanomachine? (Though I think nanotech purists would want to say that the cell has too large a size for what they want.) -- John R. Campbell, Speaker to Machines, Resident Heckler soup@jtan.com "As a SysAdmin, yes, I CAN read your e-mail, but I DON'T get that bored!"-me Disclaimer: I'm just a consultant at the bottom of the food chain, so, if you're thinking I speak for anyone but myself, you must have more lawyers than sense. From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!MOLBIOL.UCT.AC.ZA!ed From: ed@MOLBIOL.UCT.AC.ZA ("Ed Rybicki") Newsgroups: bionet.molbio.evolution Subject: Re: A possible definition of life. Date: 16 Apr 1997 06:37:22 -0700 Organization: Dept Microbiology, UCT Lines: 33 Sender: daemon@net.bio.net Distribution: world Message-ID: Reply-To: ed@molbiol.uct.ac.za NNTP-Posting-Host: net.bio.net > From: mattst@cogs.susx.ac.uk (Matthew Stanfield) > Subject: A possible definition of life. > I have, what I consider, a possible definition of life. > > I have been reading about Artificial Life (studying for college) and have hit ... Please could someone explain to me why the age-old problem of > defining life is not solved by: > > "Life (on Earth) consists of all things built by DNA." Because, Matthew, there are those of us who think viruses - at least when in their hosts - display the attributes of living things. And many viruses have RNA genomes. This is not to mention the possibility that computer viruses are, given a brand new niche of electronic labyrinths in which to electronicaly multiply, also alive (who are we to argue with Stephen Hawking?). Or memes (thought viruses - like the tune of "The Macarena"). No, Matthew: I prefer: "Life (anywhere) is the phenomenon associated with th replciaiton of self-coding informational systems". c. Rybicki, 1995. Ed Rybicki, PhD Dept Microbiology | ed@molbiol.uct.ac.za University of Cape Town | rybicki@uctvms.uct.ac.za Private Bag, Rondebosch | phone: x27-21-650-3265 7700, South Africa | fax: x27-21-689 7573 WWW URL: http://www.uct.ac.za/microbiology/ed.html "Out here on the perimeter, there are no stars..." From owner-evolution@net.bio.net Tue Apr 15 23:00:00 1997 Path: biosci!agate!newsxfer3.itd.umich.edu!cpk-news-hub1.bbnplanet.com!news.bbnplanet.com!rill.news.pipex.net!pipex!netcom.net.uk!nntpfeed.doc.ic.ac.uk!sunsite.doc.ic.ac.uk!susx.ac.uk!mattst From: mattst@cogs.susx.ac.uk (Matthew Stanfield) Newsgroups: bionet.molbio.evolution,comp.ai.genetic Subject: A possible definition of life. Date: 16 Apr 1997 13:04:01 GMT Organization: University of Sussex Lines: 15 Message-ID: <5j2io1$an6@infa.central.susx.ac.uk> NNTP-Posting-Host: tsunx.ctn.cogs.susx.ac.uk X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.molbio.evolution:5887 comp.ai.genetic:10914 I have, what I consider, a possible definition of life. I have been reading about Artificial Life (studying for college) and have hit upon what I think could be a definition of life (at least on Earth). But I am neither arrogant enough nor stupid enough to believe that this has not been thought of before and there are probably good reasons why this is not a good definit