From owner-population-bio@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!agate!usenet.ins.cwru.edu!howland.reston.ans.net!zaphod.mps.ohio-state.edu!menudo.uh.edu!jane.uh.edu!mecew6 From: mecew6@jane.uh.edu (George Broze) Newsgroups: comp.theory.dynamic-sys,bionet.population-bio,sci.fractals Subject: Re: Examples needed Message-ID: <2FEB199311394279@jane.uh.edu> Date: 2 Feb 93 17:39:00 GMT References: <1993Jan31.224819.2673@zip.eecs.umich.edu> Sender: mecew6@jane.uh.edu (Broze, J.) Organization: University of Houston Lines: 28 Xref: biosci comp.theory.dynamic-sys:118 bionet.population-bio:377 sci.fractals:787 NNTP-Posting-Host: jane.uh.edu News-Software: VAX/VMS VNEWS 1.41 In article <1993Jan31.224819.2673@zip.eecs.umich.edu>, bagchi@quip.eecs.umich.edu (Ranjan Drzzzzt! Bagchi) writes... > I do have (from Hastings and Powell, 1991) an example of >a chaotic attractor in a system type-II functional response: > >dx/dt = x(1-x) - f1(x)y >dy/dt = f1(x)y - f2(y)z - d1y >dz/dt = f2(y)z - d2z > >fn(u) = a_n u/(1 - b_n u) > >with constants -- d = ( 0.4 0.01) > a = (5 0.1) > b = (3 2.0) > >I don't see why I'm having a problem pushing this into >a logistic or simple lotka-volterra model, but I'm either >getting populations that crash or exponential. > >Ranjan Bagchi Ranjan.Bagchi@umich.edu I tried integrating this with a double-precision, 4th-order Runge-Kutta solver using the given parameter values and found a little limit cycle in the neighborhood (.3557 < x < .368), (-14.478 < y < -14.446), (-.0054 < z < +.0055). This result assumes, of course, that I copied down all the functions and parameters correctly. George From owner-population-bio@net.bio.net Mon Feb 01 22:00:00 1993 Path: biosci!ETSUACAD.bitnet!JB5369 From: JB5369@ETSUACAD.bitnet Newsgroups: bionet.population-bio Subject: GENETICS FACULTY ANNOUNCEMENT Message-ID: <9302020333.AA21876@net.bio.net> Date: 2 Feb 93 03:35:28 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 28 EAST TEXAS STATE UNIVERSITY - VACANCY ANNOUNCEMENT 1. POSITION TITLE: ASSISTANT PROFESSOR IN BIOLOGICAL SCIENCES 2. POSITION DESCRIPTION: FULL-TIME TENURE TRACK POSITION IN THE DEPARTMENT OF BIOLOGICAL SCIENCES. THIS POSITION REQUIRES TEACHING A SOPHOMORE LEVEL GENETICS COURSE FOR MAJORS, ONE UPPER LEVEL COURSE (JUNIORS/SENIORS), AND ONE OR MORE GRADUATE LEVEL COURSES IN AREA OF SPECIALIZATION. THE SUCCESSFUL APPLICANT WILL ALSO BE EXPECTED TO ASSUME SOME OF THE TEACHING RESPONSIBILITIES FOR OUR FRESHMAN LEVEL COURSES. ALTHOUGH THE SUCCESSFUL APPLICANT MUST BE AN EFFECTIVE TEACHER, IT IS ALSO EXPECTED THAT A MODEST RESEARCH PROGRAM WILL BE DEVELOPED THAT WILL INVOLVE UNDERGRADUATE AND/OR GRADUATE STUDENTS. 3. QUALIFICATIONS & EXPERIENCE: REQUIRES A Ph.D. WITH A SPECIALIZATION IN GENETICS AND THE SUCCESSFUL CANDIDATE MUST SHOW EVIDENCE OR PROMISE OF SCHOLARLY GROWTH AND A COMMITMENT TO TEACHING EXCELLENCE. THE POSITION INVOLVES TEACHING A 12-CREDIT HOUR COURSE LOAD PER SEMESTER. 4. SALARY RANGE: $32,300 - 34,300 5. STARTING DATE: FALL, 1993 6. APPLICATION REQUIREMENTS & PERSON TO CONTACT: RESUME, OFFICIAL TRANSCRIPTS, THREE LETTERS OF RECOMMENDATION, STATEMENT OF RESEARCH PLANS, AND TEACHING PHILOSOPHY. THESE MATERIALS ARE TO BE SENT TO CHAIR OF BIOLOGICAL SCIENCES SEARCH COMMITTEE, BIOLOGICAL SCIENCES DEPARTMENT, EAST TEXAS STATE UNIVERSITY, COMMERCE, TEXAS 75429-3011. CONSIDERATION OF APPLICATIONS WILL BEGIN MARCH 10, 1993. 7. LOCATION AND ENVIRONMENT: EAST TEXAS STATE UNIVERSITY, A SENIOR PUBLIC INSTITUTION, WITH AN ENROLLMENT OF APPROXIMATELY 8,000 STUDENTS IS LOCATED IN COMMERCE, TEXAS WHICH IS 65 MILES NORTHEAST OF DALLAS, TEXAS. THIS POSITION IS CONTINGENT ON FUNDING. THIS UNIVERSITY IS AN AFFIRMATIVE ACTION/EQUAL OPPORTUNITY EMPLOYER. QUALIFIED WOMEN, MINORITIES, AND DISABLE PERSONS ARE ENCOURAGED TO APPLY. From owner-population-bio@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!news.cs.indiana.edu!sgiblab!spool.mu.edu!agate!ucbvax!ucdavis!hamilton!me From: me@four.ucdavis.edu (amhastings@ucdavis.edu) Newsgroups: bionet.population-bio Subject: Re: Examples needed Message-ID: <22176@ucdavis.ucdavis.edu> Date: 3 Feb 93 20:33:44 GMT References: <1993Jan31.224819.2673@zip.eecs.umich.edu> Sender: usenet@ucdavis.ucdavis.edu Reply-To: me@four.ucdavis.edu Organization: U C DAVIS Lines: 20 In article 2673@zip.eecs.umich.edu, bagchi@quip.eecs.umich.edu (Ranjan Drzzzzt! Bagchi) writes: > > Hi. I'm having a hell of a time finding an example of > a chaotic attractor in a 3-species predator-victim system with either > Lotka-Volterra characteristics, or logistic characteristics. > > I do have (from Hastings and Powell, 1991) an example of > a chaotic attractor in a system type-II functional response: > > I don't see why I'm having a problem pushing this into > a logistic or simple lotka-volterra model, but I'm either > getting populations that crash or exponential. I fairly well convinced myself that you could not do this without the type II responses. Moreover, if the system is truly LV then some old theorems due to Goh or ??? (cannot quite remember) show that a food chain is globally stable. Alan Hastings amhastings@ucdavis.edu From owner-population-bio@net.bio.net Wed Feb 03 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!menudo.uh.edu!jane.uh.edu!mecew6 From: mecew6@jane.uh.edu (George Broze) Newsgroups: comp.theory.dynamic-sys,bionet.population-bio,sci.fractals Subject: Re: Examples needed Message-ID: <4FEB199315283062@jane.uh.edu> Date: 4 Feb 93 21:28:00 GMT References: <1993Jan31.224819.2673@zip.eecs.umich.edu> <2FEB199311394279@jane.uh.edu> Sender: mecew6@jane.uh.edu (Broze, J.) Organization: University of Houston Lines: 36 Xref: biosci comp.theory.dynamic-sys:124 bionet.population-bio:379 sci.fractals:811 NNTP-Posting-Host: jane.uh.edu News-Software: VAX/VMS VNEWS 1.41 >> I do have (from Hastings and Powell, 1991) an example of >>a chaotic attractor in a system type-II functional response: >> >>dx/dt = x(1-x) - f1(x)y >>dy/dt = f1(x)y - f2(y)z - d1y >>dz/dt = f2(y)z - d2z >> >>fn(u) = a_n u/(1 - b_n u) >> >>with constants -- d = ( 0.4 0.01) >> a = (5 0.1) >> b = (3 2.0) >> >>I don't see why I'm having a problem pushing this into >>a logistic or simple lotka-volterra model, but I'm either >>getting populations that crash or exponential. >> >>Ranjan Bagchi Ranjan.Bagchi@umich.edu > >I tried integrating this with a double-precision, 4th-order Runge-Kutta >solver using the given parameter values and found a little limit cycle >in the neighborhood (.3557 < x < .368), (-14.478 < y < -14.446), >(-.0054 < z < +.0055). This result assumes, of course, that I copied >down all the functions and parameters correctly. > >George My apologies. I miscopied the functions. I tried again and found 6 critical points, two stable [(1,0,0) and (1/6,1/12,95/9)] and four unstable [(0,0,0), (2/31,145/961,0), (7/6,1/12,-205/9) and (0,1/12,-10/3)]. Of these, I checked only (0,0,0) and (1,0,0) by hand, and tested the other four numerically. The last one (0,1/12,-10/3) blew up with regularity (for what reason I have not yet figured out), but the others headed to some stable fixed point (as I recall). George From owner-population-bio@net.bio.net Fri Feb 05 22:00:00 1993 Path: biosci!UCONNVM.bitnet!PIGLIUCC From: PIGLIUCC@UCONNVM.bitnet (Massimo Pigliucci) Newsgroups: bionet.population-bio Subject: Algorithms for fractal dimension Message-ID: <9302062000.AA01236@net.bio.net> Date: 6 Feb 93 19:55:39 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 19 Dear Pop-netters, I am currently studying applications of non-linear dynamics to problems in evolutionary biology and quantitative genetics. I am now faced with the necessity to find a reliable program that will compute the Lyapunov ex ponents and/or the dimension of an attractor based on experimental data. I am a ware of the basic literature on the subject, and I have the program TRAX (which , however, doesn't deal with experimental data...). Is anybody there able to pr ovide programs or references to programs addressing this particular problem? Th ank you very much for your input (actually, output). Any other comment or sugge stion on related matters are also very appreciated. Massimo Pigliucci Dept. of Ecology and Evol. Biology University of Connecticut Storrs, CT 06269 phone 203-486-4372, FAX 203-486-6364 bitnet PIGLIUCC@UCONNVM internet PIGLIUCC@UCONNVM.UCONN.EDU From owner-population-bio@net.bio.net Mon Feb 08 22:00:00 1993 Path: biosci!uwm.edu!zaphod.mps.ohio-state.edu!sdd.hp.com!saimiri.primate.wisc.edu!zazen!post.its.mcw.edu!not-for-mail From: gordin@post.its.mcw.edu (Erez Gordin) Newsgroups: bionet.population-bio Subject: Wright's Inbreeding Coefficient Message-ID: <1l8lrjINNpm6@post.its.mcw.edu> Date: 9 Feb 93 16:24:19 GMT Sender: gordin@post.its.mcw.edu Organization: Medical College of Wisconsin (Milwaukee, WI) Lines: 14 NNTP-Posting-Host: post.its.mcw.edu Does anyone know of a computer program to calculate Wright's Inbreeding Coefficient for a medium to large population. Please post response here or respond to: Erez Gordin Dept. of Physiology Medical College of Wisconsin E-mail : gordin@post.its.mcw.edu Phone : (414) 257-8727 Fax : (414) 257-8570 From owner-population-bio@net.bio.net Tue Feb 09 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!usenet.ins.cwru.edu!gatech!rpi!usenet.coe.montana.edu!news.u.washington.edu!evolution!joe From: joe@evolution.u.washington.edu (Joe Felsenstein) Newsgroups: bionet.population-bio Subject: Re: Wright's Inbreeding Coefficient Summary: Simple program Message-ID: <1lac32INNkn2@shelley.u.washington.edu> Date: 10 Feb 93 07:49:54 GMT References: <1l8lrjINNpm6@post.its.mcw.edu> Sender: Joe Felsenstein Organization: University of Washington, Seattle Lines: 51 NNTP-Posting-Host: evolution.genetics.washington.edu Erez Gordin writes: > Does anyone know of a computer program to calculate Wright's > Inbreeding Coefficient for a medium to large population. Don't know how big medium to large is, but here's a 27-line program in C that will compute inbreeding coefficients for all individuals in a small population. It takes space proportional to the square of the size of the population so this is for not too large a population. Number the individuals in the population consecutively, with offspring having a number larger than either of their parents. The program asks for numbers of individuals and of their two parents. These are entered blank-separated, in ascending order of individual's number. You signal the end of data input by giving all three of these numbers as 0. Parents who are not in the pedigree should have their number given as 0. An obvious extension would be to read the pedigree from a file and write the inbreeding coefficients to another file. The program: #define MAXSIZE 100 /* maximum size of pedigree */ main () { float f[MAXSIZE][MAXSIZE]; int i, ma, pa, j, n; n = 0; do { f[0][0] = 0.0; printf("Indiv Mother Father \n"); scanf("%d %d %d", &i, &ma, &pa); if (i != 0) { f[i][0] = 0; f[0][i] = f[i][0]; for (j = 1; j<=n; j++) { f[i][j] = 0.5*(f[ma][j]+f[pa][j]); f[j][i] = f[i][j]; } f[i][i] = 0.5*f[ma][pa] + 0.5; n++; } } while (i != 0); printf("\n i F(i)\n"); printf(" - ----\n"); for (i=1; i<=n; i++) printf("%4d %12.7f \n", i, 2*f[i][i]-1); } ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) Bitnet/EARN: felsenst@uwavm From owner-population-bio@net.bio.net Wed Feb 10 22:00:00 1993 Path: biosci!bcm!convex!news.utdallas.edu!corpgate!bnrgate!bnr.co.uk!pipex!warwick!mrccrc!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!news.funet.fi!hydra!klaava!saarikko From: saarikko@klaava.Helsinki.FI (Jarmo Saarikko) Newsgroups: bit.listserv.ethology,bionet.population-bio Subject: Predation risk and prey adaptations Message-ID: <1993Feb11.103403.14386@klaava.Helsinki.FI> Date: 11 Feb 93 10:34:03 GMT Organization: University of Helsinki Lines: 31 Xref: biosci bionet.population-bio:383 X-Newsreader: TIN [version 1.1 PL6] From ASAB Newsletter January 1993: --------------------------------------------------------------- A special issue of Annales Zoologici Fennici has appeared: Predation risk and behavioural adaptations of prey: ecological and evolutionary consequences. December 1992, vol. 29, No 4. Based on a Nordic Council of Ecology symposium held at Konnevesi Research Station, Finland 25th - 29th November, 1991. Edited by Hannu Ylonen and Carin Magnhagen. This issue contains 14 articles on predation risk and prey adaptations, covering theoretical models as well as empirical studies on wide range of habitats and taxa. Authors include: J. Brown, M Cassini, L. Dugatkin, H. Hakkarainen, H. Hirvonen, B. Kotler, S. Lima, C. Magnhagen, P. Palokangas, J. Saarikko, A. Sih, B. Soderback and H. Ylonen. Anyone interested in receiving a copy of this ca. 200 page issue, please contact: Hannu Ylonen, or University of Jyvaskyla, Department of Biology, Carin Magnhagen, Konnevesi Research Station, Department of Aquaculture, PO Box 35, Swedish University of Agricultural Sciences, SF-40351 JYVASKYLA, S-901 83 UMEA, Finland. Sweden. Fax +358.41.602321. Fax +46.90.123729. E-mail: ylonen@jylk.jyu.fi. E-mail: cam@nana.slu.se. ------------------------------------------------------------------- From owner-population-bio@net.bio.net Sat Feb 13 22:00:00 1993 Path: biosci!uwm.edu!wupost!howland.reston.ans.net!zaphod.mps.ohio-state.edu!rphroy!caen!batcomputer!munnari.oz.au!metro!extro.ucc.su.OZ.AU!simonb From: simonb@extro.ucc.su.OZ.AU (Simon Blomberg) Newsgroups: bit.listserv.ethology,bionet.population-bio Subject: Re: Predation risk and prey adaptations Message-ID: Date: 14 Feb 93 02:32:07 GMT References: <1993Feb11.103403.14386@klaava.Helsinki.FI> Sender: news@ucc.su.OZ.AU Organization: Sydney University Computing Service, Sydney, NSW, Australia Lines: 34 Xref: biosci bionet.population-bio:384 Nntp-Posting-Host: extro.ucc.su.oz.au saarikko@klaava.Helsinki.FI (Jarmo Saarikko) writes: >From ASAB Newsletter January 1993: >--------------------------------------------------------------- >A special issue of Annales Zoologici Fennici has appeared: > Predation risk and behavioural adaptations of prey: > ecological and evolutionary consequences. > December 1992, vol. 29, No 4. >Based on a Nordic Council of Ecology symposium held at Konnevesi >Research Station, Finland 25th - 29th November, 1991. Edited by >Hannu Ylonen and Carin Magnhagen. This issue contains 14 articles >on predation risk and prey adaptations, covering theoretical models >as well as empirical studies on wide range of habitats and taxa. >Authors include: J. Brown, M Cassini, L. Dugatkin, H. Hakkarainen, >H. Hirvonen, B. Kotler, S. Lima, C. Magnhagen, P. Palokangas, >J. Saarikko, A. Sih, B. Soderback and H. Ylonen. Hmm. Sounds interesting. Has anyone any idea about how much it will cost ($US or whatever)? Simon (poor grad. student). -- Simon Blomberg simonb@extro.ucc.su.OZ.AU School of Biol. Sciences, A08 University of Sydney We demand the right to stop to look even at NSW 2006 Australia lizards, which are nobody's property. -JBS Haldane From owner-population-bio@net.bio.net Mon Feb 15 22:00:00 1993 Path: biosci!agate!dog.ee.lbl.gov!network.ucsd.edu!usc!zaphod.mps.ohio-state.edu!uwm.edu!spool.mu.edu!news.cs.indiana.edu!nstn.ns.ca!dragon.acadiau.ca!891666t From: 891666t@dragon.acadiau.ca (Trish Turliuk) Newsgroups: bionet.population-bio Subject: Newbie pop-ecologist archive question Message-ID: <1993Feb15.234522.11971@dragon.acadiau.ca> Date: 15 Feb 93 23:45:22 GMT Organization: Acadia University Lines: 10 I'm taking my second course in Population Ecology (called "Dynamics of Populations") here at Acadia University in Wolfville, Nova Scotia. I'd like to know how to reach the archive of this newsgroup and mailing list. Hopefully, I will be able to engage in further discussions in this newsgroup. Have a natural day, Trish Turliuk trish.turliuk@acadiau.ca From owner-population-bio@net.bio.net Thu Feb 18 22:00:00 1993 Path: biosci!daresbury!daresbury!news From: M_LEAHY@ICRF.ICNET.UK (Mike Leahy) Newsgroups: bionet.population-bio Subject: Genetic anticiaption - how does it occur Message-ID: <1993Feb19.164154.5275@gserv1.dl.ac.uk> Date: 19 Feb 93 16:43:00 GMT Sender: list-admin@daresbury.ac.uk Distribution: bionet Lines: 15 Original-To: POP-BIO@UK.AC.DARESBURY Path: wheel!m_leahy From: m_leahy@icrf.icnet.uk (Mike Leahy) Newsgroups: biosci.population-biology Subject: Genetic anticiaption - how does it occur Message-ID: <56269@icrf.icnet.uk> Date: 19 Feb 93 16:43:33 GMT Organization: Imperial Cancer Research Fund, London, UK Lines: 7 I recently came across the phrase "genetic anticipation". Can anyone explain how this phenonemon is supposed to come about? thanks. Mike Leahy From owner-population-bio@net.bio.net Sun Feb 21 22:00:00 1993 Path: biosci!uwm.edu!spool.mu.edu!howland.reston.ans.net!usc!rpi!hubble.asymetrix.com!kuhub.cc.ukans.edu!husc-news.harvard.edu!husc.harvard.edu!robison1 From: robison1@husc10.harvard.edu (Keith Robison) Newsgroups: bionet.population-bio Subject: Re: Genetic anticiaption - how does it occur Message-ID: Date: 22 Feb 93 14:29:42 GMT References: <1993Feb19.164154.5275@gserv1.dl.ac.uk> Distribution: bionet Lines: 37 Nntp-Posting-Host: husc10.harvard.edu M_LEAHY@ICRF.ICNET.UK (Mike Leahy) writes: >I recently came across the phrase "genetic anticipation". >Can anyone explain how this phenonemon is supposed to come about? >thanks. >Mike Leahy This terem refers to the fact that for some genetic diseases, the disease severity worsens each time it is passed on. Myotonic dystrophy and fragile-X syndrome are two example disorders. It turns out that (of all?) the diseases which exhibit anticipation have been shown to be the result of trinucleotide repeat expansion. In normal individuals, a relatively short (10 - 20 copies) of a trinucleotide is present, but in affected individuals the copy number increases dramatically, and the longer repeat lengths correlate with stronger phenotype: F0: 40 copies moderate phenotype F1: 100 copies strong phenotype F2: 300 copies extreme phenotype There have been a large number of reviews on trinucleotide repeat expansion since it was discovered a bit over a year ago. Science had one in its last Human Genome issue, I think. Hope it helps. Keith Robison Harvard University Department of Cellular and Developmental Biology Department of Genetics / HHMI robison@ribo.harvard.edu From owner-population-bio@net.bio.net Sun Feb 21 22:00:00 1993 Path: biosci!daresbury!buzz.bmc.uu.se!corax.udac.uu.se!sunic!ugle.unit.no!lise.unit.no!mortenaa From: mortenaa@Lise.Unit.NO (Morten Aagaard) Newsgroups: bionet.population-bio Subject: Chaos in epidemics Message-ID: <1993Feb22.151245.8507@ugle.unit.no> Date: 22 Feb 93 15:12:45 GMT Sender: news@ugle.unit.no (NetNews Administrator) Organization: Norwegian Institue of Technology Lines: 4 I am interested in any pointer to information on (deterministic) chaos in epidemical models. Thanks in advance From owner-population-bio@net.bio.net Thu Feb 25 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!haven.umd.edu!mimsy!biocomp From: mbehrens@cs.utexas.edu (Mikael Behrens) Newsgroups: bionet.biology.computational,bionet.population-bio Subject: computer simulation project Message-ID: <86842@ut-emx.uucp> Date: 25 Feb 93 20:53:05 GMT Sender: news@mimsy.umd.edu Followup-To: bionet.biology.computational Distribution: bionet Lines: 24 Approved: comp-bio-moderator@genbank.bio.net Xref: biosci bionet.biology.computational:370 bionet.population-bio:389 Originator: biocomp@lerkim.umiacs.umd.edu Hi, I'm a computer science student doing a biology-related independent research project this semester. I'm interested in computer simulations based on simple rulesets or "games," that have biological relevance (usually in population or evolutionary biology.) Examples of what I mean are Conway's `Game of Life,' the Prisoners' Dilemma, and the Hawk-dove game. I plan on writing a general simulation application that can be easily modified by a user or programmer to "play" these games as well as others. It would serve as a framework for creating new rulesets and experimenting with them. Since this is a computer science project, it would focus on the DEVELOPMENT of such a system, and not a specific biological problem. I am still researching, and would be very interested in any comments about this project. Could someone suggest good sources of information about the Hawk-dove game, and the Prisoners' dilemma? So far, the three mentioned above are the only "games" I've come across. If anyone knows of others please let me know. I'm doing this project on a NeXT workstation. -- Mikael Behrens mbehrens@cs.utexas.edu (NeXTMail OK) Computer Science student University of Texas at Austin