From owner-population-bio@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CU.NIH.GOV!IAE From: IAE@CU.NIH.GOV ("Irene Anne Eckstrand") Newsgroups: bionet.population-bio Subject: AIDS Program Announcement Message-ID: <9312021544.AA06801@net.bio.net> Date: 2 Dec 93 15:42:11 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 281 BASIC RESEARCH IN SUPPORT OF TREATMENTS FOR AIDS NIH GUIDE: Volume nn, Number nn, November 19, 1993. PA NUMBER: TPA-94-003 P.T. National Institute of General Medical Sciences National Institute of Diabetes and Digestive and Kidney Diseases National Institute of Allergy and Infectious Diseases PURPOSE The purpose of this program announcement is to encourage research in areas fundamental to the development of treatments for AIDS and associated opportunistic infections. HEALTHY PEOPLE 2000 The Public Health Service (PHS) is committed to achieving the health promotion and disease prevention objectives of "Healthy People 2000," a PHS-led national activity for setting priority areas. This PA, (Title of PA), is related to the priority area of HIV infection. Potential applicants may obtain a copy of "Healthy People 2000" (Full Report: Stock No. 017-001-00474-0) or "Healthy People 2000" (Summary Report: Stock No. 017-001-00473-1) through the Superintendent of Documents, Government Printing Office, Washington, DC 20402-9325 (telephone 202-783-3238). ELIGIBILITY REQUIREMENTS Applications may be submitted by foreign (except for FIRST Award and program project grants) and domestic, for-profit and non-profit organizations, public and private, such as universities, colleges, hospitals, laboratories, units of State or local governments, and eligible agencies of the Federal government. Applications from minority individuals and women are encouraged. MECHANISM OF SUPPORT Support of this program will be through the individual research project grant (R01), the FIRST Award (R29), and the program project grant (P01) mechanisms as well as through competing supplemental awards to currently active R01, P01 or Method to Extend Research in Time (MERIT) awards (R37). Investigators holding active R01, R37, or P01 grants to study fundamental processes associated with interaction of proteins with ligands, bioavailability of drugs, crystallization of proteins, macromolecular engineering, or evolutionary adaptation, with at least one year of support remaining at the time of the anticipated award, or individuals desiring to apply for support under the R01 or R29 mechanisms, are specifically encouraged to apply for grants citing this program announcement. RESEARCH OBJECTIVES Despite all that is known about fundamental biological processes, particularly at the molecular level, and the application of this knowledge to understanding the structure and replication of HIV, there are still fundamental gaps in our understanding of basic biology that must be filled before a rational approach to the treatment of AIDS and associated secondary infections can be accomplished. These gaps include: o A basic understanding of the factors that govern the interaction of proteins with ligands--especially with respect to the flexibility of both the binding site of the protein and binding ligand. Such an understanding is essential for the de novo design of drugs to inhibit specific proteins necessary for the HIV life cycle and antibiotics to treat opportunistic infections. o A basic understanding of the factors that govern the availability of a drug at its site of action. Potential new drug candidates frequently fail due to poor bioavailability, i.e., the compounds show great receptor affinity, but fail to get to their targets in sufficient quantity. Recently, efforts to develop HIV protease inhibitors as new drugs to treat AIDS have foundered because of a failure to achieve adequate intracellular drug concentrations. The reasons why these new drug candidates fail is not well understood, and thus, cannot be accounted for in the design stage. o A basic understanding of the principles that underlie the crystallization of proteins--especially membrane and/or glycosylated proteins. The inability to routinely crystallize a given protein is a serious roadblock in the determination of the three-dimensional structure of, for example, the envelope protein of HIV, and other proteins necessary for the HIV life cycle or proteins important in the life cycle of bacteria that cause opportunistic infections. The determination of the structures of these proteins at high resolution is an essential first step in the design of drugs to inhibit the processes for which these proteins are essential. o A basic understanding of the principles of macromolecular engineering. A promising approach in the treatment of AIDS is to alter genetically AIDS infected lymphocytes so that they produce proteins or nucleic acids that inhibit either the production or escape of the AIDS virus, misdirect specific components of AIDS virus, or are toxic to infected cells. A significant limitation in this approach is the inability to engineer reliably specific functionality into an existing protein or nucleic acid scaffold or, at a more basic level, to design a protein or nucleic acid de novo to perform a specific function. o An understanding of basic evolutionary processes by which organisms adapt to complex environments. The rapid evolution of the AIDS virus, even within a single host, is a major obstacle to vaccine and drug development and underlies the phenomenon of multiple drug resistance. Knowledge about the general features which govern adaptation and evolution is an essential step to understanding the relationship between viral diversity and the course of infection, and the evolution of multiple drug resistance. These factors which must be considered in developing vaccines and designing drugs to make them effective. The purpose of this announcement is to solicit proposals that address one or more of these key issues in ways that not only take advantage of an investigator's existing expertise in these areas but also encourages the investigator to recognize the implications of his or her research to AIDS. The expectation is that the investigator will remain focused on the central question of AIDS during the course of the project. For investigators already funded by NIGMS, NIDDK or NIAID for basic research in these areas, a competitive supplement to provide key links to AIDS is encouraged. In addition to the information described in the application kit (PHS 398) required for a supplemental application, the request should detail how the requested funds will enable the investigator to enhance significantly the applicability of the research project to AIDS. APPLICATION PROCEDURES Applications for regular and supplemental awards for regular research (R01), FIRST, and MERIT grants must be submitted on the grant application form PHS 398 (rev. 9/91) and will be accepted at the receipt dates for applications for AIDS- related research: January 2, May 1, and September 1. Applications for regular and supplemental awards for program project grants (P01) have receipt dates of February 1, June 1, and October 1. Application kits are available at most institutional offices of sponsored research and may be obtained from: The Office of Grants Inquiries Division of Research Grants National Institutes of Health Westwood Building, Room 449 Bethesda, MD 20892 Telephone: (301) 594-7248. On the first (face) page, item 2a, of the application, the word "yes" must be checked and the title and number of the announcement typed in the space provided: "Basic Research in Support of Treatments for AIDS, PA-94-003". The completed original application and five legible copies must be sent or delivered to: Division of Research Grants National Institutes of Health Westwood Building, Room 240 5333 Westbard Avenue Bethesda, MD 20892** FIRST (R29) applications must include at least three sealed letters of reference attached to the face page of the original application. FIRST applications submitted without the required number of reference letters will be considered incomplete and will be returned without review. REVIEW PROCEDURES Applications will be assigned to a funding component (Institute or Center) and an Initial Review Group (IRG) on the basis of established Public Health Service referral guidelines. The IRGs will review applications for scientific and technical merit in accordance with standard NIH peer review procedures. Following the IRG review, the applications will receive a second-level review by the appropriate national advisory council. AWARD CRITERIA Applications will compete for available funds with all other approved applications. The following will be considered making funding decisions: o Quality of the proposed project as determined by peer review o Availability of funds o The implications of the project for AIDS and an intellectual environment that focuses on AIDS research o Program balance among research areas of the announcement INQUIRIES Written and telephone inquiries are encouraged. The opportunity to clarify any issues or questions from potential applicants is welcome. Direct inquiries regarding programmatic issues to: James Cassatt, Ph.D. Director, Biophysics and Physiological Sciences Program National Institute of General Medical Sciences Westwood Building, Room 907 Bethesda, MD 20892 Telephone: (301) 594-7800 FAX: (301) 594-7700 Carl W. Dieffenbach, Ph.D. Division of AIDS National Institute of Allergy and Infectious Diseases Solar Building, Room 2C05 Bethesda, MD 20892 Telephone: (301) 496-8199 FAX: (301) 402-3211 Judith Fradkin, M.D. Endocrine and Metabolic Diseases Program Branch National Institute of Diabetes and Digestive and Kidney Diseases Westwood Building, Room 621 Bethesda, MD 20892 Telephone: (301) 594-7567 FAX: (301) 594-9011 Direct inquiries regarding fiscal matters to: Ms. Carol Tippery Grants Management Officer National Institute of General Medical Sciences Westwood Building, Room 9A03 Bethesda, MD 20892 Telephone: (301) 594-7813 Ms. Donna A. Huggins Grants Management Specialist National Institute of Diabetes and Digestive and Kidney Diseases Westwood Building, Room 649 Bethesda, MD 20892 Telephone: (301) 594-7543 Ms. Carol B. Alderson Grants Management Specialist National Institute of Allergy and Infectious Diseases Solar Building, Room 4B27 Bethesda, MD 20892 Telephone: (301) 496-7075 AUTHORITY AND REGULATIONS This program is described in the Catalog of Federal Domestic Assistance Nos. 93.821, 93.859, 93.862, and 93.863. Awards are authorized by sections 301 and 405 of the Public Health Service Act, as amended, and administered under PHS grants policies and Federal Regulations 45 CFR Part 74 and 45 CFR Part 92. This program is not subject to the intergovernmental review requirements of Executive Order 12372 or Health Systems Agency review. From owner-population-bio@net.bio.net Wed Dec 01 22:00:00 1993 Path: biosci!CU.NIH.GOV!IAE From: IAE@CU.NIH.GOV ("Irene Anne Eckstrand") Newsgroups: bionet.population-bio Subject: (none) Message-ID: <9312021608.AA07878@net.bio.net> Date: 2 Dec 93 16:06:08 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 14 I am posting on this board an announcement from the National Institute of General Medical Sciences which describes the research areas it will support with AIDS money. I am delighted to say that this year, NIGMS will support research on the population biology of HIV, including how variation evolves and the effects of variation on the course of disease, and on the evolution of multiple drug resistance. If you are interested in discussing this further, please feel free to e-mail or telephone me. Irene Anne Eckstrand iae@cu.nih.gov 301-594-7762 From owner-population-bio@net.bio.net Fri Dec 03 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!library.ucla.edu!csulb.edu!nic.csu.net!nic.csu.net!nntp From: bob@biol1next.calstatela.edu (Bob Desharnais) Newsgroups: bionet.population-bio Subject: Tenure-track position, Insect Ecologist, Cal State LA Keywords: job, insect ecologist, entomologist Message-ID: <1993Dec3.182331.7670@nic.csu.net> Date: 4 Dec 93 02:23:25 GMT Distribution: bionet Lines: 63 Nntp-Posting-Host: biol1next.calstatela.edu A forthcoming advertisement in Science will announce that the Department of Biology and Microbiology at California State University, Los Angeles seeks an Insect Ecologist to fill a tenure-track, assistant professor position. A copy of the job announcement follows. We seek applicants with strong quantitative skills who conduct research in population, community or evolutionary ecology. Starting salaries are in the $35,000 to 38,000 range (nine month basis). Cal State Los Angeles is an ethnically and culturally diverse campus of 20,000 students, located east of downtown Los Angeles and south of Pasadena. Our Department has 24 faculty members, with eight in fields of environmental biology: marine ecology, population genetics, plant ecophysiology, freshwater zoology, plant evolutionary ecology, Drosophila ecological genetics, vertebrate ecophysiology, and plant community ecology. The successful candidate should expect to teach general biology, entomology and upper division courses. Enrollment in upper division courses is limited to between 16 and 32 students. The successful applicant is expected to participate in an NSF-funded initiative in multidisciplinary, environmental science education. Faculty are active in research, and start-up funds are available. New faculty are eligible for internal grants and awards. The environmental biology faculty hold grants from NSF, EPA, NASA and DOE for ecological research and environmental science education. These awards allow faculty release time from their regular teaching duties. Research facilities on campus include computer workstation labs, a greenhouse facility with outdoor research areas, GIS and image processing labs, biotechnology and electron microscopy facilities, and an aquatics laboratory. The California State University system maintains remote field stations for ecological research. Thank you in advance for bringing this opportunity to the attention of interested individuals. Dr. Robert Desharnais Chair, Insect Ecologist Search Committee Cal State LA Los Angeles, CA 90032 bob@biol1next.calstatela.edu Tel (213) 343-2056 -------------------------- ADVERTISEMENT FOR SCIENCE -------------------------- INSECT ECOLOGIST. Department of Biology and Microbiology, California State University, Los Angeles, will fill an ASSISTANT PROFESSOR tenure-track position starting fall 1994. Ph.D. required. Candidates must have strong quantitative skills and conduct research in population, community, or evolutionary ecology. Successful applicant is expected to participate in a multidisciplinary program of research and instruction in environmental biology involving undergraduate and masters students. Teaching duties in general biology, entomology, and area of specialty. Research start-up funds are available. Applicants should submit curriculum vitae, statement of research interests, and three letters of recommendation to: Dr. Robert Desharnais, Department of Biology and Microbiology, California State University, Los Angeles, CA 90032-8201. FAX: 213 343-2095. E-mail: bob@biol1next.calstatela.edu. Deadline 31 January 1994 or until filled. Equal Opportunity/Affirmative Action/Disabled Employer. From owner-population-bio@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!agate!spool.mu.edu!sgiblab!munnari.oz.au!bunyip.cc.uq.oz.au!dpi-gw!qdpii!ianst From: ianst@qdpii.ind.dpi.qld.gov.au (Ian Staples) Newsgroups: bionet.population-bio Subject: Re: Tenure-track position, Insect Ecologist, Cal State LA Keywords: job, insect ecologist, entomologist Message-ID: Date: 6 Dec 93 10:30:45 GMT References: <1993Dec3.182331.7670@nic.csu.net> Distribution: bionet Organization: Queensland Dept of Primary Industries Lines: 21 bob@biol1next.calstatela.edu (Bob Desharnais) writes: > A forthcoming advertisement in Science will announce that the >Department of Biology and Microbiology at California State University, Los >Angeles seeks an Insect Ecologist to fill a tenure-track, assistant >professor position. I showed this to a colleague who has been working on the ecology of fruit-piercing moths here in the tropics. His comment: "No thanks. I've been to Los Angeles." :-) But don't let me put you off :):):) Cheers, Ian S. -- Ian Staples E-mail : ianst@qdpii.ind.dpi.qld.gov.au c/- P.O. Box 1054 MAREEBA Phone : +61 (0)70 921 555 Home 924 847 Queensland Australia 4880 Fax : +61 (0)70 923 593 " " " From owner-population-bio@net.bio.net Sun Dec 05 22:00:00 1993 Path: biosci!lhc!darwin.sura.net!howland.reston.ans.net!spool.mu.edu!sgiblab!munnari.oz.au!bunyip.cc.uq.oz.au!dpi-gw!qdpii!ianst From: ianst@qdpii.ind.dpi.qld.gov.au (Ian Staples) Newsgroups: bionet.population-bio Subject: Re: Tenure-track position, Insect Ecologist, Cal State LA Keywords: job, insect ecologist, entomologist Message-ID: Date: 6 Dec 93 10:30:45 GMT References: <1993Dec3.182331.7670@nic.csu.net> Distribution: bionet Organization: Queensland Dept of Primary Industries Lines: 21 bob@biol1next.calstatela.edu (Bob Desharnais) writes: > A forthcoming advertisement in Science will announce that the >Department of Biology and Microbiology at California State University, Los >Angeles seeks an Insect Ecologist to fill a tenure-track, assistant >professor position. I showed this to a colleague who has been working on the ecology of fruit-piercing moths here in the tropics. His comment: "No thanks. I've been to Los Angeles." :-) But don't let me put you off :):):) Cheers, Ian S. -- Ian Staples E-mail : ianst@qdpii.ind.dpi.qld.gov.au c/- P.O. Box 1054 MAREEBA Phone : +61 (0)70 921 555 Home 924 847 Queensland Australia 4880 Fax : +61 (0)70 923 593 " " " From owner-population-bio@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.population-bio Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312061946.AA20546@judy.eng.uci.edu> Date: 6 Dec 93 19:46:10 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-population-bio@net.bio.net Mon Dec 06 22:00:00 1993 Path: biosci!JUDY.ENG.UCI.EDU!liang From: liang@JUDY.ENG.UCI.EDU (liang) Newsgroups: bionet.population-bio Subject: CHINESES_BIOTECH_NET_FOUNDED Message-ID: <9312060501.AA19445@judy.eng.uci.edu> Date: 6 Dec 93 05:01:15 GMT Sender: daemon@net.bio.net Distribution: bionet Lines: 12 CBNet (Chinese Biotechnology Network) is a non-profit organization composed of professionals in biological, chemical, medical sciences, engineering and related fields. The CBNet sponsors the Chinese Biotechnology Internet Forum (CBIF) newsletter. To subscribe CBIF, please send an email to Listserv@UCSD.Edu with the message body: Add CB-Net. From owner-population-bio@net.bio.net Mon Dec 13 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!uunet!decwrl!decwrl!morrow.stanford.edu!morrow.stanford.edu!not-for-mail From: HF.JSL@forsythe.stanford.edu (Joseph Lipsick) Newsgroups: bionet.molbio.evolution Subject: Re: Steven J Gould Date: 13 Dec 1993 22:08:40 -0800 Organization: Stanford University Lines: 3 Sender: news@morrow.stanford.edu Distribution: usa Message-ID: <2ejl98$em4@morrow.stanford.edu> NNTP-Posting-Host: morrow.stanford.edu Perhaps this bulletin board should be renamed "molecular-evil" in order to keep the would-be saints far from Darwinian temptation. Joe Lipsick From owner-population-bio@net.bio.net Tue Dec 14 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!nic.csu.net!eis.calstate.edu!eis.calstate.edu!not-for-mail Newsgroups: bionet.population-bio Subject: euthanasia Message-ID: <2eisjl$36t@eis.calstate.edu> From: cwisnia@eis.calstate.edu (Cory M Wisnia) Date: 13 Dec 1993 15:07:33 -0800 Organization: Calif State Univ/Electronic Information Services NNTP-Posting-Host: eis.calstate.edu Lines: 10 Our names are Jenny Gealey and Stephanie Mechling, and we are doing a debate for a mock trial class. We are students at the Mendocino Middle School. The subject of our debate is mercy killing. We are taking the affirmative side. We are interested in any information pertaining to mercy killing. We want to obtain any data that could support our position, such as how many people have terminal diseases, what the costs of hospital stays are, and the points of views of medical experts and of the terminally ill. You can E-mail replies to Cory Wisnia Thank you for your help. -- From owner-population-bio@net.bio.net Tue Dec 14 22:00:00 1993 Newsgroups: bionet.population-bio Path: biosci!bcm!cs.utexas.edu!uunet!pipex!sunic!news.lth.se!news.lu.se!lotka.teorekol.lu.se!siglun From: siglun@lotka.teorekol.lu.se (Sigfrid Lundberg) Subject: Re: Help with estimation problem Message-ID: <1993Dec15.171427.20363@nomina.lu.se> Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: lotka.teorekol.lu.se Organization: Lund university, Sweden References: <9312151429.AA00534@net.bio.net> Distribution: bionet Date: Wed, 15 Dec 1993 17:14:27 GMT Lines: 72 In article <9312151429.AA00534@net.bio.net> T80SMS1@MVS.CSO.NIU.EDU writes: >I need some help with a sampling estimation problem. We need >to estimate the number of genotypes in a population from a finite Well, I'm not a statistician. But I'll give you my idea anyway. >sample. The situation is as follows. We have a population of >Daphnia (small freshwater crustaceans) which reproduce asexually >(i.e., genotypes in = genotypes out). We start off the population >with a known set of genotypes (N = 34). The population grows >and some genotypes die out. Later we take a finite sample of >the population (say N = 100, but it varies). We also know the >total population size (say N = 3000 on this day). We can then With that a big difference between the sample size and population size I guess that we could, assume that the population is infinate, couldn't we? >assay the genotypes of the sampled individuals and assign them >to one of the intial 34. We wish to estimate the number of >genotypes remaining. The population now consists of a mixed >population of genotype frequencies, some common and some rare. Given that we can assume that the real population is infinate, the numbers of individuals belonging to the different genotypes in the samples must be distributed according to the multinomial distribution, from which we could estimate the genotype frequencies. >Clearly, very rare genotypes may be missing from the sample. >Is there some way to estimate this number? We have been trying >to construct a bootstrap routine but cannot figure out how >to deal with the apparant zeros. Obviously some are true >zeros and some are just unsampled. The final twist is that You could, for simplicity, consider the population as consisting of two genotypes only. That is, one that is rare and then the remaining ones pooled. Then use the binomial distribution to calculate the probability that a genotype won't turn up as a function of its frequency and the sample size. This could possibly be used for calculating how large a sample need to be in order to make the probability that a geneotype won't be detected less than (say) 0.05, given that frequency >= 1 / population size These last paragraphs are perhaps not that well written, but I hope you see what I mean. >this sampling was done 3 times. For all but the last, a >missing genotype in one sample might appear in the next. Any Three independent cultures, or three sampling events from the same culture? >help would be appreciated. >Thanks in advance, >Sam > >*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* >* Samuel M. Scheiner + * >* Department of Biological Sciences + In a bureaucracy it * >* Northern Illinois University + * >* DeKalb, Illinois 60115 + is much easier to get * >* Phone: (815) 753-7847 + * >* Fax: (815) 753-0461 + forgiveness than * >* Bitnet: t80sms1@niu.bitnet + * >* Internet: t80sms1@mvs.cso.niu.edu + permission. * >*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* Regards Sigfrid From owner-population-bio@net.bio.net Tue Dec 14 22:00:00 1993 Path: biosci!MVS.CSO.NIU.EDU!T80SMS1 From: T80SMS1@MVS.CSO.NIU.EDU Newsgroups: bionet.population-bio Subject: Help with estimation problem Date: 15 Dec 1993 06:29:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 34 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9312151429.AA00534@net.bio.net> NNTP-Posting-Host: net.bio.net I need some help with a sampling estimation problem. We need to estimate the number of genotypes in a population from a finite sample. The situation is as follows. We have a population of Daphnia (small freshwater crustaceans) which reproduce asexually (i.e., genotypes in = genotypes out). We start off the population with a known set of genotypes (N = 34). The population grows and some genotypes die out. Later we take a finite sample of the population (say N = 100, but it varies). We also know the total population size (say N = 3000 on this day). We can then assay the genotypes of the sampled individuals and assign them to one of the intial 34. We wish to estimate the number of genotypes remaining. The population now consists of a mixed population of genotype frequencies, some common and some rare. Clearly, very rare genotypes may be missing from the sample. Is there some way to estimate this number? We have been trying to construct a bootstrap routine but cannot figure out how to deal with the apparant zeros. Obviously some are true zeros and some are just unsampled. The final twist is that this sampling was done 3 times. For all but the last, a missing genotype in one sample might appear in the next. Any help would be appreciated. Thanks in advance, Sam *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* * Samuel M. Scheiner + * * Department of Biological Sciences + In a bureaucracy it * * Northern Illinois University + * * DeKalb, Illinois 60115 + is much easier to get * * Phone: (815) 753-7847 + * * Fax: (815) 753-0461 + forgiveness than * * Bitnet: t80sms1@niu.bitnet + * * Internet: t80sms1@mvs.cso.niu.edu + permission. * *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* From owner-population-bio@net.bio.net Tue Dec 14 22:00:00 1993 Path: biosci!bcm!avdms8.msfc.nasa.gov!europa.eng.gtefsd.com!howland.reston.ans.net!usc!sdd.hp.com!sgiblab!sgigate.sgi.com!olivea!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!stein1.u.washington.edu!johnreed From: johnreed@stein1.u.washington.edu (John Reed) Newsgroups: bionet.population-bio Subject: Re: Help with estimation problem Date: 15 Dec 1993 18:00:58 GMT Organization: University of Washington, Seattle Lines: 39 Distribution: bionet Message-ID: <2enjcq$kqf@news.u.washington.edu> References: <9312151429.AA00534@net.bio.net> <1993Dec15.171427.20363@nomina.lu.se> NNTP-Posting-Host: stein.u.washington.edu In article <1993Dec15.171427.20363@nomina.lu.se>, Sigfrid Lundberg wrote: >In article <9312151429.AA00534@net.bio.net> T80SMS1@MVS.CSO.NIU.EDU writes: >>I need some help with a sampling estimation problem. We need >>to estimate the number of genotypes in a population from a finite > >Well, I'm not a statistician. But I'll give you my idea anyway. > >>sample. The situation is as follows. We have a population of >>Daphnia (small freshwater crustaceans) which reproduce asexually >>(i.e., genotypes in = genotypes out). We start off the population >>with a known set of genotypes (N = 34). The population grows >>and some genotypes die out. Later we take a finite sample of >>the population (say N = 100, but it varies). We also know the >>total population size (say N = 3000 on this day). We can then > >With that a big difference between the sample size and population >size I guess that we could, assume that the population is infinate, >couldn't we? > >Sigfrid Hmm, well someone who is more knowledgable correct me if I'm wrong. I think it depends on why you think genotypes may be missing. If this is due to selection then MAYBE the infinite population size assumption is valid (1/30th doesn't seem that small to me though), but if you think the loss of some genotypes is due to genetic drift then this invalidates the infinite population size assumption immediately. You can't have drift in an infinitely large population and I think this would mess up your calculations. John -------------------------------------------------------------------------- John Reed College of Forest Resources, AR-10 University of Washington Seattle, WA 98195 Internet: johnreed@u.washington.edu -------------------------------------------------------------------------- From owner-population-bio@net.bio.net Wed Dec 15 22:00:00 1993 Newsgroups: bionet.population-bio Path: biosci!bloom-beacon.mit.edu!news.kei.com!sol.ctr.columbia.edu!usc!cs.utexas.edu!howland.reston.ans.net!EU.net!sunic!news.lth.se!news.lu.se!lotka.teorekol.lu.se!siglun From: siglun@lotka.teorekol.lu.se (Sigfrid Lundberg) Subject: Re: Help with estimation problem Message-ID: <1993Dec16.074306.12910@nomina.lu.se> Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: lotka.teorekol.lu.se Organization: Lund university, Sweden References: <9312151429.AA00534@net.bio.net> <1993Dec15.171427.20363@nomina.lu.se> <2enjcq$kqf@news.u.washington.edu> Distribution: bionet Date: Thu, 16 Dec 1993 07:43:06 GMT Lines: 67 In article <2enjcq$kqf@news.u.washington.edu> johnreed@stein1.u.washington.edu (John Reed) writes: >In article <1993Dec15.171427.20363@nomina.lu.se>, >Sigfrid Lundberg wrote: >>In article <9312151429.AA00534@net.bio.net> T80SMS1@MVS.CSO.NIU.EDU writes: >>>I need some help with a sampling estimation problem. We need >>>to estimate the number of genotypes in a population from a finite >> >>Well, I'm not a statistician. But I'll give you my idea anyway. >> >>>sample. The situation is as follows. We have a population of >>>Daphnia (small freshwater crustaceans) which reproduce asexually >>>(i.e., genotypes in = genotypes out). We start off the population >>>with a known set of genotypes (N = 34). The population grows >>>and some genotypes die out. Later we take a finite sample of >>>the population (say N = 100, but it varies). We also know the >>>total population size (say N = 3000 on this day). We can then >> >>With that a big difference between the sample size and population >>size I guess that we could, assume that the population is infinate, >>couldn't we? >> >>Sigfrid > >Hmm, well someone who is more knowledgable correct me if I'm wrong. I >think it depends on why you think genotypes may be missing. If this is >due to selection then MAYBE the infinite population size assumption is >valid (1/30th doesn't seem that small to me though), but if you think the >loss of some genotypes is due to genetic drift then this invalidates the >infinite population size assumption immediately. You can't have drift in This is a good point. And I think it is valid regardless of whether there is selection or drift (I just thought 3000 seemed to be fairly large), because the sampling procedure is *changing* the genotypic composition (sampling without replacement) if the total population size is to small. On could, however, do the same analysis using the multinomial generalization of the hypergeometric distribution (The best reference I could find on my book shelves this morning is volume 1 of Sewall Writes (1968) treatise "Evolution and genetics of populations" pp. 223-225. Chicago University Press). Using this one is more complicated, but it takes into account the fact that the population is not infinate, and that the sampling occurs without replacement. To be strict, using the bi/multi-nomial distribution requires either that the total population is infinate, or that the sampling occurs with replacement. >an infinitely large population and I think this would mess up your >calculations. >John Sure. Drift is most likely an important causes of loss of genotypes in this experimental setup. > >-------------------------------------------------------------------------- >John Reed >College of Forest Resources, AR-10 >University of Washington >Seattle, WA 98195 >Internet: johnreed@u.washington.edu >-------------------------------------------------------------------------- Regards Sigfrid From owner-population-bio@net.bio.net Wed Dec 15 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!usc!nic.csu.net!nic.csu.net!nntp Newsgroups: bionet.population-bio Subject: Job: Insect Ecologist, tenure-track, Cal State LA Message-ID: <1993Dec15.152541.7815@nic.csu.net> From: bob@biol1next.calstatela.edu (Bob Desharnais) Date: 15 Dec 93 15:25:37 PST Distribution: bionet Keywords: job, insect ecologist, entomologist Nntp-Posting-Host: biol1next.calstatela.edu Lines: 63 A recent advertisement in Science announced that the Department of Biology and Microbiology at California State University, Los Angeles is seeking an Insect Ecologist to fill a tenure-track, assistant professor position. A copy of the job announcement follows. We seek applicants with strong quantitative skills who conduct research in population, community or evolutionary ecology. Starting salaries are in the $35,000 to 38,000 range (nine month basis). Cal State Los Angeles is an ethnically and culturally diverse campus of 20,000 students, located east of downtown Los Angeles and south of Pasadena. Our Department has 24 faculty members, with eight in fields of environmental biology: marine ecology, population genetics, plant ecophysiology, freshwater zoology, plant evolutionary ecology, Drosophila ecological genetics, vertebrate ecophysiology, and plant community ecology. The successful candidate should expect to teach general biology, entomology and upper division courses. Enrollment in upper division courses is limited to between 16 and 32 students. The successful applicant is expected to participate in an NSF-funded initiative in multidisciplinary, environmental science education. Faculty are active in research, and start-up funds are available. New faculty are eligible for internal grants and awards. The environmental biology faculty hold grants from NSF, EPA, NASA and DOE for ecological research and environmental science education. These awards allow faculty release time from their regular teaching duties. Research facilities on campus include computer workstation labs, a greenhouse facility with outdoor research areas, GIS and image processing labs, biotechnology and electron microscopy facilities, and an aquatics laboratory. The California State University system maintains remote field stations for ecological research. Thank you in advance for bringing this opportunity to the attention of interested individuals. Dr. Robert Desharnais Chair, Insect Ecologist Search Committee Cal State LA Los Angeles, CA 90032 bob@biol1next.calstatela.edu Tel (213) 343-2056 -------------------------- ADVERTISEMENT FROM SCIENCE -------------------------- INSECT ECOLOGIST. Department of Biology and Microbiology, California State University, Los Angeles, will fill an ASSISTANT PROFESSOR tenure-track position starting fall 1994. Ph.D. required. Candidates must have strong quantitative skills and conduct research in population, community, or evolutionary ecology. Successful applicant is expected to participate in a multidisciplinary program of research and instruction in environmental biology involving undergraduate and masters students. Teaching duties in general biology, entomology, and area of specialty. Research start-up funds are available. Applicants should submit curriculum vitae, statement of research interests, and three letters of recommendation to: Dr. Robert Desharnais, Department of Biology and Microbiology, California State University, Los Angeles, CA 90032-8201. FAX: 213 343-2095. E-mail: bob@biol1next.calstatela.edu. Deadline 31 January 1994 or until filled. Equal Opportunity/Affirmative Action/Disabled Employer. From owner-population-bio@net.bio.net Wed Dec 15 22:00:00 1993 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!europa.eng.gtefsd.com!uunet!olivea!decwrl!decwrl!usenet.coe.montana.edu!news.uoregon.edu!netnews.nwnet.net!news.u.washington.edu!evolution!joe From: joe@evolution.u.washington.edu (Joe Felsenstein) Newsgroups: bionet.population-bio Subject: Re: Help with estimation problem Date: 16 Dec 1993 18:58:17 GMT Organization: University of Washington, Seattle Lines: 25 Distribution: bionet Message-ID: <2eqb49$gbj@news.u.washington.edu> References: <1993Dec15.171427.20363@nomina.lu.se> <2enjcq$kqf@news.u.washington.edu> <1993Dec16.074306.12910@nomina.lu.se> NNTP-Posting-Host: evolution.genetics.washington.edu Summary: Fisher problem about butterflies Keywords: species, genotypes, Fisher, Shakespeare I think this problem may be related to the one R. A. Fisher addressed in his work on how many species there are in a region. The reference is: Fisher, R. A., A. S. Corbet, and C. B. Williams. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12: 42- He was taking some consecutive samples from an area, and by seeing how many new kinds of butterfly turned up in one sample that weren't in the other he could estimate how many would be there if he sampled repeatedly. If Sam is sampling 1/3 of the population he could adapt the calculation to estimate what would happen if he sampled all of it. A derivative of this method has since been used by Bradley Efron and Ron Thisted (in 1986) to assess the authenticity of new texts attributed to Shakespeare. ----- 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 Thu Dec 16 22:00:00 1993 Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!howland.reston.ans.net!usc!nic.csu.net!nic.csu.net!nntp Newsgroups: bionet.population-bio Subject: Re: Help with estimation problem Message-ID: <1993Dec16.191108.7834@nic.csu.net> From: bob@biol1next.calstatela.edu (Bob Desharnais) Date: 16 Dec 93 19:11:05 PST References: <9312151429.AA00534@net.bio.net> Distribution: bionet Nntp-Posting-Host: biol1next.calstatela.edu Lines: 70 In article <9312151429.AA00534@net.bio.net> writes: > I need some help with a sampling estimation problem. We need > to estimate the number of genotypes in a population from a finite > sample. The situation is as follows. We have a population of > Daphnia (small freshwater crustaceans) which reproduce asexually > (i.e., genotypes in = genotypes out). We start off the population > with a known set of genotypes (N = 34). The population grows > and some genotypes die out. Later we take a finite sample of > the population (say N = 100, but it varies). We also know the > total population size (say N = 3000 on this day). We can then > assay the genotypes of the sampled individuals and assign them > to one of the intial 34. We wish to estimate the number of > genotypes remaining. The population now consists of a mixed > population of genotype frequencies, some common and some rare. > Clearly, very rare genotypes may be missing from the sample. > Is there some way to estimate this number? We have been trying > to construct a bootstrap routine but cannot figure out how > to deal with the apparant zeros. Obviously some are true > zeros and some are just unsampled. The final twist is that > this sampling was done 3 times. For all but the last, a > missing genotype in one sample might appear in the next. Any > help would be appreciated. > Thanks in advance, > Sam > > *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* > * Samuel M. Scheiner + * > * Department of Biological Sciences + In a bureaucracy it * > * Northern Illinois University + * > * DeKalb, Illinois 60115 + is much easier to get * > * Phone: (815) 753-7847 + * > * Fax: (815) 753-0461 + forgiveness than * > * Bitnet: t80sms1@niu.bitnet + * > * Internet: t80sms1@mvs.cso.niu.edu + permission. * > *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+* This problem sounds similar to the one an ecologist faces when trying to determine the number of species in a community. Heltshe and Forrester (1983a,b) describe a jacknife method of estimating the number of species (genotypes) when a total of n random samples are taken: S = s + ((n-1)/n)^k where S = jacknife estimate of number of species (genotypes) s = observed total number of genotype in the n samples n = total number of samples k = number of species (genotypes) that occur in one and only one sample They also give formulas for the variance which can be used for confidence intervals. Hope this helps. References: Heltshe, J.F. and Forrester, N.E. 1983a. Estimating species richness using the jacknife procedure. Biometrics 39:1-11. Heltshe, J.F. and Forrester, N.E. 1983b. Estimating diversity using quadrat sampling. Biometrics 39: 1073-1076. -- Bob Desharnais Associate Professor Biology Cal State LA Los Angeles, CA 90032 bob@biol1next.calstatela.edu (NeXT Mail ok) Tel (213) 343-2056 From owner-population-bio@net.bio.net Thu Dec 16 22:00:00 1993 Newsgroups: bionet.population-bio Path: biosci!daresbury!doc.ic.ac.uk!uknet!pipex!sunic!news.lth.se!news.lu.se!lotka.teorekol.lu.se!siglun From: siglun@lotka.teorekol.lu.se (Sigfrid Lundberg) Subject: Re: Help with estimation problem Message-ID: <1993Dec17.081716.24845@nomina.lu.se> Keywords: species, genotypes, Fisher, Shakespeare Sender: news@nomina.lu.se (USENET News System) Nntp-Posting-Host: lotka.teorekol.lu.se Organization: Lund university, Sweden References: <2enjcq$kqf@news.u.washington.edu> <1993Dec16.074306.12910@nomina.lu.se> <2eqb49$gbj@news.u.washington.edu> Distribution: bionet Date: Fri, 17 Dec 1993 08:17:16 GMT Lines: 34 In article <2eqb49$gbj@news.u.washington.edu> joe@evolution.u.washington.edu (Joe Felsenstein) writes: >I think this problem may be related to the one R. A. Fisher addressed in >his work on how many species there are in a region. The reference is: > >Fisher, R. A., A. S. Corbet, and C. B. Williams. 1943. The relation > between the number of species and the number of individuals in a > random sample of an animal population. Journal of Animal Ecology > 12: 42- > >He was taking some consecutive samples from an area, and >by seeing how many new kinds of butterfly turned up in one sample that >weren't in the other he could estimate how many would be there if he >sampled repeatedly. If Sam is sampling 1/3 of the population he could >adapt the calculation to estimate what would happen if he sampled all >of it. > This might be good. It requires that the genotype-abundance data in the samples can be fitted to a log-series. >A derivative of this method has since been used by Bradley Efron and Ron >Thisted (in 1986) to assess the authenticity of new texts attributed to >Shakespeare. > >----- >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 > > Sigfrid From owner-population-bio@net.bio.net Thu Dec 30 22:00:00 1993 Path: biosci!CS.Arizona.EDU!organpipe.uug.arizona.edu!uunet!cs.utexas.edu!swrinde!menudo.uh.edu!ccsvax.sfasu.edu!z_durancm From: z_durancm@ccsvax.sfasu.edu Newsgroups: bionet.population-bio Subject: small mammal home range Message-ID: <1993Dec31.133547.8609@ccsvax.sfasu.edu> Date: 31 Dec 93 13:35:47 CST Organization: Stephen F. Austin State University Lines: 11 I have just completed the data collection part of a small mammal project in which we handled over 1800 animals. Animals were live-trapped on 9 X 9 grids with 15 m spacing. My question for the group: Is there a computer program out there that will calculate distances moved between traps? And/or can someone out there tell me how to do it with SAS. I can almost see it, but not quite. Mike Duran Department of Biology Nacogdoches, TX 75962-3003 e-mail z_durancm@ccsvax.sfasu.edu