Re: Swima the swimmer]
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Re: Swima the swimmer]
by Kirk Fitzhugh
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The phylogenetic hypotheses are only
'solid' insofar as they explain a limited set of sequence data. Given
that the authors must know they are actively avoiding considering all
sorts of other relevant data that are in need of being explained in the
same context, e.g. the setae as Jim Blake noted, and the use of Bayes
Theorem is not meant for the inference of hypotheses, then Torsten's
endorsement is ill-founded at best.
But then, let's not quibble with the fine points of doing good science - it's more important to impose blind acceptance of methods by even more blind endorsement. Kirk Struck, Torsten wrote: Indeed, it is a nice discovery and very interesting. Moreover, the phylogenetic hypotheses are very solid (not at all "dubios at best") and good in comparison to several other analyses out there. Nice work Karen, Torsten. On 8/22/09 10:30 AM, "Kirk Fitzhugh" kfitzhug@... wrote:Nice discoveries indeed. It's unfortunate that the scientific merits of the phylogenetic hypotheses are dubious at best. But then, it *is* published in Science. ;-) Kirk -----Original Message----- From: annelida-bounces@... on behalf of Geoff Read Sent: Sat 8/22/2009 12:54 AM To: <Annelida list Subject: [Annelida] Swima the swimmer FYI Osborn KJ, Haddock SHD, Pleijel F, Madin LP, Rouse GW 2009. Deep-Sea, Swimming Worms with Luminescent "Bombs". Science 325: 964 (and online 'supplement'). http://www.sciencemag.org/cgi/citmgr?gca=sci;325/5943/964 Swima bombiviridis named (new genus, new species of acrocirrid) Abstract: "By using remotely operated vehicles, we found seven previously unknown species of swimming annelid worms below 1800 meters. Specimens were large and bore a variety of elaborate head appendages. In addition, five species have pairs of ellipsoidal organs homologous to branchiae that produce brilliant green bioluminescence when autotomized. Five genes were used to determine the evolutionary relationships of these worms within Cirratuliformia. These species form a clade within Acrocirridae and were not closely related to either of the two known pelagic cirratuliforms. Thus, this clade represents a third invasion of the pelagic realm from Cirratuliformia. This finding emphasizes the wealth of discoveries to be made in pelagic and deep demersal habitats." Nice discovery. I want to know what they feed on, and how. Geoff -- Geoff Read g.read@... http://www.annelida.net/ http://www.niwa.co.nz/about-niwa *************************** NIWA is the trading name of the National Institute of Water & Atmospheric Research Ltd. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net------ CONTACT INFORMATION ------ PD Dr. habil. Torsten H. Struck University of Osnabrück Department of Biology/Chemistry Zoology Barbarastrasse 11 D-49069 Osnabrück Germany Phone: +49-541-9693450 Fax: +49-541-9692587 e-mail: struck@... _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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Re: Swima the swimmer]
by Greg Rouse
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Kirk,
Please consult the Supplement for details on a maximum parsimony analysis that I assume you would not find dubious. A total evidence analysis (i.e., a "limited set of sequence data", plus what must also be called a "limited set" of morphological data) will appear in due course that may alleviate your other concern. greg On Aug 23, 2009, at 7:15 AM, J. Kirk Fitzhugh wrote:
Greg Rouse Scripps Institution of Oceanography, UCSD 9500 Gilman Drive La Jolla CA, 92093-0202 USA e-mail: grouse@... Office Ph: +1 858 534 7973 Lab Ph: +1 858 534 9941 Fax: +1 858 534 7313 Courier delivery address: Scripps Institution of Oceanography 8750 Biological Grade 2170 Hubbs Hall La Jolla, CA 92037 USA ............................................................................. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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Re: Swima the swimmer]
by Kirk Fitzhugh
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Thanks Greg. No matter what method
is used, be it 'parsimony,' quasi-Bayesianism, etc., I would never
accept the results when I know there are other relevant data that need
to be considered. In lieu of even publishing a cladogram using the
sequence data, it would have been appropriate to wait on the formal
phylogenetics until the relevant data are compiled. There is no such thing as 'total
evidence' analyses - an inference either considers one's available
relevant evidence for the sake of maximizing rationality of
explanation, or they opt
for accepting that the results are going to be more irrational.
But since you mention it, I'm also deeply concerned at the fact that systematists routinely publish phylogenetic hypotheses using a variety of different methods, often with contradictory results, regardless of what data are used. Why do it? We can't compare the results because they're inferred from very different assumptions regarding theories, and no one has ever provided any good empirical arguments for the practice. It seems we've lost sight (or maybe never had it) of why those trees are produced in the first place, and are too enamored with the fact that computers can produce branching diagrams whenever we want 'em. I'm sorry for coming across so critically, but, we have to face the fact that a critical attitude toward phylogenetics is just plain absent. It's a dangerous situation when a field of science becomes so complacent that any sort of method is acceptable and in fact condoned. Kirk Greg Rouse wrote: Kirk, -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ J. Kirk Fitzhugh, Ph.D. Curator of Polychaetes Invertebrate Zoology Section Research & Collections Branch Natural History Museum of Los Angeles County 900 Exposition Blvd Los Angeles CA 90007 Phone: 213-763-3233 FAX: 213-746-2999 e-mail: kfitzhug@... http://www.nhm.org/research/annelida/staff.html http://www.nhm.org/research/annelida/index.html ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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Re: Swima the swimmer]
by Greg Rouse
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Hi Kirk,
There are always compromises made when one is constructing papers. Otherwise we would never publish anything; endlessly waiting until we had assembled all the data that is deemed necessary by purists. Phylogenetics is an iterative process and we all felt that the sequence data analysis, which incidentally will swamp any morphological dataset when its finished, was worth putting out as short note for a broad audience. A more complete detailed analysis and assessment, for digestion by the true friends of annelids, will appear in an appropriate journal in due course, and will no doubt pass unmentioned in this forum. The methods we used produced congruent results with reference to the establishment and position of Swima, and so should satisfy phylogeneticists of various philosophies, with the exception of you of course. If we had published only the parsimony analysis, we would have expected similar disparaging rants from those who prefer model-based approaches. Being pluralistic does not diminish rigor or concern for evidence. best, greg On Aug 23, 2009, at 9:41 AM, J. Kirk Fitzhugh wrote:
Greg Rouse Scripps Institution of Oceanography, UCSD 9500 Gilman Drive La Jolla CA, 92093-0202 USA e-mail: grouse@... Office Ph: +1 858 534 7973 Lab Ph: +1 858 534 9941 Fax: +1 858 534 7313 Courier delivery address: Scripps Institution of Oceanography 8750 Biological Grade 2170 Hubbs Hall La Jolla, CA 92037 USA ............................................................................. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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RE: Swima the swimmer]
by J. Kirk Fitzhugh
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Thanks Greg. Replies inserted below. ...Kirk _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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Re: Swima the swimmer
by Geoff Read
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Besides space here, the green bombers have since been taken up by the news agencies of the world, but I think that for once the Annelida list would have heard about them not long after the story was out of embargo. National Geographic presents more photos, if you want to see a close-up green bomb. http://news.nationalgeographic.com/news/2009/08/photogalleries/worms-glowing-bombs-green-pictures/ and the Scripps release is: http://scrippsnews.ucsd.edu/Releases/?releaseID=1012 Cheers, Geoff NIWA is the trading name of the National Institute of Water & Atmospheric Research Ltd. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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Publicity is good - usually
by Geoff Read
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Hi all,
What is mentioned in this forum is up to its subscribers, and there's quite a variety of topics that come up. Annelid news items that hit the press generally come from me - don't know why, but perhaps because I'm in New Zealand which sees the next calendar date before most other countries. Feel free to post about items earlier if you're directly involved. I also am able to see the stories in the weeklys like Science and Nature. Some stories get posted because they're pet interests of mine, or I find them amusing or odd, and anyone can do that too. I don't have time to keep up with all new papers on annelids, however interesting, and the alerting systems offered by journals are pretty good these days (Greg). If anyone wants an earlier mention or there's some particular reason to do so (like a pdf available of a subscriber only journal, a controversial or significant topic, when feedback wanted) then an email can be sent direct to Annelida <Annelida@...> , most likely phrased in that modest, self-deprecating way people tend to use for their own work. However, it's especially helpful if new books are announced here by those involved, because the abstracting agencies either ignore them or take months to notice them. In this regard: New books Publication of the Zoosymposia volume "Proceedings of the 9th International Polychaete Conference" is imminent, as those who attended the conference will be aware. Watch this http://www.mapress.com/zoosymposia/content.htm space. There's a multi-authored Annelida chapter in this book below, brewing 9 years since the species 2000 program began. But the book should be of wider interest. Alert your librarians for a possible purchase. Part 1 of an attempt to document all known biota in NZ. The 3 volumes will attempt to list every one of the 55,000-plus known species of New Zealand’s animals, plants, fungi and micro-organisms, and each chapter is an authoritative, if necessarily brief overview of a phylum. New Zealand Inventory of Biodiversity. Volume 1. Kingdom Animalia: Radiata, Lophotrochozoa, Deuterostomia. Canterbury University Press, 568 [+ 16] p. NZD $89.95. www.cup.canterbury.ac.nz http://www.cup.canterbury.ac.nz/catalogue/NZ_Inventory.shtml Publicity doesn't say if the below book was commissioned, or the result of a meeting. Several of you will know this. I don't. Annelids in Modern Biology, edited by Daniel H. Shain http://au.wiley.com/WileyCDA/WileyTitle/productCd-0470344210.html ISBN: 978-0-470-34421-7 Hardcover 359 pages March 2009, Wiley-Blackwell Cheers, Geoff -- Geoff Read <g.read@...> http://www.annelida.net/ http://www.niwa.co.nz/about-niwa *************************** NIWA is the trading name of the National Institute of Water & Atmospheric Research Ltd. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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position vacant
by Pat Hutchings
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The Australian Museum is advertising for a new Assistant Director -head of Research and Collections
Assistant Director – Research and Collections, SES Grade 1, Assistant Director Australian Museum. (Pos No AM304/009). Term Appointment (SES) Full-time. Please visit AM website www.australianmuseum.net.au/position/assistant-director-research-collections Closing date:13 November 2009 Position Description:AM304 Assistant Director RC.docSummary Assistant Director, Research & Collections, SES Grade 1, Australian Museum. Term Appointment (SES). Full-time. Position No. AM304/09. An attractive remuneration package including salary in the range of $144,800 to $169,550 p.a. will be negotiated with the successful applicant for a contract period of up to 5 years, with annual performance reviews. Lead the strategic planning and management of the Research and Collections Division of the Australian Museum, and promote the scientific capacities of the Museum to external stakeholders Selection Criteria: 1.Excellent leadership, vision, management, communication and negotiation skills, with a commitment to best practice, ideally in a research context. 2.Appropriate Tertiary qualifications (PhD or equivalent experience), with practical professional experience and accumulated knowledge relevant to the management of cultural, zoological and geological research and/or collections. 3.Ability to manage the day-to-day operations of a complex multi-disciplinary research/educational division. 4.Awareness of relevant current science issues, and of the scientific community roles of modern natural history museums. 5.Ability to develop and implement strategies for the advancement of the Division with limited resources, in line with Museum and Government policy and Public Sector reform principles. 6.Ability to attract funding for research and related programs. 7.Effectiveness in formulating policy and ability to contribute to the development of Government policies relating to science, especially in the areas of biodiversity, scientific information and conservation. Applications Marked ‘Confidential’ To: Human Resources Officer, via email, hr@... or visit jobsnsw www.jobs.nsw.gov.au/ Assistant Director - Research and Collections for full job details including selection criteria, inquiries contact and the position description. Dr Pat Hutchings Senior Principal Research Scientist Research Branch Marine Invertebrates Australian Museum 6 College Street Sydney NSW 2010 t 61 2 93206243 f 61 2 93206050 m 0417486821 pat.hutchings@... www.australianmuseum.net.au Just released: The Great Barrier Reef Biology, Environment and Management edited by Pat Hutchings, Mike Kingsford and Ove Hoegh-Guldberg. CSIRO Publishing 2008. ##################################################################################### This e-mail message has been scanned for Viruses and Content and cleared by MailMarshal ##################################################################################### The Australian Museum. �Egyptian Treasures: art of the pharaohs� exhibition until 6 December 2009! The views in this email are those of the user and do not necessarily reflect the views of the Australian Museum. The information contained in this email message and any accompanying files is or may be confidential and is for the intended recipient only. If you are not the intended recipient, any use, dissemination, reliance, forwarding, printing or copying of this email or any attached files is unauthorised. If you are not the intended recipient, please delete it and notify the sender. The Australian Museum does not guarantee the accuracy of any information contained in this e-mail or attached files. As Internet communications are not secure, the Australian Museum does not accept legal responsibility for the contents of this message or attached files. Please consider the environment before printing this email. _______________________________________________ Annelida mailing list Post: Annelida@... Help/archive: http://www.bio.net/biomail/listinfo/annelida Resources: http://www.annelida.net |
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