Author: niiicholas
Date: Dec. 13 2002,01:53

Post your favorite Internet resources for searching for accurate (peer-reviewed lit., high-quality science journalism, educational websites not directly evo/creo related, sequence or fossil data, etc.) scientific information on evolution.

Related hints and tips should also be added as appropriate, perhaps this would have potential as a FAQ at some point.

When posting links to journals, please make a note regarding access.

E.g.:

PubMed
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

This is the National Library of Medicine's free search engine for "biomedical" literature, but in practice it includes all major general science journals, anything related to molecular biology, many more general biology journals (weaker on ecology etc.), and in general gobbs of evolution stuff on your topic of interest.

GUIDE:
For an author search, do "lastname firstinitials" without commas or periods.  Separate multiple authors with commas.

For example, Thornhill and Ussery wrote an article outlining the various ways that "irreducibly complexity" can evolve.  Search PubMed on "ussery d, thornhill" and you get:

A classification of possible routes of Darwinian evolution


HINT:
Searching on keywords or authors will never get you everything interesting on the first shot.  A key feature is the "Related Articles" link to the upper-right of each reference.

For example, here is an article on changes-of-function in evolutionary history:

Quote

Bioessays 1999 May;21(5):432-9   Generation of evolutionary novelty by functional shift. Ganfornina MD, Sanchez D. Biology Department, University of Utah, Salt Lake City 84112, USA. lazarillo@bioscience.utah.edu That biological features may change their function during evolution has long been recognized. Particularly, the acquisition of new functions by molecules involved in developmental pathways is suspected to cause important morphologic novelties. However, the current terminology describing functional changes during evolution (co-option or recruitment) fails to recognize important biologic distinctions between diverse evolutionary routes involving functional shifts. The main goal of our work is to stress the importance of an apparently trivial distinction: Whether or not the element that adopts a new function (anything from a morphologic structure to a protein domain) is a single or a duplicated element. We propose that natural selection must act in a radically different way, depending on the historic succession of co-option and duplication events; that is, co-option may provide the selective pressure for a subsequent gene duplication or could be a stabilizing factor that helps maintain redundancy after gene duplication. We review the evidence available on functional changes, focusing whenever possible on developmental molecules, and we propose a conceptual framework for the study of functional shifts during evolution with a level of resolution appropriate to the power of our current methodologies.

But what else exists out there on this topic?  Trying different keywords is a possibility, e.g. "cooption", "co-option", "co-optation", "change in function", "functional shift", etc., but this is tedious.  Instead, once you've found one good article, click on "Related articles":

Articles related to Ganfornina and Sanchez 1999

...and you get a pile:

Quote

1:  Ganfornina MD, Sanchez D. Related Articles, Links   Generation of evolutionary novelty by functional shift. Bioessays. 1999 May;21(5):432-9. Review. PMID: 10376014 [PubMed - indexed for MEDLINE] 2:  True JR, Carroll SB. Related Articles, Links   Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol. 2002;18:53-80. PMID: 12142278 [PubMed - in process] 3:  Van de Peer Y, Taylor JS, Braasch I, Meyer A. Related Articles, Links   The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J Mol Evol. 2001 Oct-Nov;53(4-5):436-46. PMID: 11675603 [PubMed - indexed for MEDLINE] 4:  Eizinger A, Jungblut B, Sommer RJ. Related Articles, Links   Evolutionary change in the functional specificity of genes. Trends Genet. 1999 May;15(5):197-202. Review. PMID: 10322487 [PubMed - indexed for MEDLINE] 5:  Taylor JS, Van de Peer Y, Meyer A. Related Articles, Links   Genome duplication, divergent resolution and speciation. Trends Genet. 2001 Jun;17(6):299-301. Review. PMID: 11377777 [PubMed - indexed for MEDLINE] 6:  Thornton JW, DeSalle R. Related Articles, Links   Gene family evolution and homology: genomics meets phylogenetics. Annu Rev Genomics Hum Genet. 2000;1:41-73. Review. PMID: 11701624 [PubMed - indexed for MEDLINE] 7:  Otto SP, Yong P. Related Articles, Links   The evolution of gene duplicates. Adv Genet. 2002;46:451-83. Review. PMID: 11931235 [PubMed - indexed for MEDLINE] 8:  Krakauer DC, Nowak MA. Related Articles, Links   Evolutionary preservation of redundant duplicated genes. Semin Cell Dev Biol. 1999 Oct;10(5):555-9. Review. PMID: 10597640 [PubMed - indexed for MEDLINE] 9:  Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Related Articles, Links   Selection in the evolution of gene duplications. Genome Biol. 2002;3(2):RESEARCH0008. PMID: 11864370 [PubMed - indexed for MEDLINE] [etc.]

Also, be sure to try the "Sort by" window and selected "Pub Date" to bring up the most recent articles.  Doing this on the above article brought up:

Quote

1:  Woolhouse ME, Webster JP, Domingo E, Charlesworth B, Levin BR. Related Articles, Links   Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat Genet. 2002 Dec;32(4):569-77. PMID: 12457190 [PubMed - in process] 2:  Manley GA. Related Articles, Links   Evolution of structure and function of the hearing organ of lizards. J Neurobiol. 2002 Nov 5;53(2):202-11. Review. PMID: 12382276 [PubMed - in process] 3:  Prince VE, Pickett FB. Related Articles, Links   Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet. 2002 Nov;3(11):827-37. PMID: 12415313 [PubMed - in process] 4:  Karev GP, Wolf YI, Rzhetsky AY, Berezovskaya FS, Koonin EV. Related Articles, Links   Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol Biol. 2002 Oct 14 [epub ahead of print] PMID: 12379152 [PubMed - as supplied by publisher] [etc.]

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Author: niiicholas
Date: Dec. 13 2002,02:14

PubMed Central:

http://www.pubmedcentral.nih.gov/

...is a central archive of scientific literature that is freely available to the public without subscription.  Sometimes the whole journal is free, sometimes the material is made freely available after 6 months.

Oftentimes you will have to complete a free registration to access free content.

I believe this is the current list of journals with free online content:
http://www.pubmedcentral.nih.gov/

Top journals from this list for evolution-related stuff:

Genome Biology

Proceedings of the National Academy of Sciences of the United States of America
(also at http://www.pnas.org )

Journal of Biology

A free article from the last one, advocating open access to scientific lit -- a logical position, considering how most of this research is taxpayer-funded:
Open access to the scientific journal literature
Peter Suber
J Biol. 2002; 1(1): 3
http://jbiol.com/content/1/1/3






A list of journals with full-text access for subscribers (the subscribers are usually university libraries, generally they are available to anyone within the University's edu domain) tied into the PubMed search engine is here:

http://www.ncbi.nlm.nih.gov/entrez/journals/loftext_noprov.html


nic

PS: Another important journal:

Evolution
Archives back to 1996:
http://lsvl.la.asu.edu/evolution/contents.html

From 2000 on:
http://evol.allenpress.com/

Current issue:
http://evol.allenpress.com/evolonline/?request=get-current-issue

Several critques of ID have been published in Evolution:  link to search results

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Author: niiicholas
Date: Dec. 31 2002,17:21

Regarding Google, Dunk has a very good post here.

Quote

(Go to http://groups.google.com/ ) find the desired thread    view thread   find the desired post       view this message alone then the unique message ID will be displayed at the top of the message.  It will be something like 20021231093815.02096.00000093@mb-cl.aol.com You must store the google groups prefix in a convinient place. It is: http://groups.google.com/groups?&selm= Next, append the ID to the prefix: (be sure you don't leave a space after the '='. http://groups.google.com/groups?....aol.com Voila! Dunk

E.g., Dunk's post is:
http://groups.google.com/groups?....ink.net

nic

PS: If you surf with Internet Explorer, don't forget about the Google Search Toolbar (*very* cool):

http://toolbar.google.com/

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