Tag: systematics

Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize

Compiling posts and articles discussing why Carl Woese deserves a Nobel Prize.  Will be writing a new article on this but felt like I should share the articles in case I don’t get done in time

I note I do not think Woese should win a Nobel for discovering the archaea.  That was a groundbreaking finding but it does not fit well with the Nobel Prize categories.  I think he should win it for the concept of molecular classification of microorganisms and applying this in general to the microbial world around us.  This concept (expanded by Norm Pace and colleagues to uncultured microbes) revolutionized our approach to studying single microbes in the environment, to studying single microbes infecting people and to studying communities of microbes in and on people.  And thus Woese and Pace in my opinion deserve the Nobel Prize for Medicine.  I will be expanding on this in a future post …
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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BABS meeting at #UCDavis – “Phylogenomics and Systematics”

(Please respond to psward@ucdavis.edu if you plan to attend)

BAY AREA BIOSYSTEMATISTS (BABS) MEETING

Tuesday evening, 22 May 2012

at UC Davis, 1022 Life Sciences Building

“PHYLOGENOMICS AND SYSTEMATICS”

The genomics era holds great promise (and challenge) to systematics. There is the prospect of generating sequence data that will provide unprecedented resolution of phylogenetic relationships across the Tree of Life, and a much improved understanding of the tempo and mode of evolution. Join us for two talks on phylogenomics, along with plenty of discussion, leavened by pizza and beer.

Featuring presentations by…

HOLLY BIK, Postdoctoral Researcher, Eisen Lab, UC Davis Genome Center

“Phylogeny-based taxonomy assignments from environmental metagenome data” (Note updated title)

and…

BASTIEN BOUSSAU, Postdoctoral Fellow, Huelsenbeck Lab, UC Berkeley

“Methods of phylogenetic inference for genome-scale data sets”

Schedule and venue:
5:30 pm: social gathering with beverages (beer and soft drinks) and informal
pizza dinner: cost ca. $10, to be collected at door, 1022 Life Sciences, UC Davis campus.
7:00 – 9:00 pm: talks, followed by discussion, in same room.

Reservations required for beverages and dinner (but not the talk). Please email reservations to your host, Phil Ward: psward@ucdavis.edu by Sunday, May 20

For a map of UC Davis campus and Life Sciences Building:
http://campusmap.ucdavis.edu/?b=97

Parking is available in the West Entry Parking Structure, immediately west of Life Sciences. If coming from the Bay Area take the Hwy. 113 exit off I-80, and then the first exit off Hwy 113, which is Hutchison Drive. This will bring you directly to the parking garage. Or, as Google Maps would say:
http://maps.google.com/maps?saddr=San+Francisco,+CA&daddr=West+Entry+Parking+Structure,+Davis,+CA&hl=en&sll=38.581572,-121.4944&sspn=0.289854,0.441513&geocode=FVJmQAIdKAe0-CkhAGkAbZqFgDH_rXbwZxNQSg%3BFXgRTAId-x2–CEDK9SCt6OfHw&oq=West+Entry+&t=h&mra=ls&z=9

All are welcome, members or not. If you want to join the Biosystematists, sign up for our mailing list at:
https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu

See you in Davis!

Phil

Valentine’s Special: Dating in the 21st Century: 2/8 Berkeley #BABS

Posting this email I received:

Bay Area Biosystematists Meeting

Tuesday evening, February 8th, 2011
at UC Berkeley, 2063 Valley Life Sciences Bldg.

Valentine’s Special:
“Dating in the 21st Century:
Theoretical and Empirical Issues in Putting Dates on Phylogenies”

Featuring a Diverse and Distinguished Panel of Discussants
Followed by vigorous audience discussion

Panel members representing different approaches will give short informal presentations (10 minutes each), to be followed by active audience participation (this all following traditional pizza and beer, of course!).  
Confirmed Panel Members:
Tracy Heath
Pat Holroyd
Nick Matzke (moderator)
Sarah Werning

The venerable Biosystematists group (http://www.biosystematists.org/), operating since 1936 (see the history on the website), is the only inter-institutional seminar/discussion group on evolution for the Bay Area, so we encourage everyone to join in.

Schedule and venue:
    5:30 – social gathering with beverages (beer and soft drinks) and informal pizza dinner:  cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg., UC Berkeley campus.
    7:00 – talk followed by discussion, in same room.
Reservations required for beverages and dinner (but not the talk).  Please email reservations to your host, Brent Mishler, at by Sunday, Feb. 6th  

For a map of campus and view of VLSB, use the link below.

All are welcome, members or not.  If you want to join the Biosystematists, sign up for our mailing list at: 

See you all there!
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bay Area Biosystematists Meeting: w/ Quenton Wheeler – Feb 9

Announcement below:

Bay Area Biosystematists Meeting: Tuesday, 9 February, 2010

at UC Berkeley, 2063 Valley Life Sciences Bldg.

“Biodiversity Discovery”

Featuring Quentin Wheeler from Arizona State University
Plus contributions from additional panel discussants TBA

Quentin Wheeler is a well-known insect systematist interested in biodiversity discovery, phylogenetics, and species concepts. He is University Vice President and Dean of the College of Liberal Arts and Sciences at Arizona State University. He was also one of the founders of the International Institute for Species Exploration at ASU (http://species.asu.edu/index), producers of the great You Tube video “Planet Bob” (http://www.planetbob.asu.edu/index.html), which uses humor to focus attention on biodiversity and taxonomy (and won a 2008 Webby Award).

Schedule and venue:
5:30 – social gathering with beverages and informal pizza dinner:
cost ca. $10, to be collected at door, 2063 Valley Life Sciences Bldg.,
UC Berkeley campus.
7:00 – talk followed by discussion, in same room.

Reservations required for beverages and dinner (but not the talk). Please email reservations to your host, Brent Mishler by Sunday, Feb. 7th

For a map of campus and view of VLSB, use the link below.
http://www.berkeley.edu/map/maps/ABCD123.html

All are welcome, members or not. If you want to join the Biosystematists, a venerable yet exceptionally lively group that provides the only inter-institutional seminar/discussion forum addressing evolutionary topics in the Bay Area, sign up for the mailing list at: https://calmail.berkeley.edu/manage/list/listinfo/babs-l@lists.berkeley.edu

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Barcoding, taxonomy and citizen CSI

I just love the continued coverage of the story of the students from Trinity School in New York (a high school) who do investigative DNA barcoding projects. (There is a good new story about this on the LA Times blogs at:Think that sheep’s mik cheese comes from a sheep? DNA doesn’t lie | Booster Shots | Los Angeles Times)

In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University.

Among their findings:

  • “an invasive species of insect in a box of grapefruit from Texas”
  • “what could be a new species or subspecies of New York cockroach”
  • multiple mislabelled food products including (quoted from the press release, I note)
    • An expensive specialty “sheep’s milk” cheese made in fact from cow’s milk;
    • “Venison” dog treats made of beef;
    • “Sturgeon caviar” that was really Mississippi paddlefish;
    • A delicacy called “dried shark,” which proved to be freshwater Nile perch from Africa;
    • A label of “frozen yellow catfish” on walking catfish, an invasive species;
    • “Dried olidus” (smelt) that proved to be Japanese anchovy, an unrelated fish;
    • “Caribbean red snapper” that turned out to be Malabar blood snapper, a fish from Southeast Asia.
And what I find most interesting, is this built upon work of other students from Trinity Kate Stoeckle and Louisa Strauss who had done a restaurant based barcoding study last year. 
This type of work is cool in so many ways.  It gets students into science.  It is an applied us of taxonomy (though I note, barcoding is not without controversy in the taxonomy community). It is a useful form of citizen science — and may eventually provide a way to keep dishonest sellers on their toes … Kudos to all involved in this 
More on this story can be found at
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Bay Area Biosystematists: 12/8, John Carlos Garza on Genetics & mgmt of California fishes

The Bay Area Biosystematists present:
 
“The use of genetic data to delineate management units for California fishes”

John Carlos Garza
Southwest Fisheries Science Center, NOAA
and
Dept. of Ocean Sciences, UC Santa Cruz

As lead of the Molecular Ecology and Genetic Analysis (MEGA) Team, Dr. Garza and his lab
use population genetic data and analytical techniques to address a broad array of questions in ecology,
evolution, behavior, conservation, and management of marine and anadromous organisms. This talk will focus on identifying management units for California fishes and their relationship to taxonomic units

For more about Dr. Garza’s work, visit his website:
http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=902

Tuesday, December 8th, 2009
At the California Academy of Sciences
Golden Gate Park

Dinner and social hour begin at 5:30 pm              Delicious food!!      Thirst quenching beers and healthy sodas!!

Evening presentation begins at 7:00 pm

RSVP REQUIRED FOR DINNER OR TALK
Please rsvp to Healy Hamilton hhamilton — at —- calacademy.org

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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