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Jonathan Badger
Works at J. Craig Venter Institute, San Diego, CA
Attended University of Waterloo
Lives in San Diego, California
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Jonathan Badger

commented on a post on Blogger.
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As mentioned, data can't be included if doesn't exist. I think this is more about some private feud between Graur and Paabo than any serious critique. 
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Jonathan Badger

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Torrey Pines State Reserve
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Carl Woese in NYT.
I was afraid that dying on the same day as Levi-Montalcini had deprived him of a science obit in the NYT, but I'm glad I'm wrong. I like the picture they used from my era in 1996 -- Carl looks like how I remember him -- and the woman in the background with a pipetman and graduated cylinder is my fellow graduate student and friend Leslie McNeil!

http://www.nytimes.com/2013/01/01/science/carl-woese-dies-discovered-lifes-third-domain.html
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Carl Woese 1928-2012

As you may have heard, Carl Woese died of pancreatic cancer yesterday at the age of 84. I had the honor of working with Carl in grad school at the University of Illinois where my advisor, Gary Olsen, ran a joint lab with Carl.

As the originator of the use of ribosomal RNA to distinguish and classify organisms (including obviously the Archaea), Carl both revolutionized evolutionary biology and created a method that is still very much in use today. Even in the latest metagenomic study of the oceans or of the human gut, a 16S rRNA diversity study is required as a control in addition to whatever additional markers or random sequencing is used.

One of things that fascinated me about Carl is how he constantly reinvented himself and explored new fields of biology -- his early work in the 1960s dealt with classical molecular biology and the genetic code (the origins of which continued to fascinate him for the rest of his life). He then transfered to the study of the ribosome and its structure, which in turn led to his study of 16S and its evolutionary implications. In the 1990s, when I worked with him, he was a pioneeering microbial genomicist and collaborated with TIGR to sequence the first two Archaeal genomes. And in his final years he focused on early evolution and the last common ancestor of life in the light of what genomics has taught us.

Carl also had his humorous and counter-cultural side. I remember he telling me how his lab in the 1960s heard about the rumor that compounds in banana peels were a legal narcotic and how they launched an unofficial research project to isolate these. His verdict was that there was nothing there and neither the peels nor anything in them could get you high -- but he wanted to empirically test that. Also, when reading about a supposed "Qi master" who claimed to be able to influence mutation rates with this mind, he invited him to the lab to give a demonstation -- which naturally failed to show any effect under controlled conditions -- but he wanted to see if the guy could really do it.

Genomics, metagenomics, and evolutionary biology has lost one of its greats -- but his legacy lives on.
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Jeff Beall on "predatory open access publishing" in Nature
http://www.nature.com/news/predatory-publishers-are-corrupting-open-access-1.11385

He has a point in that there are these obviously spammy OA publishers from third world countries, but much like Republicans worrying about the not very common problem of "voter fraud" by illegal aliens, there is another motive going on for Nature to publish this, I would imagine....
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My Personal Genome Project Sample kit arrives!

While I joined the Personal Genome Project (http://www.personalgenomes.org/) months ago, I had more or less forgotten about it until today when my spit-tube arrived. Looking forward to not only contributing open data, but being open data.
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Introduction
I'm the Jonathan Badger who is the author of APIS and CRITICA and who has been involved in various genomics/metagenomics projects since 1997. I'm also the Esperantist Jonathan Badger and the one who posts on Boingboing and Language Log.

However, I'm *not* the Jonathan Badger who is the musician nor the one who is the Nietzsche scholar.
Education
  • University of Waterloo
    Postdoc, Computer Science, 1999 - 2000
  • University of Illinois at Urbana-Champaign
    Ph.D., Microbiology, 1992 - 1998
  • University of Wisconsin-Madison
    B.S. Bacteriology, 1988 - 1992
Basic Information
Gender
Male
Work
Occupation
Assistant Professor, Microbial & Environmental Genomics
Employment
  • J. Craig Venter Institute, San Diego, CA
    Assistant Professor, 2009 - present
  • J. Craig Venter Institute/TIGR, Rockville, MD
    Staff Scientist, 2003 - 2009
  • Caprion Pharmaceuticals, Montreal, QC
    Senior Scientist, 2001 - 2003
Places
Map of the places this user has livedMap of the places this user has livedMap of the places this user has lived
Currently
San Diego, California
Previously
Washington, DC - Montreal, Quebec - Waterloo, Ontario - Urbana, IL - Madison, WI