Monday, December 31, 2012

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 the 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 him 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 his 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.

Tuesday, September 04, 2012

Archaea in "Bizarro" Comic

Just thought today's comic was pretty amusing -- even if "an archaeon" would be more grammatically correct. Also, the phrase "primordial soup" is actually from Alexander Oparin's 1924 work, although Darwin's comments in regard to a "warm little pond" suggest he subscribed to a similar heterotrophic beginning of life.

But Darwin did encounter archaea even if he didn't know them by name -- in "The Voyage of the Beagle" Darwin describes a salt lake in Chile  where "parts of the lake seen from a short distance appeared of a reddish colour, and this perhaps was owing to some infusorial animalcula." -- in other words he was observing haloarchaea.

Thursday, June 14, 2012

Human Microbiome Papers freely accessible at Nature

Today Nature publishes two papers on the Human Microbiome (credited to the Human Microbiome Consortium made up of nearly 200 researchers including myself), and in a laudable gesture the papers are free to the public (I hope they will continue to be; Jonathan Eisen has pointed out several times that papers labeled free tend to disappear into the Nature paywall after a while, supposedly "in error").

At any rate, they are free now and are worth a look, although being "glamour mag" papers (to use Michael Eisen's phrase), most of the meat is in the supplemental information.

A framework for human microbiome research

Structure, function and diversity of the healthy human microbiome