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

Friday, October 08, 2010

Gary Olsen's Talk on Lateral Gene Transfer at SDSU

Today Gary Olsen, who was my Ph.D advisor at the University of Illinois, gave a talk here in town at SDSU. The listed title was "Lateral Gene Transfer in Prokaryotes", which I was going to kid him about as Gary is a former postdoc of Norm Pace (who famously objects to the term "prokaryote"). But it turns out that the title was actually supplied by his host, so no dice there.

The talk dealt with further work in the Olsen lab on the topic of codon bias in relation to lateral gene transfer -- a topic which dates back to my time in the lab in the 1990s -- in fact Gary presented a figure from my dissertation near the beginning of the talk -- a PCA projection of E. coli codon usage showing the "rabbit head" pattern initially proposed by Médigue. In this projection, codon usage is shown to form three clusters, a cluster of "normal" genes (the "head"), an "ear" of known highly expressed genes, and an "ear" of genes of unusual codon usage containing many genes (such as integrases) thought to be recently transferred into the genome. The idea is that over time, transferred genes will assimilate into the codon usage of the host, much as immigrants lose their accents, making them impossible to detect through codon usage.

The obvious question is whether we can we use the codon usage of recent arrivals to determine their origin. In my day, the answer was no, we couldn't -- but we only had about 20 genomes available and so it was plausible that nothing close to the source organism had been sequenced. Now with over 1,000 genomes at our disposal, can we finally answer this question? Not exactly, but Gary and colleagues have discovered an interesting property -- the presumed transferred genes in E. coli and relatives seem to have a closer codon usage to *each other* regardless of host rather than being similar to any known organism, suggesting that they form a collection of genes that hop around from genome to genome, never staying around long enough to assimilate into the host -- it isn't a case of being transferred from the core of genome X to the fringe of genome Y as we supposed. They have found similar collections for other phylogenetic groups as well. This is really quite a different way to think about horizontally transferred genes.

Wednesday, October 06, 2010

Under the Spreading Chestnut Tree

In George Orwell's novel 1984, he mentions that the drink favored by patrons of the Chestnut Tree Cafe (frequented by dissidents after serving their jail sentence) is gin with "saccharine flavored by cloves". I actually tried that recently, although using Equal (aspartame) rather than saccharine). It was actually quite good. In fact, I don't really see the point of sweetener at all. Just gin and cloves is actually quite good. I don't understand why I never really understood cloves. Except for Christmas mincemeat pie, I'm not sure if I ever really tasted cloves. What an awesome flavor.

Saturday, September 25, 2010

"Bubbly" Pauline & the $1000 genome

I'm currently reading Kevin Davies' new book, "The $1000 Genome", which is an account of the various players trying to bring down the cost of human genome sequencing to commodity levels that would make having your own genome sequenced a practical reality. Although I know some of the technologies described in the book from my work, Davies' book focuses not only on the technical side but on the business/economic side as well and is written for the general reader. It's quite well written and interesting, and I recommend it. But what made me burst out laughing was encountering the following line:

"An important next step was to compare the data from Venter and Watson, which was first done by Pauline Ng, a bubbly Venter Institute researcher."

Pauline is a colleague and friend of mine who now leads a group at the Genome Institute of Singapore. We wrote a review chapter together on the human microbiome in a book that should be coming out soon. I suppose if you had to sum her up in a single adjective, "bubbly" works. But I guess I find the idea of someone I know being reduced to a journalistic cliché kind of amusing.

Saturday, May 08, 2010

Zoologist with awesome name new President of Nigeria

On May 6th, former Vice President Goodluck Jonathan became President of Nigeria following the death of his predecessor, Umaru Yar'Adua. It remains to be seen what this will mean for Nigeria for good or ill. However, while I was initially intrigued by his unusual name, I discovered that there is another thing about Jonathan that is unusual for a politician -- he has a Ph.D. in Zoology, and has published on issues dealing with the environment in relation to fishing. He apparently published an article as recently as last year (unfortunately not as Open Access however):

Breeding seasonality and population dynamics of the catfish Schilbe mystus (Schilbeidae) in the Cross River, Nigeria

P.E Lebo, R.P King, L Etim, B.E Akpan, G.E Jonathan


Twelve consecutive months length frequency data (N = 6999) and FiSAT software were used in the study of the dynamics of exploited population the catfish Schilbe mystus in the Cross River Nigeria. Variation in monthly mean gonadosmtic index showed two peaks, March and September and this indicates that the species spawned twice in a year. Fitting the seasonalized von Bertalantffy growth function to our length frequency data gave the following growth parameters: L∞ = 38 cm, k = 0.33 y-1, C = 0.42 and WP = 0.96. The seasonalized length converted catch curve procedure gave the instantaneous total mortality coefficient Z = 2.97 y-1, the instantaneous natural mortality coefficient M = 0.81 Y-1, the instantaneous fishing mortality coefficient F = 2.16 y-1 and the current exploitation rate E = 0.73. This high value of E points to the high fishing pressure on the stock. The analysis of probability of capture of each length class showed that the length at first capture Lc 28.67cm. The predicted maximum exploitation rate of Emax = 0.59. This stock was deemed overexploited because E>Emax. Relative yield isopleths were used to demonstrate the response of relative yield per recruit of the fish to variation Lc and E. Suitable management procedure must be instituted to avoid the collapse of the fishery.