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.

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.

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

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.

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.

"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.

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):

Zoologist (The) > Vol 7 (2009) > Lebo

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

Abstract

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.

Google Celebrates 150th Birthday of Zamenhof

You may notice that today Google has a little Esperanto flag. This is in celebration of the 150th birthday of L. L. Zamenhof, the creator of the language. Esperanto is a fascinating little language, and works as diverse as The Lord of the Rings and The Origin of Species have been translated into it. It was the first foreign language that I managed to get a good reading knowledge of, and still the only one that I can read without a dictionary by my side. Many people give up learning languages because they don't see themselves getting to the stage of doing something interesting, like reading a novel in it. My success in reading Esperanto led me to develop my reading knowledge of French and German and my interest in more obscure languages such as Jersey and Sorbian. Not to mention Volapuk!

RIP Milorad Pavić (1929-2009)

Today Milorad Pavić died at the age of 80. He was the author of numerous novels, in particular the before-its-time hypertext Dictionary of the Khazars. The Dictionary of the Khazars was supposedly an encyclopedia about the Khazars, a medieval Eastern European tribe that accepted Judaism, but in fact it was a surreal work reminiscent of Borges in which the story was not told from front to back of the book but by following the references between articles. It would have been trivial to implement in HTML, but the book was written in 1984.

Happy Origin Day!

Today, 150 years ago, the first edition of Darwin's Origin of Species was published in London. I actually just learned that today -- while there was a lot of noise about the 200th anniversary of his birth last February, I didn't hear much about this ahead of time, so no, I didn't schedule a party like I did for Darwin's/Lincoln's birthday. Not that this seems to be the most opportune time for a party, given the oddly large number of people who attended the last one who now are otherwise occupied being new parents...

So I guess everyone's responsible for their own entertainment on this one.

But I'll leave you with some interesting links at least.

1. Tired of the Origin's Victorian English? Read in in another language! Esperanto German French Spanish
2. How about the Origin as a graphic novel?
3. "Almost Like a Whale"/"Darwin's Ghost" This book, written by noted science popularizer Steve Jones, is an attempt to follow the structure of Darwin's Origin, but making adjustments to incorporate modern knowledge. While I'm a fan of the history of science and the value of primary sources, I understand that a lot of the difficulty in reading Darwin (besides his verbose Victorianisms) is that biology was a very different field in Darwin's day, both in terminology and outlook. Jones ably deals with this.
   

General Thoughts on the GRC, Part I

Well, since I guess I can't say anything specific about the talks due to the policy, I'll at least talk a bit about the topics that have been discussed so far in general terms.

1) Ken Nealson gave a nice keynote about the history of the study of metal reducing bacteria, being quite fair I thought towards the rival Lovley camp. He also ventured into what he himself called "crazy stuff" about electrobiology which I understand he might not want to be disseminated yet as he hasn't fully worked things through -- not for some secrecy reason. We also had a bit of a scare during the talk as a conference attendee suffered a seizure and paramedics had to be called. But fortunately it wasn't anything life threatening.

2) I was talking about my work on my phylogenetic pipeline APIS to a grad student of Brad Tebo's , and he mentioned "We had a woman from JCVI come up to discuss CMOP and she talked about that". Hmm. Could it be this talk?

3) On Monday morning, the main topics seemed to be Raman-Fish and Nano-SIMS. I hadn't heard of either technology before coming to the conference, but both are technologies used to track the metabolic activity of single cells. As my work in environmental microbiology is in large scale metagenomics, it is easy to forget that studies at the opposite end of the scale are also being revolutionized.

GRC on Applied and Environmental Microbiology

So here I am at the campus of one of the Seven Sisters, Mt. Holyoke, for the Gordon Research Conference on Applied and Environmental Microbiology. I had intended on blogging this conference, as I do for most conferences I attend, but actually, I'm not sure of the legality in this case: The conference schedule says "All information provided at this GRC (formal talks, poster sessions, discussions) is considered private communication from the individual making the contribution and is presented with the restriction that such information is not for public use". This seems very strange to me. Why would anyone present *anything* at a conference if they want it private? Why have conferences at all? Maybe we can go back to the medieval alchemist model where we write our discoveries in code to prevent rivals from learning of them...

In the Land of Invented Languages

I promise that I'll return to science blogging soon, but I wanted to write something about a book I've just recently read -- Arika Okrent's "In The Land of Invented Languages". And after all, linguistics is a science, just not the one I generally write about.

Okrent is a trained linguist and it is interesting to see her take on constructed languages, which often get dismissive treatment in popular works on linguistics -- one senses than many linguists actually are proud to be ignorant of the subject, much as literary scholars often are about science fiction.

While Okrent gives an interesting historical overview of the subject, starting with such early works as Hildegard of Bingen's Lingua Ignota, her work really shines when she is describing the handful of modern constructed languages that have established user communities, albeit small ones: Esperanto, Lojban, Blissymbolics, and (yes) Klingon. Okrent not only has read up on these languages, but has learned their basics and attended conferences that these language communities held.

I realise that I'm somewhat of an ideal audience for such a book, as I am a guy who reads novels in Esperanto and who has tried (on and off again) to make headway into Lojban, but I think the book would also be of interest to those who have no contact with constructed languages. Okrent truly humanizes the people she meets -- even the much reviled Klingon speakers (whom, as Okrent notes, are stigmatized even among Trekkies).

Is the name "Sea Star" more accurate than "Starfish"?

It has become common in recent popularizations to suggest that echinoderms of the family Asteroidea should be given the common name "sea star" rather than the traditional "starfish". The complaint is understandable -- starfish aren't fish. In fact, humans are more closely related to fish, as they both are vertebrates while starfish are not. But is "sea star" actually a better supported name? A taxonomic analysis suggests not.

Let's consider stars, the sea, fish, and starfish.  How can we compare such diverse entities? Obviously not by molecular means. But we can return to the traditional means of cladistic characters. In this analysis I used:  1) Living 2) Primarily water 3) Non-trivial concentration of dissolved NaCl, and 4) presence of backbone.

These characters can be encoded in a PHYLIP matrix in the following manner.

    4    4
Star      0000
Fish      1111
Sea       0110
Starfish  1110

By standard parsimony this yields the following midpoint-rooted tree

So, while "starfish" is inaccurate, "sea star" is even worse!

"The Voyages of Charles Darwin" (1978)

Yesterday, I held a "Darwin/Lincoln" party for my co-worker friends at JCVI-West. To give a suitable background flavor, I played at a low volume episodes of the 1978 BBC TV series "The Voyages of Charles Darwin", in which the adventures of young Darwin are narrated (in "The Wonder Years" fashion) by old Darwin. 

This series hasn't been released on DVD yet (reasons found on the Internet vary from Creationist conspiracy to the more plausible explanation that the BBC doesn't actually own the rights to the incidental music, and re-scoring would cost too much.) At any rate, the series can still be found on the Internet in various forms -- even at the almost legitimate site Veoh.com. I think it is worth seeing, although the dated 1970s vibe does seep through -- one person coming to my party thought I was showing "Planet of the Apes" (to be fair, it was during a scene set in a rocky region of South America.)

Pictured, Charles Darwin (Malcolm Stoddard, right) reveals to his friend Joseph Hooker (Paul Chapman, left) his suspicions that species may not be immutable.

Happy Poe-day!

While the most anticipated 200th anniversary this year is the combined Darwin/Lincoln bicentennial on Feb 12th, they weren't the only famous people that were born in 1809. Today marks the 200th anniversary of Edgar Allan Poe's birth -- which occurred in Boston -- not a town that one usually associates with the man who became an editor of the Richmond, VA based Southern Literary Messenger and who died in 1849 in Baltimore.

I'm sure that other blogs and newspapers will bring up "The Raven", but Poe was more than a macabre poet and was more sane and rational than the narrators of his fiction and poetry, which many people confuse with Poe himself. So, I present you with other sides of the man that may be new to you.

1) Poe the book reviewer. Here Poe reviews Francis Glass' bizarre "WASHINGTONII VITA" -- a biography of George Washington written in pseudo-classical Latin!

2) Poe the literary theorist. In the "Philosophy of Composition" Poe describes how he wrote -- or at least how he *thought* he wrote -- which may not be the same thing at all -- shades of the debate over whether the cliched "scientific method" actually describes what scientists do in practice. 

3) Poe the biologist! Or at least Poe the biology textbook author --The Conchologist's First Book: or, A System of Testaceous Malacology, Arranged Expressly for the Use of Schools. There's actually a lot of questions about Poe's contributions to this -- apparently he based it on an existing text and was accused of plagiarism. 

The Bloody Olive

Not really typical material for my blog, but here's a thriller even more convoluted than "Nobel Son" -- and only ten minutes long! It's a Belgian-made short film from 1996, given new life thanks to Youtube. Excellent reproduction/parody of 1940s film-noir.

The science in "Nobel Son"

Last night I saw Nobel Son, the new Alan Rickman movie where he plays an arrogant chemist who wins the Nobel prize. I don't want to talk about the actual plot, which is one of those "wheels within wheels" over-complicated thrillers that everyone has seen before at least once.

Instead, I want to discuss the Rickman character -- Professor Eli Michaelson. Granted, the plot didn't really require him to be anything else than successful and arrogant -- he could have equally been a CEO or something without changing the movie much, but let's see how well the movie captured science and its culture.

1. Michaelson's  research. Apparently it has something to do with molecular fluorescence stimulated by lasers. Given that the 2008 Nobel Prize in Chemistry (which I'm sure was picked well after this movie was completed) , did deal with fluorescence, albeit created by Green Fluorescent Protein (GFP) rather than lasers, kudos to the scriptwriters.
2. Understanding of how grad school works. This the writers did not do so well. Early on in the movie Michaelson is established as unpleasant and unethical by showing him doing a quickie in his office with one of his grad students who is unhappy with her grade. I suspect the writers only have experience with undergraduate education. Grades just aren't a major issue in grad school. If the student were complaining about her project or authorship on a paper, this would have been more plausible.
3. Choice of reading material for a chemist. During the above mentioned quickie, an issue of Cell is clearly shown on Michaelson's desk. Yes, Cell is a major journal -- but for biologists and not chemists. An issue of Science or Nature (which publish across all branches of science) or indeed a chemistry journal, would have been more plausible.
4. Amount of Prize Money. The amount "$2 million" is a major plot factor in the movie. But would a Nobel Laureate actually get that much? The prize is currently $10 million SEK (US $1.2 million at present). Plus this amount is shared with the other winners in the category (The movie never says if Michaelson is sharing the award).

10th Anniversary of my Defense -- A Retrospective

On December 2, 1998 I defended my dissertation entitled "Exploration of microbial genomic sequences via comparative analysis", the somewhat vague title referring to a collection of projects that I worked on in Gary Olsen's (pictured) laboratory at the University of Illinois at Urbana-Champaign, most notably the CRITICA genefinder (which was, until a year or so ago, still in use at JGI), and one of the earliest genomic studies of thermostability.

My thesis committee consisted of Carl Woese, Tony Crofts, and Stan Maloy (now at SDSU; I run into him at seminars occasionally). 

I don't have any pictures of the defense or the lunch afterwords after owning to a sad accident -- my parents' camera had a broken lens, and in that pre-digital era, they didn't know anything was wrong until they tried to develop the film. Still, the day sticks with me in memory. I gave what was probably the best presentation of my career (probably because I had practiced ten times or so), and the questioning was very friendly (the serious questioning had been several years before at my prelim). 

I've worked a number of jobs moving to various cities in the name of science since those days -- a postdoc in Computer Science at the University of Waterloo,  a senior bioinformatics scientist at a now-defunct biotech firm in Montreal,  living in downtown DC while working in the microbial genomics departments of TIGR and its successor JCVI,  and now in San Diego, where I'm working at the west-coast campus of JCVI. Who knows where the next ten years will take me?

Extreme 2008 and Extreme Viruses

A research expedition aboard the famed R/V Atlantis (carrying the equally well known submersible DSV Alvin) has just set sail from Manzanillo, Mexico. Its 21-day mission is to explore hydrothermal vents in the Pacific and Sea of Cortes. That's what the "Extreme" part is -- they aren't going to bungee jump or anything. 

I actually know (although not well) the two PIs who are leading the expedition -- I met Craig Cary in Australia at ISME last summer and I met Eric Wommack in Boston at ASM last spring. However, my principal interest in the expedition is that two of my JCVI co-workers, Lisa Zeigler and Doug Fadrosh, are aboard in order to collect viruses in the vent community. Viral ecology is a growing field -- viruses play a role in microbial ecology both as predators and as means of transferring genes from host to host.

The expedition has a lovely official site, and Lisa has started a blog that all of you should go visit -- blogging/journalling has a long and noble tradition in marine biology expeditions, going back at least as far as Darwin's "Voyage of the Beagle".