T. taxus

Gary Olsen's Talk on Lateral Gene Transfer at SDSU

2010-10-08T20:15:00.000-07:00

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

2010-10-06T21:19:00.000-07:00

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

2010-09-25T21:54:00.000-07:00

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

2010-05-08T13:21:00.000-07:00

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

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

2009-12-15T09:49:00.000-08:00

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)

2009-11-30T22:07:00.001-08:00

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!

2009-11-24T08:54:00.000-08:00

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.

Tired of the Origin's Victorian English? Read in in another language! Esperanto German French Spanish
How about the Origin as a graphic novel?
"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

2009-07-13T11:48:00.000-07:00

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

2009-07-12T14:23:00.000-07:00

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

2009-05-26T18:36:00.000-07:00

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"?

2009-03-08T11:48:00.000-07:00

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)

2009-02-16T08:20:00.000-08:00

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!

2009-01-19T06:47:00.000-08:00

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

2008-12-13T07:36:00.000-08:00

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"

2008-12-07T06:52:00.000-08:00

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.

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.
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.
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.
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

2008-12-02T19:24:00.001-08:00

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

2008-11-10T20:55:00.000-08:00

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".

Is that a duck? It sure sounds like one!

2008-11-10T09:21:00.000-08:00

Only a few days ago, my former TIGR colleague Steve Salzberg wrote about Johns Hopkins University's plans to open an "Integrative Medical Center" where herbalism and other "alternative" (that is, unscientific) treatments will be offered. That was disturbing enough given the great stature Johns Hopkins has in medical science.

But today I received an e-mail that the East Coast branch of the JCVI, the institute where I work, as part of their "Lunch & Learn" series, is inviting a speaker from the "North Adams Wellness Corner" to talk about

"how pressure points can help relieve cold and flu symptoms. Learn easy and effective pressure points on the hands, face, and feet to relieve sinus congestion and boost your immune system".

I've only taken one immunology course and I didn't recall "pressure points" being mentioned, so I was a bit curious. Looking them up on the web, I find out that they are part of the mysticism behind martial arts! Quoting from that page, I find that

"The Eight Brocades, an ancient Chi cultivation technique that help heal the body, prevent illness and boost your immune system while activating special pressure points. These exercises have been practised for over 1,000 years by Chinese martial arts practitioners."

Not very promising. I'd be far more convinced by peer-reviewed articles rather than the anecdotal experience of Bruce Lee and his predecessors. Why is it that nonsense sounds more profound when it is from China or India? The West also had its pre-scientific medical theories. Why not return to the Four Humours of Hippocrates? This is even older than the "eight brocades", and according to the above logic, older is better, right? I guess the reason why I'm angry about this quackery is that I have too much yellow bile ("choleric").

Badgeromics 2008, er Metagenomics 2008

2008-11-05T22:43:00.000-08:00

I'm attending the Metagenomics 2008 conference being held locally at UCSD. There's plenty of interesting talks (see Jonathan Eisen's coverage). However, today what struck me the most (egotist that I am) was how my work was brought up in three separate talks...

Alex Worden started out the day by discussing her work on picoeukaryotes (unicellular eukaryotes less than 2 microns in size) and there were a couple of slides dealing with the comparative work that Andy and I have done as part of her forthcoming Micromonas paper.

Then practically half of Shannon Williamson's talk about her metagenomics work on marine viruses was devoted to my phylogenetic pipeline, APIS (Automated Phylogenetic Inference System), which performs taxonomic binning of metagenomic data by the automated creation and interpretation of phylogenetic trees.

Then in the evening Jonathan Eisen brought up our 2005 paper as part of the justification for his new project to sequence hundreds of bacterial and archaeal genomes.

Thanks guys. Your checks are in the mail...

The Genome Sequence of Phaeodactylum tricornutum

2008-10-15T17:47:00.000-07:00

What's this? Another eukaryotic genome paper with me on it? I blame Jonathan Eisen for putting me on that road to ruin -- I never touched the nucleated rascals before Tetrahymena.

But seriously, single celled eukaryotes are cool, and not Eisen but rather Andy Allen (who doesn't have a web page or blog to link to, unfortunately) is the one to blame for getting me involved with his beloved diatoms.

P. tricornutum is the second diatom genome to be sequenced, and first of the pennate (elongated) lineage. We discovered that this genome was quite different from that of Thalassiosira pseudonana, the first diatom genome to be sequenced , which is a member of the centric (hatbox/cheesebox/petri dish) lineage. We also identified about 600 genes that we believe to be of bacterial origin in this genome. As this was part of the analysis that I did, I'm perhaps biased in that I think this one of the most interesting results in the paper. This analysis wasn't just "BLASTology" (being just based on BLAST output), but rather based on phylogenetic trees for each predicted protein coding gene in the P. tricornutum genome.

There's been some press about the paper -- including this one in the German newspaper Die Welt -- whose sub heading "Diese Lebewesen entpuppen sich als eine kuriose Mischung aus Pflanze, Tier und Bakterium" implies that P. tricornutum is a curious mix of plant, animal, and bacterium -- not exactly true, but hints at the HGT analysis that we did. There's also this press release that mentions me and Andy by name, but so far no papers have used that part :-)

Anyway, the paper (which is under a Creative Commons License, showing that even commercial publishers like Nature can be reasonable) is up on Nature's advance publication page as of yesterday. Check it out. And the supplemental, where most of the actual data is.

The Genome Sequence of Penicillium chrysogenum

2008-10-01T07:13:00.000-07:00

With all the work I've been doing in metagenomics, it's nice to be reminded that I still do some of the non-meta type -- yes, I was involved in the P. chrysogenum project, and the paper (and supplemental) is now up in Nature Biotechnology's Advance Publications page prior to the print publication.

We've actually gotten a little bit of press -- the BBC has a brief article here.

P. chrysogenum is one of those obvious genomes people are surprised to learn haven't been sequenced yet (well until now). While a "pure" biologist may yawn and say "it's just another filamentous fungus -- haven't we sequenced those already?", there is real practical potential for metabolic engineering of new antibiotics from this genome given that researchers have been doing work on the bug for over 60 years. Besides, the genome wasn't completely uninteresting even from the viewpoint of basic science -- we snuck in a fairly controversial fungal phylogeny in figure 2 -- and I stand by it as we used far more data in our alignments than in previous studies.

[updated links to final published version 10/14/08]

RIP David Foster Wallace (1962-2008)

2008-09-14T13:48:00.000-07:00

You may have heard the news; last Friday the literary Wunderkind of the 1990s, David Foster Wallace, hanged himself in his Southern Californian home. I have to admit that I haven't thought much about Wallace since the turn of the century, but his 1996 Infinite Jest was (and perhaps still is) one of my favorite novels.

In many ways, _Infinite Jest_ was the quintessential 1990s American novel -- the conceit of the story was that American economic and cultural influence would simply keep growing and growing in the future -- as indeed in those heady post-Cold War times it looked like it would. Of course, part of Wallace's point was that would not necessarily be a good thing given the crass commercialization of US culture -- his idea that names of calendar years would be sold to the highest bidder is entirely believable given that we live in the world of PETCO Park and Qualcomm Stadium.

Many people have compared Wallace to Bret Easton Ellis (Less than Zero, American Psycho), and in a way they have a point. Certainly, Wallace was far more erudite and literary, but just as Ellis captured the "soul" of Reagan-era America, Wallace did the same for the Clinton era. Who will do the same for our current era?

Jacques Ravel in the New York Times

2008-08-26T08:11:00.000-07:00

I'm back from Australia (although jet-lagged), and looking through the NYT science articles that I'd missed over the past week and a half, I discovered this article about the techniques used to establish that the mailed anthrax powder that killed photo editor Robert Stevens in 2001 was from the RMR-1029 strain (indirectly suggesting Bruce Ivins as the culprit, although the article stresses that is still as yet unproven, despite Ivins' suicide).

It's a very interesting article, but I have to admit that what drew me in initially was the photo of my former TIGR colleague Jacques Ravel - while articles featuring Craig Venter are too common to mention these days, it's nice to see some coverage of other people I've worked with.

ISME 12 -- More Highlights

2008-08-22T23:34:00.000-07:00

On Wednesday we had a free day -- a very clever thing that I wish other conferences would imitate -- having a free day in the middle allows a bit of a mental breather to prevent burn out from all the scientific sessions. We used the time to go to Kuranda and environs. Kuranda is located in a rainforest and is reached through an aerial cable tram similar to that found in Palm Springs, California (but even more impressive given the length of the trip and the beauty of the scenery). The village itself is a bit of a tourist trap, as expected.

There's a nice, although small, museum called the "Rainforest Interpretation Centre" that helps visitors learn about the forest through exhibits and interactive displays. One of the oddest things was the three languages used -- English (of course), Japanese (understandably -- much like Hawaii, North Queensland seems to be a Mecca for Japanese tourists), and finally, German of all things! Of course I couldn't resist playing with interactive displays where "Welcher Baum ist das?" was asked. I understand that Europeans visit Australia, but why German in particular and not say, French and Spanish as well?

Thursday was back to science. Craig Cary talked about metagenomics in the Antarctic Dry Valleys -- I hadn't realized that there are ice-free deserts in Antarctica, but apparently there are, and there's cyanobacteria (in particular) living in them. About midway through the talk, Craig shifted gears and started talking about (I'm not making this up) mummified seals! Apparently, Antarctic explorers have long known about these naturally mummified seal corpses (some over a thousand years old) , but Craig was interested in investigating whether the microflora underneath the seals was different than in the surrounding soil. Not surprisingly it was -- the Antarctic deserts are very carbon and nitrogen starved and a slowly rotting thousand year old seal is a much better source of nutrients than anything else around. Craig even transplanted a seal from one place to another to see if he could influence the new environment in the same way, and the experiment worked.

Rick Cavicchioli talked about the genome of Methanococcoides burtonii. I liked that. These days traditional genome projects are somewhat unfashionable (and unfundable), but not everything has to be metagenomics (although Rick is doing that too). Amino acid comparisons with relatives living at higher temperatures were a major part of the story of this genome -- and that work was pioneered by my fellow blogger (and commenter) Neil Saunders, as Rick acknowledged.

I will try to write up a final writeup on the last talks soon. And yes, that is a real live koala with me in the picture.

ISME 12 -- Highlights of Tuesday

2008-08-19T15:08:00.000-07:00

On Tuesday, Phil Hugenholtz talked about his work in metagenomics of a hypersaline mat in Guerro Negro, Mexico. What makes this project a little different from typical "bulk" metagenomics projects such as the Global Ocean Survey is that the peat-like mat has distinct layers of microorganisms even within a centimeter thick sample and these layers can be separated and analyzed individually. Phil and colleagues analyzed 10 layers of the mat and found distinct differences. Particularly interesting was the overabundance of chemotaxis genes on the oxygenic/anoxygenic boundary, which he explained by the fact that microbes that live near the border have to be able to move into their preferred layer as this boundary shifts over the duration of a day. Phil also looked at amino acid bias between layers, which brought back fond memories of my work in grad school linking amino acid differences to thermostability.

Gene Tyson talked about metatranscriptomics, or metagenomics on transcripts (well, cDNAs anyway). As I have a grant funded (with Andy Allen) to do metatranscriptomics on eukaryotic phytoplankton, I found it interesting (although depressing) that despite all the optimizations to avoid it, still 50% of their cDNAs are rRNA.

I had lunch with Rick Cavicchioli and members of his group as JCVI's field biologist Jeff Hoffman hopes to get me involved in the analysis of the Antarctic lake metagenomics data he is generating in collabioration with Rick's lab.

In the afternoon, I presented my poster on "Large Scale Analysis of Nitrogen Utilization Genes in the Indian Ocean" -- basically a bioinformatic analysis of the GOS II data in the context of several genes involved in organic vs inorganic nitrogen uptake and usage. While I wasn't swamped with visitors, a dozen or so people stopped by and gave useful suggestions.

In the evening we had more keynotes from Roberto Kolter and Norm Pace. Kolter's talk (on the genetics of biofilm production in Bacillus) was really wonderful -- and not just for the knowledge imparted -- Roberto is a truly gifted public speaker, a rarity among scientists.

Norm's talk was the same "don't use the term 'prokaryote'" talk that I've heard twice already. Now don't get me wrong -- I have enormous respect for Norm and even quite a bit of agreement for the meaningless nature of the term "prokaryote", but really, I think nearly everybody in the field has either read his paper on the topic or heard him speak on it at least once. This might be forgiven if Norm was some retired scientist who was no longer is generating any new ideas, but happily Norm and his lab are still quite active -- I think everybody would find talks on new work from his lab much more interesting than yet another version of the same "prokaryote" talk.

ISME 12 Cairns - Highlights of Sunday and Monday

2008-08-18T00:21:00.000-07:00

The first two days of ISME went quite well. First of all, I have to give the organizers high marks for actually providing a conference bag worth having (BTW, it would be interesting to figure out someday where and when the custom of "conference bags" started -- why does every conference assume that attendees need a conference-specific bag?) Rather than the nearly useless tote bags which one often gets, the ISME 12 bag is a nice high quality backpack that will be worth keeping after the conference. Conference bags may be a minor issue, but a quality bag is a nice touch.

Bo Barker Joergenson gave a nice keynote on Sunday night on the subject of the "deep biosphere" by which he means microbes living deep in the sediment at the bottom of the ocean. Ships have returned drilled cores even from a couple of kilometers down that contain microbial cells. For many years there was debate over whether these cells were actually alive or just the "corpses" of cells that drifted down and never decayed, but now there is general agreement that there are living cells. What there isn't agreement at this point is what type of cells there are. Some groups, using Q-PCR have concluded that the primary players are bacteria; others using FISH-IPL say archaea are. As a bioinformatician, I find this conflict of experimental methods disturbing. Still, the "deep biosphere" is a fascinating topic to me.

After the keynote we had appropriately Australian entertainment; a group of local indigenous Murri demonstrated some traditional songs and dances and the use of firesticks.

On Monday the main series of talks began. Curtis Suttle talked about inferring the host species of marine viruses through phylogeny. He began with some fascinating statistics; there are 10^30 viruses in the ocean, and if they were laid end to end, they would stretch for 10^7 light years! And they contain more carbon than 75 million blue whales. So what exactly are these viruses infecting? Suttle has developed an interesting method where he first calculates phylogenies of viruses with known hosts, calculates the average genetic distance between viruses that infect the same host, and uses this distance to cluster sequences of viruses that infect unknown hosts. He then looks for correlation between occurrences of members of these clusters with morphologically different hosts in micrographs to assign presumed hosts. Obviously, morphology is a crude measure of species in any set of organisms (and particularly so for microbes), but it is a useful start.

Forest Rohwer, probably the best known researcher of marine viruses, gave a talk about many different projects his lab is pursuing. What I found most interesting was his idea of measuring the energy usage of phages by measuring temperature in calorimeters containing bacterial cultures with and without phages.

C.D. Long presented a good example of what I find most interesting in science -- the application of a technique developed for one problem to a different one. In this case, she utilized the traditional "checkboard" method (developed by ecologists studying island biogeography) to analyze the co-occurrence of different microbial species living on human teeth. I'll have to read up on the method to see if maybe I could do something similar.

And Mitch Sogin presented on his idea of the "rare biosphere" -- the idea that most microbial species are very low abundance organisms. I've heard Mitch talk about this idea before, but this talk was more technical and included more details --- not only of his experimental methods but also of his VAMPS analysis system. I've spent a lot of time basically writing my own version of many of the methods there because I didn't know the system existed.

P.S. Qantas found Lisa's bags.

ISME 12 in Cairns, Australia

2008-08-16T12:27:00.000-07:00

I realize that I've been a non-blogger as of late, but on the off chance some of you still have me in your feeds, I'll try to write something about the ISME (International Society for Microbial Ecology) meeting that starts this evening in Cairns (Northeast Australia, near the Great Barrier Reef).

Getting here was a bit of an adventure; coming into Sydney we were instructed that we must go through customs and retrieve our luggage before continuing on to any domestic flights. So I dutifully did that and waited for my luggage to show up at the carousel. It didn't. It turns out that because my Sydney-Cairns flight actually was the first jump in a Sydney-Tokyo flight, it didn't count as a "domestic flight" and I was actually supposed to go through customs in Cairns and collect my baggage there. After all this was figured out I very nearly missed my flight to Cairns -- as I raced through the Sydney airport to the departure gate I was one of those annoying passengers that you hear getting paged for the last call for their flight. But I made it -- and so did my luggage-- which is more than could be said for my friend Lisa's -- she still doesn't know the status of her baggage and whether it is lost for good.

But here we are in Cairns. As Lisa notes, the city is much like the San Diego that we left from in look and weather. Well, maybe how San Diego would look if Canadians had built it or something -- it does have the distinct Commonwealth feel somehow that I recognize from my time living in Canada.

More posts (with pictures and actual science) will follow.

RIP Karlin (1924-2007) & Carlin (1937-2008)

2008-06-23T11:56:00.000-07:00

Within a span of about six months we have lost two greats with homophonic surnames -- Sam Karlin, the national academy belonging statistician whose pioneering work in computational biology lead to the statistics behind BLAST (as well as more obscure programs), and now the great comedian George Carlin. Many people may think that besides their name, these two people had nothing in common. Not true.

For example, Carlin as well as Karlin has contributed to statistics. Who can forget his great insight "Just think of how stupid the average person is, and then realize half of them are even stupider!"? And before you object that he should have used "median" in that sentence, be aware that the statistical use of "average" need not mean "mean" (in the arithmetic sense) -- the median can legitimately be called an average as well.

And Karlin was a master of the pithy one-liner himself: "The purpose of models is not to fit the data but to sharpen the questions". Well, maybe it didn't bring down the house when he said it, but it's something worth always keeping in mind.

Ralph Lewin's algal physiology papers in Esperanto

2008-06-18T21:15:00.000-07:00

Ralph Lewin's interests intersect mine in two quite different ways. First of all, Lewin is a renowned marine microbiologist, and most of my current projects are marine as well. But secondly he is well known among fans (of which I am one) of the artificial language Esperanto, even being the co-author of a translation of "Winnie The Pooh" into the language. What I hadn't known until today was that Lewin had combined his interests in two papers from the early sixties: Difektita Aŭtotrofo de Mutaciita Chlamydomonas (Defective Autotrophy of Mutated Chlamydomonas) and La Enpreno de Strontio en Kokolitoforoj (The Takeup of Strontium in Cocolithophores). In both cases Lewin wrote papers which except for an English abstract, were entirely in Esperanto. And while it's true that Esperantists have organizations such as Akademio Internacia de la Sciencoj San-Marino that occasionally publish scientific reports in Esperanto, Lewin's papers were in a mainstream journal -- Plant & Cell Physiology. Makes me wonder what the neesperantistoj thought when they saw the papers...

ASM 2008 -- Interesting Talks, Part 1

2008-06-11T22:10:00.000-07:00

Well, I'm back in San Diego, and people have been asking me about ASM (in person, if not in the comments), so I suppose I ought to fulfill my promise and actually write something about the talks.

National Academy member Lucy Shapiro gave a very interesting retrospective keynote on the history of her work on Caulobacter. Having worked on Hyphomonas, a related organism, I found it obviously relevant, but what I found especially interesting was the modest style of the talk. Lucy openly admitted that most of the work was done by her many students and postdocs over the years, and rather than just include their names on an unreadable slide at the end, she mentioned them by name in her talk in the relevant place as she discussed experiments that led to various discoveries about the development and cell cycle of Caulobacter.

Howard Frumkin of the CDC talked about doing "green science", reminding us that biomedical research uses over twice the amount of energy per unit space that the commercial sector does, and that it is important for scientists to "green their sector first" to avoid looking like hypocrites. Although he gave many interesting suggestions to reduce the environmental impact of science, I don't recall him questioning the need for big conferences like the ASM where thousands of scientists fly in from thousands of miles away. Replacing those with video conferences (admittedly much less fun) would greatly reduce the carbon footprint of science.

My ultimate boss, J. Craig Venter, gave a talk about current work in the Global Ocean Survey. Memorably, he started his talk with "I'm J. Craig Venter from an institute of similar name..."

Jonathan Eisen spoke on phylogenomics (link is to Kimmen Sjölander's page on the subject) and origin of novelty, nicely illustrating this rather theoretical notion that he originated with practical examples in his own research. Speaking of Eisen, the picture above was taken at a Red Sox game that I attended with Eisen, Eric Wommack, Jacques Ravel, and some of Eisen's Boston-based relatives. The bearded guy in my picture is Eisen himself, and if you zoom in, you may notice that he has "RecA" written on his hand. Don't we all write the name of our favorite proteins on our hands?

In Boston for ASM 2008

2008-06-02T19:46:00.000-07:00

Well, it's time for the ASM (American Society for Microbiology) general meeting, and this year the venue is Boston. So 11,000 microbiologists have descended on Beantown this week - if you're a local and were wondering why those strange people on the "T" today were talking about Bacillus anthracis, don't worry - they (probably) weren't bioterrorists.

I'll give more detailed information on the talks in later posts, but I'd just like to add to Jonathan Eisen's critique of the structure of the meeting. First of all, it is extremely annoying that they are aren't dedicated poster sessions where the rest of the conference stops -- today, for instance, I had to chose between poster sessions and attending hour long talks by such luminaries as Ed DeLong and Mary Ann Moran, which nearly completely overlapped the poster sessions in time. What's worse, several students of Moran were presenting their posters while Mary was giving her talk, presumably depriving those students of their most interested "customers".

Another exciting event in Boston is that my good friend John Tsang (no, no, not this John Tsang), who was a masters student in the group where I did my postdoc, and with whom I later worked in industry, has just earned his doctorate in biophysics from Harvard. I have to admit feeling a bit of pride in this because I encouraged John to go back to grad school and wrote one of his letters of recommendation. John is going to go through the formal convocation on Thursday, and pictured is John all dressed up (next to his wife Amelia).

Revisionist history at EPCOT

2007-12-10T09:36:00.001-08:00

Several news blogs, including BoingBoing, have reported that the new refurbished "Spaceship Earth" ride at EPCOT now includes a diorama of Wozniak's and Jobs' garage where Apple got its start in the mid 1970s. Very nice. But take a look at the computer that one of the Steves (presumably Wozniak, the more technical of the two) is working on -- is it an Apple I, the computer that was actually designed in the garage? No -- it seems to be some sort of fictional primitive Lisa or Macintosh -- machines that weren't designed until years later. Why, oh why? Are they planning an diorama with Henry Ford building a primitive Taurus?

The Internet doesn't lie...

2007-11-13T09:02:00.000-08:00

My immunologist friend Andreas Krueger has recently pointed out to me that according to a certain website the reading level of this blog is "Genius". I'm sure this is every bit as scientific as those quizzes that tell you which Star Wars character you are most like. Also, this ranking was made prior to this post -- it would be amusing if this post somehow weakened the rating...

A Life Decoded: My Genome: My Life

2007-11-09T12:32:00.000-08:00

First of all, I'll get the required whining over the title done with -- yes, RPM, myself, and TR Gregory all have written about our annoyance with the terms "decoded/deciphered/cracked" in relationship to genomes, but there's a good chance that the title was thought up by the publisher. I would have called it "A Life in Sequence", but oddly enough, nobody asked me.

Now that that's done, how was the book? Pretty good (and I'm not just saying that because Craig's my ultimate boss and could fire me, honest -- he'd have to know who I was, for starters). It's a bit snarky in places, and some of his opponents come off as caricatures, but it's entertaining in much the same way as The Double Helix was.

The book is written as an autobiography, with bits of relevant genome information inserted in -- the gimmick is that this is the first of many "molecular (auto)biographies" that will interpret lives in the context of genomic sequences and the alleles the subject carries. Right now, it is a gimmick (although an amusing one), but I can see how in the future it might really be informative.

Much of Craig's working class youth and experience in the Vietnam War have been covered by various media stories before, but it is nice to hear it straight from Craig -- for one thing, it clears up the confusion between the shark and sea snake stories -- often these anecdotes are wrongly merged into one story.

What was new to me was learning about his pre-genomics scientific career. I had no idea that Craig's background was in biochemistry, for example. He credits that with helping him getting the early (notoriously temperamental and unreliable) automated sequencing machines to work when others, mostly from genetics and molecular biology backgrounds, couldn't.

The book is also interesting for some rather open and telling quotes -- probably my favorite is

One of my critics, John Sulston, objected that I wanted to have it both ways: "to achieve recognition and acclaim from his peers for his scientific work, but also to accommodate the needs of his business partners for secrecy and enjoy the resulting profits". I plead guilty, along with the rest of humanity, to committing the most heinous crime of both wanting my cake and eating it.

The rest of humanity indeed. Later Craig shows that many in the "holier-than-thou" public genome project also had links to the biotech industry; their primary difference from Craig seems to be that they tended to hide their conflicts of interest rather than openly declaring them.

Some of Craig's interpretations may be a little off base -- at one point Craig prides himself for not having the tenure system at his institutes on the basis that "the second rate people who thrive in a tenured environment like nothing more than to surround themselves with more mediocrity and drive out those who might excel and reveal the shortcomings of the entrenched". Well, perhaps. But the simpler explanation might be that tenure is rather hard to give when everyone is working off soft money which could disappear in the next funding cycle. And there has to be more to the story that Claire was the one who suggested merging JCVI and TIGR. In what context?

But in general, Craig's observations are dead on. Venter's opponents have tried to spread the myth that he's out to be "the Bill Gates of Biology", and whatever faults the guy has, his motivations are a lot more complicated than just the pursuit of money. Shreeve's "The Genome War" covered some of this, but it is nice to finally hear Craig's story from himself.

The Third Domain

2007-11-02T17:52:00.000-07:00

Tim Friend's recent book The Third Domain is an odd book on two levels -- first of all, the story that one would think it tells, that of Carl Woese's discovery of the Archaea, the initial hostile reaction that the discovery met with at the hands of the scientific establishment, and its eventual acceptance by the majority -- makes up only one chapter (chapter 3) of the book. The rest of the book mostly follows field microbiologists like Karl Stetter and Eric Mathur as they collect samples (often, but not always, of archaea) from hot springs and thermal vents. Secondly, rather than being one unified whole, each chapter reads as its own story (which it may well have been; Friend is a former USA Today science writer and may be simply fleshing out articles he's already written). I'm of two minds about this book; as a evolutionary microbial genomicist (and one who has had the honor of working with Woese), I'm glad that there's a new book for the general public that acknowledges that microbes are worth studying for things other than their effect on human health; but on the other hand, I can't help but wonder if the story of the Archaea couldn't have been told in a more engaging manner. Bill Bryson, in his A Short History of Nearly Everything managed to tell Woese's story (if a bit too simplified) in an exciting chapter there. In conclusion, The Third Domain is worth a read (especially if you are interested in the subject), but the definitive book on Woese and the archaea has yet to be written.

Biologists are happier than Computer Scientists

2007-10-27T09:36:00.000-07:00

A recent survey conducted by the National Survey on Drug Use and Health (NSDUH) compared the percentage of US workers reporting an MDE (Major Depressive Episode) in the past year across occupation, gender, and age. Some of the results were fairly predictable, such as food and service workers having a greater than average occurrence of MDEs, and I had read before that women and older people tend to be more depressed on average, but some of the other results were quite surprising, at least to me. For example, "Mathematical and Computer Scientists" had a considerably higher rate (6.2%) of MDEs than did "Life, Physical, and Social Scientists" (4.4%). Not sure where that leaves bioinformaticians....

GME 2007 Highlights

2007-10-17T11:13:00.000-07:00

Well, I haven't blogged much lately, but there hasn't been much coverage of last week's GME 2007 (no, not this GME 2007!), other than Jonathan Eisen's brief live comments, so I figured it might be of interest to talk about some of the talks I attended there.

GME (Genomes, Medicine, and the Environment) is the meeting that was once called GSAC (Genome Sequencing and Analysis Conference), with the name change reflecting that the focus is now more on the use of genomics to understand medicine and the environment rather than on genome sequencing per se (although there was still a session on sequencing technology). It was held in San Diego, which allowed me to visit the La Jolla branch of the JCVI and to see former colleagues who have transplanted to the “left coast”.

Colleen Cavanaugh and Nancy Moran gave interesting back-to-back talks on bacterial symbionts of plants and animals and brought up many of the same issues in their evolution – namely that the genome size of symbionts seems to be correlated with the estimated age of their relationship with their host – that is that large bacterial symbiont genomes seem to shrink over time. Not that this is surprising, given that mitochondria and plastids are thought to be remnants of symbionts with larger genomes, but it is nice to see evidence of the process in progress today. The isolated environment of symbionts also seems to result in other oddities, such as increase levels of drift and chance fixation. As I am currently involved in a genome project of an endosymbiont of a cellulose-degrading shipworm, both Nancy's and Colleen's talks gave me many ideas for interesting things to look for.

JCVI's own Nobel laureate, Ham Smith, gave a pleasantly low-key talk on the status of his synthetic life project (no, bad scientific reporting to the contrary, he hasn't succeeded yet). Basically, now that his group has successfully transferred a genome from one bacterium to another, they are building an entire synthetic genome of Mycoplasma genitalium from scratch. Of course, even when they successfully transfer this they won't really have “synthetic life”, but it is clearly a step that needs to be done along the way. Again, I really liked it how Ham basically just said what he was doing without any hype – but then, when you have the Nobel, I guess you don't need hype.

A younger JCVI researcher, Yuri Gorby, presented his work on “nanowires” -- basically, structures produced by some bacteria that conduct electricity. The theory is that these allow the bacteria to disseminate electrons in a biofilm, thus freeing the bacteria from having to have direct contact with an electron acceptor. Really cool stuff, although not universally accepted yet.

Edward Bayer gave a talk about the “cellulosome”, which I hadn't heard of before, but given that I'm working on a cellulose degrading bacterium, I suppose I should have. Basically, not all cellulases are free in the cytoplasm – basically many form a complex (the aforementioned “cellulosome”) which is far more efficient than free cellulases. As Jonathan Eisen mentioned, Edward's paraphrase of Genesis at the start of the talk did seem rather off-putting, but hopefully it's just a cultural thing – perhaps in Israel such talk is just a manner of speaking and not a sign of creationism. He did mention evolution at one point, which was somewhat reassuring.

My former TIGR colleague John Heidelberg gave a talk on his work on metagenomics of cyanobacterial mats in Yellowstone Park hot-springs. Besides the interesting results, he brought up the important (if somewhat scary) observation that it is possible to assemble a genome from metagenomic data that doesn't actually exist in nature (much like nobody has the average 2.2 children).

Gene Tyson and Mary Ann Moran both talked about “metatranscriptomics”, which despite being a new “omics” (another one? geez!), is actually a really good idea – don't just sequence genomes from the environment – sequence the mRNAs to get an idea of what genes are turned on in a population in a given condition. Tyson was using microbial data from the Hawaii Ocean Time-series station ALOHA, and Moran was looking at her coastal Roseobacters.

Jonathan Eisen talked about his “Genomic Encyclopedia” which he plans to do with the JGI. Basically he plans to sequence (in a high throughput manner) hundreds of bacteria and archaea He aims to start with a pilot of 200 organisms (100 of which he'll close), but there's talk of maybe doing everything in Bergey's manual. From Jonathan's perspective, the point is to make a “happy tree of life” in which we have data to make truly representative phylogenetic analyses. As a genomicist, I find this both awesome and scary. Obviously, I'd love to have the data, but it looks like the time of “genome projects” as such is becoming as quaint as cloning and sequencing a single gene. Well, times move on, I suppose. Jonathan also talked about our Hyphomonas work as an example of how genomics helps resolve phylogenetic questions.

Shannon Williamson (now of JCVI-La Jolla) presented a talk about phage metagenomics in deep sea environments. Basically, she found that bacteria in diffuse-flow thermal vents have more lysogenic phages than do bacteria in the surrounding cold water (presumably because lytic phages would have have a hard time finding a host in a diffuse environment). Additionally, the phages are less diverse than in the surrounding waters, This talk was especially interesting to me because I helped her with some of the bioinformatics analyses, but I hadn't seen the big picture before.

Horizontal Gene Transfer from Bacteria to Eukaryotes

2007-08-30T13:39:00.000-07:00

Can bacteria transfer genes to eukaryotes? Many people may remember the rather rash assertion of evidence that they can that was made in the initial human genome paper (and the subsequent debunking of those claims by people I used to work with at TIGR).

But just because one study was flawed doesn't mean that such horizontal transfers don't happen, and today in the advance publication section of Science a new study shows solid evidence that the endosymbiotic bacterium Wolbachia has integrated parts (in some cases quite large portions) of its genome into that of numerous strains of Drosophila, the wasp Nasonia, and the worm Brugia malayi. These aren't mere cases of "BLASTology" -- they were confirmed by PCR. Even more stunningly, RT-PCR suggests that in some cases the integrated genes are actually expressed.

Again, there is a TIGR/JCVI connection -- one of the co-first authors, Julie Dunning Hotopp, has a cube only several feet from mine -- and all today I could hear her talking on the phone with science reporters -- so congratulations to her (and best wishes that the reporters don't screw things up). Also, congratulations to all the other authors, particularly the other co-first author, Michael Clark, whom I haven't met.

The results of the study have many implications both theoretical and practical. From an evolutionary perspective, it is interesting to ponder if the ancestors of many current eukaryotic genes came from such bacterial integrations. And from a practical perspective, it really makes one wonder if discarding bacterial sequences during the assembly of eukaryotic genomic data as "obvious contamination" (as is commonly done) is really the right thing to do.

Into the Great Wide Open

2007-08-26T08:29:00.000-07:00

My mother has spent the past 25 years working in the field of association management. What's that, you might ask? Well, if you're a scientist you probably belong to one or more associations such as the American Society for Microbiology (ASM). And it isn't just science; most professional fields have such organizations. There's even the American Society of Association Executives (ASAE), to which the people (such as my mom) who run the other associations belong. Associations, regardless of their topic, tend to fulfill the same functions, one of which is publishing journals. And that leads me into the topic of this posting.

My mother recently sent me a hardcopy of an article from ASAE's "Associations Now" magazine. It's entitled "Into the Great Wide Open" and it consists of an interview of Patrick Brown, one of the co-founders of PLOS. It is really significant that a publication of the ASAE would run such an article, because traditionally, the enemies of open access have not just been commercial publishers like Springer and Elsevier, but also many non-profit associations with publishing divisions. So I was expecting a hostile attack on open access, but actually it's quite a fair interview. In fact, they even printed the following exchange:

One thing that you've mentioned several times and I think is a big concern for the society publishers—especially societies that use income from their journal to subsidize other aspects of what they do for their members—is financial sustainability. What can you tell association publishers to show them that this transition can be sustainable?
There's a bunch of issues there. Number one, a lot of societies that make that claim—I would encourage people to look at their Form 990s. I get great enjoyment out of reading the Form 990s of scientific societies that talk about how important it is to preserve the income from their journals to do all these wonderful things they do, when, very often, the wonderful things they do, taken in aggregate, don't add up to the cost of their chief executive officer.
But let's just take that at face value—that their only motivation is to do good for the world and for science and for their community. One of the questions is, how important are those things that you're trying to fund with profits in your journal, compared to the good that you do for your mission through publishing itself and making access as freely available as possible?

The whole interview is interesting reading. And don't miss the informative sidebar containing a glossary of various Open Access terms. I have to admit I have a hard time remembering what the Berlin Declaration, etc. are, and I imagine most people who aren't professionally involved in the Open Access movement do too.

ISMB 2007 Vienna -- Part II Interesting Talks

2007-08-09T21:19:00.000-07:00

I'd just like to comment on some talks that I also found particularly noteworthy or interesting.

Atul Butte gave an interesting talk on nosology. No, that's not the study of noses, but rather the classification of diseases. What Butte has done is cluster gene expression patterns from various diseases. And the results were surprising. For example, he discovered that cervical cancer expression clustered with that of an autoimmune disease andmuscular dystrophy clustered with some forms of heart disease. These connections were unexpected and may lead to better understanding of these diseases. I liked the idea (even though I am not normally a disease person) because I found the idea analogous to the way unexpected phylogenetic relationships can be informative.

Christian von Merin g talked about phylogenetic analysis of samples from metagenomics projects. He is interested in this problem because contrary to what was generally believed prior to environmental sequencing, specific microbial species (& higher taxonomic levels) are not found everywhere it would be possible for them to live -- in other words, microbes have meaningful biogeography, just like plants and animals. Von Mering and colleagues have created an interesting pipeline for the interpretation of metagenomic data. Rather than try to analyze each of the millions of reads in detail, his method first identifies standard phylogenetically informative marker genes, then adds them to existing high quality alignments, and uses a custom phylogenetic program to test all possible phylogenetic positions on a reference tree. Both the limitation to markers and the custom phylogenetic component make this pipeline much more efficient than the typical phylogeny based methods.

Haipeng Li talked about a new maximum likelihood method for inferring positive selection and demographic history from chromosome-wide SNP data. His test case was Drosophila melanogaster and according to his model, the European population split off from the African lineage 16,000 years ago and underwent some sort of bottleneck. Current low levels of X-linked diversity (as opposed to the autosome) in the European population suggests a large excess of males in this population. This latter assertion was questioned by several members of the audience as it doesn't seem to be congruent with empirically measured numbers of males in the wild. Still, I find such studies fascinating. I would love to do a similar demographic study using bacteria, but I doubt we have enough data, even for things like E. coli or Bacillus anthracis.

And Alissa Resch, who works at the NCBI (just down the road from JCVI), also gave an interesting talk about positive selection. Odd that I'd have to travel thousands of miles to hear it though. Resch developed a new statistical test for positive selection that uses the rates of synonymous substitution in nearby intronic regions as a background. This allows detection of positive selection even at synonymous sites. She then applied it to orthologous gene pairs in mouse and rat.

ISMB 2007 Vienna, Part I - Keynotes

2007-08-05T04:53:00.000-07:00

I realize that I'm a bit late in covering a conference that occurred July 21-25, but I combined the conference with post-conference trips to Prague, Leipzig, and Berlin and have been busy at work since returning to Washington earlier this week.

There doesn't seem to have been much coverage of ISMB 2007 in the blogosphere (I've only found the coverage at Suicyte Notes,
and Fungal Genomes -- a few others had humorous posts about misadventures getting to Vienna, etc., but didn't cover any of the talks -- let me know if I missed any science-related postings).

In this first posting, I'll talk about my impressions of several of the keynote talks that made the most impression on me.

First of all, there was Michael Eisen's talk. Having worked with his brother, Jonathan, for some years, it was fun to finally see (and after the talk, briefly meet) the "other" Eisen. As would be expected from Mike's papers, his keynote largely dealt with the evolution of regulatory sequences in Drosophila. In the midst of this he made an offhand comment which generated both cheers and boos from the audience to the effect that bioinformaticians should stop working on microarray analysis methods "as nobody will be using microarrays in a couple of years". Well, we'll see.

Then, there was John Mattick's talk, which made me angry. Not because I disagree with his assertion that our traditional picture of gene regulation is incomplete, and that non-coding RNA-mediated gene regulation is going to be an important part of our revised picture, but I found his attitude towards non-eukaryotes (and even just non-mammals) annoying. According to John, the reason why "prokaryotes" are "simple" is that their gene regulation is just protein-based, while "higher organisms" require the use RNA as well. He even had graphs where "complexity" (how exactly is that defined objectively, now?) was the y-axis -- humans at the top, of course -- just like the medieval "Great Chain of Being" (minus the superhuman levels). The simple fact is that RNA based regulation isn't just limited to eukaryotes - non-coding RNA has been shown to be important in bacteria and archaea as well. Our picture of gene regulation in all domains of life is changing. Those on the quixotic quest to show that the evolutionary branch leading to humans is somehow "special" will have to look elsewhere.

And then there was Terry Speed's talk, which was one of those "historical" talks that some people see as a waste of time. Maybe it's because I once seriously considered becoming a historian of science, or perhaps it's just that I'm getting old, but I like such talks. And I learned a lot from it. For example, I always assumed that HMMs first entered biology from computer science in the context of sequence analysis/gene finding in the early 1990s, but Terry showed how people in pedigree analysis (including, if I recall from the talk, Eric Lander in his pre-genomics career) brought them into biology earlier.

I will write further on ISMB in subsequent posts.

British accused of releasing badgers in Iraq

2007-07-12T16:25:00.000-07:00

This article was from the BBC, and not the Weekly World News, I swear! The article (with the catchy, alliterative title British blamed for Basra badgers) claims, "British forces have denied rumours that they released a plague of ferocious badgers into the Iraqi city of Basra.". Of course, at first glance, this denial seems implausible -- what better way to solve the insane quagmire of Iraq than releasing badgers with the idea that chaos counteracts chaos? On the other hand, apparently the supposed badgers are not the noble Taxidea taxus, but apparently mere "honey badgers" (Mellivora capensis).

Anyone attending ISMB 2007 in Vienna?

2007-07-09T08:40:00.000-07:00

Anyone atttending the bioinformatics conference ISMB 2007 (held in Vienna, Austria this year)? I'll be there, along with several fellow alumni of the bioinformatics group from Waterloo -- John Tsang, Tomas Vinar, and Broňa Brejová. Perhaps we could organize a bloggers' dinner or something there if we get a critical mass.

Tagged!

2007-07-05T03:54:00.000-07:00

Well, just a few days after I did a "Friday Cat Blogging" (sort of), I find that there's another blogging tradition that I need to follow -- that of a "tagged post". I've been tagged by John Logsdon to follow up on his "eight random facts about yourself" posting and tag eight other bloggers with the same meme.

The rules are:

We have to post these rules before we give you the facts.
Players start with eight random facts/habits about themselves.
People who are tagged need to write their own blog about their eight things and post these rules.
At the end of your blog, you need to choose eight people to get tagged and list their names.
Don't forget to leave them a comment telling them they're tagged, and to read your blog.

1. I am a native Wisconsinite and my last name is indeed "Badger" (as Wisconsin is known as the 'Badger State', the sports teams of the University of Wisconsin are the 'Badgers' and so many businesses there are named Badger this and Badger that, this was the source of many jokes growing up). Apparently my name has no linguistic connection to the animal or state, though -- 'Badger' is a Scots name and my father's ancestors were Scots-Irish.

2. I don't drive. In the Midwest this fact generally generates gasps of incredulity, here on the East Coast it often generates compliments on the assumption that I've done it out of some noble principle, protesting urban sprawl or pollution or something. But really, given my poor eyesight, reflexes, and sense of direction, it's just better for everyone (including myself) that I stay off the road.

3. My s c i entific genealogy includes two Nobel Laureates (Rutherford and Chadwick) and well as a winner (Woese) of the Nobel-ish award for evolutionary biologists/ecologists, the Crafoord Prize in Bioscience. Not that that necessarily means anything for my own career -- as stock brokers say, "past performance is no guarantee of future returns".

4. I like languages. Both computer and human. The computer languages I know are Basic, Pascal, C, C++, Smalltalk, F orth, dBASE, Actor, Perl, and Ruby. The human languages I know are English, Esperanto, French, and Ger man, although to be honest, I'm far better at reading than speaking the last two.

5. As if it wasn't obvious from my "Friday Cat Blogging", I'm a cat person. I don't much care for dogs. I find the large ones vaguely threatening, and the small yippy ones are just plain annoying. Plus, they neither clean themselves nor use a litter box. Human infants have similar defects, but I guess inclusive fitness must play some role because all the people I know with infants seem to overlook this.

6. I seem to have an obsession about the former East Germany. I own 27 books about East German y and listen to albums like "Die Partei hat immer recht" and collections of Oktoberklub songs.

7. My favorite authors are John Crowley and A.S. Byatt. Besides the fact that they both write well, they both seem to be attracted to the Elizabethan and Victorian eras. These eras also attract me because they were also transitional times in the history of science -- the dawn of modern science in the early 1600s and the transition of science from hobby of the independently wealthy to practical career choice in the late 1800s.

8. I like my coffee black, and my art nerdy (Escher) or atmospheric (Hopper).

I tag:
Jacques Ravel
Neil Saunders
Eva
Steve Salzberg
Mike Hu
Naomi Ward (yes, your blog has to rise again!)
John Tsang (You need a blog!)
Marei Dose (ditto)

My 15 minutes (or 30 seconds) of fame

2007-07-03T06:30:00.000-07:00

I've worked with people like Carl Woese and Jonathan Eisen who routinely get interviewed by the media, but this is the first time that I've been in the spotlight. In May, Chris Condayan interviewed me along with several other bloggers attending the ASM 2007 meeting in Toronto, and he's edited them into an edition of his MicrobeWorld series dealing with microbiologists who blog.

Besides me, the featured bloggers are John Logsdon, "Yersinia", Tara Smith, Elio Schaechter, and Larry Moran.

Tara seems to think that she is too "animated", but I think she is undervaluing the value of animation. After all, this week, the animated Ratatouille beat out the latest "Die Hard" movie....

I could complain about my segment too, but it's probably pretty representative of me (not that I tend to talk into phones without calling someone first...)

Not your typical Friday Cat Blogging

2007-06-29T13:08:00.000-07:00

There's a tradition in blogging culture termed "Friday Cat Blogging". in which bloggers post light-hearted articles on Fridays, with the clichéd example being pictures of one's cats. Well, as you can see, I did post a picture of Bella Cat Badger, perched upon my closet door as she so often is, but I actually have a more serious reason for bringing up the topic of cats this Friday -- Driscoll and colleagues newly published paper "The Near Eastern Origin of Cat Domestication" (probably not open access, unfortunately). Anyway, as the article involves both cats and phylogenetic inference, how could I resist?

Small wild cats live (or have lived) in many places in Europe, Africa, and Asia. So an obvious question is whether domestic cats in different parts of the world are more closely related to their local wild cats (evidence of independent domestication events in different parts of the world) or to wild cats from one part of the world. Driscoll and colleagues addressed the issue by two different methods: making a neighbor-joining tree from short tandem repeat (STR) profiling (basically DNA fingerprinting) of 979 cats and by making a maximum parsimony tree from the sequence of the ND5 and ND6 genes from the mitochondria of 742 cats. The cats contained a mixture of wildcats, feral domestic cats, and domestic cats of various breeds sampled from Europe, Asia, and Africa. Both analyses supported the conclusion that the closest ancestors of both European and Asian domestic cats are wildcats from the Near East. However, the mitochondrial data suggests that there are at least five maternal lineages within that group.

Secret Messages in DNA...no

2007-06-27T06:55:00.000-07:00

There were a lot of blog postings about the evolution articles in yesterday's NYT (for example, JE's, Coturnix's and Larry's), but I don't recall anyone mentioning Dennis Overbye's article. I realize that making fun of bad science journalism is getting to be a rather repetitive joke, but this one is just weird. The article is combining two different topics. The first is about a Japanese group that encoded "E=mc^2" in DNA and introduced it into E. coli. That's a cute but in the end rather useless trick, rather like using DNA to solve cases of the traveling salesman problem (which people have also done ). Apparently, the Japanese group seriously thinks that DNA in living organisms could be a practical data storage method, and claims that the problem of mutation could be solved be using multiple copies (which would only slow down the decay, not halt it).

It gets more disturbing in the second half -- apparently actually taking seriously the idea that messages could be hidden already (by aliens?) in our DNA. I mean, everyone is amused by finding phage proteins that actually contain the word "PHAGE" using single letter amino acid abbreviations, but that's different from actually assigning meaning to the coincidence. The numerous falsified "solutions" to the Voynich manuscript, the supposed Bible Code (and the facetious Moby Dick code), and the endless reinterpretations of Nostradamus suggests that people can find secret messages even when none exist. What's the point of encouraging such nonsense by even seriously considering it in a major newspaper? I expect a crank volume on messages in our genome any day now -- in fact, were I less scrupulous, I'd write it myself under a pseudonym -- I'm sure it would sell.

Greatest BBC Headline ever

2007-06-14T07:21:00.000-07:00

"FBI tries to fight zombie hordes". Okay, I know the author knows he's being clever, and probably the people who actually have to deal with compromised Windows machines are already sick of the slang term "zombie", but still, I never expected to read such a Romero-esque headline at the BBC except maybe on April Fool's day.

Not that the zombies in the article affect me other than sending me more spam -- I'm a Linux and OS X user...

Genome of DNA Discoverer NOT Deciphered

2007-06-01T11:01:00.000-07:00

Do you recognize the man in the picture? It's Friedrich Miescher, the Swiss biologist/biochemist who discovered DNA in 1869. So, when the NYT announced today that "Genome of DNA Discoverer Is Deciphered", I was really excited, despite the annoying (and incorrect) use of "decipher" to mean "sequenced". Just think! Sequencing the genomes of Victorian scientists is now in our grasp! Who will be next? Darwin? Maxwell? Faraday?

But alas, it isn't so. It's just Jim Watson's genome.

Craig Venter "plays God" on international editions of Newsweek

2007-05-29T11:20:00.001-07:00

Apparently, on European, Asian, and Latin American editions of Newsweek this week, Craig Venter (my ultimate boss after about three levels), is shown looking, I suppose, reflective about the potential awesomeness of synthetic biology and the possibility of "playing God". Or maybe he just has indigestion. Anyway, the article is here. Interestingly enough, neither the cover nor the article appears in the US edition. The article is interesting enough, but I wish it would have clearly distinguished the public research on synthetic biology going on at the JCVI from Craig's startup. Yes, both involve Craig, but not everyone who works for Craig is on the private sector side of things.

ASM 2007 Wrapup

2007-05-25T17:33:00.000-07:00

ASM 2007 ended at noon today. This morning I attended the session dedicated to the International Polar Year (March 2007-March 2008) in relation to microbiology. My favorite talk was by Corien Bakersman and it dealt with the cold adaptation in the psychrophile (no, it doesn't love psychos, they love cold - psychro) Psychrobacter articus. Interestingly enough, instead of identifying amino acid replacements (as in common in such studies), Corien looked for other trends. She discovered that ORFs in P. articus tend to be longer than in mesophiles and she sees that as being explained by selection for encoded proteins to be "floppy" thus preventing them from freezing up in cold temperatures. She also noticed the cell walls of P. articus tend to be less rigid than in mesophiles.

Pictured is Honest Ed's, a classic independent discount store (and Toronto landmark) that started back in 1948 by Ed Mirvish (who is still around, but 91 years old).

Highlights of ASM 2007 -- May 23 and May 24

2007-05-25T02:57:00.000-07:00

On Wednesday, I attended two sessions -- one on adaptive landscapes in the morning and another on integrating ecology and evolution into the teaching of microbiology in the afternoon.

The highlight of the morning session was probably the talk by Paul Turner on the effect of co-infection on fitness variance in bacteriophage ϕ6 (which infects Pseudomonas). I hadn't heard about ϕ6 prior to this talk, but it is really quite interesting because much like the influenza virus, it is an RNA virus with multiple segments. When two or more ϕ6 phages infect the same cell, the progeny viruses can have a mixture of segments derived from different "parents". In theory, co-infection could act as a crutch for less fit viruses, as some of their (partial) progeny could be of higher fitness. Turner and colleagues showed that this indeed what happens An earlier version of the work he presented was written up in an article in PLoS Biology.

You might legitimately ask why I attended the afternoon session on integrating ecology and evolution into teaching microbiology (as I don't teach), but maybe I was just drawn to the name of Jo Handelsman, who is rightly renowned for both her teaching and her active research program. Jo is into metagenomics and microbial biodiversity these days, and she talked about how to explain the use of sampling to estimate diversity to undergraduates. She believes that it is easier to start out with concrete simple examples. One of her techniques is to use bags of candies that have different distributions of colors to show that one can underestimate diversity in populations with a majority species (If one draws out three candies and they are all green, one may be tempted to assume that all of the candies are green, perhaps incorrectly).

Thursday morning I had to attend my poster on positive selection in Geobacter. Most people stopping by were more interested in learning how to use PAML in their own systems than in the results, but that was okay as my results are fairly preliminary anyway.

In the afternoon, I attended a session on predation of bacteria. I've long been interested in predators of bacteria (particularly bacterial predators of bacteria such as Bdellovibrio). These days there is quite a battle going on over which of the three main predators (phage, protists, and bacterial predators) is the most important in regulation of bacterial populations in nature. Henry Williams (with whom last year I wrote a grant proposal to sequence environmental isolates of Bdellovibrio-like organisms, unfortunately not funded) gave an interesting talk on comparing the effects of phage versus Bdellovibrio-like predation. He came up with the conclusion that Bdellovibrio and friends are more important because their titers after controlled predation go up several orders of magnitude more than do phage, and this he explained as a result of Bdellovibrio being motile and phages not.

Mini-Blogger convention at ASM 2007

2007-05-23T20:53:00.000-07:00

I promise I'll write something up on Wednesday's talks, but that would require too much thinking and it's getting late here. Instead, I'll just show this picture demonstrating that I've finally joined the cool blogging world for real. Larry Moran organized a dinner for bloggers attending ASM and invited me as well as other (mostly more established) bloggers. Pictured are (L to R), Larry Moran (Sandwalk), Mona (Science Notes), Andrew Staroscik (Mixotrophy), John Logsdon (Sex, genes and evolution), and Tara Smith (Aetiology). Not pictured are Eva (Eastern Blot) and Chris Condayan, the ASM public outreach manager who later interviewed and filmed us for a feature on science blogging. For some reason (either out of creativity or alcohol consumption) Chris filmed me while having me stand in a phone booth. He's going to edit the interviews into something short and interesting and I'll post a link when it is available (assuming it isn't too embarrassing).

Highlights of ASM 2007 -- May 22

2007-05-22T19:17:00.000-07:00

There were many shorter (30 min) talks today, so I'll focus on a few that I found most interesting. Janet Siefert gave a interesting talk on her studies of the "living stomatolites" (large cyanobacterial colonies) of the Mexican desert and how they and associated organisms live under such phosphorous-limiting conditions. Particularly interesting was her discovery of a new species of Bacillus that had many apparent cyanobacterial-derived genes. Janet was replacing Ken Nealson (who couldn't attend for health reasons). I had been hoping to meet Ken as one of the many hats he wears is head of the environmental microbiology division of the JCVI, meaning that he's technically been my boss since mid April. Oh well.

Susan Glasauer talked about her work in studying the biodiversity of metal-reducing bacteria in the Jura mountains of Switzerland. There's more growing there than wine grapes (although the same iron-rich soil that makes for such good wine country is also partly responsible for the microbial diversity)

And to finish off the day, the father of bacterial and archaeal (no, I won't say the "p" word) biodiversity studies, Norm Pace himself, gave an special award lecture as he had been chosen for this year's Abbot-ASM Lifetime Achievement Award. While he made his usual arguments against the use of the word "prokaryote" (which I fully agree with in theory, if not entirely in practice), I found it interesting that he now considers the rRNA tree to represent the nuclear lineage (shades of Jim Lake) rather than the organismal tree.

Highlights of ASM 2007 -- May 21

2007-05-22T03:35:00.000-07:00

Monday's talks were all by well-known speakers and were pretty much overviews of topics rather than presentations of any new findings.

Gerry Wright gave an interesting talk on antibiotic resistance. He brought up the points that 1) according to molecular evolution half of all known antibiotics predate the Cambrian explosion and 2) environmental isolates that have never seen a clinical antibiotic quite often have genes for resistance. To understand the development of resistance, we have to stop thinking that the world revolves around humans; we've really stepped into a war between microbes that's been going on long before humans existed.

Ed Delong (one of my heroes) talked about the importance of oxygen-producing bacteria in the oceans and how people tend to forget about their existence and importance, despite these "prokaryotic forests of the sea" producing 50% of the atmospheric oxygen.

And E.O. Wilson (of ants and sociobiology fame) gave a keynote lecture on biodiversity, probably on the basis of his quip made some years ago that if he were a young scientist today, he would become a microbial ecologist rather than an entomologist. It was interesting to hear him talk, as I've heard his rivals Gould and Lewontin speak before, but clearly Wilson's talk was simply a recycled biodiversity of animals talk with a few slides about microbes added -- although I rather liked the (to the general public anyway) more famous Wilson talking about the importance of the work of Woese.

Pictured is the main hall of Union Station -- Toronto's version of New York's Grand Central Station.

In Toronto for ASM 2007

2007-05-20T18:19:00.000-07:00

This year the big meeting for the American Society for Microbiology is in Toronto. Which is odd, because Canada has its own professional association, the Canadian Society of Microbiologists. Are they going to hold their meeting in New York? Anyway, I'm here and enjoying a return to a city that I visited several times as a teenager and then as a postdoc in the (relatively) close University of Waterloo. I'll try to post highlights as I see them from the conference each day until Friday.

Oh, I have to tell you an amusing story that occurred when I was going through customs today as I was entering Canada: The customs official asked me why I was entering Canada and I told him that I was attending the microbiology meeting, and he asked me where I worked and I told him I worked at the J. Craig Venter Institute, and he responded with "You know, are they ever going to do studies of the ocean bacteria that live too deep for photosynthesis?". Which is a totally valid question -- the Global Ocean Survey used samples collected from Craig's yacht, not a research vessel, so the samples were from the surface. But I was a bit stunned hearing it coming from a customs official!

Concerning the pictures -- one is of Dundas Square -- which didn't even exist the last time I was in Toronto, and the other is of the so-called World's Biggest Bookstore. I went there today for old-times sake. It is quite a large bookstore, and I was blown away by it when I first visited it in the 1980s, when my idea of a bookstore was a typical Waldenbooks or B. Dalton's. But while it's still larger than than the average Barnes and Noble (or Chapters or Indigo, eh?) location of today, it isn't mindbogglingly larger.

Erdös numbers & other geekery

2007-05-16T22:48:00.000-07:00

RPM over at Evolgen has recently posted on the (perhaps facetious) need for a version of an Erdös number in biology. If you don't know what an Erdös number is, it basically is the geekier version of "six degrees of Kevin Bacon". Paul Erdös (1913-1996) was a prolific mathematician who had many co-authors. If you co-authored a paper with Erdös, you have an Erdös number of 1, if you didn't collaborate with Erdös himself but instead with one of his collaborators, you have an Erdös number of 2, and so forth. It's a point of pride among mathematicians to have a low Erdös number.

Well, shouldn't biologists join in on the fun? RPM has suggested that Richard Gibbs should be our Erdös. Of course, he's honest enough to mention that he has a Gibbs number of one, but Gibbs isn't actually a bad choice, at least in genomics. I suggested Craig Venter or Claire Fraser (as I have a both a Venter and a Fraser number of 1), but RPM suggested that I wasn't really getting into the spirit of things. Still, (as you'll see), these connections still help me.

So first of all, having done a postdoc in a Computer Science department, I'd just like to state that I have a respectable Erdös number of 4. (Paul Erdös -> Charles Colbourn -> Derek Corneil -> Paul Kearney -> me).

My Gibbs number isn't so bad either, at 2. (Richard Gibbs -> Craig Venter -> me)

Someone on evolgen suggested Eric Lander. My Lander number is 3 (Eric Lander -> Michael Eisen -> Steven Salzberg -> me).

JCVI Evolutionary Genomics Journal Club on Liu-Ochman

2007-05-12T04:31:00.000-07:00

This week I was the presenter for our "Evolutionary Genomics" journal club at JCVI and I chose to present the Liu-Ochman paper on the the stepwise formation of the bacterial flagellum and its reception (part two, three) in the blogosphere. The basic claim of the article is that the 24 core proteins are homologous to each other and this explains how the flagellum evolved through repeated gene duplication events.

Nick Matzke doesn't buy the argument for several reasons: 1) It doesn't seem to be congruent with previous studies 2) At least two of the structures of the presumed homologous proteins don't "look" homologous. and 3) The authors seem to be using the Bl2Seq tool incorrectly. It's odd that Nick focuses so much effort on points 1) and 2) because it is really 3) that is the issue. Personally, I've never been convinced that protein structure is of much use in inferring homology or the lack of it; systematists have been burned so many times by incorrectly assumed (non)homology of gross morphological traits in light of convergent and divergent evolution; why should morphology at the protein level be any different? The beauty of molecular systematics is that it's freed us from having to deal with morphology at all.

At the journal club, we were split on the value of structure for inferring homology, but we all agreed that eyeballing structures, particularly structures that seem to have drawn with different programs and rotated differently. was not a very convincing argument.

We were much more convinced, however, by Nick's demonstration that the authors seem to have performed their BLAST matches incorrectly. As Nick showed, the authors did not have sequence filters enabled, which means that matches to low-complexity regions can artificially inflate BLAST significance, and perhaps more damning, the authors used multiple pairwise BL2Seq runs without correcting for the true size of the search space. And these weren't just assumed to be the problem; Nick demonstrated on a subset of the data that using the correct parameters caused several "significant" BLAST matches to disappear.

This was the introduction to scientific blogging for many of the attendees of the journal club, and they also had some interesting comments about the phenomenon after preparing for the club.

1) While the paper was much mentioned in scientific blogs, generally the mentions were just "Nick Matzke has shown that the Liu-Ochman paper is flawed; here's the link", and not independent analyses of the paper. Yes, this is true of blogs in general, not just scientific ones. But this sort of laziness is very common in traditional media too. Take a look at your newspaper and see how many articles are from news services like AP or Reuters rather than being independent reporting.

2) Why did discussion suddenly fall off after Nick's articles? Does the blogosphere really have such a short attention span?

3) Why haven't we seen a response from Liu and Ochman? Are they not aware of the discussion, or do they simply see criticism on blogs as not being worth responding to?

Wiley and fair use of published figures by bloggers

2007-04-26T06:57:00.000-07:00

This has been all over the blogosphere -- even on boingboing (which means that it's probably going to show up on Slashdot in a day or two), but it ties in with what I just posted, and it reminds us of yet another problem with non open access publishing.

Basically, the story is that a PhD student blogger, Shelley Batts, wrote a blog posting about a much discussed recent article that claimed that antioxidants in berries are increased by alcohol (the "daiquiris are good for you" paper). As part of her blog entry, Shelly posted graphs and a table from the paper, as would seem reasonable fair use in discussion of the science. But Wiley Publishing didn't see it that way -- here's their take:

"The above article contains copyrighted material in the form of a table and graphs taken from a recently published paper in the Journal of the Science of Food and Agriculture. If these figures are not removed immediately, lawyers from John Wiley & Sons will contact you with further action."

The only good thing I see about this is that the news has gotten out about what unreasonable asses Wiley are being and hopefully people will think twice before submitting a paper to a Wiley published journal.

BTW, the Wiley E. Coyote image I'm using is supposedly fair use (it's from Wikipedia), but I'll let you know if Warner decides to threaten me over that.

UPDATE: At 1:02 pm, the legal threat against Shelly was retracted:

"There has been a misunderstanding with this issue, inadvertently caused by a junior staff member at our Society. Our official response is below: 'We apologise for any misunderstanding. In this situation the publisher would typically grant permission on request in order to ensure that figures and extracts are properly credited. We do not think there is any need to pursue this matter further.'"

Still, it is disturbing that the concept of "fair use" doesn't seem to be acknowledged in that response -- under fair use, there would be no need for any permission to be asked for in the first place.

Prototaxites a fungus? Who can tell without Open Access?

2007-04-23T11:20:00.000-07:00

Prototaxites is believed to have been the largest land organism in the Devonian period, leaving behind tree-trunk sized fossils that have stumped geologists for the 150 years since their discovery. What exactly was it? Traditionally, it was assumed to be an ancient brown algae, largely from analogy with modern giant aquatic brown algae. However, according to a recent news article Francis Hueber and colleagues have just published a paper that gives convincing evidence that it was in fact a giant fungus. An interesting idea -- but unless your institution subscribes to the journal "Geology", you can't read the actual paper to decide for yourself. It's particularly sad that this is the case because the journal isn't published by a commercial company that would be expected to put profit before science, but by a non-profit society that supposedly stands for "Fostering the human quest for understanding Earth, planets, and life". Limiting access to papers seems to be in direct conflict with their stated mission.

RIP Kurt Vonnegut (1922 - 2007)

2007-04-12T06:18:00.000-07:00

Well, besides TIGR, Kurt Vonnegut died yesterday as well. So it goes. While many of his later works were rather derivative, one is reminded of the quip about Bob Dylan: "sure, he's derivative nowadays, but the person he's plagiarizing from is his younger self." Certainly both Slaughterhouse Five and Cat's Cradle will stand the test of time, and I'm rather fond of Player Piano and Galapagos as well.

RIP TIGR (1992-2007)

2007-04-11T14:12:00.000-07:00

Well, it's official -- TIGR is no more. We had an "all hands meeting" today and Craig informed us that the TIGR name has been officially retired (as has that of the lesser known TCAG, or The Center for the Advancement of Genomics, which had been the "traditional" J, Craig Venter Institute). We are all now employees of the J. Craig Venter Institute. Even our e-mail will be at jcvi.org and not tigr.org. Personally, I don't understand the rationale behind Craig's reasoning -- TIGR means something to the scientific community, and with the possible exception of the recent Global Ocean Survey, the J. Craig Venter Institute is an unknown quantity. But hey, what do I know? In other news, the much rumored "flat organization" that would bring faculty and staff scientists to equality turned out to be just that -- a rumor. I had mixed feelings about that one, anyway. As a staff scientist, I of course would like to move up in the social scale, but I realize that many faculty would be alienated by such a move. TIGR (er, the JCVI) is hemorrhaging enough faculty as it is.

Stacey Singer's "Plasmid"

2007-04-10T07:44:00.000-07:00

Last night I when was talking to my brother on the telephone, he mentioned that Stacey Singer, whom we went to high school with, had become a science journalist for the Palm Beach Post and had started a blog, Plasmid. It's a bit anemic at the present (I suppose Stacey's mostly writing actual newspaper articles), but hey, I know someone who grew up to be a science journalist. I guess when I make a major discovery I can call her up to tell her.

You will be showered with good luch

2007-04-04T14:10:00.000-07:00

Today I received a disturbing fortune in a fortune cookie at the vaguely Pan-Asian restaurant across from TIGR. Normally, I'm annoyed by "fortunes" that are merely statements like "You have a good heart". Well, today, I received one with a concrete prediction, but a rather distressing one -- "You will be showered with good luch." What's "luch", you ask? Apparently it refers to a series of Soviet satellites. Also, it could refer to a brand of watches made in Minsk (the Communists loved to name their consumer goods after satellites; cf. the East German Trabant). The watch might hurt less.

Back to the Future

2007-04-02T19:13:00.000-07:00

Have you ever come across an old e-mail file? I recently was looking at some of my old files and discovered an archive of all of my grad school e-mails from 1992-1998. It's rather eerie to have the ability to look and see what you were doing ten years ago. (Okay, so the movie is about going back 30 years, but hey, cut me some slack). Anyway, bizarrely enough, on April 2nd and 3rd, 1997, I was arguing about gene annotation in Archaeoglobus fulgidus with people who worked at TIGR. Now I work at TIGR. (Well, technically, I now work at the J. Craig Venter Institute, TIGR subdivision -- it's like Hong Kong -- One nation two systems, or something like that).

Talk finished!

2007-03-29T11:16:00.000-07:00

This past week I've been freaking out about an internal promotion talk here at TIGR and finally it's over. It went well, I think. Some people have asked me for the slides, and so I've provided links to them in their original Apple Keynote format and as a PDF.

Classic biology books online

2007-03-20T06:33:00.000-07:00

I've always had an interest in the history of science, particularly of evolutionary biology, and enjoy reading classic works in the field. While I'm lucky that I live near the Library of Congress, with its fabled collection, it's nice to be able to read from the comfort of my own home (the LoC is non-lending). What to do? One possibility is to read online books. Everybody probably knows that the works of Darwin, Huxley, and other Victorians are available on the net, but you may not know that even early 20th century classics are now available, thanks to the digitizing efforts that have been going on in various university libraries. Some may dislike the idea of reading on-screen, but there are services like CafePress and Lulu that will print and bind a PDF file for you for a small fee (and eventually, we will have practical e-ink devices that will make printing unnecessary. Oh, and flying cars and personal robots too).

Anyway, here are a few significant books that I've discovered on-line:

Hugo de Vries' Species and Varieties, Their Origin by Mutation (1905) -- The classic "saltationist" work by one of the rediscoverers of Mendel's laws, this is a good example of early thought by geneticists on the issue of evolution -- de Vries considered mutation, rather than selection to be the primary force behind evolution.

Thomas Hunt Morgan's The Physical Basis of Heredity (1919) -- The book that established the gene as a real entity on a chromosome rather than an ideal "factor".

R.A, Fisher's The Genetical Theory of Natural Selection (1930) -- Considered the most important advance in evolutionary theory since Darwin, this book ended the "eclipse of Darwinism" caused by people like de Vries by explaining selection in terms of Mendelian genetics.

Self censorship or just common sense?

2007-03-14T12:00:00.000-07:00

In today's Nature there's another installment of Prospect by Paul Smaglik (yes, it's not open access -- unclean! unclean!). If you don't read it, Prospect is a column geared towards postdocs and other beginning researchers and aims to give them career advice, often verging on the banally obvious. Today's was a little different -- it's entitled "Could blogs replace résumés?" and suggests that "perhaps it's best to treat your blog as a public document that you wouldn't mind your next boss reading". Well, I suppose -- realizing that what you say on the Internet can come back to haunt you is not new and dates back to the early days of Usenet newsgroups, but at the same time it isn't possible to say anything interesting without potentially pissing off somebody.

The J. Craig Venter Institute's Global Ocean Sampling Expedition

2007-03-13T14:17:00.000-07:00

Well, today a series of papers on the Global Ocean Sampling Expedition (including one first-authored by my drinking buddy Rekha Seshadri and another by my former mentor Jonathan Eisen) were published in PLoS Biology. We also had an institute wide (TIGR is now part of the J. Craig Venter Institute, if you hadn't heard) happy hour to celebrate the event. I may be a fan of "free as in free speech, not as in free beer" software, but I'm not one to turn up my nose at literal free beer (which was provided). And the papers themselves are actually rather interesting. While there's currently a tension between TIGR (run by Craig's ex-wife Claire Fraser, and run rather like a university minus the teaching) and the rest of the Venter Institute (more centrally controlled by Craig), you have to admit that good science can be done in Craig's domain.

The Difference Engine

2007-03-11T05:36:00.000-07:00

I've just finished reading Doron Swade's "The Difference Engine: Charles Babbage and the Quest to Build the First Computer". In it, Swade (a curator at London's Science Museum) tells two stories: the first is a biography of Charles Babbage, the 19th century polymath who designed a series of mechanical computing devices that were never built, and the other is Swade's own story of building a working version of Babbage's Difference Engine No. 2 for the Science Museum.

I've long been fascinated by the idea of clockwork computers, and had a general idea of Babbage's story, but Swade dispels some common myths that have surrounded him. For example, one often reads that 19th century manufacturing techniques were too crude to create parts with the required tolerances, but Swade's studies on the surviving parts of Babbage's unfinished engines shows that they were sufficient. Rather, the issue was political and personal. Babbage's constant redesigning of his engines rather than creating a working version of any of them, combined with his skill at making enemies in influential places, meant that the British government finally lost patience and discontinued funding. Swade also deflates the romantic idea of Lord Byron's daughter Ada Lovelace being the "first programmer"; While Ada did provide examples of engine programs (really just algorithms) in a series of notes to her translation of a French article about the Analytical Engine, they unfortunately seem to be paraphrases of Babbage's own work.

Oh -- one last note -- the title may lead to confusion with William Gibson & Bruce Sterling's alternative history novel also entitled "The Difference Engine" in which Babbage Engines were built and started the Information Age a century early. That's a different book!