Monday, September 29, 2008


Assistant Professor - UCSB - Evolutionary Genomics

The Department of Ecology, Evolution, and Marine Biology at the University of California, Santa Barbara invites applications for a tenure-track faculty position starting at the rank of Assistant Professor. We are searching broadly for an interactive scientist who addresses fundamental questions in evolutionary biology via analysis of large-scale gene sequence and/or expression data sets. Applications from those who can take advantage of UCSB’s world class marine facilities and international standing in marine biology are especially encouraged. The successful candidate is expected to develop an internationally recognized research program and to teach graduate and undergraduate students in his or her area of expertise. The successful applicant will have a PhD and clear evidence of research productivity.

Applicants should submit 1) an application letter 2) a curriculum vitae 3) a statement of research accomplishments and future plans 4) a statement of teaching experience and interests, 5) up to three selected publications and 6) names and contact information of three persons willing to provide letters of reference (the committee will solicit letters for a short-list of candidates). Submit applications to:

Evolution Search Committee
Department of Ecology, Evolution, and Marine Biology
University of California
Santa Barbara, CA 93106-9610 U.S.A

Alternatively, applications can be sent electronically, and questions addressed to:

Review of applicants will begin November 1 and will continue until the position has been filled

The department is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research, teaching and service

UCSB is an Equal Opportunity Affirmative Action Employer

Tuesday, September 23, 2008

Chance and Necessity: The fate of graduate students

There have been a few posts relating to a story in Science about the fate of 30 students who began graduate school at Yale in 1991.

Chance and Necessity: The fate of graduate students

Sandwalk: What Happened....?

The upshot is that most of those students in the story are not currently in tenure track academic jobs. This has inspired me to complete a little exercise that I've been meaning to do for a while - to list some of my graduate colleagues from Duke and where we are now. It is truly amazing how such a large number of us have landed really good academic jobs. I'm not sure if the late 1990's was a special time at Duke, or whether the early 2000's were a ripe time for academic jobs in general (or both). Perhaps Duke grads always do well in the academic job market. This is not a scientific study. I am only conveying the awe I have for my own graduate experience, and the gratitude I have for being able to be surrounded by a tremendous group of students. I think we all raised the bar for each other, and of course this was all possible because of the collaborative and empowering environment fostered by Duke Biology faculty. Here are some of the folks who started or ended graduate school about the same time I did at Duke. I was there 1996-2001. This list is straight off the top of my head, in no particular order (except my lab and office mates are first), and I am certain that I am forgetting people. I apologize to them. Yet the point still stands, we did okay.

Todd Oakley (me) Professor Univ. CA Santa Barbara
John Wares, Professor University of Georgia
Mike Hickerson, Professor Queens College NY
Mike Gilchrist, Professor University of Tennessee
Laura Miller, Professor University of North Carolina
Rebecca Zufall, Professor University of Houston
John Stinchcomb, Professor University of Toronto
Sheila Patek, Professor U-Mass-Amhurst
Kirk Zigler, Professor Sewanee University
Armin Moczek, Professor Indiana University
Matt Hahn, Professor Indiana University
Leonie Moyle, Professor Indiana University
Matt Rockman, Professor NYU
Ehab Abouheif, Professor, McGill University
Peter Tiffin, Professor, University of Minnesota
Tami Mendelson, Professor, U Maryland-BC
Janneke Hille Ris Lambers, Professor, University of Washington
Anne Pringle, Professor Harvard University

Even now, this is a great academic network (some call it the Duke Mafia, especially after they witness the secret handshake).

Monday, September 15, 2008

It's all been done

A few people have liked the idea of bioluminescent beverages, after I posted a picture of glowing ostracods in a wine glass. Sounds like fun, but we'd have to pay royalties. An existing patent seems pretty comprehensive, even including "slimy play material".

This patent represents the origin of novel novelty items by combining entities: manufactured articles and bioluminescence.

Bioluminescent novelty items
Document Type and Number:
United States Patent 6152358

Novelty items that are combinations of articles of manufacture with bioluminescence generating systems and/or fluorescent proteins are provided. These novelty items, which are articles of manufacture, are designed for entertainment, recreation and amusement, and include toys, paints, slimy play material, textiles, particularly clothing, bubbles in bubble making toys and other toys that produce bubbles, balloons, personal items, such as cosmetics, bath powders, body lotions, gels, powders and creams, toothpastes and other dentifrices, soaps, body paints, and bubble bath, foods, such as gelatins, icings and frostings, beverages such as beer, wine, champagne, soft drinks, and glowing ice, fountains, including liquid "fireworks" and other such jets or sprays or aerosols of compositions that are solutions, mixtures, suspensions, powders, pastes, particles or other suitable formulation.

Tuesday, September 9, 2008

Ostrablog 5 - Three shows and a funeral

In 1998, I spent nine weeks in Japan in an international graduate student program co-sponsored by the National Science Foundation of the United States and the Japanese ministry of Science, Monbusho. The trip was for me a memorable and life-changing experience I many ways. Besides a high school trip to Mexico, Japan was my first trip abroad, and the magnitude of cultural differences between the US and Japan was a big part of the memories. For me, immersion in a different culture is mind-stretching. If you haven’t been to Japan and want to get a sense of what I mean, I found the film Lost In Translation to be quite a good [although decidedly amplified and somewhat stereotyped] facsimile of total immersion in the culture. Besides culture shock, another vivid memory of my Japan trip involves the subject of today’s ostra-blog, the ostracod Vargula hilgendorfii.

Vargula hilgendorfii. Male on top female on bottom. Image from

Vargula hilgendorfii is known to the Japanese as ‘umihotaru’. “Umi” means “sea” and “hotaru” means "firefly". Umihotaru are vividly, potently, bioluminescent. When threatened, they spit out a liquid cloud of light that is the blue of a sun-drenched Caribbean bay. The animal is only about 2 mm in length, roughly the size and shape of a sesame seed. Yet the “light bomb” (as one of my Japanese friends called it) can be seen from meters away. To detonate this bomb, umihotaru spits out an enzyme and its substrate from glands on its “upper lip”, an organ just above its mouth that also spits out digestive enzymes. My Japanese advisor and host, Katsumi Abe, had the idea that the light producing enzyme is actually derived from a digestive enzyme, and evolutionary novelty that arose by duplication and divergence. It was hundreds of light-vomiting umihotaru that provided one of my most potent, and decidedly surreal memories of my Japanese adventure.

Light from the ostracods of the species Vargula hilgendorfii. Image from

Imagine a nearly full sheet of plywood (4 x 8 feet) standing in the back of the room. Attached to the plywood are rows and rows of vials filled with seawater. The vials are capped and through each cap runs two thin wires, dipping into the water. The wires all bundle together behind the plywood and snake back to a console. The console looks like a mixing board at a rock concert, with a row of sliders. The consoled is plugged into an electrical outlet in the wall so that the wires can deliver a potentiated jolt of electricity to the vials of sea water. I would soon find out that swimming in the numerous vials of seawater, were hundreds of ostracods, umihotaru.

While I examined this strange contraption, trying to imagine the purpose, the room lights when dark, and cheesy, achingly theatrical, synthesized new age music filled the room. An operator took his position behind the electric console, leaning forward with his hands on the sliders like a rock star keyboard player. He dexterously began moving the sliders in time with the music, sending pulses of electricity into the bodies of the umihotaru. They felt threatened, and they were vomiting their luciferase enzymes into the vials of brine, producing effervescent azure explosions of light, pulsing in time with the music.

The vials were not the only part of the show. Hidden behind curtains, the electric console-wielding front man had assistants. Poised precariously on top of a step ladders, their instruments were funnels aquarium nets and buckets of water. Inside the nets? Hundreds more umihotaru! Precisely choreographed with the music, the assistants vigorously poured water into the nets of umihotaru. Too large to pass through the nets, the water coursing over them threatens them until they spit out their light, illuminating the coursing water. The water cascaded into the funnels, which were directly attached to clear aquarium tubing. The tubing ran the length of the room, 30 feet at least, descending and arcing gracefully like garland at Christmas time. The water stayed lit on its journey through the tubes, the entire length of the room. The same electric blue that pulsed in the vials punctuated cymbal crashes by coursing through the tubing.

As if that weren’t enough, umihotaru was on display in one more way. Larger clear tubing hung in “U” shapes in a few places in the room. One each side of the U, wires ran, connecting back to the electric console. These larger tubes stayed filled with seawater, and again, umihotaru swam in the water. Dedicated sliders jolted the U with electricity, and umihotaru swam, leaving behind illuminated contrails, like tiny psychedelic fighter jets – and again choreographed to the blaring music.

I’ve told this story many times, and depending on my mood, and how well I know the listeners, I will sometimes stop here. People laugh incredulously, ask a question or two, and we move on to other stories. Because the story takes a more somber turn here, I often leave out the most unbelievable part of the story. The kitchy, surreal display I just described actually began the funeral of my Japanese advisor Katsumi Abe. People even took pictures and video. Of a funeral.

A week earlier, Abe was tragically killed when his car struck an oncoming truck head on. He was young, in his mid-40s I suppose, full of energy, full of life. He had five children. I was one of the last people to see him alive. He left a conference that we were at late at night. He probably fell asleep at the wheel and never woke up. I felt so alone in that foreign land without my host and I felt guilty for feeling alone. What right did I have to feel bad, compared to five children who lost their dad, or to a wife who lost her husband? The night after the funeral, I had to go to Tokyo. My plane was scheduled to leave the next day. Fitting my mood, a torrential storm from a typhoon drenched me while I waited for trains with a Japanese friend who kindly escorted me. He also was at the funeral and knew Abe well. A few days later, I would be a world away in sunny Bermuda to collect other ostracods. But no matter the distance I travel, I will never forget Japan. Abe wrote a book in Japanese which translates to "The Light of the Marine Firefly". Whenever I see that electric blue light, I think of him.

Tuesday, September 2, 2008

Ostra-blog 4 - Colymbosathon ecplecticos

Last week, somewhere near the top of my mental list of candidate species for ostra-blogs was Colymbosathon ecplecticos. A couple years ago, this species burst on to the ostracod scene, causing a global media event. Ostracodologists are not used to seeing their favorite animals in the headlines, so Colymbosathon caused quite a sensation. On Friday, Eric at The Other 95% generated a post, Who's Got the Oldest?, with Colymbosathon playing the prominent role. Eric described some of the species' vitals. Yes, it's the oldest fossil with identifiable male parts. Yes, its species name means "amazing swimmer with a large penis". Eric's post prompted me to make Colymbosathon the star of this, ostra-blog #4.

Colymbosathon first exposed itself to me at a scientific conference. I was immediately drawn to its rather prominent.... eyes. We were in Seattle in November of 2003, about a month before the Science paper was to be published, and cause the aforementioned media blitz. So it came as a complete surprise to me when the first picture of this 425 year-old fossil flashed on the screen. I remember a seeing on the screen a photo similar to Figure 1 below.

Figure 1. Colymbosathon ecplecticos, a 425 million year old fossil ostracod. Image copyright Science Magazine.

I study ostracod eyes, and I've dissected many of them. My attention went directly to the compound eyes. One is marked "le" in the figure above for "lateral eye". That's the left eye, the right eye is higher on this figure, just below the "H" in the figure.

This fossil was preserved about 425 million years ago in three dimensions inside a volcanic nodule. The scientists break open such nodules in search of interesting fossils. When they find one, they make an image of the fossil at the point it broke, and then grind away a tiny bit of rock (10 microns or so, if memory serves) and take another picture. Doing this procedure over and over again gives them a stack of images, which they can put together computationally to yield full 3-dimensional reconstructions of the fossils. For ostracods and other small animals, this is completely amazing. For most ostracod fossils, only their carapace is preserved, it's made of calcium carbonate. On a few fairly rare occasions the "soft parts" of ostracods are also preserved. (Soft parts refers to the non-carapace parts, even though they are not all that soft, having a chitinous exoskeleton). But even when soft parts are preserved, there were no cases where the full 3-dimensional structure was visible. With digital reconstructions, movies can be made, and specific parts of the animal can be highlighted or removed in order to view other structures.

Figure 2 - Computer generated image of Colymbosathon (side view). Different parts of the animal are colorized differently to make them easier to see. Faint parallel lines are visible, which is where the original was ground, 10 microns at a time, to yield an image stack of the 3-dimensionally preserved fossil. Image copyright Science Magazine.

It was obvious right away that this was something very special. It clearly impacted my own work on ostracod eye evolution. This marked the oldest ostracod compound eye in the fossil record, pushing back the date some 200 million years. In 2002, I published a molecular phylogeny of ostracods that shows that ostracods with lateral compound eyes are nested phylogenetically within multiple groups that lack lateral eyes. One possible interpretation of this is that lateral eyes evolved within Ostracoda (of course eyes don't evolve from nothing, so if this idea is true, many of the genes used in all animal eyes should still be present in the ostracod lateral eyes). Colymbosathon doesn't itself change these conclusions because it is a member of the same group (myodocopids) that today have lateral eyes. Nevertheless, the Colymbosathon fossil pushes back the origin of ostracod compound eyes quite a bit.

Of course not many other people cared about the eyes. They had other things on their mind. In particular, many journalists really rose to the occasion, devising many very entertaining headlines. Some of my favorites are below, and I've taken the liberty to put them into a few categories.

1. The "size matters" category
  • Scientists Discover Ancient Gargantuan Penis
  • Sea creature impressive in its maleness
  • Well-endowed sea creature is nearly half a billion years old
  • He's 425 million years old and clearly virile
  • Male fossil makes a big impression

2. The "age before beauty" category

  • Ancient penis brings fame to lowly fossil
  • Oldest male fossil bares all
  • World's oldest genitals found in Scotland
3. Wonderful alliteration category
  • Phallic fossil found

4. And last but not least, the winkle category, a clipping of which hangs in the lab

  • Fossilised shrimp has the oldest winkle in the world