Wednesday, October 29, 2008

New Blog

I've noticed that a former student who worked in our lab has started a blog called Pleion. Bjørn enjoys discussing evolution and politics, cannibalism, and teasing Americans for not being able to pronounce "Bjørn Østman". He was made for blogging because he likes to be provocative. If you do go over there, ignore the post on predictions for Obama's first term, or else you'll get the wrong idea about him. If you do read that post, make sure to click on the links [English] to help clarify the sarcasm.

Monday, October 27, 2008

You can pick your friends - etc

When I give presentations, I always try to have a joke prepared in case of technical difficulties. This came in handy when I gave a symposium talk a few years back at Chico State, at the Botany meetings (long story, I'm no botanist... not that there's anything WRONG with being a botanist). The talks were delivered on a large stage, so my joke was that if the slides went out ... which they did temporarily... I'd offer to use the stage to do an interpretive dance of my research presentation. I got a pretty good laugh, pretending like it was completely spontaneous.

Little did I know that interpretive dance is such a powerful medium for scientific communication. Check gonzo scientist for the contest here.

And a plug for my colleague Wendy Grus. I first met Wendy at the evolution meetings in Alaska a few years back, and I took notice of her research on receptors expressed in the vomeronasal organs of vertebrates. She didn't dance in Alaska - at least not that I know of. But she does have an interpretive dance of her PhD work up on YouTube for the contest. She uses sparkly gene phylogenies to reel in odorants. Pay her video a visit - she could win a trip to Chicago, and professional choreography service:

Wendy is quite multi-talented. Check out the music video to her smash hit new single, Seminarcolepsy:

Thursday, October 23, 2008

Optical Allusions Book Review

As mentioned at The Loom, and Genomicron, there is a new issue of Evolution, Education and Outreach available, devoted to my favorite topic, the evolution of eyes. I've contributed two pieces, one is available now, and is a book review of Optical Allusions, by Jay Hosler.

Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley

The other paper I contributed is inspired in part by Behe's claim of irreducible complexity of phototransduction in Darwin's Black Box. That paper is not available yet, but should be soon. For a small taste of the paper, I will quote from the it:

"Unfortunately, instead of pointing to the molecular evolution of multi-component systems as a rich area for new scientific research and synthesis, Behe chose to commit scientific suicide by incorrectly claiming that the only way for multi-step biochemistry to arise is by intelligent design."

Monday, October 20, 2008

Phylogeny, evolution, biodiversity and ecology

We are in the midst of massive upheaval in the world’s ecosystems, driven by species invasions and the sixth mass extinction in Earth’s history. How will these changes in biodiversity affect the functions of ecological communities? Will the functions of ecological systems that humans rely on for survival, such as production of oxygen, be impacted by all this upheaval?

Answering these questions requires that biologists have a good metric for biodiversity. New research by Marc Cadotte, Brad Cardinale and I, and published this week in Proceedings of the National Academy of Sciences, indicates that one particular metric of biodiversity - evolutionary diversity - is a particularly strong predictor of the biomass produced in plant communities: The more biodiversity present (measured as evolutionary diversity), the more productive the community. In fact, for the datasets we examined, evolutionary diversity was a better predictor of productivity than raw species number or number of functional groups in the community. This suggests that the most evolutionarily diverse communities may function best, and that the most evolutionarily distinct species might be the best targets of conservation efforts aimed at maximizing ecosystem productivity.

Measuring Biodiversity
One common theme in current ecological research is to ask questions about how changes in biodiversity impact or influence ecological systems or communities. This has obvious importance when we know that many species are going extinct, and that many species are being shipped around the world by human transportation. Often in ecological research, a measure of biodiversity is placed on the X-axis, and some predicted response is placed on the Y-axis, to test if there is a strong relationship. For example, one might predict that less diverse and simpler communities are more susceptible to invasive species compared to more diverse and complex communities. One might also predict that more ecological diversity leads to a healthier ecosystem, as measured by higher production. Namely, a higher diversity of organisms could make more efficient or more complete use of available resources, ultimately leading to a healthier, better functioning ecosystem.

These types of ecological studies usually use a measure of biodiversity referred to as “species richness” as the X-axis variable. “Species richness” is simply a count of the number of species. However, simply counting species makes the assumption that, say, two very closely related grass species contribute the same amount to the diversity measure as two much more distantly related species, such as a grass and a magnolia. In contrast to this implicit assumption of “species richness”, phylogeneticists often think of biodiversity in terms of evolutionary relationships, assuming that differences between species (one way to conceive of diversity) accumulate over the time since they last shared a common ancestor. To a phylogeneticist then, species that share a very recent common ancestor – like the two similar grasses mentioned above – should be nearly identical and therefore represent less total diversity compared to the much more distantly related grass and magnolia species.

We wondered if evolutionary diversity really does matter for predicting how much biomass a community produces, one measure of the health of ecological communities. Decades of experiments have already established that species number (“species richness”) is in fact correlated with productivity – the more species of plants growing together, the more biomass is produced. We extended these studies, weighing different species by how closely related they are evolutionarily. Could we better predict biomass production by also accounting for evolutionary (phylogenetic) diversity? Based on our analyses, the answer was a clear “yes”. Incorporating evolutionary distances into our biodiversity metric resulted in better predictive power of the productiveness of experimental plant communities. The metric including evolutionary history was better than “species richness” and better than the number of functional plant groups, two commonly used metrics of biodiversity.

Our data set was a collection of 40 different previously published experimental studies, conducted around the world using a total of 177 different species of flowering plants. Researchers planted experimental ecological communities, using many different combinations of plant species, and using different numbers of species. Then they let the communities grow, and measured the biomass produced by the different combinations. We added an analysis of the phylogenetic relationships of the plants using publicly available genetic data from four different genes commonly used in other studies of plant phylogeny.

Phylogenetics and Nihilism

Do all ecologists now need to become phylogeneticists? This question is similar to one asked of comparative biologists in the mid 1980’s.

In 1985, Joe Felsenstein wrote a landmark paper introducing the method of phylogenetic independent contrasts, which is now standard in comparative biology. The core message is that we cannot treat species as independent entities because they share a nested set of common ancestors. In other words, species are similar because of descent, not only because of adaptations, and traits might be correlated across species because of shared evolutionary history. At that time, comparative biologists were told they must consider phylogeny when testing for correlations among traits. Felsenstein addressed the question, “What if we do not take phylogeny into consideration [in comparative biology]?” His answer:

“Some reviewers of this paper felt that the message was “rather nihilistic,” and suggested that it would be much improved if I could present a simple and robust method that obviated the need to have an accurate knowledge of the phylogeny. I entirely sympathize, but do not have a method that solves the problem…. Comparative biologists may understandably feel frustrated upon being told that they need to know the phylogenies of their groups in detail, when this is not something that they had much interest in knowing. Nevertheless, efforts to cope with the effects of the phylogeny will have to be made. Phylogenies are fundamental to comparative biology; there is no doing it without taking them into account.”
-Felsenstein (1985)

Although other systems and other questions might differ from our study in how diversity relates to ecological processes, it seems to me that counting species is far too simplistic of a metric of biodiversity. If adding phylogenetic information was valuable in one case, it seems worthy of strong consideration any time a metric of diversity is below the X-axis in a graph. To paraphrase Joe, ecologists may understandably feel frustrated upon being told that they need to know the phylogenies of their groups in detail, when this is not something that they had much interest in knowing. Nevertheless, the evolutionary history of their focal communities or systems will often have a lot to tell them. Species are not independent entities, and biodiversity cannot be measured as if they were.

M. W. Cadotte, B. J. Cardinale, T. H. Oakley (2008). Evolutionary history and the effect of biodiversity on plant productivity Proceedings of the National Academy of Sciences, 105 (44), 17012-17017 DOI: 10.1073/pnas.0805962105

Wednesday, October 15, 2008

Tawk Amongst Yah-selves

Anyone seen an old SNL skit called Cawfee Tawk, where Mike Myers, dressed as a women, hosted a talk show? Every once in a while s/he became vaclempt, and would throw out a topic to discuss. Tawk amongst yah-selves s/he would say, before collecting him/herself.

I keep a few topics for discussion in mind, for different situations (not directly from SNL, those were much funnier than my bio-geek stuff). Still, they are quite useful for breaking out of one of those awkward silences that can occur when a group of semi-strangers is talking together. I'll throw one out at a conference or at a bar, and think "Tawk amongst yah-selves". I usually like to sit back and listen, whether vaclempt or not.

If I am with a group of physiologists or evolutionists, I throw out this one:

Why has bioluminescence evolved SO many times in the marine environment, but almost never in freshwater environments?

Or, if you're more interested in one for a bar that includes someone other than a biologist -

Why are all the best rock bands British, but all the best individuals of rock n roll American?

Friday, October 10, 2008

A joke creationists don't get

My daughter told me a joke just the other day with two alternative punchlines, neither of which any young-earth creationist would understand:

1. Why did T. rex cross the road?

Answers in the comments

Wednesday, October 8, 2008

Ostra-blog 6 - Ostracodology and the Nobel Prize

Dagummit! I've been scooped again by the guys at the other 95% by this post: The Other 95%: The Nobel Jelly - Aequorea victoria . They point out that one of the winners of this year's Nobel Prize for chemistry is marine biologist, chemist, and one time ostracodologist, Osamu Shimomura. [By the way, I didn't invent the word ostracodologist - we actually use that to describe ourselves].

Early in his career, Shimomura studied bioluminescence in Vargula hilgendorfii (he called it Cypridina hilgendorfii, which is a synonym for Vargula hilgendorfii. Vargula is usually used today, the taxonomy is a bit complicated, and I won't go into it here). After that, Shimomura went to work on the jellyfish Aequorea and its bioluminescence. It turns out that Aequorea produces light with a protein called aequorin, which sends light to another protein (Green Flourescent Protein=GFP) that emits green fluorescence. GFP is today used in all sorts of applications, as Eric at TO95% nicely explained.

There also is one more connection between GFP and ostracodology. An ostracodologist actually named GFP (Morin and Hastings, 1971)! Jim Morin is a prominent ostracodologist, who, with Anne Cohen has described, in often exquisite detail, the biology of bioluminescent ostracods from the Caribbean. In my talks on ostracods, I often use a slide based on their work:

Fig 1. Small blue circles represent discrete flashes of light produced by male bioluminescent cypridinid ostracods. Patterns of different species are illustrated, with white arrows showing the direction of swimming of an individual animal producing the pattern over time. Each pattern is characteristic of a different species and are performed above different microhabitats. Original figure in black and white line drawing by Jim Morin and Anne Cohen. Color and photos added by T. Oakley.

Male ostracods of this family signal to females using flashes of light in rather complex species-specific patterns, often over sterotyped microhabitats. These Caribbean species are related to Vargula hilgendorfii (ostrablog 5), which does not signal. In the Caribbean species, there are even "sneaker males", males that follow a signalling male, without using the energy to signal themselves, in an attempt to mate with females attracted to those signals. I guess in bars, humans call this something like a "wing man".

I think this is a great example of how solid basic research will often lead to great advances. Shimomura was interested in bioluminescence because of pure scientific curiosity. I doubt he was aiming for a Nobel. The general public often does not understand this. In the 1970's, I'm sure some people wondered why anyone would want to spend enormous time and energy studying a glowing protein of a jellyfish. But that scientific curiosity has now paid big dividends!

Tuesday, October 7, 2008

Fallen Giants

In the 1880's loggers felled many ancient and giant sequoia trees in an area that is now in King's Canyon National Park. The wood from these majestic trees is brittle, and mostly wasted when the trees would shatter upon impacting the ground. The 50% or so of the timber that did make it to the mills was probably used for shingles, fence posts, or matchsticks. High tannin levels make sequoia wood resistant to decay, so remnants of the fallen giants remain to this day. I visited Big Stump Grove on Saturday while clouds shrouded the tops of the living trees and drips of rain fell from the skies. Giant blackened stumps were like ghosts and piles of sawdust like blood stains.

(These pictures were snapped from my little Mino Flip Video camera because I forgot to take my still camera. I like this little video camera more and more, the more I use it.)