As 2008 winds down, I thought I would look back at Evolutionary Novelties and pick some of my favorite posts of the year.
The major theme of this blog is to explore how it's possible that all life has a common origin and still has diversified into the riotous diversity/complexity/disparity that we see today. New features evolve through duplication and recombination (at all levels of biological organization).
1. Box Jellies and the Red Herring of Eye Evolution is one of my favorite posts. The main thesis is that people always ask an inappropriate question "how many times did eyes evolve?". I'd thought about this idea for quite a while, and when a paper came out in PNAS that re-inforced my thesis, I incorporated the new research into the idea.
2. Coming to grips with common descent discusses the idea that during the history of evolution, people have tended to forget that everything evolves from something else. This was not conceived as a blog post, but as a chapter of a book I've toyed around with writing. In some ways, blogging satisfies my urge to write a book, so the book probably won't happen for a long time.
3. Gould: Pluralism by Monism My thesis that Gould was practicing pluralism by taking an opposing stance to the whole field of evolutionary biology. This is perhaps my favorite post of 2008 because I've never seen anyone else with this idea, and the more I think about it the more I think it explains a lot, a general theory of Gould, if you will.
The above are posts that present an idea I've had. I've also recently been writing a few posts on others' research. I find that writing about the work helps me internalize and understand the work. I'm not a rocket-science journalist, but some of the posts have been okay, I think:
4. Evolutionary Novelty: Photosynthetic Slug
5. Evolutionary Novelty: Hair
I also have a series of posts about ostracods, my ostrablogs. I haven't had time to do these for a while, but I do have one half written, so more are coming. My favorites are probably:
6. Ostrablog 5 - Three shows and a funeral retells a story that I've told many, many times in person.
7. Ostrablog 3 - How we discovered chupacabra tells about our discovery of a new ostracod species.
8. Ostra-blog 2 - to e or not to e Ostracod or ostracode?
But much of what I do is promotion of my research and papers, or posting drafts of things I'm writing:
9. Phylogeny, evolution, biodiversity and ecology discusses some research recently published in PNAS. I also noticed this was featured at NESCENT.
10. Opsins: An amazing evolutionary convergence. Slightly expanded from part of an encyclopedia article I was asked to write.
Those are 10 of my favorites from this year. Happy New Year!!
Wednesday, December 31, 2008
Tuesday, December 30, 2008
Two New Blogs
Greetings from the frozen tundra. I've been in Milwaukee catching up with family and friends during the holidays. Visiting has been a full time job, and I've been online very little, but 2 new blogs have come to my attention, both by colleagues of mine:
First is "A Fish Eye View"
Next is "The EEB and Flow":
First is "A Fish Eye View"
Next is "The EEB and Flow":
Friday, December 19, 2008
Opsins: An amazing evolutionary convergence
How predictable is evolution? If we could travel back in time 4 billion years and make a few changes, what would remain the same upon our return? This is an enduring topic of evolutionary inquiry (and movies and sci-fi shorts for that matter).
In his book Life's Solution, Conway-Morris made the case for a semblance of predictability in evolution. He argued that convergence - the independent origin of similar traits - represents an element of predictability in evolution. Octopus and humans have outwardly similar eye designs, so if we reply animal history over and over, these camera-type eyes would likely evolve in most replays.
Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!
If we could go back a few billion years and replay the evolution of life on earth a few times, chances are, opsins would evolve in many of our replicates.
[Disclaimer - the following is text from an encyclopedia article I've been asked to write on opsin evolution, so the writing style is a bit terse from here on out. I will add a little bit though, specially for the blog. But since many people I know think opsin originated only once, I feel it's my duty to spread the word of opsin convergence, starting here, at Evolutionary Novelties].
What is opsin and rhodopsin?
Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis. Opsins are sometimes called retinylidene proteins because they bind to a light-activated, non-protein chromophore called retinal (retinaldehyde). Opsins are also in some cases called “rhodopsins”, a name originally given to isolated visual pigments that contained both opsin protein and non-protein chromophore in a time before the two separate components were known. Today, the term “Rhodopsin” is used commonly to describe the opsin expressed in vertebrate rod (dim-light) photoreceptors, and the opsins of certain organismal groups, like bacteria. All opsin proteins are embedded in cell membranes, crossing the membrane seven times.
Type I and Type II opsins
Two major classes of opsins are defined and differentiated based on primary protein sequence, chromophore chemistry, and signal transduction mechanisms. Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.
Type I opsins are present in bacteria and algae and are referred to by various names, including bacteriorhodopsin, bacterial sensory rhodopsins, channelrhodopsin, halorhodopsin, and proteorhodopsin. Type I opsins have varied function, including bacterial photosynthesis (bacteriorhodopsin), which is mediated by pumping protons into the cell, and phototaxis (channelrhodopsin), which is mediated by depolarizing the cell membrane. Type II opsins are present in eumetazoans (animals not including sponges), but are unknown from sponges or any non-animals. Because opsins are known from cnidarians and bilaterian animals (animals with bilateral symmetry, including humans, flies, and earthworms), Type II opsins are inferred to have been present in their common ancestor, which lived about 600 million years ago. Type II opsins have varied function, including phototransduction and vision, circadian rhythm entrainment, mediating papillary light reflex (pupil constriction), and photoisomerization (recycling the chromophore).
Despite their functional similarity and despite both being 7-transmembrane proteins, multiple lines of evidence indicate that Type I and Type II opsins evolved independently. First, the primary amino acid sequences of Type I and Type II opsins are no more similar than expected by chance. For example, try to align a Type I (say bacteriorhodopsin) and Type II opsin together. I just tried this with blastalign, with the following result:
Exhibit A. Blast search find "no significant similarity" of the amino acid sequences.
Sequence 1: gi|163443|rhodopsin
Length = 348
Sequence 2: gi|208055|bacteriorhodopsin >gi|208057|gb|AAA72603.1| bacteriorhodopsin
Length = 249
No significant similarity was found
CPU time: 0.04 user secs. 0.02 sys. secs 0.06 total secs.
Second, the orientation of the transmembrane domains differs between the major groups. We now have crystal structure data for both Type I and Type II opsins, and the arrangements of the parts of the protein that are stuck in the cell membrane are quite different, inconsistent with a single origin of opsins (unless this changed a lot during evolution, which is not impossible).
Exhibit B. Type I on the left, Type 2 on the right. Denser lines are positions of transmembrane domains. Figure is from Spudich et al (2000)
Third, the major opsin groups differ in chromophore chemistry. Prior to light activation, the chromophore of Type I opsins is an all-trans isomer. Light activation then involves isomerization of the chromophore to 13-cis retinal. In contrast, prior to light activation, the chromophore of type II opsins is 11-cis retinal. Light activation of Type II opsins involves isomerization to all-trans retinal.
Exhibit C. Type I on the left, Type 2 on the right. Chromophore chemistry differs. Figure is from Spudich et al (2000)
Fourth, Type II opsins belong to the larger protein family called G-protein coupled receptors (GPCRs), which transmit varied signals from outside to inside cells by activating GTPase proteins, which in turn signal to second messengers that affect the state of the cell in various ways. Type I opsins do not activate G-proteins. Furthermore, Type II opsins are more closely related to non-opsin, light insenstive GPCR’s than they are to Type I opsins. So even if there is some very, very distant and *undetectable* common origin of Type I and Type II opsins, chromophore binding likely evolved twice. Since chromophore binding is what allows photosensitivity, it is the crux of being an opsin (but see), and the realization that Type II opsins are closer to non-opsin GPCR's than Type I opsins is strong support for two separate origins.
Exhibit D. (Dashed lines mean no sequence similarity beyond random. Light bulbs mean origin of chromophore binding=light sensitivity=opsin.)
Finally, with two CS students, I tested the single origin hypothesis in a different way and found no support. Type I opsins show similarity of membrane domains 1-2-3 and 5-6-7, consistent with an origin by duplicating a 3-domain protein (and adding one). However, Type II opsins show no such similarity. If they Type I and Type II share a single origin, the duplication pattern of the domains should be shared too (unless there were drastically different rates of evolution in the 2 lineages, which is not impossible). This work is described here: Larusso et al (2008) J Mol Ev.
John L. Spudich, Chii-Shen Yang, Kwang-Hwan Jung, Elena N. Spudich (2000). RETINYLIDENE PROTEINS: Structures and Functions from Archaea to Humans Annual Review of Cell and Developmental Biology, 16 (1), 365-392 DOI: 10.1146/annurev.cellbio.16.1.365
Wednesday, December 10, 2008
Exaptation! PT flare up #2
Continuing on with my thoughts about the flare up at Panda's Thumb (part 1 here):
Basically, I think "Green" the anonymous undergrad from a University in the UK, raised a few valid issues that are worth thinking about. A lot of the evolutionists, while I agree with their points on general terms, are not addressing the concern of "Green" directly.
Her main point is (from the comments at Panda's Thumb):
This is in part true, and raises the point that we should be discussing EXAPTATION and not co-option, to most clearly convey the point.
Green is stating that even if all the components of phototransduction are present an ancestral genome that lacks phototransduction, multiple mutations would be required to assemble all those components into a phototransduction cascade. So, multiple co-option events would be required, and this is what she is having a problem with.
HOWEVER, what is false is the requirement for all these mutations to occur simultaneously. Instead, the components could be assembled one by one in a graduated, step-wise (Darwinian) fashion.
Instead of focusing on co-option, Green should focus on "exaptation". Exaptation is the idea (roughly) that features can arise for one function, and then change function later on. In the case of phototransduction, much of the phototransduction cascade originated for another purpose - sensing some signal from outside the cell to elicit changes inside the cell. (And just because a yeast pheromone cascade isn't THE phototransduction precursor, doesn't mean there wasn't one). One response to a signal evolves, changing the signal that is detected (to light) seems pretty surmountable. In fact, this has happened independently in the lineage leading to C. elegans (see my post here).
For another example of exaptation, we've found that many components used in synapses predate synapses themselves. See these posts in pharyngula, Newsweek. The open access paper and other news sites (including radio interview) are here.
Basically, I think "Green" the anonymous undergrad from a University in the UK, raised a few valid issues that are worth thinking about. A lot of the evolutionists, while I agree with their points on general terms, are not addressing the concern of "Green" directly.
Her main point is (from the comments at Panda's Thumb):
“Co-option may not be the de novo formation of genes, but it still requires mutations (such as, for example, the gain of a cis regulatory region). My whole point was that simultaneous mutations are required for the evolution of the phototransduction cascade. Correct me if I’m wrong, …”
This is in part true, and raises the point that we should be discussing EXAPTATION and not co-option, to most clearly convey the point.
Green is stating that even if all the components of phototransduction are present an ancestral genome that lacks phototransduction, multiple mutations would be required to assemble all those components into a phototransduction cascade. So, multiple co-option events would be required, and this is what she is having a problem with.
HOWEVER, what is false is the requirement for all these mutations to occur simultaneously. Instead, the components could be assembled one by one in a graduated, step-wise (Darwinian) fashion.
Instead of focusing on co-option, Green should focus on "exaptation". Exaptation is the idea (roughly) that features can arise for one function, and then change function later on. In the case of phototransduction, much of the phototransduction cascade originated for another purpose - sensing some signal from outside the cell to elicit changes inside the cell. (And just because a yeast pheromone cascade isn't THE phototransduction precursor, doesn't mean there wasn't one). One response to a signal evolves, changing the signal that is detected (to light) seems pretty surmountable. In fact, this has happened independently in the lineage leading to C. elegans (see my post here).
For another example of exaptation, we've found that many components used in synapses predate synapses themselves. See these posts in pharyngula, Newsweek. The open access paper and other news sites (including radio interview) are here.
Tuesday, December 9, 2008
PT eye evolution flare up
I was notified that there was a little flare up at Panda's Thumb about our recent article on eye evolution, entitled:
Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF) published in Evolution: Education and Outreach.
Warning: Long Post. If you only read one thing, read this:
Here is the story:
A week or two ago, I was contacted by an undergraduate from a university in the UK (I see no reason to reveal her name). She had questions about the article, writing:
Unfortunately, she misinterpreted this email, understanding it to mean (written over at PT, using the pseudonym "Green"):
First of all, this is an incorrect interpretation of what I wrote. In fact, I wrote "So, I think all that is similar is the GPCR and G-protein." This is far from "not homologous in any way", as claimed by the student. The G-protein is undeniably homologous, and the yeast pheromone receptor is a 7-transmembrane protein, at least conformationally like opsin (whether or not the opsin and pheromone receptor sequences are homologous is a trickier issue).
But the larger issue is I think an issue of "linear thinking", which I address quite often on this blog. The student seems to think that if we cannot identify in yeast (taken as a linear ancestor of animals) a cascade identical to phototransduction except for opsin, then the origin of phototransduction requires numerous simultaneous mutations. This is not the case. First of all, yeast is a more distant relative of animals with phototransduction than is sponges. I just mentioned the yeast pheromone photoreceptor in the paper as a well studied example of a pathway outside of animals with partial homology (some components homologous, some not) to photoreception. There are closer "relatives" of phototransduction in sponges (poorly studied functionally, but the genes are known) and in other animals (better studied).
Another issue is a difficulty that people have with thinking about partial homology - that some components can be homologous and some not, depending on the time scale of the comparison (see my post The Red Herring of Eye Evolution).
Partial homology is a pattern that indicates a mechanism of co-option in the evolution of features. Co-option is the combination of existing things in a new way (analogy: dijonaisse = dijon mustard plus mayonaisse). All of the components of phototransduction pre-date animals, except opsin. And if we consider opsin to be a GPCR, which it is, then all of the components of phototransduction pre-date animals. This may be considered a pattern of co-option, or exaptation. Signaling pathways were already present before phototransduction. Some of the phototransduction components function together as far back as the yeast + human common ancestor (GPCR + G-protein). Other components of phototransdcution function together in non-phototransduction cascades of other animals. This indicates that phototransduction did not assemble all at once, but built incrementally upon an existing scaffold.
One might argue that we are just pushing back the origins, changing the question of "phototransduction" origin to the question "transduction" origins. In a way this is true, but it is also a fundamental insight about how evolution works. New features are not breathed into organisms by some unknown force, they evolve by duplication/divergence or recombination of existing features. Trace a feature like phototransduction back far enough in evolutionary time, and it grades into something else, component by component.
There were other comments, too. Again at PT, she also commented:
This is also a "God in the Gaps" argument, or maybe, a "God under the surface" argument, stating that describing the origin of the keystone molecule of phototransduction (opsin) "only scratches the surface".
Also, I don't understand what the difference is between "comparisons of genes" and "biochemical explanation". What would a biochemical explanation be for the evolutionary origins of things that doesn't involve "comparisons of genes". The genes of the phototransduction pathway have biochemical interactions with each other, many mediated by interactions between specific amino acids.
Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF) published in Evolution: Education and Outreach.
Warning: Long Post. If you only read one thing, read this:
One might argue that we are just pushing back the origins, changing the question of "phototransduction" origin to the question of "transduction" origins. In a way this is true, but it is also a fundamental insight about how evolution works. New features are not breathed into organisms by some unknown force, they evolve by duplication/divergence or recombination of existing features. Trace a feature like phototransduction back far enough in evolutionary time, component by component, and it grades into something else altogether.
Here is the story:
A week or two ago, I was contacted by an undergraduate from a university in the UK (I see no reason to reveal her name). She had questions about the article, writing:
I've just been reading your 2008 paper 'Opening the Black Box: the genetic and biochemical basis of eye evolution' and found it really interesting! I'm just writing an essay on eye evolution atm and am trying to get to the crux of the issue, and find out how the phototransduction cascade itself evolved. After explaining that opsin probably arose by a mutation in a serpentine gene/protein, you mention in your paper that:
"In yeast...these receptors [GPCR's - the serpentine proteins] are sensitive to pheremones, and they even direct a signal through proteins homologous to non-opsin phototransduction proteins."
What I'm wondering is, is it this whole yeast pathway that has been modified for the metazoan phototransduction cascade? Or is it only the opsin which has been derived from it? (With the subsequent molecules involved in the phototransduction cascade being co-opted from other proteins not involved in the yeast signalling pathway).Thanks for you questions. I found out after writing the paper thatthe yeast pheromone proteins are not the "rhodopsin type" GPCR, sothey are distantly related at best to opsins. So they should not beconsidered anything like direct ancestors of opsin.
As for other components of the yeast pheromone cascade, these aredifferent than phototransduction. Yeast pheromones activate a MAPkinase cascade. So, I think all that is similar is the GPCR andG-protein.So, it really is an open question as to what the ancestral functionwas of some of the genes of phototransduction, although some of thesegenes do function in other sensory transduction pathways...Unfortunately, she misinterpreted this email, understanding it to mean (written over at PT, using the pseudonym "Green"):
But the larger issue is I think an issue of "linear thinking", which I address quite often on this blog. The student seems to think that if we cannot identify in yeast (taken as a linear ancestor of animals) a cascade identical to phototransduction except for opsin, then the origin of phototransduction requires numerous simultaneous mutations. This is not the case. First of all, yeast is a more distant relative of animals with phototransduction than is sponges. I just mentioned the yeast pheromone photoreceptor in the paper as a well studied example of a pathway outside of animals with partial homology (some components homologous, some not) to photoreception. There are closer "relatives" of phototransduction in sponges (poorly studied functionally, but the genes are known) and in other animals (better studied).
Another issue is a difficulty that people have with thinking about partial homology - that some components can be homologous and some not, depending on the time scale of the comparison (see my post The Red Herring of Eye Evolution).
Partial homology is a pattern that indicates a mechanism of co-option in the evolution of features. Co-option is the combination of existing things in a new way (analogy: dijonaisse = dijon mustard plus mayonaisse). All of the components of phototransduction pre-date animals, except opsin. And if we consider opsin to be a GPCR, which it is, then all of the components of phototransduction pre-date animals. This may be considered a pattern of co-option, or exaptation. Signaling pathways were already present before phototransduction. Some of the phototransduction components function together as far back as the yeast + human common ancestor (GPCR + G-protein). Other components of phototransdcution function together in non-phototransduction cascades of other animals. This indicates that phototransduction did not assemble all at once, but built incrementally upon an existing scaffold.
One might argue that we are just pushing back the origins, changing the question of "phototransduction" origin to the question "transduction" origins. In a way this is true, but it is also a fundamental insight about how evolution works. New features are not breathed into organisms by some unknown force, they evolve by duplication/divergence or recombination of existing features. Trace a feature like phototransduction back far enough in evolutionary time, and it grades into something else, component by component.
There were other comments, too. Again at PT, she also commented:
The difficulty with this comment is that the origin of opsin defines the origin of phototransduction. The other components of the cascade were already there, they all predate opsin, as described above.Yeah I read Oakley and Gregory’s articles on eye evolution a couple of weeks ago. Unfortuantely neither address the crux of the issue: namely the origin of the biochemical phototransduction cascade.
To be fair, Oakley’s article (the ‘Black Box’ one) at least tries to give some biochemical details. But it only scratches the surface by suggesting a potential origin of the opsin protein. Unfortunately the origin of a new opsin protein is not equivalent to the origin of an entire phototransduction cascade.
So it seems the Darwinian account still falls quite far short of any satisfactory biochemical explanation. Descriptions of morphological change, comparisons of genes, crystallins, etc. all skirt the issue if it cannot be shown how the phototransduction cascade itself arose
This is also a "God in the Gaps" argument, or maybe, a "God under the surface" argument, stating that describing the origin of the keystone molecule of phototransduction (opsin) "only scratches the surface".
Also, I don't understand what the difference is between "comparisons of genes" and "biochemical explanation". What would a biochemical explanation be for the evolutionary origins of things that doesn't involve "comparisons of genes". The genes of the phototransduction pathway have biochemical interactions with each other, many mediated by interactions between specific amino acids.
Monday, December 8, 2008
Eye evolution issue printed
The new issue of Evolution education and outreach has been printed, and the issue is all about eye evolution. The links to all the articles are below, they are available free of charge.
Evolution: Education and Outreach
Volume 1 Issue 4
Editorial
351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)
352-354. Introduction by T. Ryan Gregory (PDF)
355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)
Original science / evolution reviews
358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)
390-402. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)
403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)
415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)
427-438. Early Evolution of the Vertebrate Eye--Fossil Evidence by Gavin C. Young (PDF)
439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)
448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)
463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)
476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)
487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)
493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)
Curriculum articles
498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)
505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)
509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)
Book reviews
548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)
Evolution: Education and Outreach
Volume 1 Issue 4
Editorial
351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)
352-354. Introduction by T. Ryan Gregory (PDF)
355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)
Original science / evolution reviews
358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)
390-402. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)
403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)
415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)
427-438. Early Evolution of the Vertebrate Eye--Fossil Evidence by Gavin C. Young (PDF)
439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)
448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)
463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)
476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)
487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)
493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)
Curriculum articles
498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)
505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)
509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)
Book reviews
548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)
Friday, November 28, 2008
Online Lecture
I've been shopping around trying to find a fairly easy way to combine audio with PowerPoint slides to post lectures online. I tried some movie-editing software, but that had some problems. Then I saw that Carl Zimmer over at The Loom used a piece of software called Soundslides. I thought I'd try Soundslides with a lecture I delivered recently.
(The lecture was to help inaugurate a new organization at UCSB called SUB - Society for Undergraduate Biologists. I was asked to speak about undergraduate research. I chose to talk about "paths to undergraduate research"; my own path, the path of one undergraduate from my lab, and the path that others might take to undergraduate research.)
I concur with Carl's comments that Soundslides is mostly nice, but determining the timing for when the slides change is a bit of a hassle. The quality of the slides ends up to be very high, because it uses jpeg graphics within Macromedia Flash, I gather. Other methods make a movie, and the graphics don't come across as well, or they take much more memory. Anyway, I post the result from soundslides below, which took me a few hours to complete. There is one more program I want to try that was recommended to me, I will try to post comparisons here, in case anyone is interested. After that, I want to buy the program I like best and then get many of my lectures from my Macroevolution course online, including lectures on the basics of phylogeny reconstruction. Then I just point students to the online lectures, retire from teaching, and focus on research (wink)...
(The lecture was to help inaugurate a new organization at UCSB called SUB - Society for Undergraduate Biologists. I was asked to speak about undergraduate research. I chose to talk about "paths to undergraduate research"; my own path, the path of one undergraduate from my lab, and the path that others might take to undergraduate research.)
I concur with Carl's comments that Soundslides is mostly nice, but determining the timing for when the slides change is a bit of a hassle. The quality of the slides ends up to be very high, because it uses jpeg graphics within Macromedia Flash, I gather. Other methods make a movie, and the graphics don't come across as well, or they take much more memory. Anyway, I post the result from soundslides below, which took me a few hours to complete. There is one more program I want to try that was recommended to me, I will try to post comparisons here, in case anyone is interested. After that, I want to buy the program I like best and then get many of my lectures from my Macroevolution course online, including lectures on the basics of phylogeny reconstruction. Then I just point students to the online lectures, retire from teaching, and focus on research (wink)...
Monday, November 24, 2008
How Complexity Evolves
[Slightly altered excerpt from an invited review on the evolution of (nervous system) complexity]
The evolution of complexity is an enduring and fundamental topic in biology. Recent research is allowing new insights into the origins of complexity. Namely, scientists now have access to the components of complex structures, and their evolutionary histories. "The eye" is no longer an anonymous collection of components - Darwin may have known an eye is composed of lens retina and nerve - but he did not know what lenses or retinas were composed of, nor did he know in much detail how they functioned. We now know many of the protein components of structures like eyes and how they function, and we know that these components have evolutionary histories. Since biological entities from genes to ecosystems arise from existing entities, general patterns emerge as to where those entities came from. They either duplicate/diverge; split/diverge; or fuse in new combinations.
What is biological complexity?
Numerous definitions have been suggested for biological complexity, from mathematical and information theoretic formulas [2,3] to intuitive definitions, such as the numbers of parts or components that can be counted in a system [4,5]. In practice, a researcher’s choice of definition for complexity often boils down to his ability to measure it. In investigator-defined computer simulations [2] or circumscribed biological systems [3], information theoretic definitions using explicit mathematical formulas are tractable. However, in extensive biological systems, especially those that encompass multiple levels of biological organization with varied properties, the relationship between structure and function (e.g. genotype and phenotype) is often largely unknown, and may itself be complicated and variable. These unknowns complicate the formulation of explicit, yet general, mathematical definitions of complexity for extensive biological systems. Instead, some have argued that counting the numbers of parts of a system is an appropriate measure of complexity [4]. Although often focused on structural units, such as cell types, genes, or species, and not on the functions of those units, McShea [5] has also argued that counting structural parts should often be a good estimate of functional complexity.
Herein, we follow previous authors [4,5] and define more complex systems as those that have more parts. “Part” is used as a term that spans levels of biological organization [4]. Species are parts of ecological communities. Organs (like brains or ganglia) are parts of species. Cell types (like neuronal types) are parts of organs and of species. Proteins are parts of cells and of networks, and domains and amino acids are parts of proteins. Many other biological units are also parts [6]. For the current discussion, we are concerned less with defining or counting parts, and concerned more with how new parts originate during evolution. According to the definition of complexity that we employ, new parts (that do not come at the expense of existing parts) increase biological complexity. Therefore, those mechanisms that cause the evolution of new parts are of particular interest because those are the mechanisms that cause increases in biology complexity.
General patterns of increased complexity
By definition, complex systems have many parts, and the histories of those parts are varied. As such, we cannot expect a simple, one dimensional answer to the question of how complexity evolved. Nevertheless, at all levels of biological organization, conceptually similar patterns (Figure 1) have resulted from a varied array of mechanisms that historically increased complexity.
Figure 1 - Generalized patterns of increased biological complexity. The top of the figure represents an ancestral state, the bottom a descendant state. Shapes represent “parts”, a generic term for a biological feature at any level of organization. Parts can be species, genes, protein domains, pathways, brain regions, and many other biological units [see 6]. A. Copying and divergence B. Fission and divergence C. Copying and fusion. Without copying or fission, complexity does not increase because divergence (or fusion) maintains the same number of parts. Without differential divergence or fusion of parts, complexity only increases marginally.
First, parts may exhibit a pattern consistent with differential divergence of copied elements (Fig. 1a). A prime example of a specific mechanism leading to this pattern is gene duplication plus divergence. Duplicated genes are initially identical, and they gradually diverge over time, increasing genomic complexity. Second, parts may exhibit a pattern consistent with differential divergence of split elements (Fig. 1b). Here, a prime example is speciation, where populations of individual organisms, originally all of the same species, split into multiple populations that diverge to the point of becoming separate species. Splitting (fission) can also occur in an asymmetric fashion (Fig 1c), generating two uncoupled parts that together would sum to one ancestral part. Third, parts may exhibit a pattern consistent with fusion of copied parts (Fig. 1d). For example, copied protein domains often join together to generate a new gene. Another example of fusion is expression of genes in new combinations, a process termed co-option [reviewed in 7]. A primary goal of this paper is to review cases in nervous system evolution that provide specific and more detailed mechanisms that account for these patterns at different levels of biological organization.
The patterns in figure 1 are produce by a number of different mechanisms, including gene duplication, alternative splicing, retrotransposition, co-option, etc.
[The specific mechanisms leading to the general patterns is the topic of the rest of the paper from which this excerpt is taken].
References Cited
1. Striedter GF: Principles of Brain Evolution. Sunderland, MA: Sinauer; 2005.
2. Adami C, Ofria C, Collier TC: Evolution of biological complexity. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:4463-4468.
3. Adamowicz SJ, Purvis A, Wills MA: Increasing morphological complexity in multiple parallel lineages of the Crustacea. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:4786-4791.
4. Bonner JT: The Evolution of Complexity. Princeton: Princeton University Press; 1988.
5. McShea DW: Functional complexity in organisms: Parts as proxies. Biology & Philosophy 2000, 15:641-668.
6. McShea DW, Venit EP: What is a part? In The Character Concept in Evolutionary Biology. Edited by Wagner GP: Academic Press; 2001:259-284.
7. True JR, Carroll SB: Gene co-option in physiological and morphological evolution. Annual Review of Cell and Developmental Biology 2002, 18:53-80.
The evolution of complexity is an enduring and fundamental topic in biology. Recent research is allowing new insights into the origins of complexity. Namely, scientists now have access to the components of complex structures, and their evolutionary histories. "The eye" is no longer an anonymous collection of components - Darwin may have known an eye is composed of lens retina and nerve - but he did not know what lenses or retinas were composed of, nor did he know in much detail how they functioned. We now know many of the protein components of structures like eyes and how they function, and we know that these components have evolutionary histories. Since biological entities from genes to ecosystems arise from existing entities, general patterns emerge as to where those entities came from. They either duplicate/diverge; split/diverge; or fuse in new combinations.
What is biological complexity?
Numerous definitions have been suggested for biological complexity, from mathematical and information theoretic formulas [2,3] to intuitive definitions, such as the numbers of parts or components that can be counted in a system [4,5]. In practice, a researcher’s choice of definition for complexity often boils down to his ability to measure it. In investigator-defined computer simulations [2] or circumscribed biological systems [3], information theoretic definitions using explicit mathematical formulas are tractable. However, in extensive biological systems, especially those that encompass multiple levels of biological organization with varied properties, the relationship between structure and function (e.g. genotype and phenotype) is often largely unknown, and may itself be complicated and variable. These unknowns complicate the formulation of explicit, yet general, mathematical definitions of complexity for extensive biological systems. Instead, some have argued that counting the numbers of parts of a system is an appropriate measure of complexity [4]. Although often focused on structural units, such as cell types, genes, or species, and not on the functions of those units, McShea [5] has also argued that counting structural parts should often be a good estimate of functional complexity.
Herein, we follow previous authors [4,5] and define more complex systems as those that have more parts. “Part” is used as a term that spans levels of biological organization [4]. Species are parts of ecological communities. Organs (like brains or ganglia) are parts of species. Cell types (like neuronal types) are parts of organs and of species. Proteins are parts of cells and of networks, and domains and amino acids are parts of proteins. Many other biological units are also parts [6]. For the current discussion, we are concerned less with defining or counting parts, and concerned more with how new parts originate during evolution. According to the definition of complexity that we employ, new parts (that do not come at the expense of existing parts) increase biological complexity. Therefore, those mechanisms that cause the evolution of new parts are of particular interest because those are the mechanisms that cause increases in biology complexity.
"those mechanisms that cause the evolution of new parts are of particular interest because those are the mechanisms that cause increases in biology complexity."
General patterns of increased complexity
By definition, complex systems have many parts, and the histories of those parts are varied. As such, we cannot expect a simple, one dimensional answer to the question of how complexity evolved. Nevertheless, at all levels of biological organization, conceptually similar patterns (Figure 1) have resulted from a varied array of mechanisms that historically increased complexity.
Figure 1 - Generalized patterns of increased biological complexity. The top of the figure represents an ancestral state, the bottom a descendant state. Shapes represent “parts”, a generic term for a biological feature at any level of organization. Parts can be species, genes, protein domains, pathways, brain regions, and many other biological units [see 6]. A. Copying and divergence B. Fission and divergence C. Copying and fusion. Without copying or fission, complexity does not increase because divergence (or fusion) maintains the same number of parts. Without differential divergence or fusion of parts, complexity only increases marginally.
First, parts may exhibit a pattern consistent with differential divergence of copied elements (Fig. 1a). A prime example of a specific mechanism leading to this pattern is gene duplication plus divergence. Duplicated genes are initially identical, and they gradually diverge over time, increasing genomic complexity. Second, parts may exhibit a pattern consistent with differential divergence of split elements (Fig. 1b). Here, a prime example is speciation, where populations of individual organisms, originally all of the same species, split into multiple populations that diverge to the point of becoming separate species. Splitting (fission) can also occur in an asymmetric fashion (Fig 1c), generating two uncoupled parts that together would sum to one ancestral part. Third, parts may exhibit a pattern consistent with fusion of copied parts (Fig. 1d). For example, copied protein domains often join together to generate a new gene. Another example of fusion is expression of genes in new combinations, a process termed co-option [reviewed in 7]. A primary goal of this paper is to review cases in nervous system evolution that provide specific and more detailed mechanisms that account for these patterns at different levels of biological organization.
The patterns in figure 1 are produce by a number of different mechanisms, including gene duplication, alternative splicing, retrotransposition, co-option, etc.
[The specific mechanisms leading to the general patterns is the topic of the rest of the paper from which this excerpt is taken].
References Cited
1. Striedter GF: Principles of Brain Evolution. Sunderland, MA: Sinauer; 2005.
2. Adami C, Ofria C, Collier TC: Evolution of biological complexity. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:4463-4468.
3. Adamowicz SJ, Purvis A, Wills MA: Increasing morphological complexity in multiple parallel lineages of the Crustacea. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:4786-4791.
4. Bonner JT: The Evolution of Complexity. Princeton: Princeton University Press; 1988.
5. McShea DW: Functional complexity in organisms: Parts as proxies. Biology & Philosophy 2000, 15:641-668.
6. McShea DW, Venit EP: What is a part? In The Character Concept in Evolutionary Biology. Edited by Wagner GP: Academic Press; 2001:259-284.
7. True JR, Carroll SB: Gene co-option in physiological and morphological evolution. Annual Review of Cell and Developmental Biology 2002, 18:53-80.
Thursday, November 20, 2008
Evolutionary novelty: Photosynthetic slug
All of biology, from genes to species, is united by common descent. Therefore new biological entities – novelties – must come from the modification of existing entities. Lightening does not strike and impart new features into organisms; new features evolve from existing ones. New research in PNAS provides fascinating new insights into the evolutionary origin of a 'photosynthetic slug'.
Given new features evolve from existing ones, one way novelties originate is through duplication and divergence. Another way is through new combinations of existing biological entities. In fact, biological entities can be recombined at many levels. Protein domains fuse to form new genes, genes become expressed together in new combinations in developmental time or space, even species can merge together to form new species, as occurred at the origin of eukaryotic cells when one species merged with a bacteria that became our cells’ energy factories, the mitochondria.
Imagine if evolution happened to produce a photosynthetic animal, and ask, what are some of the ways it might happen? One likely way is to utilize existing organisms (or their genes) that already have the ability to convert light energy into chemical energy. This is exactly what has happened during the evolution of the gastropod mollusk Elysia chlorotica, a green “sea slug”. Like other types of animal including reef-building corals, E. chlorotica harbors the photosynthetic machinery of other organisms. In the case of reef corals, a symbiotic relationship with dinoflagellates provides photosynthetic ability. But in the green sea slug, only the photosynthetic machinery itself is sequestered, by ingesting an algae, and using the algae’s plastids, the photosynthetic sub-cellular structure of the algae (interestingly, the plastid joined the algal cell in an ancient novel merger of species).
This presents a puzzle. The algae’s plastid, which is being used by the green sea slug for photosynthesis, does not itself contain all of the machinery required for photosynthesis. Instead, many of the photosynthesis genes reside in the algae, only some reside in the plastid. Yet the green sea slug can photosynthesize for months using only the plastid, even in the absence of algae, and therefore in the absence of the algae’s photosynthesis machinery. How is this possible?
The authors found that at least one gene (psbO) is integrated into the genome of the green sea slug. This gene is identical in sequence to an algal gene, yet the sequence adjacent to the gene in the slug analyses make clear that the gene is in the slug’s genome and not an experimental artifact, like contamination.
As the authors indicate, this work raises many interesting questions. How does the slug’s gene target the plastids? What about all the other genes absent from the plastid that are required for photosynthesis – are those transferred to the slug, too? Or could some of the slug’s genes replace the function of the missing genes? What is the specific mechanism for horizontal transfer of genes from one species to another? Clearly, the authors are thinking about these interesting questions, and likely future research will provide us with answers.
I noticed that Carl Zimmer already posted on this article in his fine blog, The Loom
Self-promotion*
As I wrote in an article with Michael Rose called “The New Biology: Beyond the Modern Synthesis”, acceptance of biological mergers was slow, perhaps because the modern synthesis viewed genomes as sleekly functional, finely tuned to current utility. As such, moving genes from one genome to another seems like it should be suboptimal, and therefore rare. No one doubts the importance of biological mergers any more, but they are still fascinating and under-documented, in part because they were neglected for so long.
*One reason I write blog entries is to present my research interests and ideas to a potentially broader audience. As such, I like to like papers of mine when possible.
M. E. Rumpho, J. M. Worful, J. Lee, K. Kannan, M. S. Tyler, D. Bhattacharya, A. Moustafa, J. R. Manhart (2008). From the Cover: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica Proceedings of the National Academy of Sciences, 105 (46), 17867-17871 DOI: 10.1073/pnas.0804968105
Tuesday, November 18, 2008
There once was a man named Chuck
I decided to write a quick Darwin Limerick, inspired by the contest over at Dispersal of Darwin, and by the concepts of pluralistic Darwinism and common descent:
I'm still working on "There once was a man named Chuck"
There once was a man from Down House
Who convinced me I'm cousin to a brown mouse
I'm glad as can be
That all life is a tree
Toe fungus to red grouse to crown louse
I'm still working on "There once was a man named Chuck"
Tuesday, November 11, 2008
Evolutionary Novelty: Hair
Mammals have hair but no other animals do. As such, hair is a clear evolutionary novelty, present in one group but absent in all others. In my macroevolution course (EEMB 102), I use hair as a clear character that can be used in phylogenetics. Hair groups all mammals to the exclusion of other organisms. In systematics jargon, hair is therefore a “synapomorphy”, grouping mammals together.
We can map the trait of hair on a family tree of animals. From this perspective, we can infer that the ancestor of all mammals very likely had hair, but that the ancestor of sauropods (birds, reptiles, and mammals) lacked hair. Therefore, hair originated prior to the common ancestor of all mammals.
Figure 1 – Hair originated before mammals, but after the common ancestor of birds, reptiles and mammals. Grey ellipse (hard to see except as a broken branch, I'd fix it but I'm too lazy) is the origin of hair keratin protein.
So where did hair come from - how did this evolutionary novelty evolve? A new paper by Eckhart et al in PNAS [link] provides evidence that the building blocks of hair pre-date the origin of hair itself. Namely, they found alpha-keratin (“hair keratin”) proteins are encoded in the genomes of chickens and the green anole lizard. In the green anole they studied, ‘hair keratin’ proteins were used in claws.
Just ten years ago, results like this clarifying the molecular components of trait evolution were rare, but they have become common now that genome sequences are available for many species. Before we had some idea of gene function, and before genome sequencing, scientists could only examine one level of biological organization – the trait (hair in this case). And that could only get science so far. In the case of hair, it mainly got science as far as Figure 1, which leads to the inference that hair evolved a bit before the common ancestor of living mammals. But “hair” is not one thing. It is a complex of building blocks, including structural genes (like keratin) and developmental processes. Today, scientists can decompose a trait, like hair, into its components and study the evolutionary history of each part separately, tracing the parts through various genomes.
What do we expect for the evolution of hair’s components? Figure 1 suggests that “hair” and all its components arise at the same time, near the origin of mammals. The origin of “hair” on figure 1 can be considered a first-pass hypothesis for the origins of ALL the components of hair. If hair itself originated near the origin of mammals, a logical idea is that the components originated then too.
Today, we can test this first-pass hypothesis because we know some of the molecular components of hair. A particularly important part is “hair keratin”. Mutate this protein and the hair built from that mutant protein is fragile and brittle. The expectation based on figure 1 is that hair keratin proteins originated with hair itself. But the discovery of these genes in an anole indicates an earlier origin for this component. In other words, components of hair originated before hair itself. In this case the protein “hardened” by mutations to cysteine amino acids that may have functioned to molecularly harden the proteins. Since these changes were later useful in the structure of hair, they may be considered exaptations, features that originated for functions other than current utility: keratins may have hardened before that feature became useful for hair formation. [Note for scientific accuracy – the biochemistry of the anole protein has not been studied, so while it is cysteine rich, we don’t know yet if the anole protein is ‘hardened’].
This work also illustrates that in evolution, new things do not appear from nowhere [see my post Coming to Grips]. In evolution, new things come from the duplication/differential modification and recombination of existing parts. Morphologists know this, as one dominant idea about the origin of hair is that hair evolved by modification of scales. Hair keratin is not expressed in anole scales, so the scale hypothesis is not supported by the new PNAS paper. Also unfortunate for the scale hypothesis is the fact that the fossil record retains no transitional forms between scale and hair. Even though morphological relatives of hair are ambiguous, the molecular relatives in this case are clear. Hardened keratin comes as two types, which share an evolutionary relationship, and hardened keratins may share an evolutionary relationship with soft keratins, proteins that are present in numerous tetrapods, and therefore have a more ancient origin than the hard variety. In sum, keratin has an ancient heritage, and through gene duplications and differential modification, two related groups of these proteins have specialized as hair keratins. Fascinatingly, some of the hair keratin modifications pre-dated hair itself.
If you are interested phylogenetic analyses of trait evolution, and the evolutionary history of trait components, this is a common theme of research in my lab.
We’ve found:
Synaptic components are present in sponges and therefore may predate synapses. [paper] [blog]
Phototransduction components were first assembled for vision in the eumetazoan ancestor (cnidaria + bilateria), yet some components pre-date animals [blog] [blog] [paper] [paper]
See also: Red Herring Blog
We can map the trait of hair on a family tree of animals. From this perspective, we can infer that the ancestor of all mammals very likely had hair, but that the ancestor of sauropods (birds, reptiles, and mammals) lacked hair. Therefore, hair originated prior to the common ancestor of all mammals.
Figure 1 – Hair originated before mammals, but after the common ancestor of birds, reptiles and mammals. Grey ellipse (hard to see except as a broken branch, I'd fix it but I'm too lazy) is the origin of hair keratin protein.
So where did hair come from - how did this evolutionary novelty evolve? A new paper by Eckhart et al in PNAS [link] provides evidence that the building blocks of hair pre-date the origin of hair itself. Namely, they found alpha-keratin (“hair keratin”) proteins are encoded in the genomes of chickens and the green anole lizard. In the green anole they studied, ‘hair keratin’ proteins were used in claws.
Just ten years ago, results like this clarifying the molecular components of trait evolution were rare, but they have become common now that genome sequences are available for many species. Before we had some idea of gene function, and before genome sequencing, scientists could only examine one level of biological organization – the trait (hair in this case). And that could only get science so far. In the case of hair, it mainly got science as far as Figure 1, which leads to the inference that hair evolved a bit before the common ancestor of living mammals. But “hair” is not one thing. It is a complex of building blocks, including structural genes (like keratin) and developmental processes. Today, scientists can decompose a trait, like hair, into its components and study the evolutionary history of each part separately, tracing the parts through various genomes.
What do we expect for the evolution of hair’s components? Figure 1 suggests that “hair” and all its components arise at the same time, near the origin of mammals. The origin of “hair” on figure 1 can be considered a first-pass hypothesis for the origins of ALL the components of hair. If hair itself originated near the origin of mammals, a logical idea is that the components originated then too.
Today, we can test this first-pass hypothesis because we know some of the molecular components of hair. A particularly important part is “hair keratin”. Mutate this protein and the hair built from that mutant protein is fragile and brittle. The expectation based on figure 1 is that hair keratin proteins originated with hair itself. But the discovery of these genes in an anole indicates an earlier origin for this component. In other words, components of hair originated before hair itself. In this case the protein “hardened” by mutations to cysteine amino acids that may have functioned to molecularly harden the proteins. Since these changes were later useful in the structure of hair, they may be considered exaptations, features that originated for functions other than current utility: keratins may have hardened before that feature became useful for hair formation. [Note for scientific accuracy – the biochemistry of the anole protein has not been studied, so while it is cysteine rich, we don’t know yet if the anole protein is ‘hardened’].
This work also illustrates that in evolution, new things do not appear from nowhere [see my post Coming to Grips]. In evolution, new things come from the duplication/differential modification and recombination of existing parts. Morphologists know this, as one dominant idea about the origin of hair is that hair evolved by modification of scales. Hair keratin is not expressed in anole scales, so the scale hypothesis is not supported by the new PNAS paper. Also unfortunate for the scale hypothesis is the fact that the fossil record retains no transitional forms between scale and hair. Even though morphological relatives of hair are ambiguous, the molecular relatives in this case are clear. Hardened keratin comes as two types, which share an evolutionary relationship, and hardened keratins may share an evolutionary relationship with soft keratins, proteins that are present in numerous tetrapods, and therefore have a more ancient origin than the hard variety. In sum, keratin has an ancient heritage, and through gene duplications and differential modification, two related groups of these proteins have specialized as hair keratins. Fascinatingly, some of the hair keratin modifications pre-dated hair itself.
If you are interested phylogenetic analyses of trait evolution, and the evolutionary history of trait components, this is a common theme of research in my lab.
We’ve found:
Synaptic components are present in sponges and therefore may predate synapses. [paper] [blog]
Phototransduction components were first assembled for vision in the eumetazoan ancestor (cnidaria + bilateria), yet some components pre-date animals [blog] [blog] [paper] [paper]
See also: Red Herring Blog
Monday, November 10, 2008
Probing Darwin's Black Box
The 'God of the Gaps' strategy is to assert that anything we do not yet understand is attributable to a god or gods. Two thousand years ago there were a lot of gaps in our understanding, and plenty of room for inventing ad hoc explanations for things. There were a lot of gaps where gods might reside.
Even recently, the god of the gaps argument is sometimes used. One example is the idea of 'Darwin's black box', the false assertion that the exquisite details of molecular biology cannot be understood in an evolutionary context.
There are two facets of 'god of the gaps' that are particularly bankrupt, one scientific and one theological. Scientifically, god of the gaps is equivalent to suicide, an admission that one simply cannot imagine how to go on any farther. God of the gaps is giving up on science, with no reason to do so. Theologically, god of the gaps means that the realm of god gets smaller each time a gap in our knowledge is filled.
Here, I give two recent examples from my life where the molecular details of evolution have been explicated in greater detail. In neither case are the gaps fully filled - this can never be the case - split a gap in half and we have two smaller gaps. But the gaps are getting sooo small - is it really worth trying to stuff gods in those tiny little gaps?
First, I saw a seminar by Joe Thornton on his work on the evolution of steriod receptors. Joe uses statistical inference to reconstruct the sequence of ancestral proteins. Then he brings them to life in the lab and conducts experiments on the proteins. He is able to reconstruct the order of specific mutations that occurred and that change the function of the proteins he studies.
I found particularly interesting that one particular receptor could identify 3 different steroids at the origin of the protein. Later on, specializations occurred through particular mutations that Joe and his group could identify. When thinking about the evolution of novelty, we often assume that multiple functions are added over evolutionary time. However, Joe's results show how functional complexity can be the original state, and that structural complexity can follow by parsing an ancestral function across subsequently duplicated genes.
To view Joe's presentation, go here.
The second recent example is that a paper from my lab was recently published that reviews our progress on understanding the evolution of the molecular basis of vision (phototransduction). This paper is available for free from the Springer web site.
Even recently, the god of the gaps argument is sometimes used. One example is the idea of 'Darwin's black box', the false assertion that the exquisite details of molecular biology cannot be understood in an evolutionary context.
There are two facets of 'god of the gaps' that are particularly bankrupt, one scientific and one theological. Scientifically, god of the gaps is equivalent to suicide, an admission that one simply cannot imagine how to go on any farther. God of the gaps is giving up on science, with no reason to do so. Theologically, god of the gaps means that the realm of god gets smaller each time a gap in our knowledge is filled.
Here, I give two recent examples from my life where the molecular details of evolution have been explicated in greater detail. In neither case are the gaps fully filled - this can never be the case - split a gap in half and we have two smaller gaps. But the gaps are getting sooo small - is it really worth trying to stuff gods in those tiny little gaps?
First, I saw a seminar by Joe Thornton on his work on the evolution of steriod receptors. Joe uses statistical inference to reconstruct the sequence of ancestral proteins. Then he brings them to life in the lab and conducts experiments on the proteins. He is able to reconstruct the order of specific mutations that occurred and that change the function of the proteins he studies.
I found particularly interesting that one particular receptor could identify 3 different steroids at the origin of the protein. Later on, specializations occurred through particular mutations that Joe and his group could identify. When thinking about the evolution of novelty, we often assume that multiple functions are added over evolutionary time. However, Joe's results show how functional complexity can be the original state, and that structural complexity can follow by parsing an ancestral function across subsequently duplicated genes.
To view Joe's presentation, go here.
The second recent example is that a paper from my lab was recently published that reviews our progress on understanding the evolution of the molecular basis of vision (phototransduction). This paper is available for free from the Springer web site.
Todd Oakley and M. Sabrina Pankey (2008) Opening the "Black Box": The genetic and biochemical basis of eye evolution. Evolution Education and Outreach. [Link]
Monday, November 3, 2008
Linear Evolution: McCain and Obama
A common theme of this blog is to share cases of "linear evolutionary thinking". These are instances, usually graphics, that illustrate the common conception of evolution as a line of progress, from worst to best. Evolution actually occurs by branching processes. We could pull out a line of evolution from the tree, but that line by necessity has an arbitrary endpoint, often humans or a human-like feature. And living species or their traits cannot necessarily be equated with ancestral forms.
Ostracod eye evolution has been depicted as a straight line from simple to compound eye, illustrated here. Textbooks use such diagrams (see also this), and these diagrams can impact the way people think about evolution.
Here is another variation on the human march of progress, which shows Barack Obama as the more advanced political candidate, compared to John McCain.
Thanks to my brother for sending this to me.
Ostracod eye evolution has been depicted as a straight line from simple to compound eye, illustrated here. Textbooks use such diagrams (see also this), and these diagrams can impact the way people think about evolution.
Here is another variation on the human march of progress, which shows Barack Obama as the more advanced political candidate, compared to John McCain.
Thanks to my brother for sending this to me.
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:
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:
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?
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
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!
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.)
Monday, September 29, 2008
UCSB Job
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:
evolutionsearch@lifesci.ucsb.edu
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
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:
evolutionsearch@lifesci.ucsb.edu
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).
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.
This patent represents the origin of novel novelty items by combining entities: manufactured articles and bioluminescence.
Title:
Bioluminescent novelty items
Document Type and Number:
United States Patent 6152358
Abstract:
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 umiho.net
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 http://www.kanko-otakara.jp
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.