Here is an invaluable resource for learning about fishes run by UCSD:
Digital Fish Library
It's mostly fish anatomy and physiology, but it's organized by phylogeny using an intuitive Flash interface. The information they provide is really good, especially when coupled with something like FishBase and/or the Tree of Life.
February 12, 2009
February 10, 2009
Darwin's Legacy
It's about that time....
February 2009 is officially Darwin's 200 birthmonth. The New York Times has most of this week's science section devoted to his legacy. I find it interesting that in the popular imagination, Darwin is viewed as being a one-trick pony. Most people don't realize this, but Darwin was what we might call a theoretical synthesist (like myself). That is, he took all of the accumulating evidence and put it forth in a coherent form. Sometimes people don't really like what you have to say, but it needs to be said.
NY Times Darwin spread
Put yourself in 19th century Europe. Consider that until the 16th century, most people knew very little if anything about the natural world outside of Europe. Consider further that the bible purportedly held all of the answers regarding how natural diversity and the earth itself got there. From the renaissance until the 19th century, Europeans observed things like fossils in cliff walls or novel species in Australia and had no frame of reference for which to put them in other than the Bible's great flood. Darwin's work essentially built on the work of people like Cuvier, Aggaziz, and other naturalists of the time. However, he added just that little bit of extra insight that made the difference between Darwin being a household name and Lamarck (who made an earlier attempt at synthesis) being widely ridiculed.
Below is a link to a list of Darwin's publications:
List of publications
Interestingly, he published not just the Origin of Species, but books on sexual selection and facial expressions, geology, and, towards the end of his life, plant behavior. In particular, he was interested in the effects of a hormone called Auxin on phototropism. Of course, Darwin was a man of his time in that he knew little about genes or biochemistry, and didn't test his many theories in an elegant manner. On the other hand, one could make the same accusations about Einstein. But such is the life of a synthesist.
February 2009 is officially Darwin's 200 birthmonth. The New York Times has most of this week's science section devoted to his legacy. I find it interesting that in the popular imagination, Darwin is viewed as being a one-trick pony. Most people don't realize this, but Darwin was what we might call a theoretical synthesist (like myself). That is, he took all of the accumulating evidence and put it forth in a coherent form. Sometimes people don't really like what you have to say, but it needs to be said.
NY Times Darwin spread
Put yourself in 19th century Europe. Consider that until the 16th century, most people knew very little if anything about the natural world outside of Europe. Consider further that the bible purportedly held all of the answers regarding how natural diversity and the earth itself got there. From the renaissance until the 19th century, Europeans observed things like fossils in cliff walls or novel species in Australia and had no frame of reference for which to put them in other than the Bible's great flood. Darwin's work essentially built on the work of people like Cuvier, Aggaziz, and other naturalists of the time. However, he added just that little bit of extra insight that made the difference between Darwin being a household name and Lamarck (who made an earlier attempt at synthesis) being widely ridiculed.
Below is a link to a list of Darwin's publications:
List of publications
Interestingly, he published not just the Origin of Species, but books on sexual selection and facial expressions, geology, and, towards the end of his life, plant behavior. In particular, he was interested in the effects of a hormone called Auxin on phototropism. Of course, Darwin was a man of his time in that he knew little about genes or biochemistry, and didn't test his many theories in an elegant manner. On the other hand, one could make the same accusations about Einstein. But such is the life of a synthesist.
January 30, 2009
Non-razors, unite!
A central assumption of modern science is parsimony, or that the simplest explanation also serves as the best explanation for a particular phenomenon. The principle behind this is the famous idea of "Occam's razor". Einstein is even famous for his expression "A theory should be as simple as possible but no simpler". This idea seems like a match made for explaining the evolutionary origins of lifeforms, especially those that are hyper-specialized. One might even say (especially maximum parsimony people) that a good razor makes for a good phylogeny.
However, the underlying assumption of parsimony may not actually explain all instances of evolution. Consider that for as many examples of "good design" one can find in nature, there are many examples of less-than-optimal natural systems. To illustrate what I am getting at, I would point readers to the Rube Goldberg machine. Rube Goldberg was a cartoonist in the early 20th century who designed elaborate machines (many serially interacting parts) that produced a rather trivial output. For example, to turn off a light switch, we could design an elaborate mechanism that utilizes 30 different steps. Essentially, the number of parts is MAXIMIZED in the production of a particular output. I point you to these examples:
Considering the role of Rube Goldberg-like evolutionary mechanisms in a systematic way has (as far as I know) never really been done before. I have heard people mention casually that many transcriptional and metabolic pathways are of this quality, but have never seen a solid experimental or computational result. In a literature search, I did find reference to "anti-razor" advocates (who are mostly philosophers of science), but no serious inquiries into what we might call anti-razor biology.
The idea of maximizing the number of mechanisms, as the polar opposite of minimizing the number of mechanisms that people usually think of when pointing to examples of natural selection, is actually pretty intriguing to me. Let us suppose that an adaptive process in evolution operates as a game. The goal of this game is not to produce an optimal output, but to produce a unique solution that is complementary with the overall function of the organism. This could be the result of either cooperation or competition. A traditional biological arms race is similar to this: two organisms will compete in an iterative fashion to build bigger, more elaborate structures until they both end up with structures of ridiculous size. The original impetus of the arms race was to improve fitness. Ultimately, however, what becomes paramount (or enforces this runaway result) is the competition itself. It may be that two organisms (or set of genetic elements, or populations) compete against another such unit (or against nature) in a way that results in such a sub-optimal result. This would be natural selection working in a way counter to what most people would expect, but natural selection nonetheless.
Please send me examples of non-optimal mechanisms and traits in organisms (at any level of analysis -- from molecular pathways to social behavior). I am especially interested in the non-optimal products of evolution. Please post comments pointing to your own examples. In future posts, I may expand on this theme a bit more, so stay tuned.
POSTSCRIPT: I did elaborate on this a bit. Unfortunately, the empirical data is a bit sparse. Please see my arXiv paper "The 'Machinery' of Biocomplexity: understanding non-optimal architectures in biological systems" (arXiv:1104.3559, q-bio.QM) for further development of this idea.
For more information on how evolution (more specifically, natural selection) is or is not an optimizing force, please see: Orzack, S.H. and Sober, E. Adaptationism and Optimality. Cambridge University Press, Cambridge, UK (2001).
Also, watch this "Richard Dawkins Presents" video showing an example of non-optimal evolution and unintelligent design (the laryngeal nerve in the giraffe, which is an artifact of fish physiology).
Phylogeny constructed using maximum parsimony (this one exhibits long-branch attraction, which is a problem in such analyses). COURTESY: Wikipedia.
However, the underlying assumption of parsimony may not actually explain all instances of evolution. Consider that for as many examples of "good design" one can find in nature, there are many examples of less-than-optimal natural systems. To illustrate what I am getting at, I would point readers to the Rube Goldberg machine. Rube Goldberg was a cartoonist in the early 20th century who designed elaborate machines (many serially interacting parts) that produced a rather trivial output. For example, to turn off a light switch, we could design an elaborate mechanism that utilizes 30 different steps. Essentially, the number of parts is MAXIMIZED in the production of a particular output. I point you to these examples:
Example of a Rube Goldberg machine (COURTESY: Purdue University YouTube channel)
Considering the role of Rube Goldberg-like evolutionary mechanisms in a systematic way has (as far as I know) never really been done before. I have heard people mention casually that many transcriptional and metabolic pathways are of this quality, but have never seen a solid experimental or computational result. In a literature search, I did find reference to "anti-razor" advocates (who are mostly philosophers of science), but no serious inquiries into what we might call anti-razor biology.
The idea of maximizing the number of mechanisms, as the polar opposite of minimizing the number of mechanisms that people usually think of when pointing to examples of natural selection, is actually pretty intriguing to me. Let us suppose that an adaptive process in evolution operates as a game. The goal of this game is not to produce an optimal output, but to produce a unique solution that is complementary with the overall function of the organism. This could be the result of either cooperation or competition. A traditional biological arms race is similar to this: two organisms will compete in an iterative fashion to build bigger, more elaborate structures until they both end up with structures of ridiculous size. The original impetus of the arms race was to improve fitness. Ultimately, however, what becomes paramount (or enforces this runaway result) is the competition itself. It may be that two organisms (or set of genetic elements, or populations) compete against another such unit (or against nature) in a way that results in such a sub-optimal result. This would be natural selection working in a way counter to what most people would expect, but natural selection nonetheless.
Please send me examples of non-optimal mechanisms and traits in organisms (at any level of analysis -- from molecular pathways to social behavior). I am especially interested in the non-optimal products of evolution. Please post comments pointing to your own examples. In future posts, I may expand on this theme a bit more, so stay tuned.
POSTSCRIPT: I did elaborate on this a bit. Unfortunately, the empirical data is a bit sparse. Please see my arXiv paper "The 'Machinery' of Biocomplexity: understanding non-optimal architectures in biological systems" (arXiv:1104.3559, q-bio.QM) for further development of this idea.
For more information on how evolution (more specifically, natural selection) is or is not an optimizing force, please see: Orzack, S.H. and Sober, E. Adaptationism and Optimality. Cambridge University Press, Cambridge, UK (2001).
Also, watch this "Richard Dawkins Presents" video showing an example of non-optimal evolution and unintelligent design (the laryngeal nerve in the giraffe, which is an artifact of fish physiology).
Dawkins on Campus!
If you happen to be in the Michigan State University area on March 2, Richard Dawkins will be speaking at the Wharton Center:
Relevant Info
The talk is sponsored by the WorldView speaker series and the EEBB (Ecology, Evolutionary Biology, and Behavior) program. Tickets are required, but are free to anyone with an MSU ID. I got my tickets last week, and the floor seating is sold out. This is the same lecture series that brought in E.O. Wilson last Spring.
Relevant Info
The talk is sponsored by the WorldView speaker series and the EEBB (Ecology, Evolutionary Biology, and Behavior) program. Tickets are required, but are free to anyone with an MSU ID. I got my tickets last week, and the floor seating is sold out. This is the same lecture series that brought in E.O. Wilson last Spring.
December 31, 2008
Florida Museum of Natural History: prehistory on film.
This is really cool! Who says that YouTube is contributing to the downfall of civilization (I am not among those people, but whatever)? Have a look at these videos from the UF libraries archive. I used to work here as a Masters student:
This is the dedication of Dickinson Hall, which is now the "old" FLMNH (where they house most of the collections and scientific research today). By contrast, the "new" FLMNH (with the fully-functioning Butterfly rainforest) is out on Museum road near 34th Street (which is just off the lower left edge of the map shown below):
The whole buliding was designed to look (and apparently function, since it dosen't have freight elevators) like a Mayan pyramid nestled into the side of a hill. Notice how the front entrance appears tobe a single story while the plaza in back looks quite expansive with staircases and everything. In the background you can see Carrtram Hall (a portmanteau of Carr and Bartram Halls, home of the Zoology and Botany departments).
If you ever pass by (right on I-75) or visit Gainesville, FL, do yourself a favor and visit this museum. You'll learn a hell of a lot more than you will at Disney, and they have some pretty good collections, especially pertaining to Florida, Carribean, and South American biodiversity/cultural history.
More UF trivia as the opportunity presents itself......
This is the dedication of Dickinson Hall, which is now the "old" FLMNH (where they house most of the collections and scientific research today). By contrast, the "new" FLMNH (with the fully-functioning Butterfly rainforest) is out on Museum road near 34th Street (which is just off the lower left edge of the map shown below):
The whole buliding was designed to look (and apparently function, since it dosen't have freight elevators) like a Mayan pyramid nestled into the side of a hill. Notice how the front entrance appears tobe a single story while the plaza in back looks quite expansive with staircases and everything. In the background you can see Carrtram Hall (a portmanteau of Carr and Bartram Halls, home of the Zoology and Botany departments).
If you ever pass by (right on I-75) or visit Gainesville, FL, do yourself a favor and visit this museum. You'll learn a hell of a lot more than you will at Disney, and they have some pretty good collections, especially pertaining to Florida, Carribean, and South American biodiversity/cultural history.
More UF trivia as the opportunity presents itself......
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