Tuesday, July 21, 2009

Plants 1 : Anolis 0

The June 2009 number of the Carnivorous Plant Newsletter marks a low point for the lizard genus Anolis. Joel McNeal from Athens, Georgia reports the capture of a small green anole (Anolis carolinensis) by the venus flytrap (Dionaea muscipula). The lizard was dead by the time he found it, but he never got a chance to see if it would be digested because the lizard and most of the trap were gone the following day, presumably due to bird predation.

Thursday, July 16, 2009

Herptastic Articles in Science

Science magazine features some interesting herpetological research in its most recent issues. Last week's number had an interesting piece on the evolution and development of the turtle shell (see also the enlightening summaries of this article by Olivier Rieppel and Ed Yong). Although elegant, the results are unlikely to satisfy researchers who favor the account provided in the Little Golden Book. Tomorrow, we get another report on the swimming behavior of lizards in sand (already featured in the NYT). Because the article hasn't yet been posted at Science, it's difficult to tell how it differs from previous work on this subject published by Baumgartner et al. last year in PLoS ONE. In any case, the visuals are more inticing because the current study uses high speed x-ray rather than NMR (the new x-ray video can be viewed along with a press release).

Tuesday, July 7, 2009

Large Tree Extraction, Viewing, and Printing

Extracting trees from various idiosyncratically formatted databases is a pain, as is the task of printing very large trees for visual inspection of showing off. Many software packages are competent or good at one or both sets of tasks--I use some combination of APE package for R and FigTree, which work well for most of my needs, but not all. There are two new tools that help partly solve a couple of vaguely related problems.

Archaeopteryx, written by Christian Zmasek, is a Java-based application potentially useful in broad comparative analyses for extraction of trees from various source formats. With open source Java and Ruby libraries, it reads and displays trees in common formats (e.g. newick and nexus) as well as NCBI Taxonomy, TOL, and PhyloXML. For a nice example, take a look at the amphibian tree, then go to 'View as Text' and copy the newick formatted tree. Why? If you were to wish to print this or another large tree, you'd be out a nice chunk of time, and experience moderate hassle. No longer.

Tred, Rick Ree's web-based tree printing tool, can import, manipulate, and print very large trees. The most exciting feature for me is the duplication of sections near the margins for easy pasting of multi-page trees! The amphibian tree can be easily printed over three pages, taped together at convenient overlaps, and posted above your desk.

I can barely contain the urge to outdo the Hillis and Bull Lab tree, pictured above, by using the above tools to print out and unfurl a gigantic tree of life from Sears Tower. (Nevermind the uncertainty or accuracy.) A cheap way into the Guinness Book of World Records?

[Thanks to MudPuppy for pointing out Archaeopteryx!]

Thursday, July 2, 2009

Sunday Book Review: Why Evolution is True

I try to avoid reading about the science of evolution versus the dogma of creationism. Too often, I find the science presented in this type of writing to be repetitive and intolerably over-simplified. Although this is surely a symptom of my own academic elitism, I can't escape the impression that many of the journalists or professional writers discussing evolution aren't keeping up to speed on the latest advances or, in some cases, don't really get the science of evolution at its deepest levels. This is why Jerry Coyne's new book Why Evolution is True is such a welcome contribution (see also the associated blog). While many contemporary scientists have written in defense of evolution, few have the academic credentials of Coyne, whom many evolutionary biologists (myself included) regard as one of the best scientists of his generation.

Although Coyne shares Richard Dawkins's view that evolution and religion are fundamentally incompatible (as well as Dawkins's literary agent John Brockman), his book sticks mostly to scientific facts. In this sense, Coyne's book lives up to expectations by providing an excellent synthesis of the evidence supporting evolution, including reference to many recent discoveries and examples that are rarely discussed elsewhere. His lengthy chapter on human evolution was particularly enlightening because it cuts through much of the BS perpetuated by competing camps of scientists that are directly involved in this research. As Coyne notes, this field suffers from the problems endemic to many disciplines where "students far outnumber the objects of study." One problem is that the names for specific ancestral human fossils and resulting controversy "can't be taken too seriously" because there are "too few specimens, spread out over too large a geographic area, to make these decisions with any confidence." Coyne avoids this needless debate by focusing our attention on "the general trend of the fossils over time, which clearly shows a change from apelike to humanlike features."

On matters that are likely to be of particular interest to readers of this blog, I must offer a somewhat mixed review. On the one hand, Coyne's impassioned defense of biogeography and its importance is inspiring. I could identify only a few places where studies and facts were somewhat out of date (e.g., the suggestion on p. 100 that Madagascar is an old island the formed 160 million years ago when it separated from Africa, when it now seems clear that Madagascar enjoyed at Late Cretaceous connection with present-day South America and Antarctica). On the other hand, I was a bit dissapointed with the lack of coverage of modern phylogenetics and its contribution to the evidence supporting evolution. Shouldn't the the similarities seen in the DNA of related organisms be recognized as one of the most powerful lines of evidence supporting the truth of evolution? Although this subject is mentioned in passing, the scant attention devoted to it may stem from Coyne's view that "molecular methods have not produced much change in the pre-DNA era trees of life" (p. 10). I think most modern phylogeneticists could take exception to this remark by citing any number of insights on the tree of life that were only possible with the use of molecular data. Indeed, some of these insights are brushed under the carpet by the few figures of phylogenetic trees contained in Coyne's book. Figure 1 (see image) and the accompanying discussion on page 6 about the relationship between birds and reptiles, for example, exclude tuataras, turtles and crocodiles, imply that lizards and snakes are distinct groups (they're not because snakes are nested within lizards), and suggest that most modern non-avian reptiles are a monophyletic sister group to dinosaurs and birds (this is only true if crocs and turtles are included with the birds and dinosaurs). The exclusion of turtles is particularly relevant because they are one of the most striking examples of how the visible traits of organisms and their DNA sequences do not give similar information about evolutionary relationships.

Nit-picky criticisms aside, Newsweek was right to include Why Evolution is True among it's 50 top books for our time. If you're going to read one book in preparation for your next encounter with a doubter of evolution, Why Evolution is True should be at the top of your list.