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December 26, 2007

This year in intelligent design

Intelligent design and evolution both have definitions not related to biology. Therefore, as in past analyses, I’ve included “species? as an additional search term. A Google Scholar search for articles mentioning “evolution? and “species?, in publications with “journal? in the title – this eliminates some journals, of course -- gave 17,200 hits for 2007. Substituting “intelligent design? for “evolution? reduced this to 51 hits.

This was few enough that I could check each title individually, looking for papers claiming to provide data showing that living things were designed rather than evolving. I was hoping to find at least one such paper to critique in my usual way, but no luck.

A large fraction of the papers are in religious, philosophical, legal or educational journals. For example, the Journal of Anglican Studies published a paper titled “William Paley’s Natural Theology: An Anglican Classic?? Whatever.

Some biological journals mentioned intelligent design to criticize it, as in “Evo/Devo and the lungfish: the last gasp of intelligent design? in The FASEB Journal. The Journal of Agricultural Science published a symposium paper suggesting that intelligent design of photosynthesis by humans might soon be possible. I doubt that we will improve on evolution anytime soon, at least when it comes to the basic efficiency of key enzymes.

In a second Google Scholar search, I dropped the requirement for “journal? in the title, but added “flagellum? (a favorite example, claimed to be evidence for intelligent design) as a keyword. I found an interesting paper on “Stepwise formation of the bacterial flagellar system? (Proc. Nat. Acad. Sci.), which looked at DNA sequences and found that

many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

So here are some questions to think about. We can detect the signature, in DNA sequences, of gene duplication and other processes (selection, etc.) known to be important in evolution. What would the DNA-sequence signature of supernatural intervention look like? If the first life on earth had been created (perhaps by some extraterrestrial civilization, as a terra-forming project), are there any patterns (perhaps in the genetic code) that would survive four billion years of evolutionary processes? If there were a scientific discipline of intelligent design, these are the sorts of questions it would be asking. But, so far, there isn’t. One problem is that you can’t recognize any hypothetical departures from natural evolutionary processes unless you first understand those processes in considerable detail. And, as in all of science, you don't want to get too attached to a hypothesis you may end up disproving.

December 21, 2007

Lots of interesting papers...

...but I'm still working on a paper and two grant proposals due in January, so don't have time to blog this week. Maybe I can find time to review all the intelligent design papers published this year that meet my basic criteria -- that shouldn't take long! Check back in January, or you should be able to access abstracts from these links:

Sexual selection mediated by the thermoregulatory effects of male colour pattern in the ambush bug Phymata americana

Adaptive developmental plasticity in growing nestlings: sibling competition induces differential gape growth

More altruistic punishment in larger societies

Basic Math in Monkeys and College Students

December 20, 2007

MPen is mightier than MSword

You know how, whenever you edit an MS Word document, your neatly positioned figures and captions fly off in opposite directions? Someday, MPen will solve these and other problems. Meanwhile, here's a work-around I just figured out:

Layout graphs and captions you want to stay together on a single Power Point "slide." Make slide width equal the width of your printed lines, so Word won't try to squeeze text on either side. Save individual slides as WMF files. Import each WMF file into Word about where you want the slide. Slides may still jump around when you edit the document, but at least slide(s) and caption(s) will stay together.

I'm still working on grant proposals, but thought those of you who don't use LaTeX might find this useful.

December 7, 2007

The ghost of infections past, present, and future

Summary: A 39-year record of host-parasite interaction, recovered from sediment layers in a pond, is consistent with rapid coevolution.
Link: Host-parasite /`Red Queen/' dynamics archived in pond sediment

As I've discussed previously, archival samples often prove useful for answering questions that weren't being asked when the samples were collected. But what if nobody collected and preserved the samples you need for your research? Maybe you can find a "natural archive" that has what you need.

That's what Ellen Decaester and her coauthors did. They retrieved what appears to be a 39-year record of coevolution between the water flea Daphnia and its bacterial parasite Pasteuria ramosa from successive layers of sediment (24 cm total) on the bottom of a pond. To measure the coevolution of the ability of the bacterium to infect its host, and the ability of the fleas to resist infection, they exposed fleas from each layer to bacteria from the same layer (their "present") and from the next layer below (bacteria from their recent "past") and above ("future").
Daphnia.jpg
Bacteria from the past were less infectious, presumably because the flea population had evolved resistance to bacteria to which their recent ancestors had been exposed -- resistant fleas were more likely to have descendants. Bacteria from the "future" were also less infectious. Apparently the bacteria had lost some ability to attack fleas from their recent past. Perhaps there was a trade-off between retaining the ability to infect genotypes that were common in the previous flea generation versus being able to infect the present generation. Since they were able to recover live fleas and bacteria from layers thought to represent different time periods, it should be possible to work out the molecular details of this evolutionary arms race.

I say "thought to represent different time periods" because I wonder whether sediment layers preserve a perfect record of past genotypes. I'm sure the sediment layers were laid down in the order assumed, and presumably at a fairly consistent rate. A dormant flea egg from a layer laid down 20 years ago presumably represents a genotype present at that time. Dormant eggs aren't going to migrate from one layer to another. Neither would bacterial spores. Active bacteria might, however. This could just add random variation that wouldn't bias conclusions one way or another, but what if bacteria have a preferred direction (up, say, or towards particular flea genotypes)? "Parasite isolates were obtained by exposing a random set of Daphnia clones to sediment from each depth." Some method of ensuring that these bacterial isolates came from nonmotile spores rather than motile active bacteria would seem useful in future work using this approach. And I assume we will see such future work, based on this very innovative paper.

December 2, 2007

Atheism and religious satire?

That was the text on a button listed as the #4 genetics blog on DailyCells.com/community that somehow got pointed to This Week in Evolution. I know because a recent reader came here via that link. Only one reader came that way, though, so I guess I'll stick to science.