The Biologic Institute, the Seattle research arm of the Discovery Institute (not to be confused with the older North American Biologic Institute of Boca Raton, FL, lab for blood chemistry analysis and medical supplier), has a paper on PLOSone announcing a software package, Stylus. Stylus is supposed to do something relative to investigating protein chemistry by simulating evolution of, um, Chinese characters.
The authors, Douglas Axe, Brendan Dixon (he of the Microsoft moneybags), and Philip Lu, know that they are basing their whole effort here on analogy. Given the far-fetched proposition that something useful about evolution of protein chemistry can be learned by examining Chinese characters, one should give them props for making about as forceful an argument by analogy as yet has been seen from religious antievolutionists. You see, certain Chinese characters bear a resemblance to certain protein folds, if one orients the protein in question in just the right way and projects it onto a 2D space. (You knew “METHINKS IT IS LIKE A WEASEL” would be relevant in here somewhere, right?) And since Chinese is a language, and various people have talked about DNA and proteins being language-like, surely it can’t be a stretch to think that there is some deep connection between Chinese character space and protein space… OK, I think that’s enough sarcasm.
The primary fault in this paper, IMO, is that their analogy presumes that protein space is as rugged and, perhaps more importantly, as discontinuous as a Chinese character space. This is by no means established, though they try to give that appearance via citation of Axe’s previous studies.
We have no expectation that Chinese character sets should be evolvable from scratch and represent a spannable set. The significant question for the Stylus team isn’t whether they can do something with Chinese characters, but whether this has any bearing on the issue of whether observed proteomics are in fact spannable given genetic operators. Meaning of Chinese characters doesn’t offhand seem to be a good stand-in for protein function, not least because of the subjective nature of the former and objective nature of the latter.
Now, I have another issue… the Stylus software itself. The Biologic Institute has a SourceForge project set up for this, and one can get the software from there via SVN (sorry, no package for Stylus as of yet):
svn co https://biologicstylus.svn.sourceforge.net/svnroot/biologicstylus
The software is specifically stated to run on FreeBSD, and I have a FreeBSD 6.3 desktop. I should be in good shape.
The README gives some requirements for compiling, and a few “pkg_add” instructions take care of that:
pkg_add -r libxml2
pkg_add -r swig
pkg_add -r python
But the “bootstrap” configuration script provided errors out with a complaint about a bad substitution for “OSTYPE”. The help output for the script doesn’t seem to mention OSTYPE at all. I have an email off to the supplied address at the Biologic Institute to see if someone there has further details to offer.
(Given that Axe is elsewhere critical of Avida, I’ll note that at least one can obtain and compile Avida if one follows the instructions.)
Update: Reed Cartwright pointed out that they have hard-coded “make” in their scripts, and “make” differs between FreeBSD and Linux. So I downloaded Stylus to my Xubuntu, loaded the specified prerequisites, and still got the same set of errors on running “bootstrap”.
Update: I got a very nice note from Brendan Dixon in response to my inquiry on difficulty getting the program going. I’ll see if I can make progress based on that. One thing he notes is that despite what it says on SourceForge, he hasn’t installed Stylus on a FreeBSD system. So I’ll concentrate on getting it running on my Xubuntu install first.