Sunday, April 02, 2006

Junk science

Last week PZ Myers brought the excellent post he wrote about my paper on the evolution of cell lineage complexity back from the archives. In a related post, PZ took the opportunity to remind us of how Paul Nelson, a fellow of the Discovery Institute, claimed our paper offered "a workable (i.e., usable) measure of ontogenetic depth, maybe". Ontogenetic depth was a concept proposed by Nelson in an unpublished discussion paper in early 2003. I first heard of Paul Nelson and ontogenetic depth in Pharyngula. The ignorance, apparently, was mutual, even though our measure had been originally published in 2003. Despite insistent requests for clarification, and repeated assurances that "an omnibus reply" was in the making, Paul Nelson hasn't said anything substantive about ontogenetic depth for two years. PZ concludes:
"Nelson promised us an explanation of his method; months later, after giving us nothing, he showed up to point to a legitimate and interesting science paper that used an interesting technique, apparently nothing like what he was doing, and thinks that's a fair substitution? What a wonderful example of the purely parasitic nature of the Discovery Institute! No work, only promises, and the best they can do is point to the efforts of real scientists!

We're still waiting for Paul Nelson to explain the procedure and utility of "ontogenetic depth". A day wasn't enough, and I can't complain about that. A month was pushing it. A year? That's not looking so good. At two years, we ought to just give up. I'll be patient, though, and give the poor fellow a decade [...]"
Last week I encountered another example of this kind of scientific parasitism by another intelligent design creationist: Salvador Cordova. Cordova, like Nelson, regularly engages in polite discussions with evolutionary biologists. This time, the topic was "junk" DNA. Cordova joined the discussion and steered it towards the topic of robustness. Over a two comments, he wrote:
"One can do a knockout experiment on one of the develomental pathways of a nematode vulva and then an alternative develomental pathway kicks in to create the vulva. There are two independently successful redundant developmental pathways in the vulva. [...]

In the case of the nematode vulva, without some co-option, the independent path way can not be selectively advantaged unless the other develpmental pathway is knocked out. The independent pathway, would have to be pretty much functional when it appears as it is critical to perpetuation."
He then used this example to suggest that robustness cannot evolve. The problem is that his discussion of vulval development in Caenorhabditis elegans is rubbish. The fates of the six vulval precursor cells are determined by the action of two signaling pathways: the EGF receptor/RAS/RAF/MAPK inductive signaling pathway specifies the primary vulval fate, and the LIN-12/Notch lateral signaling pathway specifies the secondary fate. However, these pathways are certainly not redundant.

The redundancy he's thinking about is in the synMuv (synthetic multivulva) genes. These form two functionally redundant classes, A and B (to which a third, C, has recently been added), of regulators of RAS signalling. This class of genes gets its name from the observation that mutants from within a single class show normal vulval development, but double mutants affecting loci in different classes, known as "synthetic", show several ectopic vulvae, a phenotype known as "multivulva". However, the synMuv genes do not constitute "independently successful redundant developmental pathways". This is parasitism of the highest order: the synMuv genes were originally characterized in the lab of the Nobel Prize winner Robert Horvitz. Let's just say that he's no intelligent design creationist. When are you guys going to start doing some actual research, instead of misinterpreting the work of real scientists?

Cordova's other arguments on how robustness evolves (or rather fails to do so) bear no relationship to any real research into this problem -- for a proper review of the subject see, for example, Andreas Wagner (2005), de Visser et al. (2003) or Flatt (2006). For example, commenting on A. Wagner's paper (reviewed here and here) Cordova descended further into his strange world of make-believe:
"Regarding the paper pertaining to circadian oscillators, 'Can these results be generalized to other systems? It's impossible to tell at this stage.' The answer is likely no.

We know from mathematics that evolutionary algorithms can only solve a small fraction of design architectures. That is a given fact in engineering. Some of those architectures which evolutionary algorithms can not solve are already in evidence in biology, such as the turing machine or anything dealing with large scale software such as seen in the cell."

Notice how Cordova skiped over the entire argument from the paper without actually addressing what Wagner set out to test, and then made up some "given facts" about evolutionary biology.

Remember Cordova's prediction that Wagner's result cannot be generalized to other systems. For the record, I'll bet on the opposite outcome. I'll return to this as more evidence comes out. (Something tells me that you won't have to wait for too long.)

Read on

Saturday, April 01, 2006

The unnecessary hypothesis

Does prayer work? The New Testament is clear that it should: "Ask and it shall be given you" (Matthew 7:7). Other religions would concur. However, evidence for this prediction has been hard to come by. Francis Galton was perhaps the first to approach this problem scientifically. In his Statistical inquiries into the efficacy of prayer (1872) he wrote:
"The efficacy of prayer [...] is a perfectly appropriate and legitimate subject of scientific inquiry. Whether prayer is efficacious or not, in any given sense, is a matter of fact on which each man must form an opinion for himself. His decision will lie based upon data more or less justly handled, according to his education and habits. An unscientific reasoner will be guided by a confused recollection of crude experience. A scientific reasoner will scrutinise each separate experience before he admits it as evidence, and will compare all the cases he has selected on a methodical system."
Galton, one of the founders of modern statistics, was clear about how to proceed. He began by reducing the problem to "a simple statistical question -- are prayers answered, or are they not?" He then argued that one should "examine large classes of cases, and to be guided by broad averages". In a memorable case study, Galton considered the "longevity of persons whose lives are prayed for":
"The public prayer for the sovereign of every state, Protestant and Catholic, is and has been in the spirit of our own, "Grant her in health long to live." Now, as a simple matter of fact, has this prayer any efficacy? There is a memoir by Dr. Guy, in the (Vol. XXII. p.355), in which he compares the mean age of sovereigns with that of other classes of persons [...] The sovereigns are literally the shortest lived of all who have the advantage of affluence. The prayer has therefore no efficacy, unless the very questionable hypothesis be raised, that the conditions of royal life may naturally be yet more fatal, and that their influence is partly, though incompletely, neutralised by the effects of public prayers."
Many studies have since attempted to detect the effects of prayer in a variety of contexts, using a Galtonian approach.

The results of the largest study to date into the clinical effects of intercessory prayer were published in the American Heart Journal last week. Rhosgobel wrote an excellent summary of the research. Galton would have been proud. The study split over 1800 coronary bypass patients into three groups:
  1. Patients who were prayed for but were told that they "may or may not be prayed for"
  2. Patients who were not prayed for but were told that they "may or may not be prayed for"
  3. Patients who were prayed for and were told that they "will be prayed for"
Patients from the first two groups did not differ in the probability of developing complications within 30 days of the surgery. Patients from group 3 showed a small but statistically significant increase (!) in complications. The study cost approximately $2.4 million, mostly from the Templeton Foundation. "Unscientific reasoners" have already started to make up excuses, in much the same way as defenders of alternative medicine.

After reading Laplace's Mécanique céleste, Napoleon is said to have questioned the author on his failure to mention God. Laplace famously replied: "I have no need for such a hypothesis". I agree.

Read on