Does Intelligent Design Have Merit?

A Failure of Scholarship

This post by Casey Luskin graphically illustrates why Intelligent Design is not science. Lack of even simple standards of scholarship fatally flaw ID arguments. For example, in attempting to discuss a paper by Pancer et al., (Nature, 2004 Vol. 430: 174-180) that Luskin thinks shows that there was a big gap in the origin of the vertebrate immune system, Lusking claims:

Furthermore, when these authors say that the usage of IG domains is “untraceable,” they are not asking the question “from what were these materials co-opted during evolution?” IG domains are found throughout biology from bacteria to humans and thus it is simple to imagine where higher vertebrates might have co-opted such domains. Rather, this paper is talking about the type of deeper question Behe raises: by what Darwinian pathway did IG domains evolve into the type of IG domain used by antibodies in the adaptive immune system of higher vertebrates?

This completely misrepresents the Pancer paper. It was not in anyway about the evolution of Ig domains, and as such it did not ask questions about Darwinian pathways to Ig, contray to what Luskin implies. The Pancer et al., paper reports the discovery of the class of molecules that produced allograft rejection in Lampreys. They found it was not an Ig system, as in jawed fish and the rest of us vertebrates, but due to a completely different class of molecule. In Jawless fish, there is no adaptive Ig system. The one throwaway line line that Luskin quotes needs to be seen in the context that the paper was written (discovering the mechanism of adaptive immunity in an organism without rearranging Ig molecules), it is not saying that we have no idea of how Ig molecules evolved. In fact, it says nothing about the evolution of Ig molecules at all.

For a paper that actually does look at the evolution of Ig molecules, one need look no further than another paper Pancer et all published in 2004. Note that before this paper was published, it was already known that several Ig-like molecules had been identified in amphioxus and sea squirts that could play the role of the ancestor of Ig. This is not just proteins with the Ig fold, but deeper Ig structure. In sea squirts there are Ig fold proteins (nectin and Junctional Adehesion Molecules) with an Ig fold and a Constant-Variable domain architecture just like the immunoglobulins. Also in amphioxus there is an Ig protein which is used in innate immunity (the Variable Domain Chitin Binding proteins) that was known in 2004 (in 2006 a protein that is a very similar to the T Cell Receptor and is involved in innate immunity was found in the amphioxus, be here I'm dealing with 2004 knowledge relevant to Behe's testimony).

Pancer's paper on the evolution of Ig molecules Pancer Z, Mayer WE, Klein J, Cooper MD (2004) Prototypic T cell receptor and CD4-like coreceptor are expressed by lymphocytes in the agnathan sea lamprey. Proc Natl Acad Sci USA 101:13273-13278 . Here they report finding a molecule in the lymphocytes of Lampreys that looks very much like the immunogloblulin T Cell Receptor. Not only does it have an Ig fold, and a constant-variable domain structure, it also has a joining, constant and cytoplasmic chain structure that matches the structure of modern rearranging T Cell Receptors. It looks just like you would expect a non-rearranging ancestor of TCR/Ig to look like. SInce then several other memebrs of non-rearranging Ig like molecules have been found in Lamprey lymphocytes.

Now, it wouldn't take much to discover this paper on Ig evolution, a simple PubMed search would have found this paper, it is also listed in reviews on the evolution of adaptive immunity from 2004 to 2005. Yet Luskin ignores it completely and discusses, as his key argument against our account of the evolutuon of immunity, a paper which does not look at the evolution of Ig at all.

Let me repeat this, Luskin is using a paper that reports that a) Lampreys have an adaptive immune system and b) the Lamprey genome does not adaptive immunoglobulin genes, and then discoverers the mechanisms that produce adaptive immunity (a novel variant of an innate immunity mechanism) to claim that we have no accounts of how Ig molecules could have evolved. He ignores the paper by the same group that reports the very protein that Luskin claims is missing from our account of immune system evolution.

If a prominent ID advocate can't even get the description of one basic paper right, how are they going to handle more complicated papers on the evolution of the immune system?