The Revenge of Calvin and Hobbes




In all jawed vertebrates, the adaptive immune system “detectors” (receptors), are encoded not by single, stable genes, but by families of gene segments that change their conformation on DNA (rearrange) during the development of immune cells. By randomly joining one segment from each of the different families (called “V”, “D” or “J”, each containing from a few to a few hundred members) into a single coding sequence, the immune system can generate many thousands of different genetic combinations, each encoding a different receptor capable of recognizing a different molecular target. The proteins that mediate this DNA rearrangement process (“VDJ recombination”) are called RAG1 and RAG2, and they act on specific DNA sequences, recombination signal sequences, or “RSSs”, which flank the rearranging V, D and J segments. (For those who want to know more, Matt Inlay’s excellent summary, especially its “IC system II” section, serves as a very good primer).


In the absence of the machine [RAG1/RAG2], the parts [V, D and J gene segments] never get cut out and joined. In the absence of the signals [RSSs], it’s like expecting a machine that’s randomly cutting paper to make a paper doll. And, of course, in the absence of the message for the antibody itself, the other components would be pointless.
DBB, p. 130


Transposons are odd fellows in the DNA world, who spend their time physically hopping from genomic site to genomic site, and replicating themselves, pretty much as “molecular parasites”. They do this via a number of mechanisms, but the kind we are interested here are a class of DNA transposons which carry within their own sequences genes encoding the necessary enzymes (“transposases”) for cutting themselves off the genomic DNA (“excision”), and re-inserting somewhere else (“integration”). At the very end of each transposon element is a characteristic sequence, which is recognized by the specific transposase (I am sure you are already seeing the parallel with VDJ recombination).

A decade after the discovery of VDJ recombination the responsible enzymes, RAG1 and RAG2, were identified, and lo and behold their genes had a funny look about them: just like transposases, they were almost devoid of introns, and mapped right next to each other in the genome (transposons need to “travel light”, and cannot carry excess DNA as they hop around). This is when David Baltimore, in whose lab the RAG genes were discovered, and others wrote the review in the Proceedings of the National Academy of Sciences USA [3] that was mocked by Behe as proposing a “hop in the box of Calvin and Hobbes” for openly stating the transposon hypothesis: that RAGs/RSSs were the remnants of some sort of transposon system that integrated itself into a non-rearranging immune receptor, and became “enslaved” to it, causing the integrated portion to “pop out” whenever the gene became active, and in so doing generated useful diversity for immune target recognition.

To be fair, at the time the hypothesis was indeed quite a stretch, but still, a stretch that made some specific predictions. No sooner had Behe’s words been put to print, those predictions started coming true. What follows is a short timeline, with the major milestones:


  • DBB published. In it, Behe says:

” the complexity of the [VDJ recombination] system dooms all Darwinian explanations to frustration. [my emphasis] DBB, p. 139


1998: The Gellert and Schatz lab independently discover that RAGs can, under certain in vitro conditions, mediate actual transposition reactions by inserting cleaved DNA ends containing RSSs into double-stranded target DNA. This is the other side of the transposon “life cycle”, the insertion phase. In other words, although the RAGs’ physiological activity requires them only to cut DNA out of the genome, they bear, buried inside their structure, the ability to insert RSSs into DNA, a sort of molecular vestigial structure. This makes sense if RAGs are indeed an evolved transposase, but is harder to justify from a design perspective, because transposition events, by potentially disrupting genes, can actually be quite deleterious, for instance by causing cancer.




2005: RAGs find their long-lost family of transposases [1]. In this paper, Kapitonov and Jurka take a fully evolutionary, biocomputational approach to figure out where RAGs may have come from. Let’s look at what they did, and how.


Figure 1 “ Alignment of conserved regions in Transib transposases and RAG1 (Click on the figure to see a larger version from the original paper)



What this means is that a simple system exists, with both a RAG1-like gene and RSSs, as an independent functional unit: what we would expect for a direct, “reduced” predecessor to the supposedly irreducible VDJ recombinase system. But there’s more: while extending their search to the genome databases from various organisms, Kapitonov and Jurka found a number of other RAG1 homologues in various organisms, including some in which the similarity extended beyond the protein “core” they had originally search for, all the way to the so-called N-terminal region of the protein. There is therefore a family of close RAG1-related proteins in various organisms. The distribution of the various homologues in different lineages is shown below.




Let’s summarize: where once Behe saw an “irreducibly complex” system made of a) a receptor gene, b) a RAG recombinase, and c) RSSs, we now know that a) whole families of non-rearranging receptors and b) a whole family of functional RAG1 homologues acting on c) RSS-like sequences already existed before the emergence of the vertebrate adaptive immune system. Exactly what we would expect to see if the adaptive immune system did arise via an evolutionary process, as opposed to poof into existence in its complete form.


















