The spandrels essay always resurfaces
'A germline-encoded specificity might have arisen as an evolutionary spandrel, a byproduct of immunoglobulin gene diversification in vertebrates, and then been selected (Gould and Lewontin, 1979; Sangesland and Lingwood, 2021; Pennell et al., 2023). For instance, germline alleles with innately high affinity for bacterial antigens might be favored if they protect against commonly encountered pathogens and commensals via broad classes of epitopes shared by these organisms (Yeung et al., 2016; Collins and Jackson, 2018; Sangesland et al., 2020).'
@cyrilpedia not sure I got it from context... how is that a spandrel? Surely the high affinity being retained would imply selection to favour bacterial protection, and therefore the function is correctly interpreted, regardless of how it arose?
@MarkHanson Yeah, I think it works fine to just consider this as another source of diversity. The broader, more interesting problem, is how germline specificities (which are normally *not* high affinity) become fixed and developmentally regulated (the recombination process tends to abolish them, for some species, like the nurse shark, this is solved by having the full VDJ fused in the germline. but that's a very rare solution).
@MarkHanson I'm just hoping it will encourage some of the young 'uns to read this classic essaY (which has many flaws, including on the architectural function of spandrels, but is definitely worth reading). https://doi.org/10.1098%2Frspb.1979.0086
@foaylward @cyrilpedia Yeah, I bring it up now in the context of the classic thinking about NF-kB induction patterns vs. the modern logic of why so many genes are upregulated: the reason all the genes are induced is due to constraints on precision in activation, not a derived relevance of every gene to every possible infection.
@cyrilpedia @MarkHanson I usually discuss it my genomics class after I introduce junk DNA just to emphasize all the raw material available for evolution.