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It seems likely that much of the junk DNA in humans and other evolved species was once useful to provide an immune response to threats that no longer exist. This branch of biology would involve testing arbitrary non-disease-related proteins in blood for an immune response. If found the same reaction
should be tested in animals that have changed less over the years to see how far back the reaction holds. For example human, dog, rat, and squirrel blood might attack the protein, but frog immune systems might ignore it. In that case it can be conjectured that a threat appeared after Batrachomorpha and was more dangerous to mammals, and that the threat involved that protein.
My personal theory is that allergies could evolve to seperate individuals from potential threats. So the guy who can't eat fish had an ancestor who survived because he didn't eat the fish that, by whatever mechanism, killed people in his village who did eat it. In that case the protein ould be related to now-extinct food sources.
||//It seems likely that much of the junk DNA in humans and
other evolved species was once useful to provide an immune
response// Uh, why does it seem likely?
||...because that's a powerful force in evolution and the DNA no longer seems to be doing anything. Oh fine let me hand-wae it... there. Consider the question begged in the most humiliating fashion.
||The mutations evolution works by are random, you know
||It means DNA can be thought of as a bit like words made by
to determine how many letters to pull from a bag of
letters & arrange in the order drawn.
||How many junk words do you think you get to actual words?
||A lot, most of them.. so most of the junk really is just
||//because// Well, to be honest, most of the non-
transcribed DNA in the genome doesn't seem to be immune-
related, or at least not for the last few hundred million
years. Antibody-style immune systems go back quite a long
way, and their genetics are really cool.
||As to the underlying idea, almost any foreign protein will
produce an immune response. Your body produces
gazillions of different antibodies (by shuffling and mutating
quite a modest array of gene-parts), to ensure that there
will be something that recognizes just about any foreign
thing in your body. Once the initial immune response
happens, there's a further process of tweaking (targetted
mutations that affect the relevant antibody gene) to give a