The End of Evolution By Means of Natural Selection

I'm trying to follow along here quietly, but I'm having some trouble with things I don't know. I want to compare what Faith is suggesting with these innumerable front-loaded hidden alleles with the normal rigmarole of mutations and natural selection, see how the results might tend to differ, sort of a "thought experiment". I'm aware of the special problems in trying to imagine how an allele stays hidden for any significant number of generations, but that's not my main obstacle just yet.We normally tend to think of mutations, I imagine, as being dominant. That is, we talk about someone who has a phenotype that is unusual, perhaps they shoot ray beams out of their eyes or metal claws out of their hands, and we check them out to see how that happened, and when we look in their genes we see that they have a new gene that neither of their parents sample has in it. Unless I'm totally off base, this would be on only one of the two zygotes, yes? (why would the same thing go wrong with both zygotes of the gene?)So therefore, in order for it to be brand new in this individual, and also expressed in his phenotype, that one new trait in that one out of two zygotes would have to be dominant. But, is that how it really always happens? What I mean is, do we also get new mutations that are recessive? So then when someone is born with blue fur who can teleport, and we check them, we don't find any new genes that their parents didn't have. The mutation happened to some common ancestor back when, and the zygote has finally come together in a matched pair and the gene is finally expressed now.Does this ever happen? Does it happen about half the time? Or are they always dominant, in which case does relative dominance tend to show which genes are more recent than others?PS: Just to contribute something to the actual topic, yes, the above suggestion about how long it might take rare genes to come together and be expressed is about the closest thing to an argument I can see in favor of this hidden allele scheme. If a population is suddenly isolated, there's a much greater chance of incestuous pairings. Hard to imagine how there would be none at all until the isolation, though.

Yes I am, thanks! Chromosomes. Alleles on each chromosome? I'm reading about genes being "heterozygous" rather than "homozygous". I guess that gets all muddled up when I try to express it as "one of the two zygotes". But fine, what I mean is, a mutation tends to occur on only one chromosome, not both, right? So then, to be expressed immediately in the first generation, it would have to not be recessive, yes? Yes, I had an idea like this to start with. That is, in a given pairing, black might be dominant because in that case it represents production of a pigment, whereas white might be recessive because all it represents is the non-production of the pigment. But then I read this Dominance (genetics) - WikipediaMendel's pair-matching math tends to make me feel slightly queasy after only a few iterations, sorry to be so stupid about it.If a mutation can be recessive, then it won't be expressed in the organism in which it occurs. This means that a gene may be "hidden" for some or even many generations in the evolutionary synthesis just as it could be in Faith's "no useful mutations" world.Is that correct?

Right, so if Bob has a mutation (and I'm guessing that that mutation is liable to occur on only one chromosome of the pair he has) and that mutation is dominant, then it can be expressed right there in Bob. But if it is recessive, then it can't. And because it's a mutation, Mary whom Bob marries doesn't have it, and therefore even though about half of their kids have the new gene, it isn't expressed in any of them, because it is never reinforced. And Bob and Mary's kids dont breed, because society frowns on that sort of thing, so it doesn't get reinforced that way either.So, it isn't until several generations later, in some sort of "kissing cousins" scenario, before that gene might end up being homozygous for an individual and actually get expressed. It might never get expressed, it might get lost in the shuffle or just not get reinforced even though it persists through generations of outbreeding. Inbreeding might never occur, until suddenly one day Bob and Mary's descendant Phil gets trapped on a desert island with his wife Sally and they have two kids and then die off and those kids grow up feral and inbreed and produce children who have the gene reinforced and expressed and suddenly there are people with purple hair whereas there never were before, even though the gene for it has been in existence for many generations.Or not?

I still haven't managed to digest the polyploidy and "junk DNA" as lost alleles arguments, so forgive me for not incorporating those arguments into my "simulation" as of yet.But I see that Faith is allowing for mutation to happen, as long as it's in the form of disease and degeneration. There are a lot of diseases and disorders that directly affect the chromosomes, aren't there? I am thinking of things like Down's Syndrome, dwarfism, and hermaphroditism of various kinds. Chromosomes can fuse, split, double, or vanish.These sort of "disease" mutations could certainly contribute to speciation couldn't they? For example, we have horses and donkeys. We know they are the same "kind" because they can interbreed. These pairings are not very successful, however, they produce mules which usually cannot reproduce in turn. The occasional non-sterile mule or hinny still won't breed true, they revert to one type or another.The reason for this is that horses have 32 chromosome pairs (64 chromosomes) while donkeys have only 31 pairs (62.) As a result, the mule only has 63 chromosomes, which don't pair up properly for further reproduction. Now, isn't this a result of what we would certainly call disease if it happened to us? That is, either the horse ancestors suffered a chromosome fusion or loss which produced the donkey, or else vice-versa the donkeys suffered a split or doubling. Yes?So if something a little more severe than this happened to animals of a particular kind, they very well might not end up being able to interbreed at all. Yet they would obviously still be basically the same animal, as with hares and rabbits or whatever, camels and llamas, sheep and goats, bison and cattle; we see lots of unlikely breeding pairs and also animals who look the same to us but cannot interbreed. Isn't this mutation / defect at the chromosome level the cause of a lot of this?

Can't they acquire it via lateral transfer? Isn't this in fact pretty common in studies of things like immune resistance?Admittedly it's not a reliable standard procedure but I think you are neglecting this aspect of bacterial evolution. Don't hesitate to correct me if I have got it wrong somehow.

I tried to follow the argument but it didn't stand up at all. While it is fairly easy to get rid of dominant genes simply by killing all instances of them, it is virtually impossible to get rid of recessives. They ride along and keep popping up whether they are good for survival or not.While isolating recessives does tend to increase their likelihood of being reinforced due to the greater likelihood of inbreeding, this doesn't magically make them dominants without some further beneficial mutation. Nor does mere isolation produce anything like real speciation, the new "variety" remains capable of breeding with their cousin group unless mutation intervenes.After RAZD smacked me down about chromosome mismatches, I did better research and learned that a lot of what prevents interbreeding amongst otherwise similar species like apes and men is due to mismatches on the much more granular level of the genes themselves. This is overwhelming due to insertions and deletions which tend to cause the genetic structure for specific traits to drift away from the very similar structures in slightly different locations on cousin species.So the thread wasn't a total waste, I learned something. Thanks.Edited by Iblis, : brain mismatch