Again most claims that mutations are mostly harmless are gleaning that from mutations that are affecting sequences that are non functional in the first place,
As you have seen, most of the sites on proteins are not functional. So mutations there rarely do anything. And as you just saw, mutations to non-coding DNA are often the source of new genes which are often useful.
and/or re-defining 'harmless' as 'not all that harmful'
Indeed, neutral mutations can be very slightly harmful in some environments or in epstasis with other genes, and also can be very slightly beneficial in other environments, or with other genes. You seem hung up on the fact that very few things in biology are perfectly neutral.
the codon example is interesting in that DNA uses an additional hierarchical code convention to translate 4 nucleotides into 20 amino acids, but the overwhelming probability is still that an incorrect codon and amino acid will result.
No. Perhaps you should review probability. For example, valene can be coded by GTT, GTA, GTG, or GTC. So if there's a point mutation on that site there a one in three chance that it's at the variable site and you get the same amino acid. Two in three doesn't sound like "overwhelming probability" to me.
Again, the details matter, if you want to discuss this sort of thing.
There's an easy way to test this. I don't have any alleles that have given me any health problems. How many have caused you health problems? By you own definition, harmful mutations must have harmful effects on the health of one having them
Well you're lucky, not to have hereditary cancer in your family
But I do. Every family has lots of harmful recessives. And some have harmful dominants like Huntington's. But it's very unlikely that either of us have any mutation among the hundred or so that are unique to us, that causes us any health problems at all. As you noted in your source, a deleterious mutation is one that causes health problems.
Those with mutations that improve function are retained for the next generation
This is another very commonly repeated misconception.
The nylon mutation, for example. Or the human lactose persistence gene, or or the Milano mutation. Lots of examples. Real world beats anyone's beliefs.
Being able to run 25% faster than your sibling because of a miraculous genetic mutation during development, would be a pretty astoundingly fortunate mutation
As you learned, there's no miracles involved. And yes, there are mutations that can do that:
Scientists at Scripps Research have discovered a genetic mutation that gives tendons the ability to store more energy, letting mice jump higher and reach faster speeds than usual, as the team reported June 1, 2022, in Science Translational Medicine. Preliminary data on humans suggests that the gene variant, which is in a sensor protein known as PIEZO1, might play a similar role in people.
https://debuglies.com/2022/06/09/piezo1-mutation-give-the-ability-to-jump-higher-and-run-faster/
The Constructal Law shows that a mutation that raises the center of gravity higher on an athlete will make him or her a faster runner. Longer legs do more than add strength; they permit more energy gained from gravity in running. There are mutations for that. So no miracle involved.
surely that must be retained for the next generation? Intuitively of course.
Tends to be. The race is not always to the swift. But that's where the smart money is. If one's environment selects for speed, this is definitely an advantage.
But if the sabre toothed tiger can run 4x faster than you both, and decides you look tastier.. even that huge improbable advantage is not enough to be selected.
Fortunately, predators are good at economizing on energy output. It's tough being a predator, and they frequently starve. They pick the slow ones, always. So you don't have to outrun the sabretooth tiger; you just have to outrun the other guy. It's significant that you have to add another mutation in and effort to make your idea work. But unfortunately, it still wouldn't work.
That's just one example of chaos in the system, amongst countless millions, and it has a far larger impact that intuitively perceived, and this has been observed directly in experiments introducing bacteria with genetic advantages and watching them being routinely discarded in an inferior population that's doing just fine without the advantage.
Time and chance happen to them all. But Usain Bolt probably won't be losing races for a while, yet.
I am writing this in anticipation of you completely changing your mind and renouncing Darwinism for good
That would require evidence. And as you see...
And so it is next to impossible to remove that bias from our thought experiments.
Like adding a "looks tasty" allele to your sabre tooth tiger gedankenexperiment in an attempt to make it work for your argument. Takes some practice to keep from doing that, and it's always a possible problem, even for those of us who have done science for a long time.
Of course WE would select the advantageous mutation, however slight the advantage, because we can anticipate a hypothetical future pay off. But natural selection has no such powers of anticipation, the advantage has to be very significant, life or death, right here, right now, or no selection takes place.
That's a testable belief. And it can be mathematically tested and even examined in real life. Let's look at real life...
Evolution
NATURAL SELECTION ON BEAK AND BODY SIZE IN THE SONG SPARROW
March 1986
1986.tb00465.x
Abstract
We documented temporal patterns of natural selection on beak and body traits in a song sparrow population. We looked for evidence of selection in association with reproduction and overwinter survival in order to identify the conditions under which size in beak and body traits is adaptive. We also attempted to identify the specific traits most closely associated with fitness under these conditions.
Selection was observed in association with both survival and reproduction.
And so it is next to impossible to remove that bias from our thought experiments.
