Natural Limitation to Evolutionary Processes (2/14/05)

I hope it was helpful. Genetics is a truly fascinating subject.

If this is what you think a neutral mutation is, then somebody didn't explain neutral mutations to you.Neutral mutations are mutations to genes that alter base sequences but don't change the ultimate protein product, or the function of that product, in any significant way. For instance, if a gene had "CGA" at one position, that sequence would encode a protein that had the amino acid alanine at that homologous position. If a mutation changed that portion of the gene to read "CGG", instead, it would be a neutral mutation because that gene would still encode alanine at that position. (You can see that there are multiple, synonymous codon sequences for each amino acid at: Genetic code - WikipediaNeutral mutations have no effect on the function of a gene. Mutations that cause even a slight disease effect such as you describe cannot be neutral, by definition.

Actually, it has been. You can read about a baby that was either born with, or inherited, the mutation in this article in the NYT.

If comic-book-style superstrength is genetic degredation, then, in the words of Tevye, may God smite me with it!But that's basically the shell-game for creationists, isn't it? They define any difference from "normal" as "degredation", and then can assert by definition that any mutation cannot be beneficial.If you don't operate from a definition of "beneficial" that relates to increasing allele frequencies, then you simply have no objective basis to define "beneficial." No matter what the change, there's some trade-off that you can latch onto.

Well, it seems to me that there would be a big detectable difference between your view, where beneficial qualities were present from the beginning and are lost as time goes by; and the consensus evolutionary view that beneficial qualities spontaneously appear in individuals who then mate and spread those qualities through their successive generations.Speaking outside of human populations for a moment, because human civilization muddles the issue (and our long generational times makes these comparisons more difficult), and assuming that you agree with my extremely generalized statement of your position, which would you argue is the predominant mode of most populations? Do we observe beneficial qualities lost from most individuals over time with a net reduction in the "goodness" or "health" (or whathave you, let's avoid the term "fitness" which already has an evolutionary definition); or do we observe, as generations of a population go on, that individuals appear with beneficial qualities than then go on to dominate the population?I think the evidence, from things like bacterial studies or other efforts in population genetics - or even casual examples, like animal breeding - indicates the latter. It seems to be predominantly the case, in things like animal breeding, that the reward comes from a breeder taking advantage of an exceptional individual - say, with a long and attractive muzzle that his ancestors lacked, rather than from the breeder struggling to maintain ancestral perfection against a tide of genetic degredation. Yes. But we can see any mutation this way. For instance, the super-strong infant I linked you to earlier possesses two mutations that each knock out the gene that produces a muscle-limiting factor called "myostatin." Lacking the ability to produce this protein, the infant's musculature was able to develop unhindered, with considerable result.But, hey. Maybe we're all the mutants, with a genetic degeneracy that leaves us all 98-pound weaklings, and this infant is simply the "wild type." (That's a term that we use to refer to the nominal, unmutated version of a gene or phenotype.) Maybe he's just a reversion to a previous state of increased human perfection. But agreeing, as I know that you do, that natural selection weeds out genetic weakness, I think that you would have great difficulty explaining how weakness would come to overtake strength over 6000 years of human civilization. (From an evolutionary/anthropological perspective, I have a few speculations of my own about the evolutionary role of a muscle-limiting protein factor.)

Let's talk about what a gene is.DNA is a molecule that encodes a "recipe" for a protein in the form of, basically, a list of ingredients (amino acids): "start with a methianone, add an alanine, then a lysine, then an arginine", etc. Every one of the 20 different amino acids used in living organisms has it's own three-letter code. (In fact, there are usually several different three-letter codes for each amino acid.) When that code appears in the DNA, a part of the cell grabs the corresponding amino acid and tacks it on to the end of the protein that it's constructing. There's another three-letter code, too: "stop." It's a signal to the cell that the protein is "done", construction should stop, and the protein should be released into the cell. (It's obviously a lot more complicated than this but bear with me, and try not to draw too many conclusions from this enormously simplified description of the process.) There's no randomness in this code. If the code says "Lysine", Lysine is what you get. Every time.Different alleles are like different recipes for the same dish. My recipe for chili calls for kidney and navy beans, maybe yours doesn't. Allele 1 for a gene specifies Leucine at the 2,356th position; Allele 2 specifies Lysine there instead, maybe. Allele 3, though, specifies "stop" at that position. If the 2,356th position is only halfway through the protein, there's probably no chance that the half-completed protein product is very functional. (That's how a mutation can prevent a gene from doing it's job.)Let's relate this to Mendelian genetics. As a sexual organism, you have two copies of every chromosome. That means that, per gene, you have two alleles. It's like you and your buddy coming to the chili cook-off as a team - you each bring your own recipe, and you're each going to make your own pot of chili according to it, but to everybody else, you're acting as one unit.Your genes are the same way. Both of those copies of that gene are working independantly, they don't get mixed or blended at all. They both independantly generate proteins according to their own recipe. Maybe they have the same recipe. Maybe they don't. Maybe one of them has a recipe that's broken in the middle like I described above, but the other one is fine, and it goes on making the proteins your cells need to do a certain job. (Maybe you got Allele 3 on both your chromosomes, from both your parents, and then you're really in trouble.)All a mutation is, is a change in the recipe. Let's say that a mutation happens to Allele 3, and the "stop" is replaced with "Proline". Now, that gene produces something new. Something that hasn't been seen before. Because that's a new version of the recipe, we call it Allele 4. (It's the 4th different version we know about.)It didn't come about as a result of any kind of mixing or combination of any of the other alleles, and it wasn't hidden in the alleles, waiting to come out. It wasn't one of several "possibilities" that could have resulted from the allele. Once the allele mutated, this was the only possibile protein product that could result, and it'll be the only possible result until another mutation happens to change the gene again.Now, we have a fairly good idea about what kind of situations will result in mutations, but they're not terribly relevant. It's related to the process by which cells produce copies of themselves - along with copies of their chromosomes - and various things that can go wrong during that process. That's why you hear people call them "mistakes", because it's usually happening when a chromosome is being copied, and the new copy isn't quite exactly the same as the old one. But it's sufficient for you to realize that a mutation is simply a change in the sequence - the "recipe" - of a gene, creating a new allele from an old one. It is most definately not the revealing of any "hidden" information or possibilities that were already there. Mutations are, by definition, something new. Pseudogenes almost certainly are formerly functional genes; they're called "pseudogenes" because their sequences look a lot like other genes but they've been de-activated by the cell. A lot of junk DNA are endogenous retroviral sequences - DNA implanted by viruses for their own purposes which the cell has de-activated for its own protection. They just get copied down in their in-active state from generation to generation, forever.But a lot of it is accumulated mutations, too. Somebody pointed out that the vast majority of our DNA looks like somebody simply copied "and" over and over again. Not literally the word "and", but just the same short little sequence over and over again. That's because one very common kind of mutation occurs at sequences that are highly repetitive, and what the mutation does there is accidentally add a few repetitions. Over successive generations of reproduction and cell division, we've got all these repetitive sequences that just keep getting longer and longer. Sometimes they get removed, but that's a lot less common.Well, I do go on. Sorry this was so long. The general point of it all is - beyond the two alleles of each gene you possess, there isn't any room for hidden possibilites or hidden versions. So we know that all such changes are mutations, not the expression of dormant possibilities. There's simply no place for dormant possiblities to hide. There's plenty of dormant stuff in our genome, to be sure; but it's all sleeping right out in the open, and we know the difference between a new version of a gene and a re-activated dormant sequence somewhere else. We can actually see from what location on the chromosome a specific protein product is being generated.