A test for claimed knowledge of how macroevolution occurs

Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing/selecting a new set of alleles?Edited by Faith, : No reason given.

Just a little context for my previous posts. Here is a chart for transition and transversion substitutions: Transition mutations are substitutions for bases that are structurally similar. Adenine and guanine have two rings while thymine and cytosine have one ring. Therefore, it is more likely for the protein that is copying DNA to substitute similar bases than dissimilar bases. Due to biochemistry, we would expect naturally caused substitution mutations to be biased towards transitions over transversions.There is also a second major mechanism. If there is a two base sequence CG (called CpG because of the phosphate between them on the DNA backbone) then the C can be methylated by proteins in the cell nucleus. A methylated C can be deaminated into a T. The fingerprint of naturally occurring mutations is a high rate of CpG mutations and transitions outnumbering transversions. We know this is the natural process because we understand the biochemistry and also observe these same rates in new organisms. When we see this fingerprint in a comparison of genomes it is smoking gun evidence that those differences were produced by known and observable natural processes.

"Mutation" is defined as a change in the sequence of amino acid molecules in DNA.We get some DNA from our mother and some from our father. Any DNA we have that is different from both our mother and father is a mutation. That's by definition.We can and do compare DNA sequences and detect mutations.The differences between someone's DNA and both their parents, which we label as mutat, did not exist anywhere before. Not in the mother's DNA, not in the father's DNA, not anywhere. No amount of redefinition or argument can change that fact. It does not depend on assumptions or worldview.Mother's DNA + father's DNA + mutations = your DNA. There's no other physically possible source of your DNA.

If they were the result of recombination then the child's DNA would match one of the alleles carried by the parents. This isn't what they see. The child has a difference in its DNA not found in either parent, not in any of their alleles. This is a mutation by definition.

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Well, but aren't you just talking about observed differences, and how do you know those differences are the result of mutations rather than the result of sexual recombination producing a new set of alleles?

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What makes you think that sexual recombination would produce new alleles. If it did why wouldn’t they count as mutations ? And why do you think that actually comparing the sequences doesn’t give all the information you need ?

Easier than pie.All recombinations are identical to the corresponding sequence in one parent (or both). So we can comp the three genomes and detect the recombinations.Some relatively small amount of the offspring's DNA will not appear in either parent. Those we label as mutations. The particular mutations do not exist anywh else. (It is poss it may exist somewhere else but that wouldn't be a copy of the offspring's DNA; it would have to arise independently.) Edited by JonF, : No reason given.

But wouldn't the substitution of one allele for another show the same kinds of differences? Yes, I'm more or less winging it, so I expect to have a better understanding if the discussion progresses, but those differences in the placement of chemicals must also be the case when one allele replaces another. If there were no differences in that sequence there would be no differences in the proteins the sequence makes and no difference in the traits the protein brings about.Besides, this presentation of supposed mutations is just too organized for how mutations are normally described as random. Why should they occur in such a regular looking pattern at all if they really are random mistakes in replication? As I said before, this is revolutionary information, isn't it? It simply does not fit the definitions we usually encounter.So in fact the pattern more reasonably reflects built in variation than mutations.Edited by Faith, : No reason given.

No. The child's DNA sequence doesn't match any of the 4 alleles carried by the parents.Here is a simple example. Each parent has two alleles, and the child gets one allele from each parent:Father:AAAAAAAAAAA
AAATAAAAAAAMother:
AAAAAAAAAAA
AGAAAAAAAAAChild:
AAAAAAAACAA
AAAAAAAAAAAThe child has two all A alleles, on from each parent. However, there was a C mutation that happened in one of those alleles. We know it is a mutation because none of the parents' alleles had that sequence. The child now has a new allele due to that mutation.Are you now saying that mutations never happen? If so, that's just nuts.Edited by Taq, : No reason given.Edited by Taq, : No reason given.Edited by Taq, : No reason given.

What happens in the DNA when say a brown-eyed Bb father and a brown-eyed Bb mother produce children? The Mendelian formula is one BB, two Bb and one bb, right? How is this expressed in the DNA?Is the parents' B on one strand and b on the other?I'm sure there must be a different sequence of the four chemicals for a B versus a b, right?

No, no, no, no.If your allele is the same as your father's allele that's recombination.If your allele is the same as your mother's allele that's recombination.If your allele is different from both parent's alleles that's mutation because that's the label we use for that situation.There is no other place your allele could come from. There's no allele bank where your parents could get a special one.

What happens during the production of sperm and eggs is that the genome is split into two. Some sperm will have B and some sperm will have b. The same for eggs. Yes. There can also be new mutations that happen in either allele, making it different from the B and b alleles found in the parents.

Could we ignore the mutations issue until I get how the Bs and bs show up in the DNA?

I guess I don't see traditional breeding and mutation breeding as the same thing. The examples you mentioned of mutations in dogs and cattle have come up in previous discussions, and I wasn't forgetting them when I said that mutations play almost no role in breeding. Your sense that mutations have been responsible for more breeding results than we give credit for seems a quite a stretch to me, though I would of course concede in the face of evidence. But that populations of domestic breeds revert so quickly to wild forms once out in the wild (see, for example, When domesticated animals return to the wild) argues strongly, at least to me, against mutations playing any meaningful role in breeding.The lack of mutations at any meaningful frequency in traditional breeding on human timescales is the driving force behind efforts at mutation breeding where the mutation rate is artificially accelerated.--Percy

But I've got an allele from each parent don't I? Two alleles, one from each. If I've got a b from my father and a b from my mother are these going to be identical sequences of DNA? (if they are how are they going to reflect the complementary pairs of chemicals?)What if I've got a b from my father and a B from my mother? What will the DNA look llke?Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

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Yes, I'm more or less winging it, so I expect to have a better understanding if the discussion progresses

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Spouting nonsense because you don’t know what you are talking about is not a good way to gain understanding.

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but those differences in the placement of chemicals must also be the case when one allele replaces another

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And that is showing no sign of gaining understanding. Yes, alleles differ in sequence. But if the sequence found in the child does not match the sequence for the gene in either parent, it has to be a mutation.

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Besides, this presentation of supposed mutations is just too organized for how mutations are normally described as random

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At the level of the chemicals some substitutions are more probable than others. That is what the graphs show. (Besides the fact that we are talking about probabilities because these changes are random). If you roll two dice some totals are more likely than others. It’s still random. And that isn’t even the randomness we’re really talking about when we call mutations random.

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I said before, this is revolutionary information, isn't it? It simply does not fit the definitions we usually encounter.

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No, it’s just a detail that you won’t know about if you just skim the surface - and you haven’t even got that far.

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So in fact the pattern more reasonably reflects built in variation than mutations.

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Are you literally suggesting that differences from the parent’s genes are most likely not differences from the parent’s genes ? Because differences from the parent’s genes are mutations.Or perhaps what you are saying is better expressed as “mutations are built into the reproductive process”.