Re: Part 1 (of 3): What are major aspects of evolutionary theory?

> > I've looked at the FAQ again just now.
> "The" FAQ? There are dozens (hundreds) of FAQs. Huh?

The talk.origins FAQ, you stupid ***.
The FAQ for the newsgroup where this thread is posted.
Which FAQ for which newsgroup do you think I was referring to anyway?

> > I have a problem: I don't believe there is yet any evidence for
> > Universal Common Descent, only for very-large common descent. We might
> > be able to trace each of the three domains from a single origin (each)
> > to all modern species of such domain, but there's no clear evidence
> > that the trunks of those three large clades can be traced back to a
> > single all-encompassing common ancestor.
> Yes there is. The evidence is of a somewhat different sort than the
> evidence for the rest of the tree (roots are always a problem), but it's
> there.

Are you claiming that a single species was the LCA of all domains of
life, that the tree can indeed be traced (with current evidence) back
to a single (one, uno, ein) root species (or strain of bacteria)?
Or are you allowing that the idea of a tree breaks down beyond the
three separate domain roots, that there may have been a mixmash of
multiple ancestors into *each* domain beyond that point? For example,
could there have been pre-prokaryotes A B C D E F G and then
the three domains formed by merger of those genomes:
- archea from A + B + F + G
- eubacteria from C + D + E + F + G
- pre-eukaryotae from B + C + E + G
Then much later endosymbiosis created the true eukaryotes as we know them.

> And without arithmetic, we can't do radioactive dating. Is it therefore
> necessary to discuss the basics of arithmetic?

Perhaps I should include one extra preliminary question, as to whether
the person has graduated from eighth grade or not. If so, then
presumably the person knows arithmetic and reading and writing and
other basic stuff needed to even understand what we mean when we ask
about atoms and isotopes and radioactive decay. I wouldn't break down
the question into each particular pre-8th-grade subject since virtually
everyone would answer YES to this question.

> > I personally think a four-taxa unrooted tree is the best starting
> > example, and whoever is maintaining that example should change it to
> > four taxa if not already done.
> Nobody is maintaining it. It's a POTM, frozen in the form in which it
> first appeared.

Then perhaps I might undertake to rework it to use only four taxa, with
only three possible ways to make the 2:2 split for the unrooted tree.
Or do you assert copyright on the work and refuse to grant me license
to create a derivative work?

> And you think the way I did it was too complicated?

Yes. For a very first exercise in using DNA/genome sequences to support
an unrooted tree, I think using five species was unnecessarily
complicated. Four species would have been less work on the part of the
reader, and increase likelihood of reader-success.

Too bad I missed the vote. I would have voted for four instead of five
species. Do you happen to know the message-ID of the call-for-votes so
I use Google to look it up and see what I missed?

> > Or maybe nobody suggested my fine idea before. I don't remember whether
> > anybody thought of exactly that idea before.
> Yes, it's been suggested before. Any tree can be assembled from a set of
> quartets. There's a program that tries to do that, called
> "quartet-puzzling". Here, though, it's silly, one reason being that one
> of the two nodes just isn't well resolved by the data at hand.

So you're saying that even though we know from other studies that
*both* 3:2 splits are well supported:
chi+hum+gor / ora+gib
ora+gib+gor / chi+hum
the first of those two is supported by that particular sample evidence
whereas the second isn't supported there and would require some
different evidence? If you delete one of the three African apes from
the set, can you use that particular evidence to support the one 2:2
split that remains from the first of the 3:2 splits above?
AfApe#1+AfApe#2 / ora+gib
Which of the three African apes is best to delete from the set, so that
the evidence best supports the remaining two as distinct from ora+gib?

IMO, after that first four-species example is presented, there should
be ideas for followup experiments, such as picking a different African
ape to omit, or using different portions of the genome for comparison.
By the way, I know that virtually 100% of the human genome has been
sequenced, and most of the chimp genome likewise, but how much of the
other three species have been sequenced so-far? And for how many DNA
bases is there unique alignment across all five genomes?
(After I get those answers, then I have followup questions such as if
you divide the fully-five-aligned portions of the genomes into sections
of reasonble size, such as breaking the sequence whenever you've
accumulated one hundred SNPs, what fraction of these segments show
support for one or the other of the two 2:3 splits (or 2:2 splits with
one species omitted)?)
..

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