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

anon1@xxxxxxx wrote:

>>>No, the talk-original FAQ does not have any place where it nicely
>>>organizes the various lines of evidence and the various factors of
>>>theory. It merely answers a lot of stupid questions from YECs and
>>>IDiots, giving point-by-point rebuttals, but not putting the whole
>>>thing into any sort of coherent whole.
>>
>>I like "29+ evidences for macroevolution". Why don't you?
>
>
> I never saw it when I was browsing the talk.origins FAQ.
>
>>http://www.talkorigins.org/faqs/comdesc/
>
> Let me look again and see if I can find that specific link:

Dude, all you have to do is click on it, or if your newsreader doesn't
support that, cut and paste into a browser. Has anyone ever told you
that you work way too hard?

[snip bizarre search for what's right in front of you]

> I've looked at the FAQ again just now.

"The" FAQ? There are dozens (hundreds) of FAQs. Huh?

> There's a question:
> "I thought evolution was just a theory. Why do you call it a fact?"
> which would seem to be a good place to put the 29-evidences link, but
> there are links to three other documents, none of which link to
> 29-evidences. But better would be addition of my new question, or
> perhaps a less confrontrational question:
> "I've heard bits and pieces of evidence in favor of evolution, but I've
> never seen a coherent listing of the various types of evidence. Where
> might such be found?"
>
> By the way, I eyeballed through the entire FAQ one more time, and I
> don't see any links to any of those pages I found by working backward
> using Google. If you believe there's a path from the FAQ page-by-page
> to the 29-evidences page, please cite the path. (The note that says
> "read the entire talk.origins archive" is *not* a valid "path" IMO.)

I have no idea. I don't use the archive that way. Why should I?

> What I'm going to do now is ignore the claim that there's a path from
> the FAQ to that 29-evidences page, and use your newsgroup article as my
> only known path to the page.

At last!

>>http://www.talkorigins.org/faqs/comdesc/
>
> 29+ Evidences for Macroevolution
> The Scientific Case for Common Descent
>
> Those are not the same thing. Either can be established without the other.
> It's confusing as to whether this document is about evidence for
> macroevolution or for common descent or both.

I don't know what you, specifically, mean by macroevolution. But by any
definition I can think of, common descent requires macroevolution, and
threfore implies it. You could have macroevolution without common
descent (or without very much), but do we really need to worry about that?

> Introduction
> * Evidence for Common Descent is Independent of Mechanism
> (It sounds like it's giving evidence for common descent, *not* for
> macroevolution)

Again, evidence for common descent is necessarily evidence for
macroevolution.

> <http://www.talkorigins.org/faqs/comdesc/default.html#theorytobetested>
> In this essay, universal common descent alone is specifically
> considered and weighed against the scientific evidence.
> I.e. no evidence whatsoever for evolution is here, only for common descent?

Again, I have no idea what your definition of evolution might be that
would allow this statement to make sense.

> Let me back up to the previous section:
> * Universal Common Descent Defined
> <http://www.talkorigins.org/faqs/comdesc/default.html#common_descent>
> U niversal common descent is the hypothesis that all living,
> terrestrial organisms are genealogically related. All existing species
> originated gradually by biological, reproductive processes on a
> geological timescale. Modern organisms are the genetic descendants of
> one original species or communal gene pool.
> 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.

> So for me personally, I'd like
> to skip to the alleged such evidence. Searching for it now... couldn't
> find anything specifically showing that the three domains definitely
> have a common ancestor. I think I'll have to dismiss this Web page as
> not the kind of listing of evidence I was seeking. Its biggest problem
> is that it is all-or-nothing, evidence for Universal (not just
> large-groups) Common Ancestry, and survives or falls as a whole
> depending on whether it establishes or fails to establish this grand
> hypothesis.

That's bizarre. You throw out the whole thing because there are a couple
of sentences you don't like? If that's so, I should throw out everything
you say without reading it either.

> I just want to show abundant evidence for large clades, and leave
> Universal Common Ancestry as an unresolve question that we might answer
> at some time in the future. If we can convince the Creationists and
> IDiots that all members of any single phylum are a single clade (except
> where the classical hierarchy turns out to be wrong and needs to be
> re-organized), that would be enough in my opinion regarding common descent.
> Then once that's agreed-upon, we can the discuss what mechanism caused
> large-clade common-descent to happen.
>
> (Regarding atomic theory: Atoms, elements, isotopes.)
>
>>I don't think the modern theory of evolution has much at all to do
>>with this stuff, except peripherally (without atoms or elements, no
>>purines and pyrimidines).
>
> Without atomic theory at the level of atoms and elements, it's not
> possible to understand what a crystal really is. Without isotopes, it's
> not possible to understand what radioactive decay means. Without
> radioactive decay, it's not possible to understand what it means for
> decayed isotopes in crystals to sit there as their result instead of
> original, and it's not possible to understand the principle of isochron
> methods of dating the formation of crystals from cooling magma. Without
> dating, you have no reason to believe that fossils were distributed
> over hundreds of millions of years, nor any way to specifically date
> layers of sediment and their corresponding fossils. Without dating like
> that, if one person says a fossil of Triceratops is 100 million years
> old, and another person says that same fossil is only 4000 years old.
> there's no evidence to say who is correct, it's just a matter of
> authority, or personal belief, who is correct.

And without arithmetic, we can't do radioactive dating. Is it therefore
necessary to discuss the basics of arithmetic? Try to have a little
perspective here.

>>I disagree with your first question.
>
> Which part(s) of it do you disagree with? Materials are composed of
> atoms? Each atom has a nucleus? A nucleus defines an element per how
> many protons it has? There are different isotopes of the same element
> per how many neutrons it has in addition to the protons?

Since you snipped the question, I have no idea what I disagree with.

>>Here is one instance:
>>http://www.talkorigins.org/origins/postmonth/apr05.html
>
> Ah, I saw that several times. It shows that (assuming you already
> accept the idea of evolution, and DNA as a way to track evolution)

Why are those prior assumptions necessary?

> that
> African apes (including humans) are closer together than any of them
> are to two non-African apes, and furthermore that within the African
> apes human+chimp are tighter than with gorillas. Basically the 3:2 splits
> gib+ora / gor+chimp+human
> and
> gib+ora+gor / chimp+human
> are well supported, whereas all other 3:2 splits aren't well supported,
> although you confuse the issue by talking only about the first of those
> two 3:2 splits.

No, you confuse the issue by failing to understand what I said. In fact
the second of the two splits is not well supported by that particular
data set (try it yourself), and I ignored it for that good reason. If
you think that leaving out extraneous information is confusing the
issue, then much of your approach becomes clear to me.

> This gives the unrooted tree uniquely as:
>
> ora\ /chimp
> >--T--<
> gib/ | \human
> gorilla
>
> People suggested you trim the set to four species to make the analysis
> easier, for example prove that ora+gib / gor+hum is well supported, and
> I thought I saw an updated version with 2:2 split, but now you're
> reverting to the original confusing version.

I'm not reverting. That's what is in the TO archive. And there were
mixed opinions on trimming to 4 species; the majority vote was that
trimming was not necessary or useful.

> Caveat: I don't remember
> names of who said what, so I don't remember whether you were the author
> or one of the people who criticized it or you were neither.

Shouldn't that be obvious from the name on the post?

> 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.

> If you do four-taxa in all possible ways
> (i.e. omit one of the five at a time, hence four ways to do it), you
> should get these 2:2 splits:
> ora+gib / gor+chi
> ora+gib / gor+hum
> ora+gib / chi+hum
> ora+gor / chi+hum
> gib+gor / chi+hum
> Once you have established all four splits, you then check whether all
> five are consistent with a single 2:1:2 unrooted tree of all five taxa,
> and indeed they are, which then implies the two 3:2 splits as well.
> So I suggest a fully worked-out example for just one of the 2:2 splits,
> then exercise for the reader for each of the other four 2:2 splits,
> then worked out quickie exercise showing those five 2:2 splits are
> consistent with one and only one 5-taxa unrooted tree.

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

> Maybe the author already worked that out sometime and posted it but you
> found the older version here.
> 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.

[snip paranoia]

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