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

> > I'm just trying to collect a nice organization of the evidence,
> > to ask who accepts it and who disputes it, and then for whose who agree
> > to stipulate the evidence is correct, a nice organization of the
> > theories of evolution and common descent, and ask them whether they
> > accept those conclusions. For those who accept all the evidence, and
> > evoution and common descent, then I ask them what theory, other than
> > mutation + replication + selection/drift, they have to explain the
> > cause of evolution and common descent.
> Several people here and in the TO FAQs have done just that. But you
> have a strange way to go about it.

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.

Likewise I've never seen anybody before me posting the list of basic
kinds of evidence and various aspects of theory. If you can cite
anybody before me who did, please find it in Google Groups and cite the
message-ID and/or GG URL. Put up or shut up.

> As I recall we began this argument
> because you were trying to use the evidence above as some kind of
> argument for natural selection, not just common descent.

Yes, that's correct. You remember the original well. It's just the
middle you seem to have failed in reading comprehension where you cited
two instead of three types of evidence. Maybe that was just a slip-up
in your otherwise fine comprehension.

Anyway, I got harassed by nitpicking so much, led off the main topic to
detailed debate over language expression and mathematical factor
analysis and subtle effects of stochastic mechanisms that for a day or
so I forgot what I was originally trying to cover.

I now think I need to break the overall checklist into four sections:
- p1 p2 p3 p4 p5 p6 p7 p8 (prerequisites: atomic theory, crystal
forming, radioactive decay, sedimentation, fossilization, plate
tectonics, biochemistry, genetics)
- e1 e2 e3 (evidence: taxonomy, fossils, DNA cladograms)
- f1 f2 f3 (facts: lines of descent, branchings apparent from fossil
evidence, and the two unrooted cladogram trees and the one forest of
rooted fossil trees fitting together nicely to yield common ancestry)
- t1 t2 t3(a,b) (theory: replication, mutation, differences in
survival factored into mean (bias, "pressure") and random (noise, "drift"))

Regarding my proposed poll I've been working on developing:
> You have a strange way of going about it.

Well I think the checklist of items to stipulate (legal sense) or
dispute is a reasonble way to find out exactly where the others don't
accept the modern synthesis of neo-Darwinism.

I think I'm settled on the items in the checklist. Next I need to word
each as a poll question. For example: The modern theory of evolution is
based on several facts about nature, one of which is that all material
is divided into atoms, and those atoms are of various types based on
the number of protons in the nucleus, these types we call "elements",
such as Hydrogen or Oxygen, and for many of these elements there is a
further division into "isotopes" based on the number of neutrons
present in the nucleus, such as normal Carbon 12 (6 protons and 6
neutrons) which is the common isotope and Carbon 14 (6 protons and 8
neutrons) which is less common. Agree [ ] / Disagree [ ]

> > I really want a check-list of evidence, accept or deny, and then a
> > check-list of theory, accept or deny, so we can pin down where exactly
> > the others disagree with modern evolutionary fact or theory.
> Good luck on that. I've had trouble getting creationists to admit what
> they believe, especially in any consistent fashion, or to accept the
> consequences of what they believe.

I'll make the first few poll questions, such as the one above on atomic
theory, so very obviously correct that nobody except a pre-school child
or a Zen buddhist would disagree. Once they get warmed up on those
first few questions, then when I get the ones they might possibly not
agree with because they never heard of any such ideas, such as magnetic
impressions in solidified ferromagnetic materials, they can learn a
little science, without yet attackig their religion, after all there's
nothing in the Bible saying magnets and magnetic compasses are
impossible or that it's impossible to create a magnet by subjecting it
to a strong fixed magnetic field, or anything like that, and Bible
thumpers might actually get a kick out of understanding why lodestone
has any intrinsic magnetism in the first place (because was liquid then
cooled in the presence of Earth's magnetic field) thereby allowing it
to be used as a crude compass by hanging it from a string.

> > Then that matrix is fed to such-and-such computer program
> > which generates the best-fit tree, if any, and shows a measure of
> > fitness
> Better call that "fit"; fitness has a different meaning.

Oops, I was thinking the mathematical term was "test of fitness" but I
did a Google search just now and see it's called "Goodness-of-Fit
Test". Thanks for the correction.

> > such as a P (confidence) value for tree-ness (and/or that
> > specific tree model) preferred over the null hypothesis of random
> > number input not belonging to any tree? It would be nice to
> > have two such examples, one very small, such as apes, only five or ten
> > species, such that the whole thing could be processed by hand or at
> > least the final result verified by hand, and one much larger to show
> > how really interesting trees can be demonstrated.
> Only the one I did myself with mtDNA sequences. Did you read that post?
> I've put it up many times.

I don't remember. Please try to remember a few keywords you had in that
article, and then do a Google Groups search to find the archive copy,
and then tell me the mesasge-ID and/or the URL, and I'll take a look
and see if it looks familiar. Don't post the whole thing again if there
are already several copies online.

> > If within a single geographic area there's an isolated species that
> > lasts a few million years, then immediately afterward there's another
> > species only slightly different from the previous but clearly showing a
> > significant change from the previous, and it's in the same area as the
> > first, we can reasonably guess that the second descends from the first.
> No, we can't. We could if we could be confident that there had been no
> movement between unsampled geographic areas, and that we had sampled all
> species in that particular area, and that we could actually recognize
> which individuals belonged to the same or different species. But we
> really can't do any of those things.

I didn't say such an observation is strong evidence for the hypothesis
being true. I merely said it's reasonable to invent that hypothesis to
explain it. Then if there are many other similar linked species pairs,
we might generate a general hypothesis that one species descending from
an earlier species is a common occurrance. Once we have that
hypothesis, that it's common, not a one-time occurrance, *then* we can
perform statistical tests to see whether that general hypothesis seems
to be validated by the data. But science works only with general rules,
not one-of exceptions, so we need to have many such apparent lines of
evolution before we can even propose anything that can be tested.

So my evidence is here's an apparent line of descent. Here's another.
Here's another. Here are a hundred. Hey, do you think there's something
going on here? What do you think that might be? Yeah, that's right,
evolution from one species to another, some kind of descent with
modification, either direct biological descent, or some Intelligent
Designer who lived in that local area and released one edition of the
genus after another and never acquired means to ship his product beyond
the local area, but in any case new species whose design is somehow
modified from design of corresponding earlier species, regardless of
whether that "design" is intelligent design or merely apparent design
due to some physical mechanism, in any case the design seems to be
evolving locally.

> > Now Darwin's finches wouldn't be like that. He observed a whole bunch
> > of species, which all seemed be be variants upon a common theme, and he
> > guessed that they all descended from a common ancestor, but his "tree"
> > had a single level wherein all modern species suddenly appeared in
> > parallel, no successive splittings over time that he could discern
> > without any fossils to look at.
> In fact Darwin didn't even propose a tree for Darwin's finches, just
> common ancestry for the lot.

That's basically what I said. He envisioned common ancestry, with no
idea how the various sub-clades might have occurred over time,
whereupon the mathematical graph, with a single massive unresolved
branching node, doesn't look at all like a tree, so Darwin would have
looked silly drawing a tree like this:

ancestral finch
|
+-----+-----+-----+-----+-----+--+--+-----+-----+-----+-----+-----+
| | | | | | | | | | | |
DF1 DF2 DF3 DF4 DF5 DF6 DF7 DF8 DF9 DF10 DF11 DF12

It probably didn't even occur to him to display the common ancestry
like that, since obviously it's wrong, obviously there was sub-clading,
it's just that the details of such sub-clading were unknown to Darwin,
so rather than draw a really stupid tree, just wait until some
sub-clade information might someday be available, and let that later
researcher draw a nice tree-looking tree showing what he discovered.

> However, we don't need fossils to determine this successive
> splitting. There are several papers on the phylogeny of Darwin's
> finches, the most recent using DNA sequences.

Sorry if I sound like a Creationist attacking evolution, but:
If we believe with all our hearts that *all* variation of species in
nature is caused by evolution over time, *not* by the result of
hierarchial committees of angels (I hope you saw the first part of my
followup I posted about 2AM PST), then whenever we compute a cladogram
based on DNA we can just take it for granted that our cladogram
represents a family tree of evolution over time. But such a cladogram
by itself does nothing to prove common ancestry if not a single fossil
had ever been discovered from a species of the past.

> I don't know of any "chains", just trees.

Every monotonic path through a tree is a "line" of descent, which is a
"chain" of successive links between adjacent species.
Two paths are concident until the point where a species-split
("speciation") event occurred, then the two paths run in parallel from
that point onward until one or the other goes extinct.

> You can turn trees into chains by ignoring some of the branches, if
> you really want a chain.

If you're trying to solve a maze, but it has multiple solutions,
if you're really smart you can find all the solutions to the maze (all
the paths from start to goal) without needing the crutch of erasing all
the other paths while looking at one of them. You can just "see"
several paths simultaneously, recognizing each of them as *a* solution
to the maze, recognizing that each is not unique, that there are others
in addition to any one you are looking at.

You don't have to ignore the other branches, you can see more than one
chain all at the same time, up to five if you are human, up to seven if
you are a bird. :-)

> > I believe such trees would show low levels of confidence for some
> > branchings, expecially pre-Cambrian, and if the program is forced to
> > exclude all low-confidence parts of the tree, it would yield a bunch of
> > separate trees instead of just a single tree. (Some programs would
> > simply refuse to give any result at all.
> Not true. I only know of one such program, and I doubt sincerely that
> you have ever heard of it.

I'm a bright guy who hates cruddy software, and often I think of ways
the software could have been better. I don't need to see an already
existing better program to suggest how the other cruddy software could
have been better. If I saw a program that broke horribly, or which
generated a grossly unsupported toplevel node in the UCA cladogram, I
would surely suggest the program be fixed to simply report separate
trees that can't be confidently joined, and thereby anticipate that
wonderful but secret program you know of. By the way, what's its name?

> The node of all eukaryotes, for example, is a very high confidence
> one.

Are you merely saying that eukaryotes cluster grossly distinctly from
all prokaryotes, so that we can be really sure eukaryotes are a single
clade? But what about the next level inside eukaryotes. Do we know with
high confidence how eukaryotes divide into exactly two sub-clades?

And when you say eukaryotes, are you considering only nuclear DNA, or
only mitochondrial DNA, or both of those conflated together? I've seen
a lot of published reports in _Science_ which say the same sort of
thing you are saying but never say which part of their DNA is being
cladogrammed. (Is that a verb??)

I can't finish tonight. I gotta go to bed now.
..

.