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

anon1@xxxxxxx wrote:

>>>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.

I like "29+ evidences for macroevolution". Why don't you?

http://www.talkorigins.org/faqs/comdesc/

>>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.

No, it's your artificial division of the data that is the problem here.
Taxonomy is not, as you seem to think, something that relies on
embryology, or morphological characters, alone. It's the result of
combining all relevant data, including fossils and molecules. If you
meant to talk about morphology of extant species as being your category
e1, you used an inapplicable term to summarize it.

> 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"))

I think this is a bizarre division, and entirely artificial in its
structure from beginning to end. How can facts be separated from
evidence, for example? I would even deny that facts can be separated
from theory.

> 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 would certainly disagree. 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).

>>>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.

Bad start, since I disagree with your first question.

> 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.

>>>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.

Here is one instance:

http://www.talkorigins.org/origins/postmonth/apr05.html

>>>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.

You may like this line of argument, but very few scientists do. Tracing
of actual ancestry, by assigning one fossil species as the ancestor of
another, just isn't done, with two exceptions: 1) science journalists
hot to make things exciting for the public; 2) human paleontologists
(talking about people who work on the paleontology of hominids here --
no jokes please), who for some reason just can't do without claims of
ancestry; makes their fossils look special, I suppose.

> 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.

Good luck with your research program. You're going to have trouble
getting scientists to sign on to it, unless your description above was a
really bad one that doesn't convey what you would actually do.

>>>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.

[snip]

>>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.

As I explained in another post, this is a pathological approach to
science. It doesn't just destroy the value of hierarchical evidence, it
destroys the value of all evidence, of any sort. Fossils are not special
in this regard.

>>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.

Yes, I now that. But that's the real tree you are describing, with real
organisms at the internal nodes. In practice we probably have not found
representatives of most of the internal nodes, and for those few we have
found, we can't tell them from "side branches". So while these chains of
yours certainly did exist, we can't really identify any of their members.

>>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.

If this makes any sense, then I have no idea what you mean by a "chain".

> 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?

I forget, but the algorithm it's based on is called continuous track
analysis, or CTA, and it was published by John Alroy. The program may be
available on Alroy's web site. You may like it because it also assumes
that real specimens can occupy internal nodes.

The way we show confidence in actual phylogenetic analyses is by various
tests of support for particular nodes, which can take the form of some
kind of confidence number attached to a node, or to collapsing all nodes
below a certain level. The most popular forms of this are bootstrap,
Bremer support indices, and Bayesian posterior probabilities.

>>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?

I'm talking about the node "Eukaryota" itself. It happens that the very
basal branch of Eukaryota is a bit controversial.

> And when you say eukaryotes, are you considering only nuclear DNA, or
> only mitochondrial DNA, or both of those conflated together?

Nuclear DNA is the only thing you can use, since some eukaryotes (which
may or may not be part of the basal division) lack mitochondria.

> 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 have doubts that any paper in Science fails to tell you what data were
used in making a tree. Even the news reports reference the original
papers, which you could then look up. And yes, it's a verb, but you are
the first person ever to use it, to my knowledge.

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

.

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