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

> most fossils, of all ages, are marine, and that marine sediments are
> interbedded with terrestrial ones. So you are forced to imagine a
> pre-flood world in which there was land on top of ocean on top of land
> on top of ocean.

Aha, that's a good refutation to my strawman hypothesis of layering of
fossils due to elevation where the various species lived at the time of
a Flood. Thanks. So I'll have to think up a new strawman hypothesis to
make the geological column data fit a non-evolutionary mode. How about
this: The fossils were deliberately buried, in a massive graveyard,
according to a pattern of religious ritual, whereby more advanced
fossils are buried above more primitive fossils. Before the Flood, all
the various forms of life lived together in harmony, except for humans
who were warring and breaking the rules of harmony. During the Flood,
all the various forms of life, except a few rare survivors, died and
were buried per the ritualistic pattern. After the flood, the mud was
heated internally to convert mud to stone, except for the very topmost
part which was too close to the surface so heating the mud would have
boiled away the surface water and killed the remaining life, so that
topmost part wasn't heated, but heat leaked up from the deep heated
parts, so there was a gradient of heating from the totally-heated deep
layers to the non-heated topmost part. Towards the end of the Flood,
geological uplift occurred, which caused immense ocean waves, which
discouraged Noah and family from trying to land their boat before the
planned events were completed. Finally the deep mud was converted to
rock, the shallow mud was only partly converted, the very shallow mud
remained mud, and the residual heat leaking through the mud caused
rapid evaporation of the water to end the Flood by uncovering all the
uplifted land. For a brief time, due to unusually warm ocean waters
worldwide, there was a dislocation of ocean life away from tropical
areas toward polar regions, but as the water cooled back to normal the
life miagrated back toward the equator, leaving extreme polar regions
(especially central Antarctica) nearly devoid of life again. Now that
central Antarctica had cooled to far below freezing, the water vapor
from the evaporated Flood water rapidly froze over central Antarctica,
reducing atmospheric humidity back to normal, and built Antarctica to
somewhat larger than its above-sea landmass. So where did all the Flood
water come from in the first place? Well in that aspect of the Flood,
the Great Flooder spirit cheated a little bit, by cracking upen some
fissures under Antarctica, letting magna rise and not just melt the ice
but boil the water before it could drain into the ocean, creating steam
which flowed out to cooler parts of the world where it rained out.

> there are in fact programs that just draw trees, but you
> have to give them trees as input.)

That makes no sense, unless you're talking only about the
visual-rendering program which converts a table-description of a tree
into a raster image showing the same data in visual form. I'm more
concerned with the program that takes a matrix relating different
characters against different species or individual and performs
mathematical analysis to find a minimal (character-difference) spanning
tree connecting all the species/individuals. I don't care so much about
the program that actually draws a picture of that already-computed
mathematical tree. (And I don't really care how the miminal-spanning
program writes its output, whether it uses XML or Fortran formatted
output to express the mathematical tree it has constructed.)

> the justification for minimum-evolution or parsimony methods.

The idea that in a very high dimensional space, a branching sequence of
random walks from a single starting point is impossibly unlikely to
ever intersect itself except immediately after a branching event when
the different paths haven't diverged far from the starting point, in
fact it's impossibly unlikely for two divergent random walks to ever
get significantly closer to each other to where a minimal-spanning-tree
algorithm would use such a convergent-evolution link instead of
strictly following only the true-evolution links? Hence it's possible
to uniquely recover the *actual* evolutionary paths just by looking at
the character/DNA data.

> However, this doesn't relate at all to your odd attempt to draw a
> line from B1 to B2.

I'm simply saying that if B1 and B2 were the only data presented, the
program would draw a link directly between them, but with A1 and A2
also present, with need to link all four together, it's more efficient
to link B1-A1-A2-B2 and *not* to include any direct B1-B2 link. How
does that not relate??

> Insertions do most likely come from somewhere.

Except for extremely short insertions, such a single base, which might
come from a break in the DNA strand followed by some random molecule
attaching to the end of one strand and then the anti-copy mechanism
mistakenly making an anti-copy of that random molecule as if it were an
existing DNA base. I agree all long sequences are unlikely to be
generated de novo by such fooling of the anti-copy mechanism, so we can
assume they come from actual DNA or RNA strands that were part of some
genome somewhere else (other place in genome of same cell, or a pilus,
or a virus, etc.)

> But generally you don't know where they come from,

Most of the time they come from elsewhere in the genome of the same
cell. If they are sufficiently long, sequence comparison will show
exactly where they came from. Only a very few insertions should come
from other cells or from viruses. If we see a large number of indels
that are all in the same direction, and each indel is completely
different in pattern from any of the others, and not a single one of
them matches any DNA elsewhere in the same cell, I think we can assume
they are deletion events, not insertion events. Tandem repeats would
follow patterns, and known SINEs would be from a very limited menu of
possibilities active in that particular species, so we can eliminate
those as likely if the indels are totally unstructured and
uncorrelated.

If we see 90% of the indels in a particular direction matching segments
of DNA elsewhere in the same genome, and the remaining 10% of that
direction are of unknown source, I'd accept that 10% are unknown virus
vector or other non-local copy&paste.

> and thus there is no way to tell an insertion from a deletion without
> rooting the tree.

I disagree. Duplication-insertion events are easy to diagnose, and
hence decide which direction time's arrow goes. SINE insertions
likewise are easy to diagnose and decide time's arrow. Large numbers of
indels all going the same direction and *none* of them matching any
duplication or tandem repeat or SINE etc. would clearly be diagnosed as
all deletions, not insertions. The clearest case would be a lot of
indels in one direction all clearly duplication or SINE inserts, and a
lot of indels in the opposite direction not explainable via any such
mechanism, and tandem indels going both ways which we can ignore,
clearly showing that the first group are indeed insertions while the
second group are deletions, and the tandem indels are then assigned
accordingly.

> The fatal problem (though there are many others) is that "copies of
> something from somewhere" are distinguishable only if you know where
> they come from.

Perhaps we'll just have to leave this question unresolved until
Venter's whole-ecosystem shotgun sequencing project has catalogued 99%
of all sequences worldwide, and then there'll be a simple test via
database lookup for any sequence to tell where it could have come from.
Unless you accept my assumption that in any large (ten or more)
collection of indels, there are solid explanations for several of them,
either copies from elsewhere on same genome, or SINE inserts, and these
are sufficient to establish the time-direction for that particular link
as well as to provide true evidence not only that evolution happened
but specifically that evolution happened via a mechanism we see in the lab.

Do you have any summary statistic, regarding the complete unrooted tree
of life, how many links between internal nodes display sufficient
known-mechanism indels that we can use that information to assign a
time-direction to that particular link?

> > If you score different kinds of changes,
> > you should be able to estimate which way time occurred between two
> > genomes which differ by any insert/delete/dup.
> The chances of actually doing that might indeed increase if you had two
> or more entire genomes to examine. But usually we don't.

I was reading in a recent issue of _Science_ that we already have a
hundred or more complete genomes. I presume most of them are very small
genomes, such as viruses or bacteria, only about ten or so really large
genomes such as mustard or mammal. So what do you mean by not having
even two complete genomes?

> I never use time-directed indels to root the tree.

So what do you use to root it? You have prejudice about what came
before what else, based on what some other expert claims and your
respect for such authority, with no evidence (except fossils) to
support that prejudice, and you just go with your prejudice as if it
were Gospel?

> You can use time-directed indels (SINEs being the only such that you
> have mentioned) to root a tree.

They don't completely root the tree. At best they certify that certain
branches of the tree are true clades, and that the true root lies
somewhere in the relatively small part of the tree that connects those
clades together. Do you know how many total species are known, and
hence the total size of the unrooted tree connecting them all, and do
you furthermore know the statistics of the known-clades that result
from knowing the SINE-insert data, and hence the number of branches in
the undirected portion of the tree?

> You can use a rooted tree to determine the direction of any
> non-time-directed indels on it.

Given that only part of the tree is rooted, the known clades as given
by the SINEs, this method determines the direction of every link within
any one of the clades, but doesn't help anywhere in the undirected
backbone that connects the various clades together.

> "Directed link" is not a term I would use, nor am I sure of its meaning.

If you feed in the character and/or DNA data for current species only,
you get an unrooted tree, comprised of leaf nodes (the current species
themselves), internal nodes (the new nodes generated by the program),
half-internal links (between internal nodes and leaf nodes), and
full-internal links (between two different internal nodes). The
half-internal links are of course directed, from the internal node to
the current species. But initially there's no reason to decide which
direction the full-internal links go, so they are all undirected links
initially. If and when you have solid evidence to allow you to decide
which direction some full-internal link goes, *then* you change that
link from undirected to directed in your database. So my term "directed
link" means any link for which you know the direction of time across
that link. This term refers to our information. In nature of course
*every* link was directed, but we aren't omniscient so we don't know
the direction of every link, so in our model some links are undirected
until we get more information sometime in the future, or they remain
undirected forever if we never get sufficient information to assign a
direction to them.

> No, internal nodes are not species, even presumed species. They are
> hypothetical common ancestors, which may or may not be species.

In the case of LCA of current species that all engage in meiosis, and
presumably all ancestors back to the root of eukaryotes also engaged in
meiosis, what else would a LCA be except a species?

> Extending the meaning of "species" through time is itself problematic.

Extending the meaning so that a species lasts over time is indeed
problematic, and perhaps meaningless. But at any particular epoch
(single time), it's possible to define the species at that particular
time in a logical manner. Yes it's a fuzzy definition due to ring
species and in-progress species-splits, but still in some sense the
term can be defined just the same as it'd defined today.

> I counted the weights exactly as the data allow. Only the SINEs were
> self-polarizing. All else is your delusion.

So if I asked you: DNA-segment-duplication events are self-polarizing,
because it commonly happens that a single segment of DNA gets duplicated
and then the two copies gradually diverge over time, but it *never*
happens that two unrelated segments of DNA gradually drift toward an
exact match and then at the moment they exactly match suddenly one
of the two copies is exactly/totally deleted. Agree [ ] / Disagree [ ]
You'd check Disagree??

> You seem to think that a SINE on one branch polarizes that
> branch only, when in fact it supplies a root for the entire tree
> subsequent to that particular insertion.

No, I don't think polarizing a single link has no consequences
downstream. Indeed my opinion is as you stated there. Polarizing a
single link establishes one of the two sides of the tree, namely the
*after* side, as a true clade, which thereby defines the direction
along all links within that clade. That true-clade is thereby
eliminated from consideration as the true location of the root. The
root must be somewhere in the other side of the tree, the *before*
side.

> > So do you know of any such force-direction mutations across major links
> > in the middle of the unrooted tree of life as it is currently known,
> > which could be used to root portions of the tree and thereby establish
> > those portions as true clades, and thereby restrict the global root to
> > the rest of the tree that connects those clades together, ...
> No. I'm sure there are gene duplications that would be useful for the
> purpose. For example, all vertebrates share two duplications of the
> entire single ancestral HOX cluster.

So now you're agreeing with me that duplications have intrinsic
direction (self polarized), which is the opposite of what you said just
earlier.

> I don't know if any protists have SINEs.

What about duplications followed by later divergence of the copies?

> > By the way, I presume the unrooted metazoan tree must look like this:
> > Parazoa--------+---------Radiata
> > |
> > Bilatera
> > where the root is presumed to be somewhere within Parazoa, right?
> Radiata is not a term in modern use.

It means Cnidaria + Ctenophora. I'll re-draw the unrooted tree to show
them separately to please you.

> Nor is Parazoa.

It means Porifera + Placozoa. I'll re-draw the unrooted tree to show
them separately to please you.

Porifera--+--------+---------Bilatera
| |
Placozoa +--Cnidaria
|
Ctenophora
Do you see an unrooted tree there, or can't you see it? (Earlier you
said you don't know what an unrooted tree is, despite my frequent
drawing such trees for you. Well here's another.)

Also, do you agree all five taxa I've used there are modern usage?

Now the big question: Per the latest data, have I drawn the correct
unrooted tree connecting those five taxa? If not, which unrooted tree
would you draw to connect those same five taxa?

> ... it's unclear whether they are a clade or whether one or the other
> is closer to Bilateria than the other.

All I'm asking about here is the **unrooted** tree. With an unrooted
tree, "closer to" is meaningless, so please don't use such nonsense
wording in this part of the discussion.

Note if we include a sixth taxon, any protist, then on the assumption
that protists came before any animals, and on the assumption that
Porifera lie between the protist ancestor and the rest of the animals,
that sixth taxon would be *inside* the Porifera node on the unrooted
tree, forcing the Porifera node to be broken into multiple nodes,
causing the tree to be re-drawn something like this:

Protist--+----------+-------------+--------+---------Bilatera
| | | |
SomePorifera MorePorifera Placozoa +--Cnidaria
|
Ctenophora

As an interim measure, before we have the Porifera-related internal
nodes fully resolved, we might have an unrooted tree like this:

SomePorifera MorePorifera
\ /
Protist----------*----------+--------+---------Bilatera
| | |
EvenMorePorifera Placozoa +--Cnidaria
|
Ctenophora

So anyway, how would you draw the unrooted tree of just the five animal
taxa, not including the one protist taxon, based on the latest
information? The way I drew it 43 lines earlier, or some other way?

OK now I switch to *rooted* trees, true cladograms, are you clear on that?
> > Now I saw a rooted tree long ago that showed:
> > --Protists
> > |--ModernProtists
> > `--Animalia
> > |--Porifera
> > `--(unnamed)
> > |--Placozoa
> > `--(unnamed)
> > |--Radiata
> > `--Bilateria
> > But somebody here (you?) said we now believe the root is *within* Porifera.
> Yes. This is a bizarre tree in many other ways, such as the monophyly of
> ModernProtists, and the use of Radiata as a clade name.

If Cnidaria + Ctenophora form a single clade not including any other
phylum, and if the old name for that single clade is "Radiata", what do
you have against continued use of that name? I'll re-draw it to clearly
show that Radiata is the smallest clade including both Cnidaria +
Ctenophora if that pleases you.

As for ModernProtists: Sorry, I'll re-draw that as an unresolved node,
and I'll re-name the topmost node
Here is the result with both those changes:

--ProtistsAndAnimals
|--SomeModernProtists
|--MoreModernProtists
|--EvenMoreModernProtists
|--YetSomeMoreModernProtists
|--YetAnotherBunchOfModernProtists
`--Animalia
|--Porifera
`--(unnamed)
|--Placozoa
`--Eumetazoa
|--Radiata (or just call this node "unnamed" if you wish)
| |--Cnidaria
| `--Ctenophora
`--Bilateria

Now presumably you would break up Porifera into multiple clades which
connect at various points along the branch from Animalia down toward
Eumetazoa, correct?
..

.

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