Re: Article: On Phylogenetic Trees

(First attempt to post this failed, trying again...)
Lamarck also had a tree of life, earlier.

It's my understanding that neither Lamarck nor Darwin had *a* single
tree of life, rather each had multiple trees of life, with Lamarck's
trees comprising very small clades (one genus, or one family many
genera), while Darwin's trees comprised larger clades. Furthermore
Lamarck believed firmly that evolution was strictly segregated within
these family groups, whereas Darwin allowed for the possibility of a
single all-inclusive clade or at least a very small number of master
clades.

If one wants to use trees properly, you want not only a single estimate
of the tree, but some information about the uncertainty of different parts
of the tree.

Yes. I agree strongly. For example, considered several species
(characterized by DNA sequences, or by physical characters) where
different cladogram-generating methods, or different starting points or
parameter settings with the same method, result in slightly different
trees:

+-------------------- #1
|
+-----+
| | +------------------ #2
| +-+
| | +--- #3
| +--------------+
| +--- #4
|
+----------------------- outgroup (used to establish base for rooted tree)

+------------------- #1
++
|+------------------- #2
|
+----+
| | +--- #3
| +----------------+
| +--- #4
|
+----------------------- outgroup (used to establish base for rooted tree)

Clearly the 3,4 are much tighter to each other than they are to any
others, or than any others are to each other. But at the next higher
level, the 1/2/34 split is unresolved, and should be shown as such,
perhaps somewhat like this, with different notation for unresolved
more-than-2-way branches compared to fully resolved 2-way branches:

(+------------------- #1
()
(+------------------- #2
()
+----+)
| () +--- #3
| (+---------------+
| +--- #4
|
+----------------------- outgroup (used to establish base for rooted tree)

If branch lengths are shown by numbers as well as visual length of
segments, upper and lower bounds should be shown for any branch whose
length isn't known to the precision of the numbering system. For
example, if the branch length is known to be between 7.5 and 8.2, then
just showing 8 is fine, but if the branch length is so uncertain that
it might be anywhere between 6 and 9, 6..9 should be clearly shown. In
some cases the lower bound is very close to zero, meaning that the
next-higher branching is just barely resolved, and further data might
merge higher and lower nodes into an unresolved node, and then further
data might resolve it in a different way from what was first presumed.
Showing the lower bound (and upper bound) instead of only the mean
would be especially "honest" in such a case.

(Actually the numbers I usually see in published cladograms are
actually confidence levels, usually above 90, sometimes only in the
80's, not branch lengths, right? I'm not sure really. Enlighten me? For
really close nodes I sometimes see numbers only in the tens. What does
that mean? It can't mean that there's only 10% chance the decision is
correct, 90% chance it's wrong?? I understand the pictorial tree fine,
but I don't know what those numbers mean, sigh.)

Lamarck did come (after some resistance) to a tree of life, fifty years
before Darwin.

So it's no wonder he didn't go so radical as Darwin later did. What
Lamarck proposed was radical for his time, and apparently the French
later recanted it, even as the British continued to embrace it, and
then what Darwin proposed would have been a mortal sin in Lamarck's
time but was merely radical in his time, while Lamarck's proposal was
tame in Darwin's time, already well accepted everywhere, and *still*
accepted outside France.

But on the other difference between their theories, as to the proposed
mechanism: Lamarck was slightly before Malthus, whereas Darwin and
Wallace were well after:
- Lamarck was born 1744
- Malthus was born 1766
..... (big gap here) ...
- Charles Darwin (1809-
- Alfred Russel Wallace (1823-

And in fact both Darwin and Wallace state clearly they were spurred toward
their mechanism-theories precisely by reading Malthus:
In 1838 Darwin read the Rev. Thomas Malthus's Essay on the Principle
of Population (1798).
Wallace theorised on the basis of his findings and was influenced in
this theorising by Thomas Malthus' Essay on Population.
(Quoted from the Web somewhere, sorry I don't have the URLs, but GIYF.)

Lamarck was a really bright guy, and it's just that he didn't have
Malthus's shoulders to stand on as Darwin and Wallace did. I think
Malthus deserves half the credit for the theory of evolution by
competition per fitness and survival of the fittest, since he did the
ground work in the population dynamics whereby the Darwin/Wallace is
merely a corollary. But Darwin and Wallace deserve a majority of the
credit for their groundwork in Galapagos and East Indies respectively
that led to the idea of largescale common descent and (see below)
abolition of the idea of fixed ideal forms.

there is a force like a hundred thousand wedges trying [to] force
every kind of adapted structure into the gaps in the economy of
nature, or rather forming gaps by thrusting out weaker ones.
(Sorry, failed to keep the URL there too.)

Hmm, this also applies to the meta-science here, the "Wedge" document
of the ID movement, and their goal, not to fill a gap in science
education, but rather to force evolution out to create gaps to fill.
Their original tactic was to ban evolution, but that didn't work. Now
they intend to wedge in their ID crap so there aren't enough resources
to continue to support evolution. In this light, we must increase our
efforts to prevent ID etc. from being wedged into high schools.

<http://pages.britishlibrary.net/charles.darwin3/darwin_bio.htm>
Darwin thought in terms of populations of
diverse heritable things with no essence--not representatives of ideal
types as many earlier thinkers had done.

I think this is the *key* mental frame shift (philosophical change)
that allowed Darwin to conceive of his theory, even after Malthus had
presented the groundwork for it. Did Wallace likewise undergo this
change in philosophical view from platonic ideals and representatives
thereof to the modern view of essenceless individual characters not
existing to satisfy any ideal type-character, and essenceless
individual critters likewise not existing to approximate any ideal
type?

Note that debates over whether Homo erectus is "a human", or Archy is
"a bird" or "a dinosaur", may be fallbacks to the old expired
ideal-type system of Plato.

(Caveat: I attribute two ideas to Plato: First the idea, in my opinion
totally worthless, that everything we see in nature is unreal, merely
an illusion, a shadow of perfect types which exist in ideal-space
beyond our ability to see them directly. Second the idea, in my opinion
valid for atomic physics but not for most aspects of biology, that
things can be classified into fixed categories with no overlap. I hope
readers aren't confused by my two different uses of "Platonic".)
...

.

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