Re: Article: On Phylogenetic Trees
- From: anon1@xxxxxxx
- Date: Sun, 22 Oct 2006 02:03:32 -0400 (EDT)
(First attempt to post this failed, trying again...)
The following points are made by D.A. Baum et al (Science 2005 310:979):
The central claim of the theory of evolution as laid out in 1859 by
Charles Darwin (1809-1882) in The Origin of Species is that living species,
despite their diversity in form and way of life, are the products of descent
(with modification) from common ancestors.
*Note* the plural "ancestors", not the signular "ancestor". I.e. the theory
doesn't claim a single Universal Common Ancestor, wherein all life lies
within the single clade from that starting point, it merely says that a lot
of groupings of similar types of life fall within various clades, each
with their own group-common-ancestor, not claiming whether that number
of clades is exactly 1 or larger than 1. (And with the evidence of
endosymbiosis from Margulis et al, clearly when we're considering
whole-cell clades we must start a new clade every time a new kind of
endosymbiosis event occurs, such as when mitochondria entered
eukaryotes, and when plastids entered algae, etc.) Darwin's central
claim does not rise or fall with Universal Common Ancestry, it requires
only Gigantic-Clades Ancestry (as opposed to Lamarck who seemed to
accept only Tiny-Clades single-family multi-genera common ancestry,
with separate abiogenesis or goddiddit-ID for each new family).
To communicate this idea, Darwin developed the metaphor of the "tree
of life."
That seems slightly wrong. How about the "forest of trees of life"?
Is there a cite as to Darwin's exact words for this?
In this comparison, living species trace backward in time to common
ancestors in the same way that separate twigs on a tree trace back to
the same major branches.
Yes, back to multiple clades, multiple common ancestors (one per
clade), multiple trees each with their separate structure of branches,
each inner clade tracing back to a major branch, and all the major
branches of a single tree tracing back to their trunk. Or a single tree
but the trunk has been rotted through so only the individual major
branches still exist, and in fact we don't know whether there ever was
any central trunk, it may have been separate branches from the start,
which only seem to perhaps imply a central trunk.
Yet "tree thinking" remains widely practiced only by professional
evolutionary biologists.
There's a yin and yang to this: Some natural systems are inherently
Platonic, absolutely strict hierarchy of classes, pure tree structure
of relatedness of minor to major categories. But other natural systems
are more flexible, with lots of "chinese restaurant menu" variation,
one from column A, one from column B, etc., where a relational database
instead of of a Platonic tree is more appropriate. The wisdom is to
know the difference between them and to use each methodology when
appropriate and not otherwise. Eukaryotes seem to fit nicely into
cladistic/tree/Platonic classification, except for viruses which effect
lateral gene flow from time to time. Prokaryotes on the other hand have
so much LGF that we might need to use trees not for whole cells but
only for blocks of DNA which are kept intact, using a
relational-database instead to model the whole-cell genomes.
In a limited sense, atomic/nuclear physics uses a tree structure:
Nucleons, fermions, and charge carriers, each sub-divided into families
of particles, each further sub-divided by mass or spin or flavor or
strangness etc. But there's a nice mapping between types of particles
in one family and in another, such as the three kinds of fermions
(electron tau-something and muon I seem to recall) and the
corresponding three kinds of neutrinos, and the quarks come in three
families with two kinds in each family that somehow match perhaps, so
it's not quite like Platonic hierarchy, there's a little extra
structure also. It's like several different hierarchies which are then
combined in all possible ways. For example, fermion/neutrino, and
e/tau/mu, and regular/anti, all 2*3*2 = 12 combinations possible.
As for really deep absolutely-Platonic-trees in nature, the clades of
evolved live are the only ones I know of. Are there any other fields of
nature study where such tree thinking is really appropriate, instead of
RDBS thinking? Cultural evolution in particular is more RDBS like.
There are myths that deal with creation, and myths that deal with
morality, and myths that deal with the cause of strange spooly bumps in
the night, etc., but a lot of times a given myth belongs to more than
one such hierarchy because it conflates elements of more than one
hierarchy. So trying to classify a myth strictly as a creation myth or
a cause-of-bump-in-night myth is not likely to be correct.
In what field of nature study would you propose we should think more by
a single gestalt-object tree than with a relational database or
mathematical compositions of separate aspect-trees, and the author
laments that we don't?
Comment:(presumably quotes from here on were by Stonjek rather than Baum)
Darwin seems to have held the view that Lamarck believed in branching
AIUI, Darwin believed in massive branching, leading to very large
clades, whereas Lamarck believed in only "micro-evolution" branching by
comparison. Per Lamarck, branching was always within a fixed type,
whereas per Darwin branching generated such great divergence eventually
to yield (after hundreds of millions of years) what we'd naively regard
as multiple types from a common ancestor.
The term 'Common Descent' does not appear in any of Darwin's major works
That's quite curious! If he had been careful to state that he was
providing evidence to support major common descent but not necessarily
universal common descent, that would have been quite appropriate.
Unfortunately, all finches are of one "type", so no matter how much
such evoution he discovered on the Galapagos Islands, they didn't lend
one shred of support to the idea of clades larger than families. So
maybe he felt that without evidence it was not yet time to propose such
a radical idea in a major work? Remember he procrastinated over ten
years in publishing his first edition of Origin of Species due to
shyness about his lack of sufficient evidence, until he was spurred by
Wallace's more rapid readiness of a similar theory, so maybe he was
merely procrastinating another fifty years before he'd have sufficient
evidence of clades larger than family level, and there was nobody like
Wallace to spur him to publish any sooner, and he died of old age still
feeling not enough evidence to publish the Major Common Descent
hypothesis?
(Letter by Darwin:)
You ask how far I go in attributing organisms to a common descent; I answer
I know not; the way in which I intend treating the subject, is to show (AS
FAR AS I CAN) the facts and arguments for and against the common descent of
the species of the same genus; and then show how far the same arguments
tell for or against forms, more and more widely different: and when we
come to forms of different orders and classes, there remain only some such
arguments as those which can perhaps be deduced from similar rudimentary
structures, and very soon not an argument is left...
I actually mostly agree with him here, even nowadays where there is so
much more evidence of common descent. I'd push the evidence up to
higher levels nowadays, but still as we reach the highest (most
general) levels in the hierarchy we get past the point where there is
any fossil evidence whatsoever of any common ancestry, and the other
two lines of evidence aren't yet ufficient to prove UCA either.
(Darwin again, regarding his changing belief while on voyage of Beagle:)
I did not become convinced that species were mutable until, I think,
two or three years had elapsed.
Hmm, if it took Darwin so long to convert, maybe it would take several
years of intense presentation of the evidence, with no other
distrations, to convince an ardent YEC or IDiot that evoution really
has been happening. Anybody willing to break the law regarding
kidnapping certain people and holding them for years to enlighten them?
I'm not talking about brainwashing them, or "showing them the
instruments", merely showing them massive quantities of evidence, each
of which they must try to explain, and also testing them with
non-evidence such as cross-time cross-space chimeras, so they must also
try to explain why such critters never appear within the evidence, and
let them take their own sweet time to come up with a model that
explains the evidence and anti-explains the chimeras.
At the least, it seems we need not just one year of high school
biology, emphasizing evolutionary theory, to enlighten the new
generations of students. At least two years required for every student,
with good students able to quickly "challenge" the basic theory and
spend the rest of their two years helping with actual research, such as
abiogenesis or protein expression or knockout experiments with
non-human analogs of all unknown-function human-genome open reading
frames, while remedial students spend the whole time studying one line
of evidence after another until they either accept common descent or
totally surprise us by finding a valid alternative theory, either way
they can eventually pass the course and graduate from high school.
...
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