Tim Ikeda wrote:
> Then again, one could take common ancestry to mean that
> organisms share many parts from an earlier pool of components
> (possibly not shared by all progenitors, but largely in common).
One could say that, sure, but it's unclear what biological
meaning it has. A "pool of components" is not a living
thing. Functional cells may possibly exchange genes
laterally -- a "pool of components" cannot.
>> In the concluding section of his paper, Doolittle grapples
>> with the consequences of his view for the standard definition
>> of homology (i.e., similarity due to common ancestry).
>
> Paul, would you care to recount Doolittle's discussion in this
> area and perhaps extrapolate to how it may pertain to things
> such as mitochondrial phylogeny, deuterosomes or vertebrates?
Doolittle argues that we may have to cash in the standard
view of homology. "[H]omology is still a funny word," he
writes (2000, p. 357). "In the context of proteins and
genes, it makes sense only if we don't think about it too
deeply." If there never was a common ancestor, Doolittle
continues, then perhaps "*all genes are homologous*" (p. 357,
emphasis in original).
If all genes are homologous, however, "we might still be
able to distinguish between orthologs and paralogs, as a
matter of logical principle but, in practice, this will
often be impossible....It is ironic that the words we seem
to need in order to think productively about biology, words
such as 'homology', 'individual', 'organism' and 'species',
have no precise meaning" (pp. 357-358).
I leave it to your imagination, Tim, to sort out the implications
of that position for phylogenetic reconstruction. Of anything.
>> These are minority viewpoints, of course. Most evolutionary
>> biologists accept the monophyly of life as a background theory
>> in their day-to-day research.
>>
>> But that's not the point at issue. It is increasingly possible
>> to cast doubt on monophyly at various levels in the taxonomic
>> hierarchy without stepping outside the arena of reasonable
>> scientific discourse.
>
> Which levels for instance? Eukaryotes? Plastid phylogeny?
> Higher primates?
Doolittle and Woese doubt the common ancestry of the three
primary domains. Gordon doubts that, too, and throws in
skepticism about the common ancestry of the tetrapods for
good measure: "Based on all these considerations the case
seems strong that the tetrapods were polyphyletic in origin"
(1999, p. 342). Fryer (1996) thinks the arthropods are
polyphyletic. Conway Morris speculates that the animals
may be polyphyletic, and favors monophyly only very weakly
over polyphyly:
For what it is worth my own belief is that metazoans
are indeed monophyletic, but to my mind the argument
is not yet won. More importantly, the question of
biological constraint, the prevalence of convergence
and the inevitability of polyphyly are not only
interconnected topics, but also unjustly neglected.
In part I suggest this is because of the atomistic
emphasis now given to biology, as well as an
obsession with cladistic methodology, which although
freely acknowledges homoplasy regards it as an
irritating diversion rather than a profoundly
interesting problem in its own right. (1998, p. 13)
At the Baylor naturalism conference in April, Conway Morris
told me in conversation that the molecular evidence on the
polyphyly of the animals was equivocal, but that in the near
future, it may favor polyphyly. His mind, he said, is more
than open to that possibility.
> In actuality, what is being discussed by Doolittle et al.
> is whether large bouts of horizontal transfer preceded the
> split between the eubacteria, archeabacteria and eukaryotes,
> which would obscure the past evolutionary trajectories of
> these groups. There are certainly instances of horizontal
> transfer after the split, so there is no reason to suspect
> that genomes were necessarily as fixed as many are today.
> I personally would not be surprised if this was the case and
> I would like to note further that most of proposed episodes
> of horizontal transfers discussed by Doolittle are confined
> to single-celled
> organisms.
Well, that's simplifying the situation a tad, wouldn't you say? ;-)
What really happened is the advent of whole genome sequencing
blew a massive hole in the received view of the tree of life,
and each new genome that comes in makes that hole wider.
As Nierman et al. summarize the situation:
As a result of the completion of genome sequences from
representatives of all three domains of life, it is
now possible to examine evolutionary relationships
among living things in a more comprehensive way.
However, this task has turned out to be anything but
straightforward. Incongruities can be seen everywhere
in the phylogenetic tree, from its root to the major
branchings, when single protein phylogenies are
examined. (2000, p. 345)
The hypothesis of promiscuous early lateral gene transfer
(LGT) has come to the rescue, so to speak, but at a rather
high cost. One must invoke entities very unlike modern
cells, which carefully regulate their LGT. There is little
specificity to these hypotheses of early widespread LGT,
perhaps because, as Woese observes (2000, p. 8395),
LGT today doesn't resemble what (putatively) happened
early in the history of life:
Modern cells are fully evolved entities. They are
sufficiently complex, integrated, and "indivdualized"
that further major change in their designs does not
appear possible...there will come a point at which
certain of the cell's componentry becomes sufficiently
complex (idiosyncratic) and sufficiently integrated into
the emerging cellular fabric that horizontal gene
displacement (especially of the phylogenetically
distant variety) will not strongly influence them.
One day soon some investigator is going to wake up in a
huffy mood and write a paper questioning the extent of
early LGT currently being invoked, on the grounds that
one simply do not know what one talking about when one
postulates "simple" cells with "primitive, error-prone"
systems freely exchanging basic functional components
(e.g., aminoacyl tRNA synthetases). Maybe that paper
is being drafted even now.
>> But based on current evidence, can one truely question
>> monophyly at "various levels" much higher than that
>> delimited by, say, higher eukaryotes?
See the papers cited above. I should also mention that
phylogenetic reconstruction is not the molecules-confirm-
morphology story often depicted in popular presentations.
For a strikingly different perspective, see Lynch (1999, p.
323):
Clarification of the phylogenetic relationships of the
major animal phyla has been an elusive problem, with
analyses based on different genes and even analyses
based on the same genes yielding a diversity of
phylogenetic trees. For example, considerable effort
has gone into resolving the relationships of the three
major protostome lineages (annelids, arthropods, and
molluscs). Analyses with 18S rRNA consistently identify
annelids and molluscs as sister taxa, as does a
morphology-based analysis and the analysis of Guigo
et al. (1996). However, results based on partial 28S
rRNA sequences are not even consistent with the
monophyly of protostomes, suggesting instead a
mollusc-deuterostome affiliation. Two studies employing
elongation factor 1-alpha have also yielded different
topological relationships involving annelids, arthropods,
and molluscs. Similarly, the phylogenetic position of
nematodes has been controversial. Of the two studies
that are based on 18S rDNA sequences, one positions
nematodes basally with respect to the coelomate lineages,
while the other joins them with arthropods. Aguinaldo
et al. (1997) have argued that this inconsistency is an
artifact of using nematode sequences that have evolved
at unusually high rates. In still another example of
phylogenetic inconsistency, in a study involving two
protein-coding genes thought to be ideally suited to
phylogenetic analysis, Nikoh et al. (1997) found amphioxus
to cluster in its expected position with the chordates in
one case, but to branch off prior to the deuterostome-
protostome divergence in the other case.
Given the substantial evolutionary time separating the
animal phyla, it is not surprising that single-gene analyses
yield such discordant results.
Tim continues:
>> I realize Paul, that you question human/ape monophyly,
>> but do you suppose that Ford's comments could be used
>> to reasonably cast doubt on many vertebrate phylogenies?
I think so, once one follows out the logic of his position
("all genes are homologous"). Phylogenetic reconstruction
is entering a revolutionary period; where the debris will
land is anyone's guess.
>> Does another Fellow at your institute, Mike Behe, question
>> common descent at such levels?
No, but he and Jonathan Wells and I have a long-standing
friendly discussion going about the strengths and weaknesses
of theories of common descent. Mike accepts common descent
provisionally. As he's said on more than one occasion, however,
if the theory turns out to be false, OK. I think he's waiting
to see what Wells and I have to say (in the refereed
literature) about the theory.
>> BTW, Paul - Here's a question I've always wondered about,
>> but for which 've never seen a clear answer: What's Phil
>> Johnson's position on common descent? Largely in agreement,
>> partially in agreement, not in agreement, strongly in
>> disagreement?
I'd guess that Phil doubts common descent, but he holds his
skepticism lightly. He's at the hub of a growing research
community (the ID group) where views on common descent
differ. The real issue for Phil is naturalism.
Paul Nelson
Senior Fellow
The Discovery Institute
www.discovery.org/crsc
References
Conway Morris, S. 1998. The Question of Metazoan Monophyly and
the Fossil Record. _Progress in Molecular and Subcellular
Biology_ 21:1-19.
Doolittle, W. Ford. 2000. The nature of the universal ancestor
and the evolution of the proteome. _Current Opinion in
Structural Biology_ 10:355-358.
Fryer, Geoffrey. 1996. Reflection on arthropod evolution.
_Biological Journal of the Linnean Society_ 58 (1996):1-55.
Gordon, Malcolm S. 1999. The Concept of Monophyly: A Speculative
Essay. _Biology and Philosophy_ 14:331-348.
Lynch, Michael. 1999. The Age and Relationships of the
Major Animal Phyla. _Evolution_ 53:319-325.
Nierman, William C. 2000. Genome data: what do we learn?
_Current Opinion in Structural Biology_ 10:343-348.
Woese, Carl R. 2000. Interpreting the universal phylogenetic
tree. _PNAS_ 97:8392-8396.
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