on 8/2/00 3:02 PM, David Campbell at bivalve@email.unc.edu wrote:
Thanks for the help.
>> Doug Hayworth strongly supports common ancestry and Paul Nelson questions
>> it. I'm not sure where others stand.
>
> Common ancestry of what needs specified.
This becomes more apparent as I search the library catalogues.
> I think common ancestry of all organisms is likely, from the available
evidence.
Is this actually the hypothesis for specific areas rather than an initial
assumption?
>
>> Paul Nelson said in a response to Terry Gray, "Common descent is not a
>> hypothesis being tested by the data. Rather, the data are being interpreted
>> with common descent as a given."
>
> However, the results of this interpretation may or may not fit the initial
> assumption of common descent. My 1998 paper on bivalve evolution assumed
> common descent of myoids and anomalodesmatans from a single ancestor. Now
> I have data for anomalodesmatans, and they show that the common ancestor of
> myoids and anomalodesmatans was also the ancestor of lots of other
> bivalves, so that they do not have an immediate common ancestor.
I presume the test of consistency is done with specific similarities.
How does this fit in with Paul Nelson's statement?
_"Modus Darwin" (Sober's term for Darwin's argument of "similarity,
ergo common ancestry") is "not a deductively valid form of inference,"
Sober writes. "Similarity does not deductively guarantee common
ancestry"_
>
>> If common ancestry is a given and it is used to structure scientific
>> classification in biology, the two together appear to create a "design"
>> condition as a pattern for evolution. My CD encyclopedia states that "The
>> classification of organisms is a science called taxonomy or systematics.
>> Scientific classification is an interpretation of facts". There is , of
>> course, more to the theory of evolution. This design condition would affect
>> the creation of hypotheses and the interpretations of the evidence.
>> Repeated tests of consistency with theory would show how well the evidence
>> fits the theory that assumes common ancestry. Is this not circular
>> reasoning?
>
> Not entirely circular, because if the test of consistency is not met, there
> could be evidence against common ancestry. Certainly there are examples
> that have shown that immediate common ancestry is not true, although not
> contradicting ultimate common ancestry. For example, a few years ago it
> was discovered that some bivalves have biparental inheritance of
> mitochondria. Thus, the mitochondrial DNA of a male and a female clam of
> the same species may be more different than that of males from two
> different species. The assumption that the mitochondrial DNA of males and
> females had an immediate common ancestor was disproved.
One example of using common ancestry as a hypothesis.
> A similar problem comes from gene duplications. If the duplication occurred
>before the evolutionary event that you want to analyze, then you run the risk
>of comparing the descendants of one copy with the descendants of the other
> copy and messing up the analysis. A different example comes from spacer
> sequences from certain plants. They evolve so fast that different copies
> in the same individual differ more than do the different species. Thus,
> they are useless for analyzing common ancestry.
>
>> How can someone say that the evidence supporting common ancestry is
>> overwhelming? We seem to be force fitting the evidence. It seems that we
>> need a new kind of scientific classification that is not dependent on the
>> assumption of common ancestry.
>
> The current Linnaean system is not dependent on assuming common ancestry,
Thanks for this clarification. My CD encyclopedia gave me the impression
that it was dependent.
> as Linnaeus did not assume common ancestry above the genus level; I am not
> certain whether he thought evolution below the genus level to usually be
> the case or just possible. (It is somewhat notable in that regard that
> chimps were assigned to Homo, though they were not well known at the time).
> There are various schemes, of which I am generally sceptical, to try to
> replace it with a cladistic classification. Most importantly to my mind,
> the Linnaean system provides a simple way of identifying everything,
> whereas a diagram is the best way to show proposed relationships.
I assume this diagram would be for possible close connections. Or perhaps a
possible branch?
>
> Paleontological evidence supports common ancestry to the phylum level in
> most animal phyla with good fossil records, but the most primitive phyla
> (Cnidaria, Porifera) already have recognizable classes in the Precambrian,
> when the oldest known fossils are present. A few phyla show
> paleontological transitions, such as the arthropod-onychophoran transitions
> discussed before on this list. What is a transition between phyla is also
> dependant on how you define phyla; some of the attempts at cladistic
> definitions do strange things in that regard. There are also some good
> transitions in plants and protists, but I do not know many details.
>
> Molecular patterns support universal common ancestry, although as Doolittle
> and many others note, the pattern is almost certainly complicated by
> lateral gene transfer. The transfer of genes from mitochondria to
> eukaryotic nuclei is still going on, for example, and there are several
> examples of gene transfer between symbionts. DNA transfer happens quite
> readily in bacteria. It has been about ten years, so I do not remember all
> the details, but bacteria can get the "copy this during conjunction"
> sequence in the main genome (Hfr bacteria) and send large amounts of DNA
> over, not just plasmid sequences. Bacteria can also take up DNA from the
> environment (one experiment widely cited as early evidence for the role of
> DNA had non-pathogenetic bacteria turning pathogenetic on exposure to DNA
> from killed pathogenetic bacteria) or get insertions from bacteriophage
> activity, so lateral transfer is not at all surprising. Conversely, not
> all the examples cited by Doolittle may be lateral transfer. Instead, some
> of them may be convergent evolution. Perhaps the common ancestor had a
> good precursor to the particular system, and so convergent evolution
> produced the same system more than once. Testing that would require a good
> understanding of the evolutionary dynamics of the system, something as of
> yet usually poorly known.
>
> The similarity of basic biochemical methods among all living organisms yet
> studied suggests common ancestry. Everything uses DNA to make RNA to make
> proteins, except for some viruses and the like that start with RNA or
> possibly protein and exploit an existing DNA-RNA-protein system, and
> whether they are alive is moot. The details of this process are very
> similar, with the same genes involved, and in fact some features of the
> construction of this system can be found in all kinds of living organisms.
> Currently, DNA gets copied into mRNA, which goes to the rRNA. tRNA brings
> the amino acids to make protein with to the rRNA. About 20 kinds of tRNA
> are needed by modern organisms. However, some of the tRNA genes show
> distinct similarities, suggesting that they were originally copied from
> each other and then modified to form the two or more modern genes before
> the last common ancestor of all living things.
>
> The patterns obtained by studies on different genes are reasonably similar
> for the groups I study. Strange results or disagreements between genetic
> analyses correlate well with areas of limited data, long branches, etc.
> Disagreements with morphological evidence generally correspond with authors
> who put too much emphasis on a single feature rather than the whole range
> of anatomical and shell features.
>
>> Am I wrong in my current impression about common ancestry? Can anyone
>> suggest clarifying material to read? Searching library catalogues for common
>> ancestry comes up with no responses.
>
> Universal root
no luck
> might be another keyword to try. Archaea (a major group of
> bacteria) might also be productive, as a lot of the work is trying to
> determine how they relate to ordinary bacteria and to eukaryotes.
> Phylogenetics, cladistics, phylogeny, monophyly, polyphyly could all give
> lots of references looking at common descent of various groups, though the
> number of references found could be overwhelming.
Phylogeny worked well. Cladistics gave no references. Now I need to go to
the library.
> Browsing contents for Journal of Molecular Evolution, Molecular Phylogenetics
and Evolution, Molecular Biology and Evolution, or Systematic Biology may be
productive; every once in a while Science or Nature will have something.
You may also run across arguments about cladistic methods.
I have not done this yet. Thanks again for the help.
>
> David C.
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