Re: Common ancestry and Scientific Classification

From: James W Stark (
Date: Thu Aug 03 2000 - 14:20:38 EDT

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    on 8/2/00 3:02 PM, David Campbell at 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
    Is this actually the hypothesis for specific areas rather than an initial
    >> 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
    >> 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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