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Re: Classification: A Definition



Tim Williams wrote:


I would have said the same thing (though perhaps not as articulately as Jerry). At the end of the day, phylogenetic nomenclature does "classify" organisms, insofar as taxa are grouped by common descent to produce a hierarchy. _Tyrannosaurus_ is inside Tyrannosauridae, which is inside Coelurosauria, which is inside Theropoda, and so on... Similarly, _Passer_ is inside Passeridae, which is inside Passeriformes, which is inside Aves, which is inside Coelurosauria, and so on...


Hear, hear. The question is, if you're not putting together the phylocode as an alternative classification system, then why are you doing it?


As for the example of protists (which also surfaced on this list), the old "Protista" is the poster child for just how BAD the Linnaean system was (and still is). Not only did the "Protista" concept vastly understate the huge phylogenetic diversity of single-celled eukaryotes, but we even had a situation where certain protists were classified as BOTH animals and plants (e.g., _Euglena_). The latter was a product of grouping organisms based on "key features" or "gross physical similarities" (as Jerry puts it). Euglenids moved and fed like animals, but they also possessed chlorophyll like plants, therefore they got put into both Animalia and Plantae.



Hang on, I think this is a little unfair on Linnaeanists. Whilst the old system was absolutely and horribly biased towards multicellular eukaryotes, I don't think it's fair to say that this was due to the ills of the Linnaean system. I think that the available technologies were more of a factor in this - without a damned good light microscope, the incredible differences in cellular organisation between Homo, Amoeba, Paramecium, and a bacterium aren't as obvious as we know them to be today. The two kingdom classification that many of us were taught (I still shudder at the thought of it - I remember my high school biology teacher talking about Euglena: "it's a plant! No, it's an animal. No, wait...") was a result of ignorance stemming from the lack of the right tools, not the fault of the classification system.

It was only when we were able to appreciate the vast range of cellular anatomy in eukaryotes, thanks to the uptake of electron microscopy, and the profound differences in biochemistry between the prokaryotes and eukaryotes, that people realised that the old system wasn't an accurate representation of life's diversity. And the attempts to address this - the three kingdom, the five kingdom, and then Woese's three domain system - were all made within a traditional Linnaean framework. Even though Woese used results from molecular biology to highlight the existance of an important new clade, his proposed classification explicitly used ranks to accomodate the deepest divisions in the tree of life. So to claim that our improved understanding of basic diversity is thanks to people abandoning Linnaeus is something I would dispute. Insistance of the importance recognising major monophyletic groups? Sure. Committment to abandoning ranks? No.

Of course, if Margulis is right about the eukaryote cytoskeleton being a result of endosymbiosis with a spirochaete-type bacteria, then the Eucarya are merely a symbiosis between one branch of the Bacteria and one branch of the Archea. I'm still confused about how the Phylocode will deal with these sorts of tree topologies; if the e.g. Archea includes all of its descendants, including the Eukarya, and the Eukarya include the descendants of one branch of the Spirochaetes, then surely the clade that contains all spirochaetes contains the Eukarya (which are a subclade of the Archaea) as well. So how does the Archaea not contain the Spirochaeta and the Spirochaeta not contain the Archaea? Maybe there's a simple way for a logical system based around divergent branching patterns to deal with convergent branching episodes: I just haven't figured out how it works. Maybe I should just read the Phylocode - does it cover this issue?

Cheers
Col


-- ***************** Colin McHenry School of Engineering (Mechanical Engineering) University of Newcastle Callaghan NSW 2308 Australia Tel: +61 2 4921 8879 Fax: + 61 2 4921 6946

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