A few comments on specific points...
>>One begins with pathogens X and ends up with pathogens X. In the case of AIDS, why do we still call them AIDS viruses if they have changed their nature so dramatically? <<
>We don't. It looks like HIV descended from SIV and other lentiviruses. These have significantly different pathologies and host ranges. Also, HIV variants are also assigned sub-types, depending on distinguishable factors such as infection modes, sequences or epitope markers.<
In addition, bacteria and viruses have their own rules for taxonomy, quite different from those for eukaryotes. In terms of distinctiveness, a species of bacteria is probably equivalent to a much higher taxonomic level for other organisms. Viruses are not even really assigned to species. In part this reflects the high variability-it is not practical to identify every new variant as a new kind. This also reflects the difficulty of working with them. Unless they grow happily in petri dishes, lab organisms, or us, we generally know very little about bacteria. Trying to come up with useful features to distinguish something as small as that also poses problems. Biochemistry (especially sequencing) gives the most detailed differences, but the magnitude of variation there is much greater than between animal species, for example.
>Similarly, in a large, freshwater body of water in Africa called Lake Victoria, there were once only a few species of cichlids living there. Yes, they are still fish, cichlids, even, but we may as well call gorillas, chimps and humans, "just a bunch of indistinguishable great apes" by similar metrics.<
The Lake Victoria cichlids are (or were-introduction of a large predatory fish has severaly damaged the ecosystem) of quite recent origin. Other lakes have a more ancient population of cichlid species, but the differentiation of humans from chimps is a bit older still, and the genetic variation may be correspondingly somewhat bigger. I have not seen morphological analysis on the cichlids, but humans are morphologically quite distinctive despite the close genetic similarity to chimps. Some years back, Cherry, L. M., S. M. Case, and A. C. Wilson (1978. Frog perspective on the morphological difference between humans and chimpanzees. Science, v.200, p. 209-211)used major morphological features used in frog taxonomy to analyze humans and chips and found the differences to be extreme by ranine standards. As all frogs use basically similar locomotion, but we are highly specialized for bipedal terrestrial locomotion whereas chimps combine climbing and knuckle-walking, the highly!
distincitve morphology is not surprising.
Dr. David Campbell
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