Dear John, (01)
> I think we're mostly in agreement, but I'd like to emphasize
> some critical details.
> MW> I expect that biologists are using ontologies in much the
> > same way as engineers do: as a common language which can be
> > used to communicate with with minimum ambiguity.
> Yes, but most practicing biologists are basically engineers:
> they apply established principles and paradigms to some aspect
> of medicine, agriculture, etc. (02)
MW: I don't see a sharp distinction between science and
engineering/applied science. Science uses engineering to construct
and conduct experiments, and engineers do science on how their
> At the level of pure research, all the words and principles,
> even the oldest and most firmly established, are subject to
> radical revision and redefinition. For example, the old
> textbooks classified fish, amphibians, reptiles, birds, and
> mammals at the same level of the tree of life.
> But the more recent work in cladistics led to a major overhaul
> of the tree at the most basic levels. Now amphibians are
> placed on a branch of the fish clade, reptiles are on a
> branch of the amphibian clade, and birds and mammals are
> on two different branches of the reptile clade.
> Most of the lower branches of the tree are still connected
> at the same points, and there is little change for most
> biological engineers. It is still correct to talk about
> fish, amphibians, reptiles, birds, and mammals as coherent
> But there has been a major restructuring of how the trees
> are derived -- including the inheritance hierarchy. For
> example, we now know that the same gene encodes the plan
> for the photoreceptors of the human eye, the eye of a
> fruitfly, and the light-sensitive spots of a marine worm. (03)
MW: This is just a matter of labels being assigned by perhaps
different communities at different times to designate different
(or the same) classes. (04)
MW: The practical consequence is that a standard ontology will
reflect a standard (accepted) scientific view.
> MW> Agreement as to [an ontology's] use for communication
> > within a community is necessary for it to achieve its
> > purpose.
> Yes, but all such agreements are subject to revision, even
> at very basic levels. (05)
MW: Of course. (06)
> Engineers don't change the terminology
> as rapidly as pure scientists, largely because they apply
> aspects of science that are not at the forefront of research.
> The latest trains on the New York subway conform to the
> mechanical and electrical interfaces of a century ago. (07)
MW: Well this is one of those arbitrary things like using
singular or plural terms. Once you've made the decision there
is little benefit in changing it. (08)
> And many programming standards were determined by the size
> of the punched card on the 1890 Hollerith machines --
> including the fact that today's email handlers wrap the
> line at 72 characters, leaving 8 columns for a line id
> on an 80-column card.
> MW> There are standards at two levels here:
> > - standards for ontology development,
> > - standard ontologies.
> I agree.
> But I want to emphasize that those standards are largely at
> the low levels of ontologies. (09)
MW: For example? (010)
> The standards for the tracks
> and voltage of the NY subway were set before anyone knew
> anything about relativity or quantum electrodynamics. (011)
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