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Re: a rose is a rose (Philidor's questions)

I'll address the Archaeopteryx question first, which is easier to answer (assuming I'm interpreting your question correctly) than is the scientific-popular split. I will use your genealogy analogy, but to make it fit the species examples in biology, we should assume that your Greataunt Katherine has one parent only (and of course, we are talking about millions of generations ago).
The unknown parent (common ancestor) has two children, Greataunt Katharine (Archaeopteryx) and an unknown sibling (ancestor to the rest of the birds). We assume Katharine is very very similar to the unknown parent and sibling. We probably will never have fossils of the direct ancestors (unknown sibling and common ancestor), but Katharine gives us very good idea what they were like (even if Katharine is really just a distant cousin further out on that branch).
In fact, fossil gaps are so large that Katharine may be the only example we have to work with for hundreds of generations before and after the unknown sibling and parent. Thousands of generations later, we find Confuciornis (an aunt or cousin of our ancestor at that time). We see the bird lineage has evolved some new synapomorphies along the way, and so on.
Having drawn a solid bird-"dinosaur" boundary line just before the Archaeopteryx branching, this gives us a framework in which to fit other forms. Did Mononykus and other Alvarezsaurids branch off the line between the Archaeopteryx and Confuciornis branches as Chiappe originally proposed (and thus considering them birds)? Or did the Alvarezsaurids split off before Archaeopteryx, which by our definition would make them non-birds. That is the kind of controversy that is really scientifically interesting.
****But the MAIN POINT (and I hope this answers your question) is that we cannot safely assume that any known fossil species gave rise to descendants. In cladistics we treat all fossils as though they are collateral relatives like aunts and cousins (and usually rather distant cousins). Archaeopteryx is no exception. The trick is getting all the branches in the right order, and inserting newly-discovered branches in the correct place.
By longheld convention (both popular and cladistic), the branch with Archaeopteryx on it is the basalmost branch of birds (Aves). Unfortunately mammals and many other groups do not have "an Archaeopteryx" upon which a widely agreed-upon convention can be based. That is one reason I think the PhyloCode is not a good idea.
As for your phrases "lazy social biases" and "pettifogging elitism", these are two extremes (on opposite ends of a continuum) representing very few people and with most people on a sort of bell curve in between. And although there will always be a sort of split between popular names and scientific names, I think the problems can be minimized by recognizing fewer formal scientific names (and use coding to store much of the phylogenetic information instead)---strict cladistics are going the other way (rapidly increasing formal names with no end in sight).
And what is really, really scarey is that we may soon have a enormous split among just the scientific names when a parallel PhyloCode becomes a reality. Michael Benton's recent paper clearly points out the kind of havoc this will undoubtedly cause, exacerbated when some of the more elitist cladists start butting heads. Hostility and confusion will probably increase in all quarters, which REALLY irks me to no end, because I think it is avoidable.
And the trouble is that the bickering will give all of systematics a black eye in the minds of the public. Not that I think cladists are going to be "pettifogging" on purpose (their intentions are good), but I fear we will end up with a similar result. To be quite frank, I could care less if cladistic "classification" gets a black eye, but worry that it will also cast a shadow over cladistic "analysis" (which I think is a very important tool).
----So it goes, Ken Kinman
P.S. Hang onto your hats, it's going to get worse before it gets better (unless by chance PhyloCode gets scrapped; well I can dream can't I?).
From: "philidor11":
The alternative to 'lazy social biases', as has been observed in other posts, is pettifogging elitism..... Can there be a split between the scientific and popular conventions, which is one compromise, or will hostility result from the mutual recognition of different ways of thinking? I'm learning about that too.

By the way (again), I would appreciate clarification on why Archaeopteryx is included in the bird definition. If I say I am descended from my grandaunt Katherine (who did not have children) and the 4 family names of my grandparents, my lineage among people, this seems an inconsistency. Assuming Archie has no living descendants, why include Archaeopteryx and not any other specific species?
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