The final of my comments on this topic (see one and two here) addresses the question whether or not there is a rank of species.
Once I had a paper knocked back by a reviewer in which I argued that there was nothing unique to being species. This became my 2003 paper. The reviewer said that the paper failed to accept that there was a "grade of organisation" in biology that comprised species. This was not surprising as the paper argued that no such grade existed (and I was able to convince the editor that this was a decent argument to make). However, many biologists are convinced such a rank, that is, a grade of biology, exists out there in the world.
The term "rank" assumes a scale, and the traditional taxonomy deriving from Linnaeus held that there were such ranks, beginning with Kingdoms at the top, and being divided respectively into various subranks such as Phylum (or Division), Order, Class, Family, Genus and Species. Linnaeus held no illusions about ranks - he knew and said they were artificial, mere constructs, except for genus and species. Species was the work of God, and possibly genus, while all else was the work of the understanding. But some people have been subsequently convinced that other ranks were in God's mind: phylum is one that zoologists held to be natural objects; and Louis Agassiz, the founder of the Harvard Museum of Comparative Zoology, believed that all these ranks were real. Agassiz was the exception, though.
In the light of recent developments in taxonomy (and for a taxonomist, "recent" means "sometime after 1860"), however, it has become widely, though not universally, accepted that there are no ranks in biology... but one: species. To deny that there was a species rank was to deny that species existed at all. If there was no rank, there was no species category, and if no species category there could be no species.
I invite you to say out loud the following: "If there is no rank of 'games', there is no 'game' category, and if there is no 'game' category, there can be no games." Does that work for you? Wittgenstein famously stated that there was nothing that all and only games had in common, but he did not from this infer that there were no games, but that terms like "game" got their meaning by way of a "family resemblance". All games have some or other aspects of the exemplary notions of games. It doesn't matter that there is no "rank" from which the category gets its definition; games are real things, we recognise their existence, and describe them as we can.
So denying that species have a single definition that constitutes a rank doesn't commit us to thinking there are no species. On my account, where a species is something that has most of the lineages of biology – genes, parent-child lineages, populational lineages, haplotype lineages, etc. – traveling together, it doesn't matter than there is a substantial fraction of cases that lack one or two of these coincidences. Species remain real things without there being a rank; or, to return to my geological analogy, species, like mountains, come in various arrangements, sizes, and so on, and in neither case is there a "rank" of those objects.
Some rankless proposals take the illusory nature of species as an implication of their ranklessness, and embrace it. I am trying to suggest they do not need to do this. If species lacks a definition, and there is no species rank, there may still be species in nature. God might be a nominalist, but he's not a flatus vocis nominalist. There can be universals without there being Universals.
To deny there is a species rank doesn't automatically endorse the Phylocode, either. Classifications without ranks are possible even in a Linnean system: all you have to do is understand that the ranks are conventions even if the species and clades are not. To use a sporting analogy, the leagues might be conventional (and a second ranked team might be capable of defeating a first ranked one), but the teams that comprise the leagues are real, and the matches they play are real. In systematics, the groups can be real (in virtue of being monophyletic, in either scheme of classification), and the names given refer to real taxa, without the rankings meaning much more than "this looks like it would be useful to group together for this or that reason".
So let us disentangle species denialism from rankless taxonomy, and recognise that we very well can describe and refer to groups (including species) the same way that we refer to real taxa of any kind. As was noted by Gareth Nelson some time ago, "species" are just like any other taxon. Well, almost...
One thing species do not need to be is monophyletic. All other taxa must be, but a species can be paraphyletic is one part of it evolves into another species (in other words, I do not accept the need for the Hennigian Convention that a species must be considered extinct at speciation). Some phylogenetic species proponents think species must be monophyletic (the Hennigians and a few of the other kinds, but only a few), but that makes no sense to me, nor is it supported by my phenomenality proposal.
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I'm not sure I understood exactly what you were trying to say (due to my own ignorance), but aren't the broader taxonomic categories just as "real" as species, to the extent that they attempt to embody the real actual history of descent from a common ancestor? Just because it reflects shit that happened in the past doesn't make it less real, does it?
The Hennigian rule that the ancestral species goes extinct when the speciation event creating the two sister species occurs was quite troubling to me. Suppose an ancestral species, 100,000 strong, has 50 individuals rafted across the Atlantic to new lands where they speciate away. So we are supposed to think that the loss of those 50 individuals changed the gene pool of the 99,950 so greatly that they have become a new species, the plesiomorphic sister species of the distant species? Suppose that 50,000 had rafted away and speciated; would this change our thinking? What was the 50,000 left behind doing all this time? Are they still the ancestral species?
I finaly came see the Hennig extinct ancestor rule is a simplifying assumption, rather a cosmic statement about how nature works. It does give us monophyletic species. In my own work I have not found it an impediment, although I'm aware of situations where it does not well reflect nature.
IMHO the problem is that people mean at least 25 different things when they say "species". There are in fact entities out there to which one or the other Biological Species Concept applies. There are also entities to which some Phylogenetic Species Concept applies. There are also internodes (Hennigian species) out there. And so on. These concepts just aren't congruent in most cases. Depending on the species concept, there are between 101 and 249 endemic bird species in Mexico.
In other words, the word "species" is the problem. The species concepts don't really have anything in common. We are looking at a desperate essentialist enterprise: people start with the premise that the word "species" must apply to something, ask what that should be, and find all manner of interesting things, just not the same ones.
Toward the end of his long career, yes. Even later, as you mention, he started having doubts about the genera, too. Earlier, on the other hand, he ascribed universal philosophical, if not outright divine, significance to the "fact" that there were exactly five ranks (variety, species, genus, order, class) in each kingdom.
On Linnaeus, it has been my experience that many things are said of him that are not borne out by what he wrote, so I'd like to see a cite for the divine nature of the ranks.
Jim, I find it helpful to think of Hennig's rule as a point about the reference of names, not a substantial point about species. If you had paraphyletic groups, then the reference would be vague. In those terms it is a sensible (albeit useless IMO) rule.
Perhaps we should think of Hennig's rules as instructions about how to do a Hennigian analysis, rather than as hypotheses about the nature of the universe.
The taxa (clades) themselves are. The ranks that their names have (genus, family, order...) are not.
Something I once read in the original Latin in the geosciences library in Vienna. Perhaps Philosophia Botanica. Near the beginning of the book anyway.
Given how the named hierarchies get remanmed and shuffled about (i.e. Pongidae/-inae vs. Hominidae/-inae/-ini) I don't see how any modern biologist would say that any rank above species actually exists in nature. They are arbitrary groupings. Even the whole species rank and how it can be difficult to decide upon the dividing lines with things like ring species should make it obvious to anyone that even species rank is, to some extent, quite arbitrary as well.
Having said that, I must also say that these arbitrary groupings are eminently useful because they help us humans keep organisms organized and because sometimes we need to refer to all organisms which are part of that named rank, whether it be all hominids, all hominoids or all opisthokonts.
The problem, I feel, is when we get too attached to a specific name as a specific rank (i.e. "It must be Pongidae, it can't be Ponginae") or when we insitently equate a specific rank with a specific time of divergence from the last common ancestor (i.e. saying that if Hominidae diverged in the late Miocene then Canidae has to have diverged then, too, instead of in the late Eocene).
Philosphy is hard slogging for me, so I think I am agreeing with you, John, but then I'm just a simple geek and I don't ratiocinate at the same level as you. :-)
Interesting discussion, and the analogies lead me to emphasize how this applies to basically _all_ language. Words are created and definitions change based on common observations and useful groupings thereof ("useful" in all kinds of ways, not just for scientific purposes).
I'm personally fascinated with situations where we are trapped by language -- where the terminology that developed is trumped by observable reality, but the words haven't evolved. I had a long argument about "human rights" with someone who could only conceive of a "right" as inherent -- therefore, it was "obvious" that any human would inherently have equal human rights. It didn't matter how many examples I gave... but yes, we think about and talk about rights this way, but in reality, the "rights" of an individual are purely based on what the people around her believe she deserves. Those beliefs vary by time period, by culture, by locale, by class, etc. etc., and they continue to change.
Lovely stuff to think about, though. The world is a messy thing -- we have to group it and box it up to be able to talk about it, but there are so rarely solid boundaries to point to!
I am not entirely convinced on your point on the Hennigian Convention. The point at which they seperate (if infact you meant spacially) may not be the best measurein the gradient, but to make a reductio: a penguin is most definitly not a maniraptor, and where to you draw the line? Maniaptors are extinct, penguins, evolved from maniraptors and somehwere along the line a maniraptor stopped being one and started being something else, a non-avian dinosaur.
One of the issues of a phenomenological perspective of species is that the boundry is indistinct. You know already that I am more concerned than many zoologists about time and its relationship to species, but if the two seperate and gradually distinguishing populations are of comparable size, which do you call the species still and which do you say is diverging? If you took one from each in 100 generations and say phenomenologically, these are different, species, and if you could also take a member of the ancestral population and say, this is also distinct, when do you claim the divergence and revise the species nomenclature for that group? Is it the point at which a novel character arises? How important does the character need to be for us to recognise it as phenomenologically different? and what if the groups diverge unequally such that a previously bimodal distribution of a character in a single population, is split amongst the diverging groups?
The other problem with demanding reciprocal monophyly for separate species, of course, is that it seems to assume that reciprocal monophyly happens as soon as the populations separate, which of course is not the case. And the larger and more widespread one (or both) of the populations is, the longer this would take. To extend the small rafting population example used by Jim Thomerson, what if the parent population is spread over the entirety of North America, with a small number of individuals rafting to (say) Hawaii?
"a penguin is most definitly not a maniraptor, and where to you draw the line? Maniaptors are extinct, penguins, evolved from maniraptors and somehwere along the line a maniraptor stopped being one and started being something else, a non-avian dinosaur."
This is silly. Penguins ARE a part of Maniraptora.
Interesting. Is this because the ranks define branch points in different lineages as being at the same "level", even though there is no basis for assigning any "level" at all to a branch point?
I'm overstating and oversimplifying this, but when I sort and identify a collection of fishes comprised of species I know well, I feel like I am dealing with facts of nature. I have no doubt that this pile of individuals is this species and that pile of similar, but different, individuals is another species, and that I have them identified correctly (as of today). I expect any other knowlegable person will sort them into the same species piles I did. Sort of like sorting a pocket full of change into stacks of pennies, nickles, dimes, etc.
On the other hand when I wonder if two species should be in the same genus, I am thinking about how names should reflect an hypothesis of relationship. Higher category names are objective; however another worker and I may look at the same set of data and come to different conclusions as to what the data infer, and thus how the names should be arranged. So, down in my gut, I think species and higher categories are not the same breed of cat.
Nick (#11). Excuse my ignorance, but I am not sure exactly what your point is. If you are seriously argueing the penguins are maniraptors, then we may as well argue humans are fish. There is a point where things that become different enough that they are no longer what they were, and the point in time, and the point of reference which we choose is an interesting subject.
We cladists think humans, and all bony vertebrates, belong to the group osteichthyes. When I explained this to one of my colleagues, a developmental biologist, she replied, "That's the stupidest thing I ever heard." So the concept is not universally accepted.