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Re: About Capes

Postby entrancedbymyGCC » Sun Feb 06, 2011 8:16 pm

This turns out to be more of an academic research issue than I properly have time for... here is what I think I know. Feel free to correct me if I have something wrong. I cannot actually find either an accepted modern definition of species which refers to genetic difference (fraction of DNA similiarity) nor can I find a single organization that is truly responsible for making these decisions at the species level. I gather the American Federation of Aviculturists gave teh nod to the resclassification, but I've been unable to determine if there is another official documentation of it, other than in the realm of scientific journals.

Michael wrote:Yes. Because if we start manipulating science for political purposes (not that it doesn't happen, but it would be much worse if we flat our approved of it), then what will be left of science? We have to separate our bias/desires from achieving a truthful understanding of the world.


This is true, but it is also true that scientific conventions -- nomenclature, for example -- do change as a function of time. IMO this is very different from falsifying data or falsifying an experimental result. The DNA profiles of P.r.r., P.f.f and P.f.s should be similar/different by a measurable amount, and that result -- the data-- should not change even if we label them differently. Taxonomy is a tool of science, it is not the science itself.

If the P. r. robustus Cape Parrot can be considered to be a different species from the P. r. fuscicollis based on some discrete differences (such as hue of plumage, weight, and beak size), then we have to entirely rethink the concept of a species.


The discrete difference is the DNA profile. I have found numerous references to degree of commonality in DNA in a group compared to degree of differentiation of those profiles in a different group as being used to reevaluate species classifications in animals other than the Cape Parrot. I cannot find a solid guideline as to how this discriminator is applied but IMO it is actually more quantifiable and less subjective than the interbreeding discriminator. It could not have been proposed at the time the interbreeding discriminator was proposed. I don't see anything inherently wrong with it. The idea is to have a way to quantify a unique group. The devil is of course in the details, but it should be possible to have a viable definition.

At this rate, we will soon be calling people of different races a different species too.


Well, now you are putting a very fine point on it. But I think the range in human DNA is very small, less than 1%. I can't find a number for the genetic difference between P.r and P.f but I would assume it was considerably greater than that for the argument to carry weight.

I have heard a suggestion that there is no such thing as a species, that every individual is their own species.


That's obviously going too far. I would think most scientists would agree that's going too far. You could just as well argue any individual has cells of several species, because mutations may occur... Sure every individual has unique DNA, but you CAN do commonality statistics and do something usefulo with that. Just because it is possible to define a meaningless discriminator using DNA does not mean that it is impossible to define a meaningful one.

You cannot violate the taxonomic principles by changing the definition of a species but then still labeling it a species.


As far as I can tell, there is no ironclad taxonomic "code". The driving principle is to rationally classify living things by grouping them according to their similarity. Utilizing genetic information to do that is IMO no violation of the principle -- creatures do often get reclassified when new information surfaces. Really "species" was the only level that ever had a common observational definition suggested as a razor -- and it doesn't apply to plants, only animals. Maybe we have a better discriminator for uniqueness now -- that was truly the intent of the system in the first place, to organize and name things in accordance with their similarities and uniquenesses.

If they want to create a new organization system of categorizing living things where genetics (or something else) rather than reproductive viability defines a species, then they can do so without breaking the existing system.


I think "they" already have. The only thing that "breaks" the current system is strict adherence to the interbreeding criterion. I'm open to arguments that just because interbreeding is possible, if a population is sufficiently isolated to have developed a unique genetic signature, interbreeding would in fact never naturally occur and that unique population is sufficiently unique to be worthy of calling a different species. I've found references to several other proposed reclassification based on genetic diversity -- in elephants and in worms, specifically. It is not just a Cape Parrot issue.

How do you feel about poor old Pluto? Seriously, that's another thing we all learned in school was a FACT, and now that we know a bit more about the taxonomy of our solar system, we realize it is really more similar to a whole host of other things just like it, and less similar to the other planets. Because of where it is, it was the first thing "like it" that we discovered. But over time, that was insufficient to allow it to be considered unique. This seem very analogous to me. The science was never bent or broken, but the definitions were refined based on data, and a mistake that was made a long time ago was corrected, causing much trauma. But now that we are finding planets around other stars right and left, the definition of "planet" needed to be reevaluated and made clearer.

BTW I have a strong feeling that Scotty is a Grey Headed Cape Parrot while Truman is a Brown Necked.


It should be possible to figure that out, but I don't have his breeder info and he isn't banded or chipped. The seller keeps promising me to dig it out, but she seems sufficiently disorganized that I may never know. She says he came from EB Cravens, and EB confirms he sold her some chicks, so... I don't know if he has only Grey Heads or Brown Necks or both. Certainly from a distance Scotty's head and neck seem quite silvery but if you look very closely there is maroon blended into the feathers giving a brownish tinge.... I can take some closeups if you want.
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Re: About Capes

Postby Dave » Sun Feb 06, 2011 9:36 pm

A little extra time on your hands?
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Re: About Capes

Postby Rueae » Sun Feb 06, 2011 11:02 pm

entrancedbymyGCC wrote:It should be possible to figure that out, but I don't have his breeder info and he isn't banded or chipped. The seller keeps promising me to dig it out, but she seems sufficiently disorganized that I may never know. She says he came from EB Cravens, and EB confirms he sold her some chicks, so... I don't know if he has only Grey Heads or Brown Necks or both. Certainly from a distance Scotty's head and neck seem quite silvery but if you look very closely there is maroon blended into the feathers giving a brownish tinge.... I can take some closeups if you want.

I don't know about Michael, but I'd love to see close ups of him. :D
I think it'd be super nifty to have both Brown Necked and Grey Headed on the forum.
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Re: About Capes

Postby Michael » Sun Feb 06, 2011 11:33 pm

I believe that for all intents and purposes, the definition of a species being defined by reproductive viability is the only one that carries any importance. The extreme example of every individual being their own species can hold true if you look at degrees of genetic difference. You can always change the increments and argue over how much is required for species categorization to apply. However, there are examples of genetically more distinct organisms being the same species and interbreeding while others are more akin and cannot. The reproductive viability definition carries importance because it means that these organisms can continue producing offspring of that genetic lineage.

Geographic (or other forms of) isolation alone cannot be used to define a species because there are endless examples of isolated populations that remain the same species and if put in contact can interbreed. So while the habitat of the P. r. robustus and the P. r. suahelicus does not overlap (and while close, maintain altitude separation), this is insufficient to label them separate species.

Considering that all of these parrots are alive and available for research, I cannot accept a species reclassification without either research proving non-compatible reproduction or a redefinition of species accepted on a global level as the new standard. The proponents of the species reclassification have argued based on politics, conservation, and aesthetics and not empirical science. It's one thing to be having a debate about classifying something that is already extinct, but since they are still around, it is ridiculous to let politics overwhelm the science and blind us from a truer understanding of Cape Parrots (as the tiniest sub component of understanding the greater universe). If you legitimize for science to be led by politics and bias rather than by the best possible attempt to discover how things really are, then science is not science. Science cannot be trusted if the basic principles and understandings we have are broken for selfish personal purposes.

I accept that definitions and classifications can, do, and should change with solid scientific justification. This is called progress and without it we'd be nowhere. However, the cases I've read for reclassifying the Cape Parrot are a hack job at best. The only convincing case they make is that the Cape Parrot should be classified as a different subspecies in its variation but gives no reason to believe that Cape Parrots cannot interbreed and produce viable offspring with other subspecies of their kind. Since the species is the basic building block of our categorization system of living organisms, because these organisms can come together and produce more of their kind, the only logical conclusion at this point is to accept that there are three subspecies of Cape Parrots.

PS I'm really not holding a personal bias either way in this Cape Parrot classification debate (overall, not specifically with you). Originally I blindly accepted the split because I had read that there was such a split. However, since getting Truman I've further looked into it and it didn't seem to make sense why the species were split. So I researched some of the papers (many of them I couldn't get but I did get some) and read the reasons they gave for splitting the species. That's when I realized it was all a load of crap and just political. If Cape Parrots are in fact a different species (based on the definition of species I am best aware of) from the "UnCapes," I would love to know this. I am entirely willing to accept such a split without personal favor of naming them either way. However, I am not willing to taint my understanding of these parrots and science overall by accepting a politically motivated, unscientific scheme to achieve an end goal that was determined before the research even commenced.
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Re: About Capes

Postby entrancedbymyGCC » Mon Feb 07, 2011 12:52 pm

Can you post links to the references? So far I have only found the one in the AFA news, not anything in refereed journals. I have access to the Caltech library system, so I'm sure I can get at the papers -- in fact, if I even knew the salient journals in the field, I could probably find suitable search tools. I don't know the biological literature at all.

I guess I disagree with you that interbreeding must be the acid test. I work in a field where quantification of similarity or difference is very often the subject of research papers and it does not at all bother me to have a DNA-similarity based system of taxonomy in principle.

The case with the Cape itself, I have not been able to assess the details for myself.

In addition, I think getting funding for research should not rest solely on the species designation -- in my field getting funding to do observations rests on being able to demonstrate that the result of the observations is of interest -- and on that proposal being more compelling than the next one over. However, getting protected status probably does because of rather circular logic -- being a "species" carries the implication of having a level of uniqueness that makes a creature "worth saving". Otherwise it is deemed "just the same as the others, really". The modern definition of species might just as well be "sufficiently unique to be worth trying to preserve". IMO changing those rules so that a subspecies can be granted protection would take longer than any extant endangered subspecies has, so you'd be fighting the good fight but losing the creatures you were trying to protect.

I guess we agree to disagree, at least until I've convinced you I'm right! (Joke). Perhaps as I become more educated, I'll change my mind, but as an employed scientist, admittedly an Astronomer not a Biologist, I don't see the concept of DNA-based taxonomy as inherently flawed. What it may be is not sufficiently mature to have a coherent definition and method.
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Re: About Capes

Postby Michael » Mon Feb 07, 2011 2:49 pm

What you will find is that the published papers promoting the Cape Parrot species split are all coming from the same circle. You'll find the same names on all the papers supporting the species split: Clancy, Symes, Perrin, Wirminghaus, Downs. Many of these are the same people that get money for their Cape Parrot counting days and other pet projects. I have yet to see an unbiased third party weigh in on this species split that is not concerned with Cape Parrot conservation or research money for Capes in either way.

All of the evidence I have encountered talks about how the groups of Capes are different and how the robustus are more different from the others. However, they don't present any case why this would mandate the robustus to be classified as a separate species. Clancy's reasoning for splitting the Cape Parrot species was because "The two austral forms of robustus-type parrots are distinguishable on the basis of the head-top and neck coloration, body plumage-colour and the nature of the bill." His case is simple laughable because it does not explain why this is sufficient evidence to call them separate species. Simply look at the variation of Grey parrots (whether congo, timneh or other). Humans come in a greater variation of colors than Cape Parrots and are still considered to be the same species.

Once again, the evidence that Wirminguas et al. use to support the species is split does nothing to prove that they cannot be the same species. He states that "the behavioral evidence, distribution data, specific habitat requirements, and morphological differences presented here support that the souther taxon P. r. robustus is a separate species from the northern subspecies P. r. suahelicus and P. r. fuscicollis." However, none of this necessarily proves that they are separate species. All it shows is justification for naming them as separate subspecies.

They make a really really bad case for calling them separate species. The papers are only believable to those who are willing to suspend their logic and skepticism in favor of personal bias. This is why it's not a wonder that the IUCN and the Parrots of the World Guide still haven't accepted the Cape Parrot species split to date (13+ years since it's proposal). South Africa would love to be able to call itself home to an endangered species of parrot. The CapeParrot project wants to solicit funds under false pretenses that they are saving the last of a species. While they are working on conserving a small population of Cape Parrots that is unique from the others, they are lying when they say that these are the last of the species (and a species being a group of organisms that can interbreed producing viable offspring).

I invited everyone to read the papers while putting their parrot loving bias aside. Even if the South African Capes are nothing more than a subspecies, that should not change our perspective about their conservation but will at least help us better understand them. So separate bias from science and determine if the evidence proves that they are in fact different species. One problem is that you will not find any opposing papers because generally no one cares (or ignores the split) while the proponents of it are very very vocal and make it look as though everyone is supporting it. Do not let this false majority impression sway your understanding based on the evidence.

The only conclusion I can make is that based on currently available evidence and the classic definition of a species, the three races of Cape Parrot are the same species and that the split was not sufficiently justified.

If anyone comes across a more convincing justification for the species split than I have already read/referenced, please show me because I am very interested in this and open to changing my opinion with sufficient evidence. However, I will not unquestioningly follow what a group of biased scientists want everyone to believe to benefit their own personal agendas.
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Re: About Capes

Postby entrancedbymyGCC » Mon Feb 07, 2011 5:11 pm

In what journals are they published?

I understood the argument that carried the decision was DNA-based. Can you tell me more about that? That's where I think precedent exists in other species.
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Re: About Capes

Postby entrancedbymyGCC » Mon Feb 07, 2011 7:24 pm

OK, I think I found the fundamental article, but it was published in "African Journal of Ornithology" which the Caltech Library does not carry. I guess I can pay for a copy of the article, but if you actually have a copy, could you PM me? Perhaps I could read it? I have the same issue with the "Journal of Natural History". Guess we really are "Big Bang Theory" and don't have access to the squishier biology journals.

I found the JNH article on Thor's site in PDF form. I'll grant you that's not wildly convincing, but some of the references therein are interesting. I'm feeling stubborn about this, so I'm going to keep digging around as I have time. The obscure article in "Honeydipper" by Clancy seems to be the one that talked about DNA sequencing differences, but that is a seriously obscure publication. There is a review on the topic in African Journal of Ornithology I'm going to see if I can get my hands on. What a morass.
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Re: About Capes

Postby Michael » Mon Feb 07, 2011 9:50 pm

You didn't say the title of the article...

As you read according to Wirminghaus et al that the reasons for Cape Parrot species split are really insufficient. Clancy was even more pointless and uninteresting. The journal you mentioned sounds familiar but I don't remember if I read that or not without the title.
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Re: About Capes

Postby entrancedbymyGCC » Mon Feb 07, 2011 11:27 pm

I'm not rejecting the paper out of hand, just that without DNA evidence it seems suggestive but not conclusive. It does have some interesting references I'd pursue if I had access to the journals. I keep reading hearsay here and there that there is DNA evidence at the basis of the species declaration, but I've not been able to locate the paper which documents that, unless it is the Clancy paper in the seemingly-obscure publication, which may not be peer-reviewed. I'd have to go back and look for the citations to find the titles, but I guess I file them mentally in astronomical journal form.... author, year, journal, issue page without title. Couldn't these guys publish in "Nature" or something?
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