I don't know if you all would be interested, but I've been thinking quite a bit about taxonomy recently. Specifically, the naming, classification and organization of living organisms into a hierarchical structure. It's sorta what I do in school and in research so the subject finds it's way into my mind space quite often.
Traditionally, there were four schools of thought on the basic reasons for classifying organisms. The first was the essentialist school, which held via Plato that all living things were reflection of divine eidos set down by god, immutable types. Around the time of Darwin, a second school called phenetics came about, which classified organisms via overall similarity. Both of these two systems have been more or less abandoned, though the Linnaean hierarchy is still used to this day.
Post Darwin, two basic systems have come about, the Cladist system ala Will Hennig which held taxa (the holder of a name) to be monophyletic (have one common ancestor) clades, and the other, the Evolutionary Synthesis system which borrowed from both cladistics and phenetics. Both try to place organisms in an evolutionary hierarchy, but Cladistics puts a high emphasis on monophyly and strict branching events based on genetic and morphological evidence, while Evolutionary Synthesis (ES) alows for paraphyletic taxa (groupings that include the common ancestor but not all of the descendents), with higher emphasis on apomorphies (specially unique characters; this is in contrast to plesiomorphies, more general shared characters).
For an easy example, Cladists would consider the Clade Aves to be part of Clade Reptilia, as the former is nested within the other via fossil and genetic evidence; as Reptillia would need to include all of the descendants to be monophyletic, and as birds are descended from the same ancestors as all other reptiles, then a bird would be considered a reptile. ES considers Class Aves to be distinct enough in it's apomorphies (feathered wings, for example) to give it "higher importance" in the classification, and therefore place it outside of Reptilia in it's own group, equal in the hierarchy; this is a paraphyletic grouping, which is completely okay under ES.
Obviously neither of these work well in situations where horizontal gene transfer takes place (bacteria, for example); in this case a more traditional phenetic approach is favored.
Now, if you looked at the example above, you can see the two systems are at odds much of the time. The Cladists and Synthesist get into big arguments over what is right and what is wrong. The cladists argue for a strict phylogenetic system where names are matched to clade which occur at branching events and follow lineages; they believe the synthesists system to be far too vague as far as evolutionary relationships go, and completely disregard lineages in their hierarchy. The synthesists argue for a more easy naming system communication wise, putting more emphasis on unique characters and the Linnaean naming system; they believe the cladist system to be an affront to the traditional taxonomy and ease of communications about organisms. Both complain of the other's "taxonomic inflation" (I've also heard the term "taxonomic terrorism" before), of the cladist's "excessive naming" of clades, and of the synthesists "excessive raising" of taxa (from genus to family for example) as "some sort of political exercise".
Some of these arguments get quite nasty. This: http://www.mapress.com/zootaxa/2008/f/zt01950p086.pdf is one of the more mild ones. The writer is coming from a synthesists background, claiming that the use of clades violates Linnaean hierarchical naming systems.
Okay, theres another argument I should cover, one that I'm a bit less neutral about, but I'll try anyway. Due to the way the International Code of Zoological Nomenclature is worded, whenever a rank change occurs the name assigned to that particular taxon must change as well. This tends to be quite political, with people raising names associated with pet projects and deleting names that they don't care for. Only the specific name (Genus species) is somewhat fixed. So, with people changing names of higher taxa all over the place, this pisses a whole bunch of people off. The ranking system which leads to the tendency to put more importance on some taxa than others is the culprit.
The alternative to this is the PhyloCode (http://www.ohio.edu/phylocode/). Many many taxonomists hate this (and will say so in rather vile language). People have a love affair with Linnaeus, what can I say. Phylocode will destroy traditional taxonomy and kill your cat, its the end of the world as we know it, or so goes the argument. People who like phylocode for being rankless with higher taxa having fixed names similar to the way species are handled under the ICZN believe it works, and will avoid all the political name changes and confusion associated with them. The understanding is thus: If we know via evidence that a particular taxon is monophyletic (thereby being a clade) why not fix the name until someone comes along with evidence to the contrary, thus saving us the confusion of the other system? I'll admit, I like PhyloCode, even with the current issues (it doesn't cover species names, for example, only higher taxa).
So the people who love Linnaeus argue with the people who love PhyloCode, and the Cladists argue with the Synthesists. And the problems continue. Names have a lot of power, and just like the person who has the gold makes the rules, the person who names taxa tends to have power and respect within the scientific community.
Follow up thoughts:
Although the idea of immutable types has been formally rejected and is not spoken of except as something quaint, the way taxonomists often talk of naming taxa often comes with this feeling of eidos, that is, comes with this feeling of power of speaking of something beyond our physical reality. Names have power. So while the eidos of Plato has been rejected subconsciously it's being carried on. The way taxonomists talk of species feels this way, like invoking words of power, like wizardry. I don't know if we can ever really escape that.
Reading back through the first paper above, I'm struck by how it covers everything except the very thing I have trouble with, that people are humans and humans suck. In other words, you can talk all day about how ranks are meaningless and are only useful in explanation, as every taxonomist very well knows, but outside the little group of friends you have that live with great honour and stoicism placing ranks is not this perfect code blessed with "being above it all". Changing rank while naming is a backstabbing political process used to establish pet projects and get rid of those names you dislike, cause ranks are to the rest of us not meaningless. Refusing to accept that just leads to a third circuit disconnect from reality. The map may not be the territory but when enough people treat it as the territory you have to adjust the way you go about doing things or they'll use your maps against you. It's hard to talk about something you don't have a name for, something we've talked about before.
Enough out of me.
Quote from: Kai on August 18, 2009, 09:18:44 PM
Although the idea of immutable types has been formally rejected and is not spoken of except as something quaint
Python has immutable types, though.
Quote from: Triple Zero on August 18, 2009, 10:37:58 PM
Quote from: Kai on August 18, 2009, 09:18:44 PM
Although the idea of immutable types has been formally rejected and is not spoken of except as something quaint
Python has immutable types, though.
:lulz: :argh!:
Very interesting reading, Kai. thx.
It sounds like the Linnaean system was very useful for a good while, and so has momentum, but will innevitably be replaced by the more accurate map of the cladists....
the argument of 'easy communication' seems to be pretty weak when discussing the incredibly complex subject of classification of living things...
does there seem to be a sentiment of whispered admission from the ES guys that this is the case when it's two taxonomists at a bar, rather than in the thick of the fray?
Quote from: Iptuous on August 19, 2009, 01:53:09 PM
Very interesting reading, Kai. thx.
It sounds like the Linnaean system was very useful for a good while, and so has momentum, but will innevitably be replaced by the more accurate map of the cladists....
the argument of 'easy communication' seems to be pretty weak when discussing the incredibly complex subject of classification of living things...
does there seem to be a sentiment of whispered admission from the ES guys that this is the case when it's two taxonomists at a bar, rather than in the thick of the fray?
I don't know. I interact with people who generally follow cladistics and agree with true monophyletic groupings.
The ranked vs nonranked system thing isn't generally a cladist versus synthesist question, but rather a Linnaean vs phylocode (and other classification methods) question. http://3lbmonkeybrain.blogspot.com/2008/08/what-is-it-that-you-hate-about.html is an example of what I mean. People are really in love with Linnaeus, regardless of him being an arrogant creationist. The ranking hierarchy is what's seen as the heart of the system, something that biologists have been working with for the past 300 years, and old habits die hard. You can agree with cladistic methods and yet use the ranked system as long as you ignore the political issue of ranks (which is frankly hard for me to ignore).
To me, the heart of communication is using terms, which are unambiguous. The way taxonomy is now is ambiguous: some people use the system with a strict phylogenetic basis only giving ranks because the ICZN requires it and some people are much closer to phenetics than they'd like to admit. In other words, some people use it as a basis for examining the relationships of descent, and some people use it for the basis of primaring naming and constructing classification for the names sake.
Honestly the whole mess confuses me to hell, much less anyone else reading this.
Quote from: Triple Zero on August 18, 2009, 10:37:58 PM
Quote from: Kai on August 18, 2009, 09:18:44 PM
Although the idea of immutable types has been formally rejected and is not spoken of except as something quaint
Your Mom has immutable types, though.
Quote from: Ratatosk on August 19, 2009, 06:20:32 PM
Quote from: Triple Zero on August 18, 2009, 10:37:58 PM
Quote from: Kai on August 18, 2009, 09:18:44 PM
Although the idea of immutable types has been formally rejected and is not spoken of except as something quaint
Your Mom has immutable types, though.
FUCK YOU MY MOM DIED OF IMMUTABLE TYPES!
Today, I had a long discussion with my adviser about phylogeny, taxonomy, and naming.
The crux of the problem seems to me now not to be of rank. Ranks occur in any hierarchical system no matter how rankless it may claim to be; a hierarchy requires some way to determine individual placement within the higher groupings. There are ways you can illustrate this without named ranks, via indentations and such, or you can erect new ranks to describe placement. Those that would be in to the "fossil" classical methods are a dying breed in any case.
The real conflict here is between those that require a flexible system, that is, those people doing the science of naming and phylogeny, and those people that require a stable system, that is, those people doing the technology of modern systematics, which includes storage and retrieval of information, description, organization, cataloging and identification of organisms.
Again, conflict between "pure and applied science".
In identification I require a stable system so I know what to call an organism. This allows me to organize store and retrieve information about the group or lineage in question. In phylogenetics, I need a flexible system so I can allow the scientific method to test my hypotheses and falsify them. Depending on what I'm doing I have to view my work through different filters.
HH Ross, the preeminent entomologist who studied more than anything the group I work with, Caddisflies, was known to say, "If you need to talk about something, give it a name". Something I'm keeping in mind.
Maybe not your exact point, but this came to mind the other weekend. I was tlakign with some folks from NOAA, and looking at a psoter of northern Atlantic fish species they had up. It had 6 different kinds of flounder with their latin genus / species names. NO commonality between any of the 6 to actually tell you, or suggest "Flounder"
Quote from: Richter on August 21, 2009, 01:41:52 PM
Maybe not your exact point, but this came to mind the other weekend. I was tlakign with some folks from NOAA, and looking at a psoter of northern Atlantic fish species they had up. It had 6 different kinds of flounder with their latin genus / species names. NO commonality between any of the 6 to actually tell you, or suggest "Flounder"
This is the reason that common names don't do much good. What's a flounder for one person is different than whats a flounder for another.
Plecoptera are sometimes called salmonflies, the same name used often for mayflies (Ephemeroptera), which are also called fishflies, a name used for many different kinds of aquatic insects.
"Common names are for common people", as someone once said, not because they're less intelligent, but because they're more ambiguous.
So Kai, which "granddaddy longlegs" is supposedly the most venomous spider in the world but has such tiny fangs that they can't penetrate human skin?
I've heard this several times, been told that it is a myth, and and then told that no, it is not a myth, but a scientific fact. It is difficult to research since there are apparently several unrelated species called "granddaddy longlegs".
Also, there seem to be several different species that people call "June Bugs". Where I live, it's a metallic green beetle approximately 3/4" in length that usually shows up in early July.
Quote from: Jerry_Frankster on August 21, 2009, 10:15:16 PM
So Kai, which "granddaddy longlegs" is supposedly the most venomous spider in the world but has such tiny fangs that they can't penetrate human skin?
I've heard this several times, been told that it is a myth, and and then told that no, it is not a myth, but a scientific fact. It is difficult to research since there are apparently several unrelated species called "granddaddy longlegs".
Also, there seem to be several different species that people call "June Bugs". Where I live, it's a metallic green beetle approximately 3/4" in length that usually shows up in early July.
The first one is a bullshit myth. http://en.wikipedia.org/wiki/Opiliones They don't have venom or fangs but rather a set of palps called chelicerae. If you want to learn more about this group check out the Catalogue of Organisms blog, the author studies harvestmen almost exclusively.
There's also the confusion that "daddy longlegs" often refers to crane flies (http://en.wikipedia.org/wiki/Tipulidae) which also have long legs. One's an arachnid, the other is a family of true flies (Diptera), an insect.
June bugs are almost always in reference to several genera from the family Scarabaeidae, also known as the scarabs. The larger ones you find here in north america that are a tan-brown to bronze brown color and come out often in may are
Phyllophaga (http://en.wikipedia.org/wiki/Phyllophaga_(genus)). There are many other smaller scarabs that look similar. The green june bug, or metallic green june beetle is probably
Cotinus nitida (http://en.wikipedia.org/wiki/Green_June_beetle). Most of these are turf grass pests as larvae.
When I use the common name, it could mean various things, but when I give a scientific name, its very unambiguous, and if it is, the qualifier "
sensu lato" or "
sensu stricto" might be added afterwards (or
confer or cf.).
Thanks for setting me straight on that, Kai.
I should have known better than to listen to commune-dwelling hippies.
Quote from: Jerry_Frankster on August 22, 2009, 01:19:59 AM
Thanks for setting me straight on that, Kai.
I should have known better than to listen to commune-dwelling hippies.
Heh, next you'll be telling me not to go to the ever reliable Discovery Institute website for information on evolutionary biology.
They have their fields of expertise, such as mycology, and tye-dyeology, but apparently entomology arthropology bugology isn't one of them.
Quote from: Jerry_Frankster on August 22, 2009, 04:42:26 PM
They have their fields of expertise, such as mycology, and tye-dyeology, but apparently entomology arthropology bugology isn't one of them.
Entomology comes from the greek en-tome, meaning cut into, essentially to be jointed or segmented. It covers all arthropods except arachnids (Arachnidology) and crustaceans (Carcinology), although these groups often fall under the umbrella of Entomology in academics.
I've been plagued by a very similar problem—if not the same one—for quite some time now.
Recently I've come across Sorites Paradox (http://plato.stanford.edu/entries/sorites-paradox/), which really is a set of similar ideas. It goes, "Would you call 1 grain of wheat a heap?" ... "How about 2 grains?" ... "When does it become a heap then?"
The link has some interesting responses to it:
Quote from: Stanford Encyclopedia of Philosophy (http://plato.stanford.edu/entries/sorites-paradox/#3.2)
The inclination to validate all the premises of a sorites argument (along with the inference pattern employed, which the Stoics accepted) was to be explained via ignorance—more exactly, the unknowable nature of the relevant sharp semantic boundary.
In this way the threat of wholesale scepticism urged by the Sceptics was met by the limited scepticism arising from our inability to know the precise boundaries to knowledge. 'Nothing can be known' was rejected in favour of 'The precise boundaries to knowledge itself cannot be known'.
and especially this one:
Quote from: Stanford Encyclopedia of Philosophy (http://plato.stanford.edu/entries/sorites-paradox/#3.2)
In the second half of this century there have been a number of attempts to develop non-classical logics of vagueness, a major constraint being the provision of a solution to the sorites paradox. The extent of the proposed logical innovation varies.
Do any of the responses to the sorite's paradox relate to the competing taxonomic systems you discussed?