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Author Topic:   Why heirarchical taxonomy? Linnean system vs. Phylocode?
gnojek
Inactive Member


Message 1 of 33 (197296)
04-06-2005 4:30 PM


Howdy.
In another thread one poster made reference to another's usage of the word "man" or "mankind" and asked him why he used that phrasing. It seemed to the other poster that this was similar to using the term "kind" as YECs do when talking about the ark story. The poster then explained that he used the term "man" to describe anything in the genus "homo." So what he was saying (even though he didn't mean to) is that "homo" is a sort of Biblical "kind."
The classification of a species usually relies on the ability of an organism in a species to interbreed with other organisms of the same species. If two organisms can't interbreed then they are of a different species (you know, and they are of opposite sex and reproduce by sex, and are sexually viable). Even though some individuals of what we classify as species can interbreed, say members of the cats or dogs, and some others. Yet we put them into separate species for whatever reason.
In this regard, the Linnean heirarchical classification system seems to be largely arbitrary in many places, especially to a non-biologist such as myself. So that the term "genus" (maybe even other types of division) really could be supplanted by the term "kind".
My question is this: Why continue to bother with the heirarchical Linnean classification system when sometimes it seems that assignments to certain genuses and species seem arbitrary and use the same type subjective classification used to assign species to a certain "kind"?
What I mean is this: Say a paleontologist discovers an extinct species of bear. What is the difference between how he assigns this fossil to the genus "Ursus" and how a creationist would assign it to the kind "bear" (or some other name)?
Should we start using this Phylocode or some other non-heirarchical scheme?

Replies to this message:
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AdminNosy
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Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 33 (197331)
04-06-2005 7:11 PM


Thread moved here from the Proposed New Topics forum.

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 3 of 33 (197349)
04-06-2005 9:01 PM
Reply to: Message 1 by gnojek
04-06-2005 4:30 PM


why? because it is the best way to differentiate species that we currently have. without some system then every creature is a human being.
there are efforts to revise it from the old system to one based on genetics, but this is not raising too many {hackles\problems}, mostly because the genetic tree of life matches the old one pretty well (something like over 99% if I read another post correctly)
for more on the current classification system go here: http://www.msu.edu/%7Enixonjos/armadillo/taxonomy.html
your definition of species is also incomplete, as it makes no reference to non-breeding behavior as a barrier to reproduction even while breeding is genetically possible.
the horse and the donkey do not, left to their own devices, mate: they have to be tricked (usually raising one only in the company of the other) to do it.
they are not alone. there is also the asian greenish warbler that has several subspecies that make a continuous ring around a high area in tibet, overlapping in china with two subspecies that do not interbreed even though all other overlaps between subspecies do interbreed. the behavior of these two subspecies is different enough that they are not viewed as potential mates.
see http://www.zoology.ubc.ca/~irwin/Greenish%20warblers.html for more
it is not natural selection (survival) that is making this happen, but sexual selection.
meanwhile I have yet to hear one clear definition of what "kind" represents ... it used to be variety, then it became species, then it became genus and is currently flirting with family if not order.
this is due to defining "kind" as the upper level where evolution has definitely been observed so as to make "macro"evolution questionable.
when it comes to the bear, the paleontologist has a framework of species from which to work, complete with timelines for the different species that are known.
see http://www.geol.umd.edu/%7Ecandela/pbevol.html for some of the information.
thus the paleontologist will be able to compare his bear to the others and see how it relates, how that fits with the time line and whether or not it provides new information that can lead to new theories or that challenge old ones.
this picture is for horses, but the same sort of thing can be developed for any group of related species:
the creationist likely says "it's a bear" and is usually satisfied with the answer, seemingly unconcerned that at some point "it's not a bear" becomes evident in the fossil record, along with "there are no bears there" before a certain date (as in no bear fossils appear in the geological record below the iridium layer that blanketed the earth only 65 million years ago).
I'll choose a well defined system that has some problems, knowing what the problems are (and the work being done to resolve those problems), rather than an undefined system that not only cannot provide any information, but doesn't provide a framework for determining information, and say thanks.
this is said, knowing that at the other extreme, like the asian greenish warbler, we are all related to past species by a chain of small changes that wouldn't even be enough to warrent classification as a different variety, and thus if we only look at the changes within a brief period of time while delving further and further into the past we will find a continuous line of one "species" from human back to bacteria, as well as a similar line for virtually every other critter on earth. this obviously does not give us a framework to map out species, evolution and changes over time, so usually some point is reached where we draw an, albeit arbitrary, line that in essence says "we believe that the total changes between {that} species and {this} one are sufficient that should they happen to coexist we would classify them as different species" and thus break the line into a chain with links that are connected but where each link is distinct enough to distinguish and which only covers descrete segments of the lines of continuous life. this solves the messy {we are all one kind} question and sorts the data into useful bits.
hope that helps.
enjoy.
This message has been edited by RAZD, 04*06*2005 08:01 PM

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

This message is a reply to:
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Minnemooseus
Member
Posts: 3941
From: Duluth, Minnesota, U.S. (West end of Lake Superior)
Joined: 11-11-2001
Member Rating: 10.0


Message 4 of 33 (197382)
04-07-2005 4:40 AM


Phylocode in Discover magazine
In the April 2005 issue - Pushing Phylocode.
A very truncated version can be found here.
I afraid that link is pretty worthless, unless you subscribe to Discover. But I thought I'd point it out anyway.
Moose

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Andya Primanda
Inactive Member


Message 5 of 33 (197407)
04-07-2005 8:34 AM


Phylocode
Personally, I think people had been using the phylocode system unconsciously. I think most workers are just happy to refer to a taxon just by its name without any attempt to force a neat 'Linnaean' rank into it. Dictyoptera, for instance. It's the name for the clade of termites (Isoptera), cockroaches (Blattaria), and mantises (Mantodea). Some regard Dictyoptera as an order, while the three groups are suborders. Others retain the traditional ranking of Isoptera, Blattaria, and Mantodea as orders, elevating Dictyoptera as a super-order. This in itself is problematic because Isoptera is nested within Blattaria, therefore making a paraphyletic Order Blattaria. In the end people just forget the ranks and use the names.

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mark24
Member (Idle past 5195 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 6 of 33 (197414)
04-07-2005 9:39 AM
Reply to: Message 1 by gnojek
04-06-2005 4:30 PM


gnojek,
Why continue to bother with the heirarchical Linnean classification system when sometimes it seems that assignments to certain genuses and species seem arbitrary and use the same type subjective classification used to assign species to a certain "kind"?
The Linnaean system is slowly being supplanted by the cladistic system, the only retention being the genus & species binomen. This should remove the arbitrariness of the Linnaean system.
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
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Chiroptera
Inactive Member


Message 7 of 33 (197418)
04-07-2005 9:57 AM
Reply to: Message 6 by mark24
04-07-2005 9:39 AM


It served its purpose
Remember that the Linnean system came about before Darwin proposed his theory of common descent. Like Mendeleev's periodic table of elements, it must have been remarkable that animal species (and later plant species) could be arranged in such a heirarchical system.
Once common descent was proposed, this classification became very important evidence for this theory. The system retained its importance over the years, as new living species that were discovered, and, more importantly, the multitude of fossil species also fit very nicely into the system, providing further evidence for common descent.
But you are now correct. There is no longer any reasonable objection to the theory of common descent, and since the Linnean system is possible only because of common descent, then the logical next step is to use common descent directly in classification. I am a big fan of cladistics (even though I am not a biologist).
Still, one can see why some people would prefer the Linnean system. One really wants to say the lungfish, for example, are obviously fish, and, despite a phylogenic relationship to tetrapods, it does almost seem perverse to group lungfish with mammals as a group that is very separate from the teleosts. Stephen J. Gould even remarks on this in an essay (although I forgot which one).
There is certainly nothing wrong with grouping and classifying species according to physical and molecular morphology. All classifying systems are arbitrary. However, I feel that since the Linnean system is really based on phylogenic relationships to begin with, going directly to cladistics is a bit less arbitrary.
Edited to add: I don't see this post anywhere; I may have hit a wrong button. I am going to submit it again and hope I don't make a double posting.

This message is a reply to:
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mark24
Member (Idle past 5195 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 8 of 33 (197429)
04-07-2005 10:49 AM
Reply to: Message 7 by Chiroptera
04-07-2005 9:57 AM


Re: It served its purpose
Chiroptera,
Still, one can see why some people would prefer the Linnean system. One really wants to say the lungfish, for example, are obviously fish, and, despite a phylogenic relationship to tetrapods, it does almost seem perverse to group lungfish with mammals as a group that is very separate from the teleosts. Stephen J. Gould even remarks on this in an essay (although I forgot which one).
It does seem wierd that humans ARE Sarcopterygians, but it's only a name of an inclusive group. The problem people have is when they try to jive Linnaean & Cladistics names, end up conflating them, & causing themselves confusion (got the T-shirt). Humans aren't fish! Right? Is there still such a thing as a "fish"?
Mark

There are 10 kinds of people in this world; those that understand binary, & those that don't

This message is a reply to:
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Chiroptera
Inactive Member


Message 9 of 33 (197436)
04-07-2005 10:54 AM
Reply to: Message 8 by mark24
04-07-2005 10:49 AM


Re: It served its purpose
Of course there are still fish. I know a fish when I see one. Like the picture in your avatar -- obviously a fish. No, wait a minute, I guess it's not really. No, maybe it is. AAAGH!

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gnojek
Inactive Member


Message 10 of 33 (197495)
04-07-2005 3:24 PM
Reply to: Message 4 by Minnemooseus
04-07-2005 4:40 AM


Re: Phylocode in Discover magazine
Yeah, I have that issue.

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gnojek
Inactive Member


Message 11 of 33 (197499)
04-07-2005 3:54 PM
Reply to: Message 3 by RAZD
04-06-2005 9:01 PM


RAZD writes:
why? because it is the best way to differentiate species that we currently have.
What I meant is what does a biologist do in order to say "this goes in genus ursus" and how is that different from a biologist who might also be a creationist saying "I could put this in kind 'bear'" which to me is only a name game.
What features let us differentiate with the current system? What thought process goes into putting a specimen into a certain genus and is it as "arbitrary" as someone who also had a similar heirarchicy but just happened to have the category "kind" instead of "genus."
there are efforts to revise it from the old system to one based on genetics, but this is not raising too many {hackles\problems}, mostly because the genetic tree of life matches the old one pretty well (something like over 99% if I read another post correctly)
Well, from what I understand, in order to make it fit 99%, people had to invent new categories like sub-phylum, super-class, sub-species and things like this. It just seems really slapdash and not very adaptable to new knowledge. All these sub-divisions and such get really hairy and confusing.
when it comes to the bear, the paleontologist has a framework of species from which to work, complete with timelines for the different species that are known.
This is exactly what someone would do if they wanted to classify a specimen as a certain "kind." They have a framework of other species that we call bears based on the construction of the skeleton and other features. To me this seems kind of subjective. It may seem less subjective to "the trained eye."
the creationist likely says "it's a bear" and is usually satisfied with the answer, seemingly unconcerned that at some point "it's not a bear" becomes evident in the fossil record, along with "there are no bears there" before a certain date (as in no bear fossils appear in the geological record below the iridium layer that blanketed the earth only 65 million years ago).
I would imagine that a biologist will also say "it's a bear." Let's say hypothetically that the biologist is a creationist and he does all the other things that a biologist would do to classify the specimen as a bear, but instead of using the Linnean classification system, he just says that this specimen is of the bear "kind." How is that so different than putting him in the genus ursus? If the alternate classification scheme was also heirarchical then "kind" could come under "variety" and maybe "type." It would be the same thing but would stick to the literal Noah story.
Yeah, and from what I understand, the iridium layer is spotty around the world but when it is found it's always at the K-T boundary.
I'll choose a well defined system that has some problems, knowing what the problems are (and the work being done to resolve those problems), rather than an undefined system that not only cannot provide any information, but doesn't provide a framework for determining information, and say thanks.
Are you talking about Phylocode?
Well, the Linnean system doesn't provide any more information than a similar system under a creationist framework with the names changed.
It doesn't provide information on the linneage of the organism in question. The way it's set up, it's as if all organisms could be alive at the same time and it would still work the same.
this is said, knowing that at the other extreme, like the asian greenish warbler, we are all related to past species by a chain of small changes that wouldn't even be enough to warrent classification as a different variety, and thus if we only look at the changes within a brief period of time while delving further and further into the past we will find a continuous line of one "species" from human back to bacteria, as well as a similar line for virtually every other critter on earth. this obviously does not give us a framework to map out species, evolution and changes over time, so usually some point is reached where we draw an, albeit arbitrary, line that in essence says "we believe that the total changes between {that} species and {this} one are sufficient that should they happen to coexist we would classify them as different species" and thus break the line into a chain with links that are connected but where each link is distinct enough to distinguish and which only covers descrete segments of the lines of continuous life. this solves the messy {we are all one kind} question and sorts the data into useful bits.
Yeah, that's what phylocode would be better at doing than the Linnean system. The Linnean system (and this may be the whole point of this thread I think) was invented before evolutionary theory took off and is in essence a creationist system. Or, it would be identical to a system devised by a creationist that happened to have the classification "kind."

This message is a reply to:
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Replies to this message:
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gnojek
Inactive Member


Message 12 of 33 (197500)
04-07-2005 3:59 PM
Reply to: Message 5 by Andya Primanda
04-07-2005 8:34 AM


Re: Phylocode
Exactly!
The Linnean system goes to hell in some circumstances.
Sometimes there are just too many differences to just cubby a classification into a specific ranking.
From what I read in that Discover article ( I had heard of Phylocode about a year before, but anyway... ) the people who like Phylocode are the ones working in fields where the old system is most problematic.
The ones who are against it are the ones working in fields where the Linnean system works.
I think it was the insect people versus the mammal people.

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gnojek
Inactive Member


Message 13 of 33 (197502)
04-07-2005 4:08 PM
Reply to: Message 7 by Chiroptera
04-07-2005 9:57 AM


Re: It served its purpose
Chiroptera writes:
Once common descent was proposed, this classification became very important evidence for this theory. The system retained its importance over the years, as new living species that were discovered, and, more importantly, the multitude of fossil species also fit very nicely into the system, providing further evidence for common descent.
I know above I said the Linnean system was identical to a creationist system, but I did forget that the heirarchical scheme of it became a sort of evidence for common descent. But I still think that the Linnean system would work whether there was common descent or not. I may be totally wrong, but the way it seems, the system could work if every organism ever alive was alive today (crap, but so would phyolocode )
Still, one can see why some people would prefer the Linnean system. One really wants to say the lungfish, for example, are obviously fish, and, despite a phylogenic relationship to tetrapods, it does almost seem perverse to group lungfish with mammals as a group that is very separate from the teleosts. Stephen J. Gould even remarks on this in an essay (although I forgot which one).
Yeah, this is the kind of "arbitrary" subjectivity I was talking about. New knowledge comes along and it becomes really hard to change the classification of an organism. It's like someone looked at it, evev fully characterized it in every way, measured everything and then some, but the final shelving into a cubby with a name on it is pretty damned subjective it seems.
All classifying systems are arbitrary.
Ah! Thanks for that! I was hoping someone would give me some validation for my concerns.

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Loudmouth
Inactive Member


Message 14 of 33 (197503)
04-07-2005 4:14 PM
Reply to: Message 11 by gnojek
04-07-2005 3:54 PM


quote:
I would imagine that a biologist will also say "it's a bear." Let's say hypothetically that the biologist is a creationist and he does all the other things that a biologist would do to classify the specimen as a bear, but instead of using the Linnean classification system, he just says that this specimen is of the bear "kind."
I think this is a good place to start. What we have, in the case of cladistics, is a nested hiearchy that is continuous. What we have with the "created kinds" are separate trees that do not interconnect.
The creationists stop at "bear kind" but give no clear reason why it shouldn't continue back to "mammal kind". Or even "vertebrate kind" and further back to "eukaryote kind". The construction of separate, unlinked trees is arbitrary. The only reasoning, from what I have read, is the amount of evolution that creationists will allow in 4,000 years since their supposed flood or 6,000 years since their creation week. Professional taxonimsts, on the other hand, make no boundaries since none are seen in living species beyond reproductive barriers.

This message is a reply to:
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gnojek
Inactive Member


Message 15 of 33 (197519)
04-07-2005 4:56 PM
Reply to: Message 14 by Loudmouth
04-07-2005 4:14 PM


I think it's finally clearing up for me.
I keep thinking of the way a creationist might think in my biased evolutionary way of thinking. It never occured to me that a creationist would not want to make a heirarchy because that would then suggest to him a common descent.
Now I wonder, since most creationists must have encountered at least the classical Linnean system in school, do they reject it?
I guess there is no real need to reject it since it doesn't necessitate common descent, it only implies it. One could still use the Linnean scheme and just say that it's based on physical similarity (as I guess it was done before evolutionary theory was applied).
BTW, I haven't heard from a creationist on this. I was hoping they could clear up my misinterpretations of how an organism might be placed into a certain kind.

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