0867: "Herpetology"

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Re: 0867: "Herpetology"

Postby bmonk » Wed Mar 02, 2011 5:35 pm UTC

He he he. It's just that early classification depended a lot on shapes, and most extant reptiles, being "lizard-like things", look generally a lot like many extant amphibian "newt-like things". But birds, despite being descended from the reptilian clade, aren't lizard-shaped.

Of course, this analysis ignores snakes and other legless amphibians and reptiles, and frogs and toads. On the other hand, it's a lot easier to change tree diagrams than to change the coverage of different fields of study. And, as was pointed out, sometimes things that look similar to each other share other similar characteristics that make it easier to study them together, despite what the official classifications say.
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Re: 0867: "Herpetology"

Postby existentialpanda » Wed Mar 02, 2011 5:50 pm UTC

KShrike wrote:ehhh.... I like the world we are allowed to manipulate better. Besides, DNA is a closed source, so genetic engineers are breaking our bodily license agreement when they are hacking our birth.


DNA is totally open source. The code's right there. It's just hard to figure out what to do with it because we can't find the documentation.
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Re: 0867: "Herpetology"

Postby keithc » Wed Mar 02, 2011 6:17 pm UTC

PHDrillSergeant wrote:
Birds are Aves, which is part of the clade Theropoda, which is in Saurischia, which is in Dinosauria. Those birds outside our windows are dinosaurs. We can clear out the rest of our brains because we now have the best fact.


This is not completely correct.

Birds are Aves, which are part of the clade Paraves, which is in Maniraptora, which is in Maniraptoriformes, which is in Tyrannoraptora, which is in Coelurosauria, which is in Avetheropodia, which is in Tetanurae, which is in Theropodia, which which is in Saurischia, which is in Dinosauria.

possibly more accurate to say "this is correct, but incomplete", after all Aves are part of Theropod(i)a. Hmm, I guess that "i" is all-important. As in the Arian heresy.
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Re: 0867: "Herpetology"

Postby Amora » Wed Mar 02, 2011 6:21 pm UTC

This comic reminds me of something my zoology professor would always say:
Salvador de la Cruz wrote:Dinosaurs aren't extinct. We just call them birds now.
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Re: 0867: "Herpetology"

Postby jimhsu » Wed Mar 02, 2011 7:57 pm UTC

existentialpanda wrote:
KShrike wrote:ehhh.... I like the world we are allowed to manipulate better. Besides, DNA is a closed source, so genetic engineers are breaking our bodily license agreement when they are hacking our birth.


DNA is totally open source. The code's right there. It's just hard to figure out what to do with it because we can't find the documentation.


Technically DNA is machine language (or if you call polypeptides machine language, then DNA would be something like assembly) -- the challenge is try to reverse-engineer (i.e. decompile) it into something ... well, meaningful. People are working at decompiling it (BLAST, for instance, to find patterns between organisms that would suggest a putative function), as well as compiling it (aka BioBricks, and the rest of synthetic biology). Problem is, as you alluded to, there is no documentation, and there never was. Oh, it also may contain read errors, be self-modifying, is polymorphic, has directionality, and is OS (organism) dependent. Fun.

There was my moment of geekery.
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Re: 0867: "Herpetology"

Postby neoliminal » Wed Mar 02, 2011 8:31 pm UTC

...and I suspect DNA is dynamically typed, object oriented, compiled, concurrent, no error reporting, highly expressive.

but that's just me.
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Re: 0867: "Herpetology"

Postby dash » Wed Mar 02, 2011 8:32 pm UTC

This one really sucked. Nothing whatsoever worthy of attention.
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Re: 0867: "Herpetology"

Postby mattbob » Wed Mar 02, 2011 9:05 pm UTC

dash wrote:This one really sucked. Nothing whatsoever worthy of attention.

I'd have to agree, except for one thing. The alt-text comes off as kind of snobbish to me; no Randy, it's not that amazing of a fact that I'd need to clear out the rest of my brain to fit it in. Sure, it's an interesting observation, but it's pretty well known and doesn't really deserve the attention it got in the comic.

Besides that, there wasn't anything that was too bad-just kind of bland.
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Re: 0867: "Herpetology"

Postby some_dude » Wed Mar 02, 2011 9:33 pm UTC

Knowing nothing about either field, what I noticed mostly about this comic was that unlike the standard definition of douchebag=asshole, Randall suggests that douchebag refer only to the slightly smaller subset of assholes who aren't ornithologists :P
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Re: 0867: "Herpetology"

Postby cluck40 » Wed Mar 02, 2011 10:24 pm UTC

Actually, new scientific research has proved that crocodilians are more closely related to birds than they are to reptiles. This would imply that birds are reptiles, because crocodilians are still considered reptiles.
As an aspring herpetologist, I have no qualms with ornithologists, only the name 'herp'.
BTW, all the info is from Lillywhite's Dictionary of Herpetology
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Re: 0867: "Herpetology"

Postby rcox1 » Wed Mar 02, 2011 11:15 pm UTC

aaronasterling wrote:There's sort of a science fail here which makes me sad :(

Lizards are squamates. Why single out lizards for inclusion in ornithology when birds and the crocodilians are both archosaurs? He's making ornithology polyphyletic and making herpetology even more paraphyletic than it already is.

For shame for shame.

Did you know that if we think monophyletically, you're a monkey? That's cooler than a bird being a dinosaur. Knowing that a bird is a dinosaur doesn't give you an excuse to shit in your hand and throw it at people.


One can pick on the lizard and reptiles, and mock the choice by using monkey instead of primte, but the joke, IMHO, is the prevalence of anachronistic grouping and preference in some that study nature. This anachronism can be interpreted as an effort to deny the current research in an attempt to reclaim some past, better time.

I see this in other situations. There are physics people who still hold on the Maxwell and Einstein, but think Feynman is just a bongo playing playboy. I see this as an attempt to hang onto some illusion that the world is deterministic and godlike. When Feynman showed that the two formulation of quantum mechanics were equivalent, it fundamentally changed the way we were forced to interpret the world. The fact that he turns Einstien's theories into a mess of ugly infinities does not help either. Denying Feynman's work sort of stops QM at a point where it is useful but not too destructive to the weltanschauung.
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Re: 0867: "Herpetology"

Postby addams » Thu Mar 03, 2011 1:22 am UTC

In a Universe of facts, many of them, good facts.

This, may be, the best fact.

I, also, like the fact, that, my appendix is from our common bird/reptile past.
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Re: 0867: "Herpetology"

Postby KShrike » Thu Mar 03, 2011 3:04 am UTC

existentialpanda wrote:
Spoiler:
KShrike wrote:ehhh.... I like the world we are allowed to manipulate better. Besides, DNA is a closed source, so genetic engineers are breaking our bodily license agreement when they are hacking our birth.


DNA is totally open source. The code's right there. It's just hard to figure out what to do with it because we can't find the documentation.


No, not really. DNA is at the lowest level (analogous to Binary/machine language), as jimshu says below.

jimhsu wrote:
Spoiler:
existentialpanda wrote:
KShrike wrote:ehhh.... I like the world we are allowed to manipulate better. Besides, DNA is a closed source, so genetic engineers are breaking our bodily license agreement when they are hacking our birth.


DNA is totally open source. The code's right there. It's just hard to figure out what to do with it because we can't find the documentation.


Technically DNA is machine language (or if you call polypeptides machine language, then DNA would be something like assembly) -- the challenge is try to reverse-engineer (i.e. decompile) it into something ... well, meaningful. People are working at decompiling it (BLAST, for instance, to find patterns between organisms that would suggest a putative function), as well as compiling it (aka BioBricks, and the rest of synthetic biology). Problem is, as you alluded to, there is no documentation, and there never was. Oh, it also may contain read errors, be self-modifying, is polymorphic, has directionality, and is OS (organism) dependent. Fun.

There was my moment of geekery.


That is hacking...... well, it is, isn't it? It's definitely hacking. Think of it in this analogy:
Our human bodies are the output of DNA (well, kinda. The programs are still being run, because DNA and RNA are being used to make proteins if I remember AP Bio correctly). The only code we have is the executable (DNA). We are trying to disassemble it to find out how it works, what genes do what, etc. For example, trying to find the gene for red hair, or maybe even what scientists claim might be the "homosexuality gene" (another story). Then they do try to rewrite the DNA (not what you would call it I guess, but you know what I mean) to produce geniuses, people without down syndrome, etc. That is the practice, and it is well intended.

In the analogous sense, it is hacking. I mean:
Image
^this.
Not
Spoiler:
Image


Sorry for the ridiculously large post, but I suck at BBCodes due to lack of experience.

edit:
dash wrote:This one really sucked. Nothing whatsoever worthy of attention.

http://www.youtube.com/watch?v=R5kPUFxXYLs

I put spoilers to conserve space. Sorry for editing it twice after posting.
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Re: 0867: "Herpetology"

Postby Hypnosifl » Thu Mar 03, 2011 3:46 am UTC

cluck40 wrote:Actually, new scientific research has proved that crocodilians are more closely related to birds than they are to reptiles. This would imply that birds are reptiles, because crocodilians are still considered reptiles.
As an aspring herpetologist, I have no qualms with ornithologists, only the name 'herp'.
BTW, all the info is from Lillywhite's Dictionary of Herpetology

That's not really a new finding, even before DNA evidence both birds and crocodilians were classed as archosaurs (along with dinosaurs and pterosaurs) based on similarities in their skull structure, so it was understood that the crocodile-bird common ancestor would be more recent than the crocodile-snake common ancestor or the crocodile-lizard common ancestor. Anyway, I think the term "reptile" has just been abandoned in modern cladistics (for those who don't know the term "cladistics", the wikipedia entry is pretty good), but you're right that if we try to define "reptile" as a clade then we have to say that birds are reptiles (and depending on whether you put mammal-like reptiles like Dimetrodon in the "reptile" clade, you might have to say mammals are too).

The page at http://www.emc.maricopa.edu/faculty/farabee/biobk/biobookdivers_class.html has a cladogram with the major reptile groups along with birds and mammals:

http://www.emc.maricopa.edu/faculty/farabee/biobk/cladclass.gif

So if the biologist in Randall's comic wanted to draw an equally simple diagram but one that was actually accurate, the branch labeled "birds" could be changed to "birds & crocodilians" while the branch labeled "reptiles" could be changed to "lizards, snakes & turtles" (or just "non-crocodilian reptiles")
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Re: 0867: "Herpetology"

Postby reason » Thu Mar 03, 2011 4:47 am UTC

mattbob wrote:
dash wrote:This one really sucked. Nothing whatsoever worthy of attention.

I'd have to agree, except for one thing. The alt-text comes off as kind of snobbish to me; no Randy, it's not that amazing of a fact that I'd need to clear out the rest of my brain to fit it in. Sure, it's an interesting observation, but it's pretty well known and doesn't really deserve the attention it got in the comic.

Besides that, there wasn't anything that was too bad-just kind of bland.


I think that the alt-text if anything should be taking more as Randall poking fun at himself (and I'm sure many others on this forum) for his obsession with dinosaurs. It is a common theme in the comic. http://xkcd.com/155/ That's the first one that comes to mind (although I realize it has more specifically to do with velociraptors).

Edit: Sorry, I don't think I have enough posts for links to show up yet.
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Re: 0867: "Herpetology"

Postby udqbpn » Thu Mar 03, 2011 6:46 am UTC

...but birds and mammals have diverged so much phenotypically from the common ancestor of birds mammals amphibians and reptiles, whereas I don't think reptiles or amphibians have changed their body plan much over the billions of years...?
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Re: 0867: "Herpetology"

Postby MolBio » Thu Mar 03, 2011 8:46 am UTC

Guest15 wrote:
KShrike wrote:
Coffee wrote:ehhh.... I like the world we are allowed to manipulate better. Besides, DNA is a closed source, so genetic engineers are breaking our bodily license agreement when they are hacking our birth.


Next time you think we don't manipulate biology, take a good look at a chihuahua. Or better yet, a banana.


Or just look at this paper: A novel triple-regulated oncolytic adenovirus carrying PDCD5 gene exerts potent antitumor efficacy on common human leukemic cell lines. Apoptosis.;14(9):1086-94. (Sep 2009)
For my Masters project, I made 4 conditionally replicating Adenoviruses by replacing endogenous viral promoters with human tissue/tumor specific promoters of a previous version of the virus described in: http://www.ncbi.nlm.nih.gov/pubmed/1648 ... olding=npg
I'm currently trying to generate interest for a PhD project where the entire human mitochondria genome will be "re-encoded" to use a different genetic code.
Any arbitrary DNA sequence can be synthesized, its just a matter of cost, and the costs (much like sequencing costs) have been dropping considerably. So we can "write code"


maastrictian wrote:I created an account to grouse over the use of the term "reptile", so I'm glad to see that others got there first :) In any case, I fixed the diagram on the left side of the comic.

http://gloria-mundi.net/herpetologyFixed.png

As MolBio points out, there is some doubt about the placement of Turtles, so they could be included with lizards and snakes rather than placed where I've put them or they could branch off from the tree after mammals rather than before. I went for the version with more pretty lines.

(Ornithologists may be assholes, but paleontologists are pedants)


I thought it was pretty well established that they branched off after synapsids did
I find this to be a good site, with scientific references, curated by people with PhDs, although the maintenance of the site is somewhat lacking, and it may not be in line with the most recent findings:
http://tolweb.org/Amniota/14990

jc wrote:One thing about the comic's diagram is that the branch that includes reptiles and birds is sorta shaky, and it's still reasonable to be skeptical of this. The old "further research is needed" mantra applies, and until that branch is firmed up a bit, it might be better to continue to view the reptile/dinosaur/mammal divergence as an unresolved 3-way split. It almost certainly was two 2-way splits, and there's some evidence that the mammals branched off first, but we really should get some more evidence before declaring this official doctrine.

Ummmm..... WHAT?!
There is absolute consensus that birds are archosaurs, even from the BAND ("Birds Are Not Dinosaurs") camp nuts.
Molecular biology confirms this. Anatomy confirms this, paleontology confirms this.
This debate is closed as far as I am concerned, there isn't a shred of evidence that calls the link into question, and there are piles of evidence supporting the link.

jc wrote:The splits that produced the modern amphibia and crocodilia are also still pretty fuzzy, so those are good areas for playing the skeptic when people claim that the tree is known in detail.

Yes, that basically all depends on if Frogs are a lineage of Temnospondyl.
I always get annoyed with they call stem tetrapods "amphibians", because it implies we are all members of the Amphibia clade (which may actually be true, depending on if lissamphibia is monophyletic, or if temnospondyls left descendants), when there is considerable doubt about that. I think the term "tetrapod" is much better, as many early tetrapods certainly lie outside the amphibia crown clade. Its not clear if Amniotes lie outside the Amphibia crown clade, but I'm leaning towards "yes" (we do lie outside it).

zmatt wrote:I've known about birds being dinosaurs for some time now. I've also known that for the most part sharks and alligators/crocs have made it to the modern day more or less the way they were pre KT. That's what I get for filling my youth with the Discovery channel, you know, back when it was actually educational.

Sharks have been around in their current general form a lot longer than the crocodiles. In the grand scheme of things, the Cretaceous was not that long ago (65 mya, the cambrian explosion on the other hand- 500 mya).
By the cretaceous you had pretty much all the modern groups. Flowering plants, eusocial insects (ants, bees, termites), neornithes, etc
What is more interesting IMO, is the crocodile body plan has been around a lot longer than Crocodiles.
Google "phytosaurs" - a lineage closely related to crocodiles, essentially the same morphology, except their nostrils were on top of their head (like whales, dolphins), instead of at the tip of their snout. Crocodiles actually come from warm blooded terrestrial ancestors similar to this:
Image
When the Phytosaurs died, the crocodiles rapidly evolved almost the same form, and took their place.
Did you know that crocodiles develop a 4 chambered heart (unlike other reptiles except birds) as an embryo, until a bypass develops making it functionally three chambered?
Too many people consider being "cold blooded" as an inferior, primitive state. It was the primitive condition, but in crocodiles it is derived, or reversion to the primitive condition, because being "cold blooded" is superior in some cases.


Hypnosifl wrote: I think the term "reptile" has just been abandoned in modern cladistics (for those who don't know the term "cladistics", the wikipedia entry is pretty good), but you're right that if we try to define "reptile" as a clade then we have to say that birds are reptiles (and depending on whether you put mammal-like reptiles like Dimetrodon in the "reptile" clade, you might have to say mammals are too).

No, it hasn't been abandoned, though I am on a paleontology e-mailing list, and periodically the debate comes up, with many people arguing in favor of abandoning it.
It basically comes down to:
"We should keep it because we can make a monophyletic clade including all living things called reptiles, if we also include birds. Also, the term Reptile is far too entrenched to get rid of, we are better off just twerking the public understanding of it (ie, retain a traditional term, but with modified meaning)"
or:
"We should discard the term because it creates misunderstanding, as most people do not consider 'reptile' to include 'birds', and far too many people call extinct synapsids 'reptiles', for which there is no monophyletic clade without including Mammals, in which case Reptiles=Amniotes"
Currently, the majority leans towards the first view.

The page at http://www.emc.maricopa.edu/faculty/far ... class.html has a cladogram with the major reptile groups along with birds and mammals:

http://www.emc.maricopa.edu/faculty/far ... dclass.gif

So if the biologist in Randall's comic wanted to draw an equally simple diagram but one that was actually accurate, the branch labeled "birds" could be changed to "birds & crocodilians" while the branch labeled "reptiles" could be changed to "lizards, snakes & turtles" (or just "non-crocodilian reptiles")

Not the best cladeogram (go to tolweb.org again), your placement of turtles is highly suspect, and you left out Tuataras (or did you accidentally type the wrong thing. BTW "Lepidosaur" includes Lizards, Snakes, and Tuataras, and would save labeling space.

udqbpn wrote:...but birds and mammals have diverged so much phenotypically from the common ancestor of birds mammals amphibians and reptiles, whereas I don't think reptiles or amphibians have changed their body plan much over the billions of years...?
[/quote]
Ever seen a Frog? yea... thats at least as diverged as a a mouse is. Amphibian skin is highly specialized. Consider (this is assuming Amniotes are not part of the Amphibia crown clade) the common ancestor of Reptiles, Mammals, and Amphibians likely had skin more like that seen in a lungfish or Coelacanth.

Image
or
Image

Frog legs are highly modified.
Some frogs don't even have lungs.
External gills (as in many amphibians), are not an ancestral tetrapod characteristic.
Note that fish scales are completely different from Reptile scales (dermal vs epidermal origin, different molecular composition as well).
All three clades (amphibia, Mammalia, and Reptilia) are highly derived from the first tetrapods
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Re: 0867: "Herpetology"

Postby Sire Styx » Thu Mar 03, 2011 9:04 am UTC

Lol I loved today's comic :)
Reminds me a bit about how fungi/plants were supposed to be in the same group XD
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Re: 0867: "Herpetology"

Postby MolBio » Thu Mar 03, 2011 9:43 am UTC

I know my posts are really long, sorry :lol:
One more thing
udqbpn wrote: I don't think reptiles or amphibians have changed their body plan much over the billions of years...?

When discussing Reptiles and Amphibians, we are only talkinf 300-350 million years ago.
Life has been around for almost 4 billion years, but evidence for multicellular life doesn't seem to go back more than about 0.63 billion years
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Re: 0867: "Herpetology"

Postby vultur-10 » Thu Mar 03, 2011 10:57 am UTC

Tiercelet wrote:Y'see, human brains actually create categories not by necessary/sufficient conditions forming in-or-out rules, but as radial structures branching off of more and less paradigmatic examples.

Example: "Mother." Central case: your dad's wife, who gave birth to you. But what about less central cases? Your dad's new wife? (Does it matter whether your birth mother is still alive?) The surrogate who bore you, after embryonic-you was implanted in her from the genetic material of the parents who have cared for you? What if the surrogate, the caring parent, and the egg donor were all different people? Is a woman a mother who had a child that died in infancy, and is now childless? What if the child was stillborn? Is an egg donor a mother? What about a nulliparous woman who married a widower with children, but has subsequently divorced him (or the children subsequently died) -- was she ever a mother, and if so, is she still one? You'll feel a need to come up with a clear set of rules to make consistent judgments on all these cases, but that's not actually relevant. Legitimate disagreement with the rules you established would be possible, because that's how human minds conceive of categories -- better and worse examples which are related to a central case everyone agrees on.


Which is basically a concept of 'form' - more and less perfect expressions of the essential concept ('form') of 'mother'.

(Now, Aristotelian or Platonic concept of forms?)
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Re: 0867: "Herpetology"

Postby MolBio » Thu Mar 03, 2011 12:23 pm UTC

Tiercelet wrote:Y'see, human brains actually create categories not by necessary/sufficient conditions forming in-or-out rules, but as radial structures branching off of more and less paradigmatic examples.

Cladistics does consist of "in-or-out" rules.

For example, Either the most recent common ancestor of Iguanadon and Megalosaurus was your ancestor, or it wasn't.

If it was, you are a dinosaur.
All the evidence suggests it was the ancestor of Birds, so birds are "in" and are dinosaurs.

Unfortunately, this definition excludes some very "dinosaur-like" triassic forms that diversified before the Ornithischia-Saurischia split.
So they make a new class "Dinosauromorpha", and something is "in" that clade if it shares a more recent common ancestor with *some arbitrary dinosaur species* than with *some arbitrary pterodactyl species*.

Yes, under current cladistics, this is merely a dinosauromorph, not a dinosaur:
Image

but this, is a dinosaur:
Image
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Re: 0867: "Herpetology"

Postby aversglay » Thu Mar 03, 2011 2:14 pm UTC

Despite their differences, they learn to work together when the nanobot attack!
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Re: 0867: "Herpetology"

Postby Hypnosifl » Thu Mar 03, 2011 8:42 pm UTC

MolBio wrote:
Hypnosifl wrote: I think the term "reptile" has just been abandoned in modern cladistics (for those who don't know the term "cladistics", the wikipedia entry is pretty good), but you're right that if we try to define "reptile" as a clade then we have to say that birds are reptiles (and depending on whether you put mammal-like reptiles like Dimetrodon in the "reptile" clade, you might have to say mammals are too).

No, it hasn't been abandoned, though I am on a paleontology e-mailing list, and periodically the debate comes up, with many people arguing in favor of abandoning it.

So do the professionals use the term in journal articles and such when discussing cladistic classification? Obviously it's still used in the Linnean system which hasn't been abandoned, but I was thinking specifically about cladistics.
MolBio wrote:
Hypnosifl wrote:The page at http://www.emc.maricopa.edu/faculty/farabee/biobk/biobookdivers_class.html has a cladogram with the major reptile groups along with birds and mammals:

http://www.emc.maricopa.edu/faculty/farabee/biobk/cladclass.gif

So if the biologist in Randall's comic wanted to draw an equally simple diagram but one that was actually accurate, the branch labeled "birds" could be changed to "birds & crocodilians" while the branch labeled "reptiles" could be changed to "lizards, snakes & turtles" (or just "non-crocodilian reptiles")

Not the best cladeogram (go to tolweb.org again), your placement of turtles is highly suspect, and you left out Tuataras (or did you accidentally type the wrong thing. BTW "Lepidosaur" includes Lizards, Snakes, and Tuataras, and would save labeling space.

It's not my placement of turtles, just the cladogram I found on the linked page when searching for info on the relationships, I don't claim to be an expert. But you're right, looking at tolweb.org and also at the DNA-based tree of amniotes from timetree.org on p.3 of the pdf at http://www.timetree.org/pdf/Shedlock2009Chap52.pdf (where testudines=turtles, squamata=lizards and snakes, and sphenodontia=tuataras) it looks like turtles should be grouped with crocodilians/birds.
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Re: 0867: "Herpetology"

Postby Cotila » Thu Mar 03, 2011 9:45 pm UTC

I originally read it as saying "with lizards folded into origami" I'm still picturing little flattened and folded lizards.
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Re: 0867: "Herpetology"

Postby imantodes » Thu Mar 03, 2011 10:02 pm UTC

Hypnosifl wrote:
cluck40 wrote:Actually, new scientific research has proved that crocodilians are more closely related to birds than they are to reptiles. This would imply that birds are reptiles, because crocodilians are still considered reptiles.
As an aspring herpetologist, I have no qualms with ornithologists, only the name 'herp'.
BTW, all the info is from Lillywhite's Dictionary of Herpetology

That's not really a new finding, even before DNA evidence both birds and crocodilians were classed as archosaurs (along with dinosaurs and pterosaurs) based on similarities in their skull structure, so it was understood that the crocodile-bird common ancestor would be more recent than the crocodile-snake common ancestor or the crocodile-lizard common ancestor. Anyway, I think the term "reptile" has just been abandoned in modern cladistics (for those who don't know the term "cladistics", the wikipedia entry is pretty good), but you're right that if we try to define "reptile" as a clade then we have to say that birds are reptiles (and depending on whether you put mammal-like reptiles like Dimetrodon in the "reptile" clade, you might have to say mammals are too).


Just one comment here: the wikipedia page on cladistics sucks. Don't trust it; you'll be misled.

And, yeah, if I had infinite free time I'd re-write it. Alas, I do not.
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Re: 0867: "Herpetology"

Postby imantodes » Thu Mar 03, 2011 10:15 pm UTC

Hypnosifl wrote:So do the professionals use the term in journal articles and such when discussing cladistic classification? Obviously it's still used in the Linnean system which hasn't been abandoned, but I was thinking specifically about cladistics.


Linnaean nomenclature (the set of rules for the formation and use of names that originates with Linnaeus) has not been abandoned, yes, but there also is no functioning alternative. On the other hand, if by Linnaean classification we mean the specific taxa recognized by Linnaeus, then it has most certainly been abandoned.

PhyloCode, which is a proposed alternative to Linnaean nomenclature (and which is representative of the views of only a small number of cladists, not of the group as a whole), is not yet operational (and may never be, it's hard to tell). Interestingly, the International Code of Zoological Nomenclature (which governs zoological use of Linnaean nomenclature) does not apply to higher taxonomic levels. This has the result that names like "Reptilia" and "Theropoda" are not covered by any formal nomenclatural system.

As for the original quesiton, yes, academic authors still use "reptiles" in a paraphyletic sense. Those authors can be divided into two groups: those who use the term for convenience with full understanding that it refers to a paraphyletic grouping; and those who are still stuck in the 19th century and tend to reject newfangled ideas in general.
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Re: 0867: "Herpetology"

Postby Ichapp » Thu Mar 03, 2011 10:24 pm UTC

keithc wrote:
PHDrillSergeant wrote:
Birds are Aves, which is part of the clade Theropoda, which is in Saurischia, which is in Dinosauria. Those birds outside our windows are dinosaurs. We can clear out the rest of our brains because we now have the best fact.


This is not completely correct.

Birds are Aves, which are part of the clade Paraves, which is in Maniraptora, which is in Maniraptoriformes, which is in Tyrannoraptora, which is in Coelurosauria, which is in Avetheropodia, which is in Tetanurae, which is in Theropodia, which which is in Saurischia, which is in Dinosauria.

possibly more accurate to say "this is correct, but incomplete", after all Aves are part of Theropod(i)a. Hmm, I guess that "i" is all-important. As in the Arian heresy.


I was going to dispute just this. It's like nesting dolls: sure one can tell you that the smallest is inside the next smallest, which is inside the third smallest all the way up to the second largest which is inside the second largest, but one can save a lot of breath by saying that the smallest is inside the next smallest which is inside the largest.
Beasts move. Men reflect. Gods make real.
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Re: 0867: "Herpetology"

Postby raugust » Fri Mar 04, 2011 5:11 am UTC

wackojacko1138 wrote:Ornithology should be absorbed into herpetology, and batrachology should be split off on its own.

Why retain the vague name 'herpetology' if we're losing so many of its members? Also, if mammals evolved from reptiles ('mammal-like' reptiles), then mammals would also need to be included under herpetology, which seems a bit vague. And since herpetology literally means 'the study of creeping things,' the Greek in me rebels at the thought of classing birds -- which are bipedal and tend to fly, not 'creep' -- in a field so named. :)

And, yes, 'herpes' and 'herpetology' are cousins. Herpes is a creepy creepy disease, after all.

aaronasterling wrote:Did you know that if we think monophyletically, you're a monkey?

No, if you think monophyletically you're an ape. 'Monkey' is not a monophyletic group to begin with; 'Old World monkey' and 'New World monkey' are truly monophyletic, though. Humans are great apes (i.e., hominoids), apes and Old World monkeys are catarrhines, and catarrhines and New World monkeys are simians. So humans are apes, catarrhines, and simians, but not 'monkeys' -- because 'monkey' already excludes 'ape,' and vice versa.

Which is why 'monkey,' like 'reptile,' is simply not a valid monophyletic term; if you want to radically redefine it to make it monophyletic, you can equally legitimately restrict it (e.g., claim that only lizards, snakes, and tuataras are really 'reptiles') rather than expand it (by encompassing birds, and perhaps mammals). If you care about preventing ambiguities, you're probably better off just coining a new folk term for the monophyletic grouping rather than trying to squeeze the English language into evolutionary boxes. Though I do have a soft place in my heart for language-squeezing....

MolBio wrote:What is a fish anyway? a morphology term? then why aren't whales/ dolphins fish, why weren't ichthyosaurs fish?

While conceding that 'fish' isn't monophyletic, there are still plenty of ways to morphologically define it such that it will exclude icthyosaurs and cetaceans (and the many other aquatic non-fish). For instance, we can eliminate mammals by requiring scales (and thus rescue sharks from the bin of non-fishdom). But such a definition will need a looot more qualification if we want to keep scaleless fish like catfish on the list....

I'm not sure there's any elegant and concise way to morphologically keep all things we intuitively call 'fish' on the list while excluding everything else; but there are plenty of ways to approximate our current list of 'fish' while keeping out amniotes. For example: 'No amniotes allowed.' (Amniote, of course, is of morphological significance and not just hereditary.)

Birds are reptiles.

I don't think redefining 'reptile' to become monophyletic has been 'settled' in the same way that redefining 'dinosaur' to encompass birds has been. Birds are clearly dinosaurs, but whether they're reptiles depends on how concerned we are about making mammals reptiles too (or, alternatively, restrict the scope of prehistoric 'reptiles' so that the common ancestor of mammals and non-mammalian amniotes is no longer deemed a 'reptile').

In any case, there is some value to studying the features non-bird non-mammal amniotes have in common, precisely because mammals and birds both diverge from a number of features that other amniotes have retained from their common ancestor. Imagine that some bacteria were more closely related to eukaryotes and archaea than to other bacteria; would that necessarily entail that it's illegitimate to study polyphletic 'bacteria' in a single field devoted, at least in part, to their morphological commonalities? Field boundaries are defined by the pragmatics of what information most commonly needs to be closely associated; they aren't defined as Aristotelian Categories segregating the natural world Objectively into the most disinterested hierarchies possible.

deepbass2k5 wrote:as a zoology major

'Zoology' is paraphyletic. Don't you mean a heterozoology major? :)

jc wrote:If your definition of "fish" includes sharks and tunas, but not humans or dolphins, then your definition is biologically meaningless.

This is absurd because it requires that any biological definition which appeals to morphological rather than hereditary considerations be 'meaningless.' This would disqualify all terms for properties that have convergently evolved -- the paraphyletic and anatomical 'quadruped' as contrasted with the monophyletic and genetic 'tetrapod,' Latin/Greek once-synonyms, both of which are clearly useful terms. Likewise 'carnivore' can be both meaningful and useful without being monophyletic. This restriction would also disqualify terms uniting organisms with a property they (but not all immediate relatives) share with an ancestor -- e.g., one could not speak of prokaryotes or jawless fish, since although they share an obvious feature in common -- and a highly useful one to discuss, in fact one derived from a common ancestor -- this feature has been lost in certain other members of the same clade.

Why is this 'biologically meaningless'? The most interesting and enlightening facts in biology -- the ones that tell us the most about the laws and possibilities of life, as opposed to the contingent 'one damned thing after another' of history -- are the patterns and repetitions which transcend strict inheritance.

there's some evidence that the mammals branched off first, but we really should get some more evidence before declaring this official doctrine.

? The first synapsid (mammal-like reptile) arose some 325 mya. The first dinosaurs arose some 230 mya. That's a gap of nearly 100 million years. So yes, I think it's safe to say that mammals branched off first. :p

To doubt this would be of the same order of magnitude as doubting whether humans evolved before or after bees. (First bees appear in the fossil record 100 mya).
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Re: 0867: "Herpetology"

Postby Tiggydong » Fri Mar 04, 2011 4:34 pm UTC

Are these real subjects? They dont sound real...
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Re: 0867: "Herpetology"

Postby Rio » Fri Mar 04, 2011 6:06 pm UTC

Cotila wrote:I originally read it as saying "with lizards folded into origami" I'm still picturing little flattened and folded lizards.


I wonder if the wings on Draco genus lizards would qualify? :) They are really neat.

My flying gecko has a flattened body plan, and lots of flappy thin bits, so she looks origami-ish to me.
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Re: 0867: "Herpetology"

Postby MolBio » Sun Mar 06, 2011 12:24 am UTC

raugust wrote:
aaronasterling wrote:Did you know that if we think monophyletically, you're a monkey?

No, if you think monophyletically you're an ape. 'Monkey' is not a monophyletic group to begin with; 'Old World monkey' and 'New World monkey' are truly monophyletic, though. Humans are great apes (i.e., hominoids), apes and Old World monkeys are catarrhines, and catarrhines and New World monkeys are simians. So humans are apes, catarrhines, and simians, but not 'monkeys' -- because 'monkey' already excludes 'ape,' and vice versa.

But the only way to make "monkeys" monophyletic, is to include the apes and gibbons.

Which is why 'monkey,' like 'reptile,' is simply not a valid monophyletic term; if you want to radically redefine it to make it monophyletic, you can equally legitimately restrict it (e.g., claim that only lizards, snakes, and tuataras are really 'reptiles') rather than expand it (by encompassing birds, and perhaps mammals). If you care about preventing ambiguities, you're probably better off just coining a new folk term for the monophyletic grouping rather than trying to squeeze the English language into evolutionary boxes. Though I do have a soft place in my heart for language-squeezing....

Yes, you could restrict it - which is why the old term "mammal like Reptile" is not used in scientific paleontology papers anymore - they use the term coined for that group "synapsids" (or stem mammals, etc). Likewise they've generally stopped calling things like "icthyostega" an amphibian (or the contect makes it clear the term describes their lifestyle, and not grouping) - and instead use the term "tetrapod"/"Stem/basal tetrapod"
However, old groups like "reptile" are completely arbitrary groups. Restricting reptiles to mean lepidosaurs wouldn't be as arbitrary as the traditional meaning - but I think its better to throw birds in, rather than take Crocodiles and Turtles out.

Image
Those feet are clearly reptilian (its an Emu).

The term "fish" is somewhat useful as a hybrid term describing members of a clade that occupy certain ecological niches

MolBio wrote:What is a fish anyway? a morphology term? then why aren't whales/ dolphins fish, why weren't ichthyosaurs fish?

While conceding that 'fish' isn't monophyletic, there are still plenty of ways to morphologically define it such that it will exclude icthyosaurs and cetaceans (and the many other aquatic non-fish). For instance, we can eliminate mammals by requiring scales (and thus rescue sharks from the bin of non-fishdom). But such a definition will need a looot more qualification if we want to keep scaleless fish like catfish on the list....

I'm not sure there's any elegant and concise way to morphologically keep all things we intuitively call 'fish' on the list while excluding everything else; but there are plenty of ways to approximate our current list of 'fish' while keeping out amniotes. For example: 'No amniotes allowed.' (Amniote, of course, is of morphological significance and not just hereditary.)

As you note, not all fish have scales.
You can't define it by the lack of a lung: Lungfish have a lung, some frogs have none.
If we restrict them to vertebrates that have a respiratory system/gas exchange system that works in water (such as gills), we exclude all amniotes, and may adult forms of amphibians.
If we don't look at the adult forms... it is very hard to draw any distinctions between fish and tadpoles, and some amphibians remain quite tadpole like, or are completely aquatic their whole life - even if they do develop limbs.
Its even harder when you go back and look at fossils - so called "Fishapods" - many which had 4 limbs with fingers, that never left the water.

We can construct a cladistic, but paraphyletic definition: all vertebrates (or chordates, if you want to include hagfish), excluding those which share the last common ancestor of a *pick an amphibian species* and *pick a reptile or mammal species*

But when most people think fish, do you really think something like a Manta ray? or a Whale Shark, it always seemed weird to me calling a Whale Shark the largest fish, or calling a manta ray a fish.
Among extant species, I'd have no problem restricting "Fish" to mean osteoichthyes... r just the ray finned fish, ignoring the very rare relics: lungfish and Coelocanths.
But looking back at early agnathans and gnathostomes... the only other term I can think to call them (aside from agnathans and gnathostomes), is "fish"

In any case, there is some value to studying the features non-bird non-mammal amniotes have in common, precisely because mammals and birds both diverge from a number of features that other amniotes have retained from their common ancestor. Imagine that some bacteria were more closely related to eukaryotes and archaea than to other bacteria; would that necessarily entail that it's illegitimate to study polyphletic 'bacteria' in a single field devoted, at least in part, to their morphological commonalities?

#1) As I mentioned about crocodiles, crocodiles are not as similar to the other traditional reptiles as they appear. The 3 chambered crocodile heart is not retained from a common ancestor of lizards, it is a modification of a 4 chambered heart, which it seems the common ancestor of archosaurs (birds and crocodiles) had. The same is probably true for body temperature.
Birds do share many things with other reptiles (such as Keratin structure), and thus there is some grouping of "common features" that includes birds, and thus there should be some field of study that considers birds and the rest of the reptiles.

Consider: I don't doubt the validity of the field "marine biology". You can study ecological niches, and draw parrallels between various sharks and other"fish" throughout time, ichthyosaurs, pliosaurs, cetaceans, etc.
Instances of convergent evolution do suggest there is great value to studying morpphology independent of evolutionary relationships.

But the general history of the biological classification system is more concerned with natural groups, than niches and general morphology (though specifics of morphology can help determine placement).

Its why we don't group bats and birds together (they are, after all, vertebrates with homologous forelimbs which have been modified for flight).

Most of the old group classifications were generally monophyletic.

Switching to cladistics just makes it more rigorous.
The mammal group is unchanged, as are arachnids, insects, sharks, most plants, etc.
But when it reveals one or two changes people didn't foresee, people freak out.

In hindsight, based only on morphology/ phenotype, birds should have been grouped with reptiles all along.
Study of croc embryos shows that a 3 chambered heart is not a shared feature among the reptiles.
Studies of the Keratin composition, forms a nice group that includes birds and the rest of the reptiles, but excludes everything else.
So too do studies of brain structure (despite the term "reptilian brain" to refer to the brain stem and more primitive brain structure, which are actually found in amphibians as well).
Study bird eyes and reptile eyes, and a grouping becomes apparent... and so on
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Re: 0867: "Herpetology"

Postby nomadofthehills » Wed Mar 16, 2011 3:25 am UTC

As an aspiring herpetologist (post bachelors, pre-grad, working seasonal herpetology field positions), I approve of this comic, but prefer the modified one posted on the first page:

Image
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Re: 0867: "Herpetology"

Postby raugust » Tue Mar 22, 2011 1:38 am UTC

MolBio wrote:But the only way to make "monkeys" monophyletic, is to include the apes and gibbons.

Not true. The point of my post was that you can make a paraphyletic group monophletic either by expanding it or by restricting it. For instance, we could call Old World monkeys 'true monkeys,' and say that New World monkeys aren't really monkeys -- thus allowing us to differentiate (true) monkeys, 'fake' monkeys, and apes as valid and exclusive monophyletic groups. Or we could do the opposite, and make the Old Worlders 'pseudo-monkeys.'

This is an extremely common practice. When we learned that some things we called 'bacteria' were really closer to eukaryotes, we did not draw the conclusion that eukaryotes must also be deemed bacterial in order to make 'bacteria' monophyletic. Instead, we restricted the definition, coined a new term for the offshoot -- Archaea -- and said that only the non-archaeans were really bacteria, were 'true bacteria' -- eubacteria. To see how often this occurs, simply note how often 'eu-' and 'true' occur in taxa designations. :) Heck, even we primates and primatoids are called 'Euarchonta.' Bats were once thought to be close to primates, and were grouped with primates (and treeshrews and colugos) in 'Archonta;' when we learned that bats were much more distant, we did not expand 'Archonta' (which would have engulfed the overwhelming majority of mammals), but restricted it as the bat-free 'Euarchonta.' A 'eu-monkey,' a true monkey, could be a monophyletic group excluding both the apes (including humans) and the 'false monkeys.' Thus we have three options, not two -- paraphyly, expanded monophyly, or restricted monophyly. I see no knock-down argument for any of the three options.

However, old groups like "reptile" are completely arbitrary groups. Restricting reptiles to mean lepidosaurs wouldn't be as arbitrary as the traditional meaning - but I think its better to throw birds in, rather than take Crocodiles and Turtles out.

I'm open to the idea of making birds reptiles. But I don't see any strong grounds for thinking that this will cause less confusion than excluding crocodiles and turtles. In either case we have to re-teach people the intension of 'reptile;' is it better to have to teach them to call birds 'reptiles,' or to teach them not to call crocs and turtles 'reptiles'? My goal is to remind us that restriction is just as legitimate in principle as expansion, and to suggest that we may simply want to ditch 'reptile' altogether rather than try to severely warp it to fit our new knowledge. Teaching people that our naive folk classifications may be genetically arbitrary is surely more valuable than just reprogramming their classifications, since it informs them about the general principles at work rather than simply replacing one mindlessly memorized classification with another.

Image
Those feet are clearly reptilian (its an Emu).

That's a bit cheap. You could just as easily have pointed to thousands of anatomical features of mammals which they share in common with reptiles. Birds are just as radically distinct in their morphology from stereotypical 'reptiles' as are mammals: Traditional 'reptiles' never have feathers, never have wings or any other flight mechanisms, never have beaks, never have hollow bones, never have warm blood, and are almost never bipedal. So they have other similar features. So what? In innumerable respects the average mammal is more reptile-like than the average bird. Cherry-picking the particular traits birds and reptiles do have in common that mammals lack won't get us anywhere, without an agreed upon criterion for how to sort the important similarities from the unimportant ones for renaming purposes.

The term "fish" is somewhat useful as a hybrid term describing members of a clade that occupy certain ecological niches

So is "reptile." What's wrong with having a common-language term for designating all cold-blooded amniotes, eh? Turtles and lepidosaurs and crocodiles have thousands more interesting features in common than do 'fish' as a whole.

We can construct a cladistic, but paraphyletic definition: all vertebrates (or chordates, if you want to include hagfish), excluding those which share the last common ancestor of a *pick an amphibian species* and *pick a reptile or mammal species*

But when most people think fish, do you really think something like a Manta ray? or a Whale Shark, it always seemed weird to me calling a Whale Shark the largest fish, or calling a manta ray a fish.

I think this is a good definition. Manta rays may not be prototypical fish, but I do think most people would classify them as fish, if they were asked to classify/describe manta rays at all. Prototypical fish (things that look like trout, basically) may have a certain stereotyped look, even while in practice people can end up with ridiculously broad conceptions of what can be a 'fish' -- I could easily imagine someone thinking of even a jellyfish or a starfish as a 'fish,' in casual contexts.

#1) As I mentioned about crocodiles, crocodiles are not as similar to the other traditional reptiles as they appear.

I know. Turtles have plenty of weird features too. But we can't notice the differences distinguishing crocodiles from lepidosaurs and turtles, without also noticing the far greater differences distinguishing these three groups from birds. This in spite of the fact that birds and croocdiles are genetically more similar to each other than either is to lepidosaurs and turtles.

And we should not be surprised if crocodiles do have a lot of crucial similarities to other traditional reptiles, which they do not have with birds; birds, after all, have specialized and diverged into an extremely distinct niche, just as have the aquatic mammals. The fully aquatic mammals, even though they arose multiple times from very different mammal taxa (sirenians vs. cetaceans) and are quite recently diverged from groups like the artiodactyls, have plenty of scientifically important features in common which could very well have justified using some term that groups them all together, especially if sirenians were a more robust and diversified group. I would have seen nothing wrong with a term uniting sirenians and cetaceans on morphological grounds, even though these similarities be largely convergent; even less would I have a problem with a term uniting all the non-aquatic mammals, e.g., 'beast.' For the same reason as the latter, I see no problem in principle with a term uniting the commonalities of the 'reptiles' (which unlike 'aquatic mammals' is an important issue of inheritance and not simply a convergence), so long as it is ever useful to make a quick reference to the non-bird non-mammal amniotes.

But the general history of the biological classification system is more concerned with natural groups, than niches and general morphology (though specifics of morphology can help determine placement).

Granted. I'm all for abolishing 'herpetology' as a field. There's no reason to make amphibian-reptile comparative work any less explicitly interdisciplinary than reptile-bird or reptile-mammal comparative work. I'm just less gung-ho about radically redefining our traditional terms, which seems to be begging for confusion and misunderstanding. At a bare minimum, if we want to retain 'reptile,' I'd prefer if we modified it to something like 'true reptiles' or 'reptilians' or some other way of differentiating it from traditional usage. I'd also like to see more actual arguments for restriction vs. expansion vs. abandonment of paraphyletic terms, since it's now obvious that the choice between these is a messy affair and there is no strict algorithm for deciding which terms get tossed out, which get broadened, and which get shrunk.
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