I've just realized I'm being fairly stupid.
This entire line of argument is a farce, from the very beginning. I've been focused on the paleo side of things, but ignored the biochemical side. Simply put, many cladograms are built via genetic data--meaning they are constructed using the DNA strands of the animals in question.
Anyone who wants to delve into the math can go to PAST's website and find all the information they want there, but the basic idea is that a cladogram, using one of several algerithms, attempts to put organisms onto a tree with the fewest number of character changes possible. The assumption is that evolution is hard--things don't tend to evolve, then lose, then evolve, then lose traits. Once it evolves, it sticks around, and once it's gone, it's gone.
What this does is construct a tree that shows you what specific traits are the most likely to change. In my field, these are morphological changes--the presence or absence of an antorbital phenestra, for example. In many cladograms, however, these changes are GENETIC changes--specific changes in the genetic code. In other words, these cladograms provide precisely what Patrick1000 says we can't provide. And they're ubiquitous in taxonomy. These trees say "The genetic code of these organisms changed in these specific ways".
Patrick1000: Any continuation of this discussion should probably include this type of diagram. Please show specifically where you think some other mechanism took hold, on a genetic cladogram of birds and reptiles.
So really, any cladogram that uses genetic data is a counter-argument to what Patrick1000 is saying. And the fact that Patrick1000 doesn't know this indicates that he doesn't know as much as he wants us to think he knows. My excuse is that it isn't my field, and I don't think of evolution this way--I know enough to know that the mechanism is well-founded, and I can play with it certainly, but I focus on the effects (ie, the morphological changes). Patrick1000, who claims to be working with DNA and pathogens on a daily basis, has no such justification. Simply put, he should know this stuff, forward, backwards, and inside out.
A second reason that this argument is a farce is that Patrick1000 is limiting gentic changes to those caused by internal mechanisms. We know that things like viruses (specifically retroviruses) can alter the DNA strand, and there's evidence of lateral genetic transfer between parasites and hosts. Patrick1000 has artificially constricted the potential sources of genetic variation.
This entire line of argument is a farce, from the very beginning. I've been focused on the paleo side of things, but ignored the biochemical side. Simply put, many cladograms are built via genetic data--meaning they are constructed using the DNA strands of the animals in question.
Anyone who wants to delve into the math can go to PAST's website and find all the information they want there, but the basic idea is that a cladogram, using one of several algerithms, attempts to put organisms onto a tree with the fewest number of character changes possible. The assumption is that evolution is hard--things don't tend to evolve, then lose, then evolve, then lose traits. Once it evolves, it sticks around, and once it's gone, it's gone.
What this does is construct a tree that shows you what specific traits are the most likely to change. In my field, these are morphological changes--the presence or absence of an antorbital phenestra, for example. In many cladograms, however, these changes are GENETIC changes--specific changes in the genetic code. In other words, these cladograms provide precisely what Patrick1000 says we can't provide. And they're ubiquitous in taxonomy. These trees say "The genetic code of these organisms changed in these specific ways".
Patrick1000: Any continuation of this discussion should probably include this type of diagram. Please show specifically where you think some other mechanism took hold, on a genetic cladogram of birds and reptiles.
So really, any cladogram that uses genetic data is a counter-argument to what Patrick1000 is saying. And the fact that Patrick1000 doesn't know this indicates that he doesn't know as much as he wants us to think he knows. My excuse is that it isn't my field, and I don't think of evolution this way--I know enough to know that the mechanism is well-founded, and I can play with it certainly, but I focus on the effects (ie, the morphological changes). Patrick1000, who claims to be working with DNA and pathogens on a daily basis, has no such justification. Simply put, he should know this stuff, forward, backwards, and inside out.
A second reason that this argument is a farce is that Patrick1000 is limiting gentic changes to those caused by internal mechanisms. We know that things like viruses (specifically retroviruses) can alter the DNA strand, and there's evidence of lateral genetic transfer between parasites and hosts. Patrick1000 has artificially constricted the potential sources of genetic variation.
