Shorter Luskin (comments, not in height): DIFRENT JEANS MAEK DIFRENT TREAHS TEHEREFORE JESUS!!! DIRP!
You know how we always laugh at the fact Creationists dont ever have degrees in biology? This illustrates one of the many, many times it would be handy for Caseytits to have taken a couple bio classes in college.
Darwins Tree of Life is a metaphor. It is very clearly a metaphor in Origin of Species:
The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have at all times overmastered other species in the great battle for life.
Darwin didnt know shit about DNA or phylogenetic analyses. He didnt know how, but maybe, just maybe, all species are related, thus connected– like branches of a tree. And maybe this means we all came from the same seed– one universal common ancestor.
The general idea of Darwins ToL is still 100% accurate. We are all ‘related’ to every other living thing on this planet. But we know now we probably didnt come from *one* LUCA, but probably lots of LUCAs swapping genes around through horizontal gene transfer. Gene soup. heh.
Now, what is a phylogenetic tree? These trees are not metaphorical. They are graphical representations of genetic similarities/differences between your input sequences. The ‘tree’ you get out the end of your analysis is one of many possible ‘trees’– usually the program you use to make these gives you, say, the top 5 most likely trees. When we do this with viruses, we might get a tree like this:
We can see HIV-1 clusters with the SIV from chimpanzees, so we probably got HIV-1 from them. HIV-2 clusters with SIV from sooty mangabeys, so we got it from them. And all HIV/SIVs cluster together, while FIV sits as more of an outsider.
But whats this Caseytits says about ‘different genes, different trees of life’? Well, lets assume Caseytits meant ‘different genes, different phylogenetic trees’. Well DUH. Every gene has its own evolutionary history. Lets look at three trees from one paper– ‘Genetic and phylogenetic evolution of HIV-1 in a low subtype heterogeneity epidemic: the Italian example‘.
The first tree they made used env. The env gene is under intense selective pressure from the environment (your immune system), and the Env protein can tolerate very high levels of mutation, thus when they made a phylogenetic tree of their patient sequences, they got this tree:
They next made a tree with pro (part of pol). Pro has its own evolutionary problems to deal with: protease inhibitors. Pro was sitting pretty till we invented those bad boys.
They then analyzed gag, a gene that actually has something called a ‘major homology region’– even distantly related HIV-1s have the same sequence. Its critical, so things dont like to change much here unless they have to (MHC I).
OH MY GOD!
OH MY GOD!
Three different genes, THREE DIFFERENT TREES!
If we believe Caseytits logic, this means that HIV-1 is not transmitted from person-to-person. HIV-1 is specially created in each infected individual, thus genetic comparisons between patient isolates of HIV-1 are impossible, which is why three genes=three trees.
Or, you could understand that each gene has its own evolutionary history, thus trees constructed from each gene need to be taken into the appropriate context. You might also notice that these patient Subtype B sequences, though they create different trees, always cluster with… Subtype B. They never clustered with Subtype A or D or any other, in any tree.
Just like we never construct a ‘human’ phylogenetic tree and see we are more closely related to ‘chickens and cows’ than we are to chimpanzees.
Pay attention in school, kids. Drink your milk. Dont grow up to be a little IDiot.