*(eg. 1,2, 3, etc; oh, and this pile of shit that erupted in the media recently)
Did you forget about cells???
There is more to organisms than genome sequences. ie. there's this whole world of cell structure that is vertically inherited along with the genome, and that is a very well-defined solid tree. Especially among prokaryotes, where cellular conjugation is practically nonexistent (never mind the pili). A few genes getting thrown around from time to time doesn't suddenly invalidate the very identity of those organisms!
I argued on a forum once with this...strange person...who insisted unicellular life were all 'one species'! (Seriously, what the fuck!?) Apparently biology stops shortly outside the metazoan clade, since there's only 99% of total biodiversity outside. But see, they're 'pre-animals', and thus don't matter.
Ok, he had the argument that the biological species concept (the only one worthy of recognition, according to the
But then the biological species concept doesn't hold for all animals... Bdelloid rotifers, some insects and lizards, to name a few. Are those now all 'one species' too? Oh right, they can't be... because they're animals, and it's bloody obvious whether two animals are the same type or now, duh!
Now, endosymbiosis is an interesting point, but not sufficient to destroy the tree of life. Yes, there is a few fusions of branches (around 3 times overall it seems, once of alpha-proteobacteria (mitochondria) and twice of cyanobacteria (plastids in archaeplastid ancestor, and in Paulinella)). However... even some real [botanical] trees have branch fusion! It's not big deal if it happens a couple times here and there, we can still follow.
I think the diagrams like the one below may be a bit misleading:
(Doolittle WF February 2000 © Scientific American; the trained reader will probably see another reason this makes me cringe. (the 'crown eukaryote' positioning of Animals, Fungi and Plants. Although this was still during the age of Archaezoa...))
Those lateral transfer lines aren't all of one gene; and even if this were a single gene tree, there are thousands of others out there. This diagram represents some well-documented lateral gene transfer events among all the organisms and all the genes we know of; if one were to represent all the genes that didn't undergo a transfer event of any sort, the importance of LGT would quickly be put back in its place. It's not as if entire genomes have been shifted around! (except in the case of endosymbiosis...)
Don't get me wrong, I still think LGT is important and awesome, but do we really need to chop down the entire tree because of a few loopy branches?