Eric Smith gave the presentation on the pool idea, and I've had a hard time finding a paper which actually cites it, unfortunately. The small bit on the codons was as related as I can find.
I'll see if I can find something better- the presentation was in early 2008 so the idea may be in press or may never have left the ground. It was an intriguing hypothesis, but perhaps never made it past peer-review.
Iunno. I tend to see the three domains as separate trees, considering how much they have diverged even if they shared common ancestry.
So... even though they all share a common ancestor, you're going to view them as different trees of life anyway? o_O
I can only think you're using a different meaning of "Tree of Life" to the rest of us. In any case it's not a particularly useful view (any more than it's useful to view different phyla as different "trees of life"), firstly because the homologies between the different domains mean that discoveries from one domain can be transferred to others (for example, discoveries of certain proteins in Archaea have been used to search for homologous proteins in Eukarya and then, using the archaeon as a model, to understand what the proteins do in the eukaryote) and, secondly, because the borders between the domains are not clear cut: horizontal gene transfer occurs between Archaea and Bacteria, and organelles such as mitochondria and chloroplasts have their endosymbiotic origin in Bacteria, meaning Eukarya cannot be fully understood without investigating other domains.
Look, you have to draw the line somewhere. The more we look at life, the more the line between life and non-life blurs. Even if we do find a completely different "tree" of life that did not share the same genetic ancestry as the life we normally know, one could still make the argument that technically both "trees" are made of the same recycled nitrogen and carbon from the same planet, so it's technically one tree.
But don't stop there. If we find life on another planet, it's still the same tree. Both life on that planet and life on this planet probably share the same matter that came from the same supernovas.
As far as I see, trying to pin down this so-called "tree" thing is futile.
There's a huge difference between arguing that two things are related because they're both made out of matter from supernovae, and arguing that two things are related because both descended from exactly the same living cell, which used RNA and DNA with the same (or almost exactly the same) transcription language; already possessed some of the same copying machinery and shared parts of the genome with both descendants.
Somebody mentioned viruses. Viruses have their own trees of life, and for that reason some biologists exclude them from being "life." But I would count them as life.
Most biologists do not count viruses as life, but not for that reason. Rather they're not normally considered life because they have no metabolism and are incapable of reproducing themselves but instead only capable of inducing others to reproduce them for them.
I think you are right, MrJack. At least that is the reason they give, and I don't have much reason to doubt it. There was a discussion about this in my high school biology class. But I still suspect the underlying reason is that viruses don't fit into the patterns that all of the rest of life fits into. And the root cause of the mismatch is that viruses don't belong to the standard phylogenetic tree. The definitions of "life" are made by finding characters that encompass every fringe clade of the standard tree of life, which means that the definitions are likely to exclude viruses and perhaps outerspace alien beings that otherwise seem like life.
Actually calling it a 'tree' of life is a simplification when you get down to the level of bacteria etc. We now know that horizontal as well as vertical (treelike) gene transfers occur which join up some of the branches and it gets to be spaghetti at the bottom of the trunk e.g.