Of trees of life and straw men

I am trying to write a grant proposal, but cannot help but get distracted by all this discussion (stemming from a recent new Scientist article) about Darwin supposedly being wrong about the tree of life. All the new evidence about the role of horizontal gene transfer in bacteria and even in unicellular eukaryotes is of course all very interesting. But to try and depict this as a Darwin-was-wrong argument strikes me as misleading and risks casting Darwin into the role of a straw man. In fact, Darwin was ignorant of the existence of bacteria until late in his life and as far as I am aware never commented on their evolution. 

But more than that, he never said any so simplistic as "all life follows a tree-like pattern of evolution right back its origin and that's that!". 

The first point to note is that Darwin was always quick to point out the caveats and counter-arguments of any given proposition. Secondly, his discussion in The Origin of the tree of life sets the "universe of discourse" at the taxonomic level of Class, rather than universally applying to all life. 

Here is what he actually wrote, with my emphasis added:

From Chapter 4

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications. 

(And even Dawkins can't top the elegance of Darwin's prose here!)

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From the final chapter:

Therefore I cannot doubt that the theory of descent with modification embraces all the members of the same class. I believe that animals have descended from at most only four or five progenitors, and plants from an equal or lesser number.

Analogy would lead me one step further, namely, to the belief that all animals and plants have descended from some one prototype. But analogy may be a deceitful guide.
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Darwin's wasn't wrong about the tree of life—he accepted that the evidence before him was limited and it was unsafe to generalise it to the whole of life. Give the poor man--or should that be "straw man"--a break!