Is Horizontal Gene Transfer a Force for Evolution?

Two more genomes were published last week: the information libraries of two tiny microbes.  They are members of Micromonas, green algae less than two microns across.  The original paper and summary both bragged about how the genetic information is helping shed light on evolution, but did the data really contain any light?  If so, the light was pointing downward.
    Worden et al published the genomes of RCC299 and CCMP1545, two isolates of the picophytoplankton clade Micromonas.¹  John M. Archibald commented on the paper in Perspectives article in the same issue.²  Three observations cast doubt on whether evolution generated any new functional information:

1. Reduction:  Both genomes have been stripped of unnecessary baggage for their simple marine lifestyle.  Two alga species sequenced earlier are the “reining [sic] champions of eukaryotic cellular miniaturization,” Archibald said.  The two genomes are also stripped down, but less so than Ostreococcus. 
2. Stasis.  Is there anything new that these organisms invented by evolution?  “Of particular note among the 1384 genes shared by both Micromonas strains but absent in Ostreococcus is an impressive suite of transcription factor genes, the origins of some of which can now reasonably be moved to the common ancestor of chlorophytes and streptophytes.”  This is the “not invented here” response.  Archibald also said of the paper by Worden et al, “Their analyses provide crucial insights into the plasticity of the eukaryotic genome over short evolutionary time scales and also shed light on the genetic “toolkit” that may have been present in the ancestors of today’s land plants and green algae.  If there was any evolution, it did not involve new tools.  It only involved sorting out what had already been invented.
3. Transfer:  Horizontal gene transfer (HGT) scrambles the picture of who invented what.  One surprise found in these genomes is that one of them contained stuff the other did not: “many genes that occur in one Micromonas genome, but not the other,” Archibald noted, “are very similar to those found in organisms as evolutionarily distant as animals, fungi, and bacteria.”  This can only mean that the alga checked the information out of someone else’s library: “One interpretation is that such genes are the product of horizontal gene transfer, through which an organism incorporates genetic material from an unrelated or distantly related species; this process is gaining increasing acceptance as a real force in eukaryotic genome evolution.”  But is HGT really a force?  The explanation does not explain the origin of the information, but only its distribution.  If genes from “an unrelated or distantly related species” can be found, without knowing which species it came from, it would seem increasingly difficult to trace the path of evolution, or to know whether the information evolved along any particular branch of the tree.

Worden et al said the same things, only in more technical detail.  They also claimed that these genomes “offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.”

1.  Worden et al, “Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas,” Science, 10 April 2009: Vol. 324. no. 5924, pp. 268-272, DOI: 10.1126/science.1167222.
2.  John M. Archibald, “Green Evolution, Green Revolution,” Science, 10 April 2009: Vol. 324. no. 5924, pp. 191-192, DOI: 10.1126/science.1172972.

Anyone see any light here?  Pre-existing toolkits, shared information, stripped-down genomes, supposedly ancient organisms doing just fine in real time: where is the evolution?  Claiming that evolution explains these phenomena is piracy, just like in the next entry.