Strikes blow against “ominous specter of irreducible complexity”
Thus, eukaryotes show a qualitatively different level of cellular organization from that of archaea and bacteria, and there are no detectable evolutionary intermediates. Comparative analysis of eukaryotic cells and genomes indicates that the signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor (LECA). These ancestral features include the actin and tubulin-based forms of cytoskeleton, the nuclear pore, the spliceosome, and the ubiquitin signaling network, to mention only several aspects of the inherent organizational complexity of eukaryotic cells -. The emergence of these fundamental facets of advanced cellular organization presents a challenge of such scale that Darwin’s famous scenario for the evolution of the eye looks like a straightforward solution to an easy problem. To some, the enigma of eukaryogenesis can appear so perplexing that the infamous concept of ‘irreducible complexity’ has sneaked into the scientific mainstream , although debunking of these ideas has not been long in coming . Below I discuss the recent advances in evolutionary genomics that make the origin of eukaryotes much less mysterious than it appeared even recently.
Also dumps on Tree of Life:
The newly achieved clarity in our understanding of these key aspects of eukaryogenesis calls for reassessment of some of the most general concepts in biology. The first one is the representation of the entire history of life as a single evolutionary tree, a grand idea that goes back to the famous single illustration of Darwin’s Origin of Species. The symbiogenetic scenario of eukaryogenesis flatly defies this concept because under this scenario, a major kingdom of life, the eukaryotes, emerged in a non-tree-like manner, through fusion of different, distant branches of the tree. The importance of trees for understanding the evolution of individual genes, gene ensembles and major taxa, especially those that encompass multicellular eukaryotes, is undeniable . However, the new findings on the origin of eukaryotes as well as the origin of archaeal phyla  indicate that major transitions in evolution often, perhaps typically, occur through the fusion of cells and/or genomes of distantly related organisms. The second, not unrelated general theme is the number and nature of the primary domains of life. In the late 1980s, based on the rRNA trees, Woese and colleagues developed the three-domain scheme (Fig. 1a) . The placement of eukaryotes within the archaeal branch that has been clinched by the discovery of Loki refutes this scheme and shows that the only consistent interpretation of the phylogeny of the universal (primarily informational) genes involves two primary domains: bacteria and archaea (with eukaryotes included) (Fig. 1b) .
Wanna bet the Tree of Life will still be in the textbooks a dozen years from now? Here’s why, probably.
Here’s the abstract:
The origin of eukaryotes is one of the hardest problems in evolutionary biology and sometimes raises the ominous specter of irreducible complexity. Reconstruction of the gene repertoire of the last eukaryotic common ancestor (LECA) has revealed a highly complex organism with a variety of advanced features but no detectable evolutionary intermediates to explain their origin. Recently, however, genome analysis of diverse archaea led to the discovery of apparent ancestral versions of several signature eukaryotic systems, such as the actin cytoskeleton and the ubiquitin network, that are scattered among archaea. These findings inspired the hypothesis that the archaeal ancestor of eukaryotes was an unusually complex form with an elaborate intracellular organization. The latest striking discovery made by deep metagenomic sequencing vindicates this hypothesis by showing that in phylogenetic trees eukaryotes fall within a newly identified archaeal group, the Lokiarchaeota, which combine several eukaryotic signatures previously identified in different archaea. The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis. (Open access) – BMC Biology 5 October 2015, 13:84 | doi:10.1186/s12915-015-0194-5
So I wouldn’t bet anything I needed on his current suggestions making “the origin of eukaryotes much less mysterious than it appeared even recently.”
When a researcher wants to discredit something (irreducible complexity, in this case) this badly, he is apt to swat at just anything whistling past. When he uses terms like “ominous specter” and “much less mysterious” to describe his battle, we can be fairly certain of one thing: The next round of conundrums and complexities will blow the speculations high.
Eventually, such theorists will get around to addressing the enigma of information. But don’t cancel any engagements in anticipation; they have hardly begun to speculate yet. 😉
See also: In a Darwinian multiverse, Eugene Koonin could be both right and wrong an infinite number of times
The multiverse: Where everything turns out to be true, except philosophy and religion
Multiverse cosmology: Assuming that evidence still matters, what does it say?
In search of a road to reality