Science Literature

What can be said about the origin of the eukaryotic cell? "Until recently, everyone assumed, based on a single ribosomal RNA gene, that eukaryotes descended from archaebacteria - extremophilic prokaryotes distinct from 'true' bacteria, or eubacteria. Now we know that's not the case.' Genome studies reveal links with eubacteria as well as archaebacteria. There are also numerous losses of genes that are puzzling: "But how did evolution come up with the strange distribution of eubacterial and archaebacterial genes we see in eukaryotes today?"
In passing, we must note that an explanation in terms of evolutionary theory is assumed as a 'given'. It is as though no other avenues need be explored.
A remarkable paradox is introduced thus: "Because eukaryotes are derived from archaebacteria and eubacteria, one might expect to find an archaebacterial and a eubacterial copy of each nuclear gene. But strangely, archaebacterial operational and eubacterial informational genes are almost completely absent from eukaryotes, even though the first eukaryote contained two sets of informational and operational genes."
The author, James Lake, uses the analogy of the Roman god Janus. "Like the two faces of the Roman god Janus, thought to represent the Moon and the Sun, the phylogenetic origins of informational and operational genes in eukaryotes are as different as night and day. Finding a gene distribution such as this is the statistical equivalent of finding that a coin tossed at night (Janus's archaebacterial face) always comes up heads (informational genes), and tossed during the day (Janus's eubacterial face) always comes up tails (operational genes)."
Lake then discusses possible explanations of the Janus paradox. He offers a possible explanation as to why the eubacterial informational genes disappeared, but that's as far as he goes. "Unfortunately, I have no good suggestion for why the archaebacterial operational genes were eliminated." He concludes: "How the eukaryotic cell came to be is one of the greatest enigmas in biology. It is a story so complex that no single gene can tell it. Only entire genomes can."
The more we look at eukaryotes, the more obvious it becomes that an evolutionary story of simple to complex is woefully inadequate. But will genome studies help? Last year, the authors of a research paper wrote: "we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage". Some paradoxes can only be solved by changing the paradigm: maybe the avenue to be explored is signposted "intelligent design".

Disappearing act
James A. Lake
Nature 446, 983, (26 April 2007) | doi:10.1038/446983a
The bizarre absence of certain gene classes in eukaryotes is key to understanding their evolution and complex links with prokaryotes.

See also:
Kurland, C.G., Collins, L.J. and Penny, D. Genomics and the Irreducible Nature of Eukaryote Cells, Science 312, 19 May 2006: 1011-1014.