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“Genomics and the Irreducible Nature of Eukaryote Cells”

[From a colleague:] Hot on the heels of Embley and Martin (Nature 440, 623-630, 30 March 2006), Kurland and colleagues take the plunge and sever the link between eukaryotes and prokaryotes. Their title refers to the “Irreducible Nature of Eukaryote Cells,” which reads like an echo of Mike Behe. The logic of their argument confirms this: the structures and the genetics of eukaryotes mean that an evolutionary pathway from prokaryotes must be rejected. However, they do not again use the word “irreducible” in their paper. What is clear is that the “simple” pathway that the textbooks have proclaimed for years must now be abandoned. Surely there are lessons here about the way darwinism gives false leads in its appetite for a narrative about the origins of complexity.

Evolution by Reduction? (Science Highlights)

The origins of eukaryotes remain controversial and somewhat enigmatic. Kurland et al. (p. 1011) provide a counterpoint to current models in which the eukaryotic cell is derived from structurally and genetically less complex prokaryotic cells. On the basis of genomic and proteomic evidence, they suggest that the essence of eukaryotic cellular complexity existed in the common ancestor of eucarya, bacteria, and archaea, and that the bacteria and archaea have evolved by genome reduction driven by specialization for fast growth and cell division and/or adaptation to extreme environments.

Genomics and the Irreducible Nature of Eukaryote Cells
C. G. Kurland, L. J. Collins, and D. Penny
Science 19 May 2006: Vol. 312. no. 5776, pp. 1011 – 1014
http://www.sciencemag.org/cgi/content/abstract/312/5776/1011

Abstract: Large-scale comparative genomics in harness with proteomics has substantiated fundamental features of eukaryote cellular evolution. The evolutionary trajectory of modern eukaryotes is distinct from that of prokaryotes. Data from many sources give no direct evidence that eukaryotes evolved by genome fusion between archaea and bacteria. Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution. Subcellular architecture of eukaryote cells is in part a physical-chemical consequence of molecular crowding; subcellular compartmentation with specialized proteomes is required for the efficient functioning of proteins.

Comparative genomics and proteomics have strengthened the view that modern eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes (1*4). Nevertheless, comparative genomics has confirmed a lesson from paleontology: Evolution does not proceed monotonically from the simpler to the more complex (5*9). Here, we review recent data from proteomics and genome sequences suggesting that eukaryotes are a unique primordial lineage.

Mitochondria, mitosomes, and hydrogenosomes are a related family of organelles that distinguish eukaryotes from all prokaryotes (10). Recent analyses also suggest that early eukaryotes had many introns (11, 12), and RNAs and proteins found in modern spliceosomes (13). Indeed, it seems that life-history parameters affect intron numbers (14, 15). In addition, “molecular crowding” is now recognized as an important physical-chemical factor contributing to the compartmentation of even the earliest eukaryote cells (16, 17).

Nuclei, nucleoli, Golgi apparatus, centrioles, and endoplasmic reticulum are examples of cellular signature structures (CSSs) that distinguish eukaryote cells from archaea and bacteria. Comparative genomics, aided by proteomics of CSSs such as the mitochondria (18, 19), nucleoli (20, 21), and spliceosomes (13, 22), reveals hundreds of proteins with no orthologs evident in the genomes of prokaryotes; these are the eukaryotic signature proteins (ESPs) (23, 24). The many ESPs within the subcellular structures of eukaryote cells provide landmarks to track the trajectory of eukaryote genomes from their origins. In contrast, hypotheses that attribute eukaryote origins to genome fusion between archaea and bacteria (25*30) are surprisingly uninformative about the emergence of the cellular and genomic signatures of eukaryotes (CSSs and ESPs). The failure of genome fusion to directly explain any characteristic feature of the eukaryote cell is a critical starting point for studying eukaryote origins. . . .

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6 Responses to “Genomics and the Irreducible Nature of Eukaryote Cells”

  1. And here’s the big question — if it is now appropriate to argue that eukaryotes can’t have evolved from prokaryotes because of irreducible complexity (or some modified version thereof), why is it not appropriate to argue that eukaryotes can’t have evolved from nothing?

    Another question — is the new trend now going to be to co-opt ID ideas without attribution?

    This just opened up a huge can of worms. I am stunned and shocked that Science printed this. What will Leshner say now?

  2. I think that these people are only reporting what they find. They are not pushing the conclusions too far. The ongoing implications may be huge of saying;

    “Comparative genomics shows that, under certain ecological settings, sequence loss and cellular simplification are common modes of evolution.”

    I wonder if they were told, after the initial submission, to add the qualifying phrase “under certain ecological settings” to minimise the impact of whet they are saying.

    If we start with something very complex in all three cell lines, we have to suppose at least three massive chemical evolutionary events instead of only one.

    How far can we stretch our imaginations before we get to breaking point?

    ID the future!

  3. “How far can we stretch our imaginations before we get to breaking point?” –idnet.com.au

    I contend that our imaginations are already at the breaking point on several key fronts. The problem is that the truth pays no regard to what our little minds might fathom.

  4. Making the conceptual step that prokaryotes cleaved off from eukaryotes is a big step towards accepting the possibility of front loading. This is because it acknowledges that more complex preceded less complex and that’s what front loading is all about. All the empirical evidence falls neatly into place when a LUCA with a complex genome is hypothesized. Nothing makes sense in evolution except in light of a LUCA with a complex genome preprogrammed to diversify into all we see today.

  5. Mike Gene recently made a post about the possibility that eukaryotes are not descended from prokaryotes. But of course we know scientifically that they did originate by way of unintelligent natural processes because…um…uh…well, we just know, okay! :roll:

  6. > Another question — is the new trend now going to be to co-opt ID ideas
    > without attribution?

    > This just opened up a huge can of worms. I am stunned and shocked that
    > Science printed this. What will Leshner say now?

    I simply see it as a VERY VERY GOOD NEWS. My impression is that:

    1. ID concepts are more and more influencing the way scientists do research in biology. IMHO it’s AMAZING to see that the term “irreducible” is actually used in a Science title.

    2. I don’t see as negative the absence of any direct reference to ID. Probably it is necessary that science mainstream do adopt ID concepts gradually and with the self-conviction that they have been reached “scientifically”

    Remeber, as Bill stated we are in the transition from phase 2 to phase 3

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