I’ve been wading through the recent tome edited by Bruce Gordon and Bill Dembski, The Nature of Nature. It’s a tour de force indeed, though every reader is bound to find whole areas of discussion where their eyes glaze over from incomprehension. That’s no bad thing if it reminds us how little we know even when we think we’re well educated.
So far, the piece that’s intrigued me most is Fazale Rana’s essay on molecular convergence, simply because I was unaware of the extent of this (and, of course, because I actually understood it, which helps). What most unsettled me was his drawing our attention to the confusing origins of DNA replication.
The paper cited is available online . The starting observation is that the core of DNA replication is the same in bacteria as in the other two superkingdoms (Archaea and Eukaryotes:)
These common features can be roughly summarized as follows: (i) replication is semi-conservative; (ii) replication always initiates at defined origins with the participation of an origin recognition system; (iii) replication fork movement is typically bidirectional; (iv) replication is continuous on the leading strand and discontinuous on the lagging strand; (v) RNA primers are needed to start DNA replication; (vi) nucleases, polymerases and ligases replace the RNA primers with DNA and seal the remaining nicks.
In other words, it’s a complex system (see here ) other alternatives to which could be conceived.
Yet the researchers found that some of the many ancillary proteins involved in DNA replication were completely different in the Archaea/Eukaryotes:
It is therefore surprising that the protein sequences of several central components of the DNA replication machinery, above all the principal replicative polymerases, show very little or no sequence similarity between bacteria and archaea/ eukaryotes. These observations suggest that some of the replication system components may not be homologs at all, whereas others, while homologous, are highly diverged.
What amazes me is how basic a finding this is. These three superkingdoms constitute all life. The archaea are thought to have branched off from the bacteria early on, and the eukaryotes (like us) from the archaea. The original branching point, in essence, is LUCA, the last universal common ancestor. All non-viral life is based on DNA – RNA world is still entirely hypothetical – so the business of DNA replication is at the very heart of the whole thing. You’d have expected it to have been sorted out pretty early on.
This is particularly so because it is a complicated process involving many proteins (as the video link above shows). Indeed it is Eugene Koonin, one of the study’s authors, who actually considers it such an evolutionary challenge for random mutation/ natural selection that in 2007 he seriously proposed the multiverse as an explanation:
Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent requisites of biological evolution… The [Many Worlds in One] version of the cosmological model of eternal inflation could suggest a way out of this conundrum…
But the research here seems to suggest the core system was already present in LUCA, and was conserved after the divergence, yet that one or both of the ensuing branches evolved, completely independently, near-identical support systems.
This looks for all the world like after-market customisation: a stock Ferrari with a Mercedes engine or (more in my own field) a standard Fender Stratocaster with Seymour-Duncan stacked humbuckers and Grover machines (don’t worry – you can’t expect to understand every piece of technical literature…). But we’re not talking about a peripheral function – even a bacterial flagellum – that could conceivably be having its R&D done by neutral mutation in the background to make new biological function. This is a classic case of redesigning the 747’s engines in flight. How (or why) could that happen?
The writers are not without a hypothesis to explain it, together with the alternatives. It involves LUCA having a mixed DNA and RNA genetic system, which explains the molecular homology of the core function, which is then redesigned in the separate groups some time after they separate:
As an alternative to all these explanations, we hypothesize that the modern-type systems for dsDNA replication evolved independently in bacteria and in the archaeal/eukaryotic lineage.
Admittedly, this scenario cannot completely invalidate the competing hypothesis of an origin of the DNA replication machinery in the LCA followed by as yet unknown (but clearly dramatic) evolutionary events causing the observed dissimilarity. We may never know the final answer.
I’m not sure if this explanation is any more plausible than that of a designer retro-fitting new molecules to one of the two divergent branches. I can’t see why the laytter would be desirable – though the alternative would be that he re-used the proven basic system with a new, improved, protein chipset. As the writers say, their explanation is more parsimonious than the evolutionary alternatives. But it still places a huge amount of faith in an undirected, random process turning up two teams at the racetrack with two near-identical major modifications to a basic system, supposedly developed independently. Look at the DNA video again. If you were a steward at the race meeting, would you be happy to put it all down to chance?
Koonin (2007) thinks that the evolution of DNA replication is an unexplained and pretty unlikely occurrence. Koonin (1999) suggests it probably happened twice. Small wonder, perhaps, that he feels it necessary to invoke the multiverse.