July 5, 2006 | David F. Coppedge

Genetic Code Began by Lamarckian Evolution

It takes guts to tackle the origin of the genetic code from a naturalist perspective.  It also takes guts to resurrect Lamarck in the age of Darwin.  Carl Woese and colleagues tried a new hypothesis in PNAS1 that boldly goes headlong into both challenges.  To preserve a natural explanation for the genetic code, they felt it necessary to abandon Darwinian “survival of the fittest” for a stage, in favor of an admittedly Lamarckian process.  “Evolution of the genetic code, translation, and cellular organization itself,” they confessed in their last sentence, “follows a dynamic whose mode is, if anything, Lamarckian.”  In this paper, they picture a more cooperative living soup of theoretical semi-genetic entities.  With apologies to Darwin, they introduce the prebiological commune:

If Darwin had been a microbiologist, he surely would not have pictured a “struggle” for existence as “red in tooth and claw.”  Our view of competition in a communal world as a dynamical process is very different from the widely understood notion of Darwinian evolution.  “Survival of the fittest” literally implies that there can only be one winner from the forces of selection [sic], whereas in a communal world, the entire distributed community benefits and its structure becomes modified by the forces of a selection that is an inherently biocomplex phenomenon involving the dynamics between the community elements and the interaction with the environment.  The most general sense in which we mean competition in this article is the complex dynamical rearrangement of the community structure.

Their hypothesis is dominated by Horizontal Gene Transfer (HGT).  In their imaginary scenario, early organisms were more tolerant of ambiguity.  They had similar but variable genetic codes instead of the universal code we see today.  Blocks of code were freely shared between organisms, with mutation and variation exploring the functional landscape.  Transcription and translation processes were less precise.  At some undefined moment, this horizontal process of sharing became fixed, and vertical evolution of the Darwinian kind took over:

With this work, we have revisited the largely overlooked problem of genetic code universality and the conceptual difficulties associated with it.  These difficulties can all be avoided if one takes, as we do, the stance that evolution was essentially communal from the very beginning.  We have argued that there are three distinct stages of evolution, which we might classify as (i) weak communal evolution, which gave way via development of an innovation-sharing protocol and the emergence of a universal genetic code to (ii) strong communal evolution, which developed exponential complexity of genes, finally leading via the Darwinian transition to (iii) individual evolution—vertical, and so, Darwinian.

They provided a computer software model that demonstrated these stages:

Most of our analysis explored the transition between regimes i and ii, through detailed consideration of the way in which a generalized form of HGT operating on long evolutionary time scales brings universality via dynamic competition between a wide variety of collective innovation-sharing protocols.  In particular, we argued how such protocols emerge through the important coevolutionary mechanism of code attraction and presented a specific model that is capable of explaining the simultaneous universality and optimality of the genetic code.

Since “the genetic code is an expression of the translation process,” more work will be required to understand the origin and dynamics of the translation mechanism; that is, the “evolutionary development of translation and the organization of the cell” and its hardware components, the transfer RNAs and aminoacyl-tRNA synthetase family (see 06/09/2003).


1Vetsigian, Woese and Goldenfeld, “Collective evolution and the genetic code,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0603780103, published online before print July 3, 2006.

Time fails to pick apart this paper, but is it even worth it?  Their hypothesis fails on the meagerest application of common sense.  It’s a story riddled with personification, wishful thinking and naturalistic miracles.  The scenario only makes sense to people so blinded by evolutionary naturalism that they cannot imagine seeing outside the cave of their own making.
    If you are impressed with computer models, then you don’t know the magic tricks of programmers who can sneak intelligently-designed information in the side door while you are distracted.  Do these models have anything to do with the real history of the world?  How could they ever know?  Anything is possible with the magic wand of “long evolutionary time scales.”   What if the time scales are not evolutionary, but entropic?  The apparatus for evolutionary magic is always hidden in the black boxes of millions of years where nobody can watch.  Abracadabra!  You see that “collective information-sharing protocols emerge” through “code attraction.”  Why, they even have a computer to demonstrate it.  Dime-store magic tricks are more credible than this.  These guys just stole ID words (information, sharing, protocol) to make translation machinery “emerge” from a black, purposeless hat.  Presto, change-o.  Demand your money back.
    Ann Coulter in her new book Godless retells the joke about three hungry scientists on a desert island with a can of food, wondering how to open it.  The physicist suggests dropping it from a height.  The chemist suggests heating it till it pops open.  The economist says, “Assume a can opener.”  Woese, the king of Archaea with his underlings, has assumed not only a can opener but a whole kitchen in his imaginary world where evolutionary dreams come true (because – you see, we’re here – so that proves they did come true, doesn’t it, now?).  In his fantasyland, primitive organisms already possess rudimentary genetic codes and translation machinery, which he has assumed came from an RNA world preceding it (see 07/11/2002 for all the problems in that tale).  Unlike Darwin’s nasty beasts red in tooth and claw, his organisms start out like friendly smurfs in kindergarten, eager to play and share and learn new things.  They all freely exchange genetic subroutines that once in awhile prove “beneficial” (whatever that means).  The translations can be clumsy and incomplete, and the machinery might only partly work, but accuracy is not a concern in this land where mistakes always eventually lead to higher good.
    Out of this hodgepodge of chaos, Woese imagines not a junkyard as a result, but the emergence of the most elegant and efficient system of transcription and translation known to the mind of man.  At a magical moment, a consensus code emerges, becomes frozen and universal.  Soon it includes elaborate redundancy, backup and proofreading routines.  Here, Woese hands off to Charlie, who takes over to convert the Lamarckian horizontal evolution into Darwinian vertical evolution.  With this new genetic code and an unguided hand, he proceeds to craft giraffes and blue whales and fruit flies and philosophers.
    This is about as good as good grief.  A child could see through this scenario.  Since imagination rules in the evolutionary science journals these days, let’s play the game, too:

Imagine of world of simple robots without souls, bumping into each other occasionally.  (Where the robots came from is our “assume a can opener” part of the story.)  One robot speaks broken Chinese, one speaks broken English, one speaks broken Spanish, and another speaks broken Eskimo.  They have a few words in common, like McDonalds, Google, soccer and barf.  They mumble nonsense phrases in their own languages without understanding what they mean, but once in awhile they can pick up new words from one another.  They can’t reproduce.  They have no desire to improve (because, remember, they have no souls).  Nobody cares about what they do; nobody is there cheering them on.  The second law of thermodynamics is in operation.  No intelligent designers are around.  Once in awhile a big meteor hits the planet.

Come back in a few hundred million years.  Will you expect to find democratic governments, concerts, and departments of evolutionary robotics at universities?  If so, what planet are you from?*

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Categories: Genetics, Origin of Life

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