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James A. Shapiro

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Natural Genetic Engineering and Natural Selection: Perplexing Delusions of Certain Neo-Darwinist Advocates

Posted: 04/23/2012 7:32 pm

In my last blog, I received repeated accusations of being "anti-evolution" from John Kwok and Keith Roragen. These accusations puzzled me, and I tried to explain why I was puzzled in my online answers to them. But they continued to insist.

My basic argument on the blog (and in my book) was the following: We need to pay far more attention to non-random cell-mediated genome change ("natural genetic engineering") in evolution.

Here's what John Kwok said:

I must concur with Jerry Coyne's assessment of you: "My own theory is that the man simply doesn't understand the kind of population thinking in which 'natural genetic engineering' can result from garden-variety natural selection. (I often find that molecular biologists fail to grasp natural selection, even though it seems conceptually simple.)"

And here's what Keith Roragen said:

Where genome changes come from in the first place is irrelevant. Darwin had no knowledge of genomes. He didn't need it. Darwinism isn't concerned with how genomes change but how those changes propagate through populations and accumulate to form new species. You haven't even come close to explaining that.

Both John and Keith invoked natural selection and population genetics in a way that makes no logical sense. They seemed to believe that incanting "natural selection" would somehow invalidate what I said about the importance of natural genetic engineering. (Readers are invited to dig out the full exchanges and judge for themselves.)

The Jerry Coyne statement that John quoted does not even make sense within the context of the neo-Darwinian Modern Synthesis. Population geneticists recognize the need to use "mutation rates" and recombination events (i.e., genome changes) to generate new allelic variants and combinations as the raw material for selection. There is no way that natural selection can substitute for natural genetic engineering; by definition, it can only work after heritable change has occurred.

Keith simply sticks his head in the sand and introduces stubborn ignorance in place of explanation.

It is difficult to imagine how evolution could occur without genome change according to virtually any theory. Perhaps a purely neo-Lamarckian process, depending exclusively on epigenetic modifications, might conceivably generate heritable (and hence selectable) organism change without alterations to DNA sequences. But I do not think this is what my antagonists had in mind.

The curious responses to my position exposed a fundamental difference in understanding of biological functions between molecular geneticists and these particular proponents of population genetics. Because I can only speak for the molecular side, let me elaborate. I will leave it to John, Keith, and Jerry to explain their assertions.

Molecular geneticists recognize the essential roles of genome structures and multi-molecular networks for cell activities and for morphogenesis.

  • Cell reproduction would not happen without signals in the DNA for replication, for synthesizing and processing RNA, and for genome transmission to daughter cells.
  • Cells would not be able to survive the many changes they undergo, both internally and externally, without cell receptors, signaling molecules, and regulatory complexes.
  • Cells could not differentiate, form tissues, and carry out morphogenesis to produce multicellular organisms without genomic signals and cell networks.

To a molecular geneticist, evolution is the story of how essential genome structures and networks have changed over the history of life. DNA-based evolution science traces the histories of genome features among distinct life forms.

The basic fact is that natural selection can only pick out the most adaptive existing genome structures once they exist. There is simply no way, even theoretically, that population genetics and natural selection can account for how these structures and networks originated in the first place and then changed over time. That is why John's and Keith's assertions are so perplexing.

Novel genome structures have repeatedly played key roles in evolution of all aspects of biological function:

  • Proteins evolved to acquire novel functions by domain accretion and shuffling, a natural genetic engineering process.
  • New protein domains appeared in evolution by the incorporation of coding sequences from mobile elements ("exonization").
  • Protein coding sequences were amplified and diversified so that "protein families" can carry out the metabolic and regulatory processes characteristic of distinct species and higher taxa.
  • Regulatory RNA molecules evolved by a variety of natural genetic engineering processes, including reverse transcription and reinsertion of the newly made DNA into the genome.
  • Multicellular development depends upon intricate genomic systems like the Hox complexes, which are amalgams constructed from multiple coding and regulatory sequences; from the DNA record, it seems evident that bilaterally symmetric animals (including ourselves) could not have evolved without the assembly of the earliest Hox complex near the end of the Ediacaran period.
  • Species evolved in significant measure through changes in the cis-regulatory networks inscribed in their genomes.
  • Formation of new taxa frequently involved changes in chromosome number and structure.

(Thousands of references [including Scientific American articles] for these and other natural genetic engineering processes in evolutionary history can be accessed through clickable links at shapiro.bsd.uchicago.edu/evolution21.shtml.)

John, Keith, and Jerry have stated that I am mistaken (and dangerously misleading others) by expressing my position that natural genetic engineering is essential to evolution. If they wish to maintain that stance, then I think they need to explain why in detail. Fiat assertions and personal attacks are no substitute for rigorous argument.

 
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