Shapiro, Evolution and Theology Part 1

James Shapiro is a microbiologist who has been advancing a new way to look at evolution for many decades. Jon Garvey has mentioned Shapiro a number of times on blog posts, and Shapiro’s ideas have been discussed by many evangelicals interested in faith and evolution, including followers of ID. Shapiro himself is not a theist, and is not interested in supporting ID or any other theological ideas. But his scientific ideas are interesting and somewhat controversial in biology (although they shouldn’t be). And, despite his own views on theism, Shapiro’s approach has highly significant implications for theistic evolution.

James Shapiro is a leading pioneer in the discovery that bacteria can somehow manipulate their own genomes to produce directed, non random mutations, which are targeted to specific genes in order to relieve the stress caused by starvation or other environmental shocks. This phenomenon was pure heresy to the orthodox Neo Darwinians, who followed (and some still do) the Luria and Delbruck paradigm that all mutations are random and selection chooses which ones are useful.

I will insert here, that while the conceptual framework of random mutations being the source of all variation, followed by natural selection to choose winners and losers is a hallmark of NeoDarwinian dogma, it is not Darwinian. In the Origin of Species, Darwin wrote that nobody knew anything about the source of hereditable variations, and if he implied that such events were due to chance, he didn’t mean it. He simply didn’t know. In fact Darwin’s theory does not at all depend on the random nature of mutations.

In 1988, when John Cairns published in Nature a confirmation and extension of Shapiro’s work, I was a struggling Associate Professor, who had just gotten tenure. Like the majority of my colleagues in biology, my reaction was negative. Nonsense, I thought, Lamarck and Lysenko making a comeback. (It was neither the first, nor by far, the last time I was wrong about something important).

By now, these controversial findings have been substantiated in many systems, mechanisms have been found to explain them (and they don’t involve thinking bacteria or theistic intervention). And what is clear is that, at least in bacteria, life has evolved some truly splendid and unexpected ways to find a way to survive dire threats.

But Shapiro has gone much further than this. He takes his own work on directed mutations and applies them and many other findings on how cells accomplish change, to develop a model he calls Natural Genetic Engineering (NGE). His view is that the cell can control the genome as much as the genome controls the cell. And then he applies this to evolution. The source of invention, or variation or creativity in biology, is not natural selection, but natural genetic engineering. And such sources of variation do not fit the Darwinian model of slow progressive changes,  but are rapid, and dramatic, and involve large events such as whole genome duplications, transposition of DNA sections leading to massive re-engineering of proteins, horizontal transfer of coding regions from plastids, viruses and other organisms, and so on.

Shapiro’s ideas are more consonant with those of Gould’s punctuated equilibrium, though Gould, not being a molecular biologist never postulated any mechanism for this. Dawkins, Coyne and friends, attack this model vigorously, and claim that there is nothing new there, and it does nothing to disprove or even dent Neo-Darwinism.

In some ways they are right. All of the phenomena cited by Shapiro are well known. One of his favorite examples is the huge evolutionary step that led to the eukaryotes when a prokaryotic cell engulfed a bacteria which remained alive and functional within its host, and gave rise to cells with mitochondria. Nobody thinks that event was a slow stepwise process. Dawkins has described it as a one time incredibly lucky accident, more or less equivalent to the origin of life.

But Shapiro says that if such a thing happened once, it shows that revolutionary explosions in the nature of life are at least possible, and in fact have happened numerous times. (In fact it happened at least twice, since chloroplasts were also swallowed by an ancient plant cell). Shapiro’s view is that all of these rapid, dramatic, revolutionary events that result from accidents or deliberate biochemical control of genomes by cells, are the real drivers of evolution.

In the next part I will give my own thoughts on Shapiro’s ideas and try to tie in the theological aspects of his theory.

Sy Garte

About Sy Garte

Dr Sy Garte earned his Ph.D. in biochemistry from the City University of New York, where he also holds a bachelor’s of science degree in chemistry. In addition to publishing more than 200 scientific publications in genetics, epidemiology, the environment and other areas, Dr. Garte is the author of Where We Stand: A Surprising Look at the Real State of Our Planet (Amacom) and Genetic Susceptibility to Environmental Carcinogenesis (Kluwer) and is co-editor of Molecular Epidemiology of Chronic Diseases (Wiley).
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2 Responses to Shapiro, Evolution and Theology Part 1

  1. Jon Garvey Jon Garvey says:

    Thanks for this, Sy. I was reading recently here how mutations caused by ionising radiation came to be seen as a magic bullet for evolution in the ND synthesis (which explains all those superheroes of the 30s and 40s resulting from laboratory accidents). But as Lonnig documents, practical biologists eventually found not only that vanishingly few useful mutations could be induced that way, but that the same mutations were happening time and again. So while mutation has remained an assumption behind Neodarwinism, in breeding experiments it just hasn’t carried the weight put upon it.

    In Shapiro’s science that’s not surprising, because mutations from ionisation are shown to be not a result of damage, but a response to damage, by the cell. And given the extreme circumstances of that response, it’s hardly likely to be a source of evolutionary innovation, any more than the flight-or-fright response is likely to lead to novel behaviours.

    But if that’s so, where does that leave variation in ND theory? Such mutation is seen as the final common path for gene (or genome) duplications, symbiotic events and so on. If mutations are predominantly either repetitive or fatal, do we really have a realistic mechanism for the arrival of the fittest? Why is random mutation as the source of evolutionary variation not considered a 1930s hypothesis that didn’t deliver as was hoped (and isn’t even completely random with regard to fitness?)

    • Sy Garte Sy Garte says:

      That is a good question, Jon, and the answer I think is complex. (big surprise). We know that polymorphic alleles can produce recognizable phenotypic variation in many genes. And the majority of these allelic polymorphisms are caused by single point mutations. So it is certainly possible for mutations of the classical kind to lead to changes in fitness and evolutionary progress. What Shapiro claims (with good justification) is that this is not what actually happens. And the fact that something is possible doesn’t mean its true. (Which neoDarwinians are quick to point in other contexts).

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