Shapiro Buries Naturalism

Shapiro is awesome! James Shapiro that is – bacterial geneticist at the University of Chicago. (Note: I’m not praising him because he is a creationist – he’s not) Two of his papers are a must read for anyone questioning naturalism. First, there is his 1997 paper, “A Third Way” – read the whole thing. It’s short and laymen like me can understand it. Secondly his 2010 paper, “Mobile DNA and Evolution in the 21st Century.” Read the conclusion. It’s all you need. Now let me whet your appetite … From “Third Way” …

Localized random mutation, selection operating “one gene at a time” (John Maynard Smith’s formulation), and gradual modification of individual functions are unable to provide satisfactory explanations for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for.

It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability.

(3) Mobile Genetic Elements and Natural Genetic Engineering. The second major lesson of molecular studies into the origins of genetic change is that all cells possess multiple biochemical agents for natural genetic engineering–processes that include the cutting and splicing of DNA molecules into new sequence arrangements.

In other words, genetic change can be massive and non-random. Some organisms, such as the ciliated protozooan Oxytricha, completely reorganize their genetic apparatus within a single cell generation, fragmenting the germ-line chromosomes into thousands of pieces and then reassembling a particular subset of them into a distinct kind of functional genome.

The point of this discussion is that our current knowledge of genetic change is fundamentally at variance with neo-Darwinist postulates.  We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutation rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures. Inevitably, such a profound advance in awareness of genetic capabilities will dramatically alter our understanding of the evolutionary process. Nonetheless, neo-Darwinist writers like Dawkins continue to ignore or trivialize the new knowledge and insist on gradualism as the only path for evolutionary change.

Wow! Did you catch all that? Shapiro – a non-creationist and a guy who should know – basically buries naturalism – that is, the view that random mutation plus natural selection created life.  It didn’t.  It couldn’t. Change happens of course — massive change in fact — and rapidly at times, but it’s all under cellular control.  In other words cells are actually pre-programmed to rearrange their DNA intelligently in response to environmental changes. Wow.

And the elephant in the room is the question – how did this pre-programmed functionality arise? Shapiro doesn’t say. I can’t find where he attempts to guess anywhere in his writings.  So it appears to me that his studies have buried naturalism.

13 years later, just last year (2010), Shapiro wrote …

The genome DNA record also bears witness to sudden changes that affect multiple characters at once: horizontal transfer of large DNA segments, cell fusions and WGDs. These data are not readily compatible with earlier gradualist views on the nature of evolutionary variation.

Although there remain many gaps in our knowledge, we are now in a position to outline a distinctively 21st
century scenario for evolutionary change. The scenario includes the following elements:

(1) hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;[emphasis mine]
(2) major disruptions of an organism’s ecology trigger cell and genome restructuring. The ecological disruptions can act directly, through stress on individuals, or indirectly, through changes in the biota that favour unusual interactions between individuals (cell fusions, interspecific hybridizations). Triggering events continue until a new ecology has emerged that is filled with organisms capable of utilizing the available resources;
(3) ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered environment. Novel adaptive features can be complex from the beginning because they result from processes that operate on pre-existing functional systems, whose components can be amplified and rearranged in new combinations. Competition for resources (purifying selection) serves to eliminate those novel system architectures that are not functional in the new ecology;
(4) once ecological stability has been achieved, natural genetic engineering functions are silenced, the tempo of innovation abates, and microevolution can occur to fine-tune recent evolutionary inventions through successions of minor changes.

This 21st century scenario assumes a major role for the kind of cellular sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel Prize address [1]. Such a cognitive component is absent from conventional evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. This 21st century view of evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions.

While Shapiro is very knowledgeable about mobile DNA, it appears he doesn’t really understand creationist views. He goes on to say

It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties. In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.

Shapiro seems to think that modern creationists hold a view that God created all modern species as they are today. This is not the modern creationist view. The modern creationist view is that God created ‘kinds’ originally (Todd Wood calls them “baramins”) and that these original kinds were pre-programmed to adapt rapidly to new environments. I became familiar with this topic back in 2008 (and wrote about it HERE and HERE) thanks to a paper by creationist Chris Ashcraft called “Genetic Variability by Design.” While Shapiro is brilliant and fearless at elucidating the natural genetic engineering properties of cells and how this new knowledge exposes the shortcomings of the neo-Darwinian paradigm, it appears to me that he avoids the elephant in the room – the question of how did this incredibly sophisticated “natural genetic engineering system” originate? He simply avoids the topic and I think I know why.  It appears to me that there is no rational answer other than “In the beginning God …”

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