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Does the article criticise neo-Darwinism (the modern synthesis)?

Yes. The 2013 article criticises neo-Darwinism (the modern synthesis) as being too restrictive and too dogmatic. That view becomes a special case that holds under certain circumstances.

 “As with other breaks from the Modern Synthesis, that synthesis emerges as only part of the evolutionary story.”

 The modern synthesis is also criticised for the unwarranted and virulent denigration of Lamarck.

“In 1998, the great contributor to the development of the Modern Synthesis, John Maynard Smith, made a very significant and even prophetic admission when he wrote ‘it [Lamarckism] is not so obviously false as is sometimes made out’ (Maynard Smith, 1998), a statement that is all the more important from being made by someone working within the Modern Synthesis framework. The time was long overdue for such an acknowledgement. Nearly 50 years before, Waddington had written ‘Lamarck is the only major figure in the history of biology whose name has become to all extents and purposes, a term of abuse. Most scientists’ contributions are fated to be outgrown, but very few authors have written works which, two centuries later, are still rejected with an indignation so intense that the skeptic may suspect something akin to an uneasy conscience. In point of fact, Lamarck has, I think, been somewhat unfairly judged.’ (Waddington, 1954).”

Maynard Smith J (1998). Evolutionary Genetics. Oxford University Press, New York, NY, USA.

Waddington CH (1954). Evolution and epistemology. Nature 173, 880–881.

The inheritance of acquired characteristics, usually called Lamarckism, has now been demonstrated, it can persist for many generations, and some of the molecular mechanisms of such inheritance have been found. It is time that this was openly acknowledged.

The reason that the new developments are ‘rocking the foundations’ is that it was clearly an aim of the modern synthesis to exclude the inheritance of acquired characteristics.  It is precisely that aspect of the modern synthesis that has now been shown to be incorrect. 

The question whether neo-Darwinism has been proven wrong therefore depends on what exactly is being questioned. The dogmatic claims (a) that the inheritance of acquired characteristics is impossible, (b) that all evolutionary change is incremental accumulation of ‘random’ mutations, (c) that the tree of life does not include lateral transfer to form a network of life, have quite clearly been disproven by experimental work. I can’t understand why neo-darwinists cannot accept this. But we must also avoid the reverse dogma: the neo-darwinist view of evolutionary mechanisms has not been disproven. It has simply become one of several mechanisms of evolutionary change. See also The Language of Neo-Darwinism.

 

   
  The MUSIC of Life: Biology Beyond the Genome                                                                                                                                 ©Denis Noble