Is Darwinian evolution true?

Question: Darwinism (or Neo-Darwinism) is any view of evolution which places special emphasize on natural selection. This natural selection, acting on random variations, is hypothesized to have produced virtually all of the diverse complexity in species on Earth. Is Darwinism true?

Some critics object to the use of the term Darwinism, but the term has long been canonized in reputable academic sources and standard works. See:

Oxford's "A Dictionary of Science" (entry: Evolution): “Darwin proposed a feasible mechanism for evolution and backed it up with evidence from the fossil record and studies of comparative anatomy and embryology (see DARWINISM; NATURAL SELECTION). The modern version of Darwinism, which incorporates discoveries in genetics made since Darwin’s time, remains the most acceptable theory of species evolution.” [304.]; “natural selection The process that, according to Darwinism, brings about the evolution of new species of animals and plants.” [Elizabeth Martin (Oxford, 2010), 549.]

princeton.edu: [“Darwinism”] “a theory of organic evolution claiming that new species arise and are perpetuated by natural selection”

A Dictionary of Zoology: “Darwinism The theory of evolution by natural selection, often used incorrectly as a synonym for the theory of evolution itself. The term ‘neo-Darwinism’ is often used to denote the ‘new synthesis’ (i.e. synthetic theory).” [Ed. Michael Allaby. (Oxford, 2009), online.]

William Dembski & Michael Ruse: “Is the appearance of design in organisms as exhibited in their functional complexity the result of purely natural forces acting without prevision or teleology? Or does the appearance of design signify genuine prevision and teleology, and, if so, is that design empirically detectable and thus open to scientific inquiry? Four main positions have emerged in response to these questions: Darwinism, self-organization, theistic evolution, and intelligent design.” [Debating Design (Cambridge, 2004, 2006).]; Francisco Ayala (Professor of Biological Sciences, Ecology & Evolutionary Biology at California; 2001 National Medal of Science): “There are many thoughtful discussions of the dialogue between Darwinism and Christianity” [“Design without Designer” in Debating Design (Cambridge, 2004, 2006), 74.]

Eugene Koonin is one of the most renowned living evolutionary biologists. and on the recent 150th anniversary of Darwin’s “Origin of Species,” his entry in the Journal “Trends in Genetics” was the introductory piece. It was a synopsis of where he and many others feel the field of evolutionary biology is today.

Eugene Koonin: “The summary of the state of affairs on the 150th anniversary of Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the modern synthesis is gone.” [“The Origin at 150: Is a New Evolutionary Synthesis in Sight?,” Trends in Genetics Vol. 25:473, (2009): 474.] (Internal citations omitted).¹

Similarly, in Nature,…

Kevin Laland and colleagues: “The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day. Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders — such as physiologists or developmental biologists — flood into their field.” [“Does evolutionary theory need a rethink? Nature 514 (October 2014), online]

Some other examples

Lynn Margulis (US Presidential Medal for Science recipient; originator of endosymbiotic theory): “At that meeting [Francisco] Ayala agreed with me when I stated that this doctrinaire neo-Darwinism is dead. He was a practitioner of neo-Darwinism, but advances in molecular genetics, evolution, ecology, biochemistry, and other news had led him to agree that neo-Darwinism’s now dead” [Suzan Mazur, The Altenberg 16 (Berkeley, 2010), p. 285)]

David J. Depew & Bruce H. Weber: “We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. … Darwinism in its current scientific incarnation has pretty much reached the end of its rope. … it is largely because Lamarckism, saltationist (sudden) mutationism, and inner-driven orthogenesis, to name the most enduring alternative traditions in evolutionary biology, failed to become mathematized empirical sciences with at least a foothold on value-neutrality that Darwinism still rules the evolutionary roost … in the past, improved versions of Darwinism have taken the place of inadequate ones and that a new version -- a Darwinism of the future -- may well displace population genetical Darwinism without ending, but instead enriching, Darwinism as such. [The Fate of Darwinism: Evolution After the Modern Synthesis, Biol Theory (2011) 6:89-102]

Scott Gilbert: “[t]he modern synthesis is remarkably good at modeling the survival of the fittest, but not good at modeling the arrival of the fittest.” Evolutionary paleobiologist Graham Budd was similarly open in the article saying, “When the public thinks about evolution, they think about the origin of wings and the invasion of the land … [b]ut these are things that evolutionary theory has told us little about. [John Whitfield, "Biological Theory: Postmodern Evolution?,” Nature 455 (2008): 281.] (quoting Scott Gilbert).]

Nicola Nadeau & Chris Jiggins.: “Nonetheless, most studies of recent evolution involve the loss of traits, and we still understand little of the genetic changes needed in the origin of novel traits. [“A golden age for evolutionary genetics?” Trends in Genetics 26(11)(2010): 484-92. Epub 2010 Sep 28.]

William Provine (Cornell University historian of science and evo-biologist): “[e]very assertion of the evolutionary synthesis below is false": Natural selection was the primary mechanism at every level of the evolutionary process. Natural selection caused genetic adaptation…. Macroevolution was a simple extension of microevolution. … Evolution is a process of sharing common ancestors back to the origin of life, or in other words, evolution produces a tree of… The evolutionary synthesis was actually a synthesis.” [Abstract of talk before the History of Science Society titled “Random Drift and the Evolutionary Synthesis.” [online at hssonline.org]

Adam Wilkins (Editor of BioEssays, edits commentaries section of Genetics): “the book’s [Shapiro's] contention that natural selection’s importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (A few months ago, I was amazed to hear it expressed, in the strongest terms, from another highly eminent microbiologist.) My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a ‘creative’ and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it.” [Review of Evolution: a view from the 21st century (2011) by James A. Shapiro, Genome Biology and Evolution (2012) [online]²