University of Zurich evolutionary biologist Andreas Wagner acknowledges that
"Biologists know many fascinating examples of evolutionary innovations, and they know that natural selection can preserve an innovation once it has originated. However, they know little about the principles that allow innovations to originate in the first place."
A press release from the Santa Fe Institute, about a Nature paper co-authored by Wagner, states much the same thing:
"Exactly how new traits emerge in evolution is a question that has long puzzled evolutionary biologists."
Writing in Nature, Wagner says:
"How evolutionary adaptations and innovations originate is one of the most profound questions in evolutionary biology."
Other biologists concur.
In 2009, Günter Theißen of the Department of Genetics at Friedrich Schiller University in Jena, Germany wrote in the journal Theory in Biosciences that modern Darwinian theory has not fully explained the origin of novel biological complexity:
While we already have a quite good understanding of how organisms adapt to the environment, much less is known about the mechanisms behind the origin of evolutionary novelties, a process that is arguably different from adaptation. Despite Darwin's undeniable merits, explaining how the enormous complexity and diversity of living beings on our planet originated remains one of the greatest challenges of biology.
An even more striking criticism of what he called the "dogmatic science" of neo-Darwinian thinking can be found in a 2006 paper by Theißen:
Explaining exactly how the great complexity and diversity of life on earth originated is still an enormous scientific challenge . . . . There is the widespread attitude in the scientific community that, despite some problems in detail, textbook accounts on evolution have essentially solved the problem already. In my view, this is not quite correct.
U.S. National Academy of Sciences member biologist Lynn Margulis is also a notorious critic of neo-Darwinism, having written that
"Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambigious evidence that random mutation itself, even with geographical isolation of populations, leads to speciation."
In a 2011 interview a few months before her death, Margulis continued:
"Natural selection eliminates and maybe maintains, but it doesn't create.... neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change -- led to new species. I believed it until I looked for evidence."
Evolutionary biologist Stanley Salthe likewise describes himself as "a critic of Darwinian evolutionary theory," which he insists "cannot explain origins, or the actual presence of forms and behaviors"9 in organisms.
Journalist Susan Mazur elaborates on Salthe's criticisms of Darwinism:
Stanley Salthe, a natural philosopher at Binghamton University with a PhD in zoology -- who says he can't get published in the mainstream media with his views .. . . told me the following: "Oh sure natural selection's been demonstrated . . . the interesting point, however, is that it has rarely if ever been demonstrated to have anything to do with evolution in the sense of long-term changes in populations . . . . Summing up we can see that the import of the Darwinian theory of evolution is just unexplainable caprice from top to bottom. What evolves is just what happened to happen."
In 2008, Nature published an article covering the Altenberg 16 conference, quoting biologist Scott Gilbert. He said that
"the modern synthesis is remarkably good at modeling the survival of the fittest, but not good at modeling the arrival of the fittest." Stuart Newman stated in the same article, "You can't deny the force of selection in genetic evolution . . . but in my view this is stabilizing and fine-tuning forms that originate due to other processes."Evolutionary paleobiologist Graham Budd was similarly open in the article about deficiencies in explanations of key evolutionary transitions: "When the public thinks about evolution, they think about the origin of wings and the invasion of the land, . . . but these are things that evolutionary theory has told us little about."
Pearson replies to these kinds of arguments by stating that "the reviewer may have taken this statement out of context, implying that it suggests evolution proceeds only by natural selection." But just because there are other mechanism of evolution doesn't mean those other mechanisms can produce novelty. As Jerry Coyne explains, other evolutionary mechanisms like neutral drift are impotent to create new features: "Both drift and natural selection produce genetic change that we recognize as evolution. But there's an important difference. Drift is a random process ... As a purely random process, genetic drift can't cause the evolution of adaptations. It could never build a wing or an eye."
In its response to the reviewer, Pearson cites two papers which supposedly show that "several mechanisms for the generation of evolutionary novelty have indeed been 'firmly established.'" The first of these papers is a short comment by Manyuan Long on the standard model of the evolution of genes by duplication followed by divergence. That Pearson would cite this paper shows how little the publisher appreciates what's wrong with neo-Darwinian evolution.
The duplication/divergence model of gene evolution ignores the problem of multiple coordinated mutations. There's no question that gene can duplicate. The question is whether duplicated genes can traverse likely evolutionary pathways to acquire new functions before they are subfunctionalized. This is typically held to be a neutral walk , detached from selection pressure. However, population genetics imposes limits on how many specific neutral mutations a gene is likely to accumulate.
In 2010, Douglas Axe published evidence indicating that despite high mutation rates and generous assumptions favoring a Darwinian process, molecular adaptations requiring more than six mutations before yielding any advantage would be extremely unlikely to arise in the history of the Earth. The following year, Axe published research with developmental biologist Ann Gauger describing the results of their experiments seeking to convert one bacterial enzyme into another closely related enzyme. That is the kind of conversion that evolutionists claim can easily happen. For this case they found that the conversion would require a minimum of at least seven simultaneous changes,15 exceeding the six-mutation-limit that Axe had previously established as a boundary of what Darwinian evolution is likely to accomplish in bacteria. Because this conversion is thought to be relatively simple, it suggests that the model of evolution by gene duplication could not produce even many modest gene conversions.
In experiments led by Gauger and biologist Ralph Seelke of the University of Wisconsin, Superior, their research team broke a gene in the bacterium E. coli required for synthesizing the amino acid tryptophan. When the bacteria's genome was broken in just one place, random mutations were capable of "fixing" the gene. But even when only two mutations were required to restore function, Darwinian evolution got stuck, apparently unable to restore full function.16 This is because it was more advantageous to delete a gene with low functionality or none than it was to continue to express it. This suggests that it is highly unlikely that the standard gene duplication model would produce new complex functions because gene duplicates are likely to be deleted before evolving some new function.
Another paper cited by Pearson deals with an unusual protein, an antifreeze protein, which acts more like "debris" in the cytoplasm to prevent freezing rather than performing a specific and complex function. This is not likely a viable model for explaining the origin of typical proteins.
Pearson's textbook makes no mention of controversies over the ability of natural selection and other evolutionary mechanisms to explain the origin of biological novelty. This controversy is well represented in the peer-reviewed technical literature, and it should be acknowledged in the textbook. Unfortunately, neither Pearson nor the panel of reviewers in Texas want students exposed to fundamental controversies over natural selection.
Indeed, elsewhere Pearson's textbook asserts that even given the entire history of the Earth, there is "plenty of time for evolution by natural selection to take place." (p. 466) But much evidence contradicts this claim.
Biochemist Michael Behe and physicist David Snoke have performed computer simulations and theoretical calculations showing that the Darwinian evolution of a functional bond between two proteins would be highly unlikely to occur in populations of multicellular organisms under reasonable evolutionary timescales. They found:
The fact that very large population sizes -- 109 or greater -- are required to build even a minimal MR feature requiring two nucleotide alterations within 108 generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
In other words, in multicellular species, Darwinian evolution would be unlikely to produce features requiring more than just two simultaneous mutations on any reasonable timescale or population size.
In 2008, Rick Durrett and Deena Schmidt sought to refute Behe in the journal Genetics with a paper titled "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution." But Durrett and Schmidt found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale."
The context of Pearson's claim makes its omission of this controversy even more egregious. Pearson makes this claim when discussing the evolution of whales, however the evolution of whales from land-mammals is thought to have occurred in less than 10 million years. This timespan allowed by the fossil record is far shorter than the 4.5 billion year age of the Earth, mentioned by the textbook in this section. Indeed, the research by Douglas Axe and Ann Gauger, as noted above, also shows that many modest evolutionary conversions of one protein to a closely related protein would likely require more coordinated mutations than could arise in the entire history of the Earth. In short, there is a genuine scientific controversy here, despite Pearson's claim that there is "plenty of time for evolution by natural selection to take place." The facts of the matter should have been disclosed to students.