Evidence for the Evolutionary Model

The Evolutionary Process ...accounts for biological change over time and causes the proliferation of life


(p.20-21)                 The pdf of the entire book, with Ray's 50 page introduction, can be found here.

      Darwin theorized that all living things evolved from simpler life forms through an undirected process of mutations and natural selection. If a mutation (a “copying error”) occurred in the genes, and it provided the creature some survival advantage, this benefit would be passed on to its offspring through the process of natural selection.

      If Ray means ‘undirected’ as in ‘undirected by an intelligent force,’ he is correct. But if he means it as in ‘random,’ he is incorrect. Although mutation is random, natural selection is the nonrandom change in allele frequencies in a population, with time, as per environmental pressures on genetic configurations that make the organisms in that population either more or less able to survive and to compete for resources.




      Species do of course change over time by adaptation and natural selection, but some disagree that this indicates Darwinian evolution. For example, in looking at the variety available within dogs—from the tiny Chihuahua to the huge Great Dane—some would label this simply microevolution. Small-scale variations occur within a kind, though nothing new actually comes into being (“evolves”) in microevolution. While dogs can have incredible differences, all are still dogs. Within the horse family are the donkey, zebra, draft horse, and the dwarf pony, yet all are horses.

      It is always interesting to see the process of dog breeding used as part of an argument against the evolutionary model, given how well it actually supports it. Dog breeding is a form of artificial selection. Based on the desirability of given traits, a breeder decides the size and nature of the contribution given dogs make to his or her small, segregated population. By doing so, this acts as a drastic environmental change. The effect is a rapid change in phenotype, relative to the usual timescales of speciation in the evolutionary model. Over the past few centuries, more than 400 breeds of domestic dogs have been created—displaying a vast array of phenotypic variation (Young & Bannasch, n.d.). Since the timescale is so small, the selection is predominantly acting on preexisting genotypic variation, rather than on new variation introduced by mutation. This is confirmed by the large genetic variation observed in these dog breeds (Parker, Sutter, & Ostrander, n.d.), and by the extremely small genetic difference between them and the grey wolves from which they recently diverged (Savolainen, n.d.; Leonard, Vila, & Wayne, n.d.). What dog breeding demonstrates is how large genetic variation in even phenotypically uniform populations correlates to an enormous range of potential phenotypes. This allows populations to adapt to new environmental pressures, even when the change is rapid and drastic. Rather than simply being wiped out, the population can persist long enough for further adaptation by natural selection acting on the genetic variation slowly introduced by mutation. Populations with larger variation have more of a built-in safeguard against being decimated by a changing environment.


There are tremendous variations among humans—from Asian to African to Aboriginal to Caucasian— but all are within the same species, Homo sapiens.

      Bringing up human genetic variation is ironic, considering how it runs contrary to what Ray wrote in his section on DNA similarities about comparative genetic research between chimpanzees and humans. As I mentioned in my response to that section, regardless of how comparatively high or low human genetic variation is, it is observed to be significantly lower than that of chimpanzees (Stone et al., 2002; Fischer et al., 2004; Chimpanzee Sequencing and Analysis Consortium, 2005); as much as four time less (Kaessmann, 1999).That Ray mentioned such inter-species variability here, yet remained previously silent on it demonstrates his inconsistency and ignorance of the subject.



      Darwin’s theory of evolution is instead based on the concept of macroevolution. This is the inference that the small changes seen in adaptation (these variations within species) accumulate and lead to large changes over long periods of time. In macroevolution, one kind of creature (such as a reptile) becomes another kind of creature (such as a bird), requiring the creation of entirely new features and body types. Evolution opponents argue that this would be a bit like observing a car going from 0 to 60 mph in 60 seconds, and inferring that it can therefore go 0 to 6,000 mph in 100 minutes—and become an airplane in the process.

      Admittedly, this puts a tremendous responsibility on mutations to accidentally create complex new body parts, and on natural selection to recognize the benefit these new parts will eventually convey and make sure the creatures with those new parts survive. As Stephen J. Gould explains:

      The essence of Darwinism lies in a single phrase: natural selection is the creative force of evolutionary change. No one denies that selection will play a negative role in eliminating the unfit. Darwinian theories require that it create the fit as well.34

       Firstly, Ray’s assertion that mutations somehow randomly happen to “create complex new body parts,” and that natural selection merely insures their persistence in the populations upon somehow “[recognizing their] benefit” is so outlandish a misrepresentation of the evolutionary model, that it is hard to believe he has any real understanding of the information pertinent to the model that he reports in this introduction. The following portions of my response to similar assertions Ray has made in his sections on vestiges and DNA similarities should adequately explain how mutation and natural selection really work:

      Proteins do more than just catalyze reactions in an organism—they bind and interact with many other proteins and chemicals, as well as provide much of the organism’s structure. Mutations in genes that code for these proteins change the way the proteins interact, the way they arrange into structures, and the way they catalyze reactions. As in the example above, a mutation can change the efficiency of an enzyme in binding to its substrates and its rate of catalyzation; but it can also cause the enzyme to bind with additional substrates or to different ones all together. Regardless of a given protein’s roll in the organism, mutation can either change or replace the way it interacts, reacts, or arranges.

      When the replaced function is necessary, and when there is only one copy of the gene that codes for the protein, mutations are often detrimental. But when the gene is a duplicate, resulting from a duplication of chromosomal DNA, mutations are often neutral, as the original function is retained in the other copy. Further mutations to duplicate genes acted on by natural selection can then cause them to form into entirely new ones, allowing organisms and their genomes to grow in size and complexity by purely natural means. There are several processes by which this occurs:

  1. A gene’s domains are rearranged (Moore et al., 2008).
  2. A new domain is formed when point mutations or insertions within an intron cause the acquisition of a splice donor and splice acceptor, witch forms a novel alternatively splicable exon (Schmidt & Davies, 2008).
  3. A frameshift mutation forms a new gene by causing the resulting polypeptide chain to be comprised of entirely different amino acids (Okamura, 2006).
  4. Mutations in random genetic sequences can convert them into genes, as observed when the D2 domain of coliphage fd's minor coat protein g3p (crucial for infectivity) was replaced with a random sequence of 139 amino acids and subjected to random mutagenesis. A 240-fold increase in fitness was observed after only 7 generations, eventually reaching a maximum of a 17,000-fold increase (Hayashi et al., 2006).

       So how does natural selection achieve such a feat? Well, all living organisms reproduce. They also pass on a large amount of the information that makes their configuration what it is to their offspring. The third critical trait of living things is that there is a consistent increase in variability caused by mutation from each generation to the next. And finally, living organisms exist in populations for finite amounts of time, and must stave off their demise while competing for limited resources. All of these principles together have an interesting result. As new variation is introduced by mutation, modifications to proteins, such as the way the catalyze reactions and configure to form anatomical structures, that allow for more efficient performance of tasks in the organisms’ environment, the organisms become either more or less able to both survive and compete for resources (thrive) in their environment. The measure of this efficiency is called fitness. Configurations that increase fitness make the organism more able—and thus more likely—to make significant contributions to their populations’ gene pools. This increases the frequencies of the alleles with those configurations, with time. Likewise, the frequencies of alleles with configurations that decrease fitness decrease, with time. This process is called natural selection. Since the differences between species are observed to be structural and functional modifications that increase fitness in the organisms’ environments, this is powerful evidence that these differences were the result of decent with modification caused by mutation and natural selection.


       Secondly, Ray also shows that he doesn’t even understand the quotes he cites on evolutionary theory. That quote by Gould affirms that in the evolutionary model, natural selection is the primary creator of structural and functional change. That directly contradicts Ray’s misinformed assertion in the preceding sentence that this roll is filled by mutation, and that natural selection merely acts on the organs created ex nihilo by mutation.


      Scientific advances since Darwin’s day have shed light on how mutations and natural selection work, though the findings were not always as expected.

      This is true. It is also true that, as has been repeatedly shown, those advances thoroughly confirm that the effect of natural selection on preexisting and new mutational genetic variation accounts for biological change over time and causes the proliferation of life.

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My References

Chimpanzee Sequencing and Analysis Consortium. "Initial sequence of the chimpanzee genome and comparison with the human genome." Nature 437.7055 (2005): 69-87. <http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html>.

Fischer, A., V. Wiebe, S. Paabo, and M. Przeworski. "Evidence for a Complex Demographic History of Chimpanzees." Molecular Biology and Evolution 21.5 (2004): 799-808. <http://mbe.oxfordjournals.org/cgi/content/full/21/5/799>.

Hayashi, Y., T. Aita, H. Toyota, Y. Husimi, I. Urabe, and T. Yomo. "Experimental rugged fitness landscape in protein sequence space." PLoS One 1.E96 (2006). <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1762315/>.

Kaessmann, H., V. Wiebe, and S. Pääbo. "Extensive nuclear DNA sequence diversity among chimpanzees." Sciencehttp://www.sciencemag.org/cgi/content/full/286/5442/1159>. 286.5442 (1999): 1159-162. <

Leonard,  J. A., C.  Vila, and R. K. Wayne. "From Wild Wolf to Domestic Dog." In: Ostrander, E. A., U. Giger, and K. Lindblad-Toh, eds. The genome of the domestic dog. New York: Cold Spring Harbor, 2006. 95–118.

Moore, A. D., A. K. Bjorklund, D. Ekman, E. Bornberg-Bauer, and A. Elofsson. "Arrangements in the modular evolution of proteins." Trends in Biochemical Sciences 33.9 (2008): 444-51. <http://www.ncbi.nlm.nih.gov/pubmed/18656364>.


Okamura, K., L. Feuk, T. Marquès-Bonet, A. Navarro, and S. W. Scherer. "Frequent appearance of novel protein-coding sequences by frameshift translation." Genomics 88.6 (2006): 690-97. <http://tinyurl.com/lds4jg>.

Parker, H. G., N. B. Sutter, E. A. Ostrander. "Understanding Genetic Relationships Among Purebred Dogs: The PhyDo Project." In: Ostrander, E. A., U. Giger, and K. Lindblad-Toh, eds. The genome of the domestic dog. New York: Cold Spring Harbor, 2006. 141–158.

Savolainen, P. "mtDNA Studies of the Origin of Dogs." In: Ostrander, E. A., U. Giger, and K. Lindblad-Toh, eds. The genome of the domestic dog. New York: Cold Spring Harbor, 2006. 119–140.

Schmidt, E. E., and C. J. Davies. "The origins of polypeptide domains." Bioessays 29.3 (2007): 262-70. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994825/?tool=pubmed>.

Stone, A. C., R. C. Griffiths, S. L. Zegura, and M. F. Hammer. "High levels of Y-chromosome nucleotide diversity in the genus Pan." Proceedings of the National Academy of Sciences 99.1 (2002): 43-48.  <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117511/?tool=pubmed>. 

Young, A., D. Bannasch. "Morphological variation in the dog." In: Ostrander, E. A., U. Giger, and K. Lindblad-Toh, eds. The genome of the domestic dog. New York: Cold Spring Harbor, 2006. 47–65.

Ray’s Reference

30.   Stephen J. Gould, “The Return of Hopeful Monsters,” Natural History, vol. 86, June/July 1977, p. 28.