[Note: For a more comprehensive defense of Ben Stein’s documentary Expelled: No Intelligence Allowed, please see: NCSE Exposed at NCSEExposed.org]

In Part 1 I explained how Alan Boyle and Sean B. Carroll unashamedly agree that scientists should keep “quiet” about their support intelligent design (ID). In this final response, I will discuss how the scientific evidence cited by Boyle does little to demonstrate the power of the neo-Darwinian mechanism. In Alan Boyle’s attack upon Expelled, he uses biologist Sean B. Carroll as his big gun scientist to attack intelligent design, touting Carroll’s book Making of the Fittest. In that book, Carroll argues that “[t]he argument for design by some external intelligence is eviscerated.”

Last year I wrote a response to Carroll showing that many of his arguments are frankly unimpressive. As I recounted at that time, “If the loss of function by turning off genes, and the usage of the same genes to build organs in vastly diverse organisms–a fact cited by design-proponents as supporting common design–are the best facts [Carroll] can muster against design, then it would appear that ID has very little to fear from the discoveries of evo-devo.”

Boyle claims that ID proponents are wrong to state that “that no new genetic information can possibly be created.” He purports to refute the claims of ID-proponents through the examples of “insertion” and “duplication”– but the examples he uses actually represent trivial increases in genetic “information,” and are not increases in meaningful genetic information, i.e. they do not generate new specified complexity. Boyle also claims that there can be “beneficial revision of genetic code.” Let’s check Boyle’s citation for that claim.

Boyle cites to a study which makes the trivial finding that some humans have slightly different biochemical or genetic mechanisms for digesting milk. Interestingly, the article assumes that “[h]uman adults were not designed to digest milk,” and therefore “[i]t took a genetic mutation to enable humans to tolerate lactose.” But what if human adults originally were designed to digest milk, and the fact that some humans have different biochemical mechanisms for lactose digestion, and that some have lost that ability, simply reflects variations or degeneration upon the original design? This evidence might show that evolution is only good at degenerating or destroying function rather than creating it.

Moreover, there are 2 reasons to understand that this study did not really document the evolution of something “new.” Note that the article states “human adults” cannot digest milk. This is because most children can digest milk, and lactose intolerance is typically caused by environmental conditions, i.e. the less milk you drink as you age, the more likely you are to become lactose intolerant. In fact, lactose intolerance takes place when your small intestine does not make enough lactase, an enzyme used to break down lactose in milk. So the difference between a lactose intolerant person and a lactose tolerant person is not the presence of a new enzyme, but the production of more of a pre-existing enzyme.

This study did not actually find evidence of the evolutionary acquisition of a new trait here, but rather found evidence for the prolonging of a pre-existing trait. And all humans produce lactase, so there has been no evolution of a new enzyme. Does this example represent the “evolution” of something impressive or new?

Boyle quotes biologist Sean Carroll asserting that when it comes to the validity of neo-Darwinism, “the ballgame is over.” This is a premature calling of the game. According to Boyle, “Evo-devo” has solved all the serious problems in evolutionary biology. (Keep in mind that in his book Making of the Fittest, the best “evo-devo” evidence for evolution that Carroll could muster were trivial examples of loss-of-function, like loss of spots on butterfly wings or loss of eyes on blind cave-fish, or an ID-favorite, the re-usage of the same genes in different organisms!) Nonetheless, Boyle argues that we have seen evolution produce new features: “Scientists are analyzing and comparing the genetic codes for hundreds of species, and the results are shedding new light on long-running posers such as the evolution of the eye or the cousinly relationship between elephants and manatees.” The truth that Boyle misses is that, as scientists analyze and compare the genetic codes for more and more species, they are finding that Phylogenetic trees are often in sharp conflict with one another. Again, let’s check Boyle’s references.

He cites an article that claims that “[s]cientists knew that elephants are related to modern aquatic creatures such as manatees.” This relationship has been claimed on the basis of DNA evidence, where Phylogenetic studies have compared the DNA of elephants and manatees and researchers suggest that they are closely related. But all that such studies have actually found is that elephants and manatees have similar DNA. Since their DNA might be similar due to functional requirements and not inheritance from a common ancestor, there’s no reason to presume that this data necessarily indicates common ancestry. But even if the similarities are derived from a common ancestor, the allegedly clear Phylogenetic relationship between elephants and sea cows seems to be the exception, and not the rule in systematics. De Jong (1998) observed that “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.”

Another severe Phylogenetic conflict is seen in Boyle’s reference regarding the “evolution of the eye” which opens by admitting, “While morphological comparisons of eye anatomy and photoreceptor cell types led to the view that animal eyes evolved multiple times independently, the molecular conservation of the pax6 eye-specifying cascade has indicated the contrary – that animal eyes evolved from a common, simple precursor, the proto-eye.” In other words, evolutionary scientists were surprised to use that very different types of eyes use the same regulatory genes to control eye growth, because the standard Darwinian phylogeny would never have predicted this. In fact, such unexpected genetic similarity may instead provide strong evidence for common design.

Indeed, some of the very research of Boyle’s big gun, Sean Carroll, also shows that Phylogenetic trees commonly conflict with one another. In 2006, Carroll co-authored a study which acknowledged that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” Such a selective use of data does not inspire confidence in the methods evolutionary biologists use to construct their phylogenetic trees.

The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The excuse that Phylogenetic trees are difficult to construct because of insufficient data is no longer feasible. The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.” Carroll of course is a committed neo-Darwinist. One assumption he does not re-evaluate is the assumption of common ancestry.

Carroll attempts to reconcile the genetic data with common descent by postulating rapid phases of evolution where there was insufficient time for enough differences in the DNA of different lineages to accumulate to allow modern biologists to resolve the evolutionary relationships. This becomes an exercise in neo-Darwinism explaining away the data. Perhaps the inability to construct robust phylogenetic trees using molecular data simply stems from the fact that neo-Darwinian common descent is wrong.

In the end, Boyle’s evidence for neo-Darwinism might be seen from a different angle–as evidence for intelligent design. Unfortunately, as I discussed in part 1, Boyle does not believe that scientists should not have the academic freedom to think such thoughts because they are too “wacky.”