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Adam and the Genome — Review and Conclusion

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Adam and the Genome

We’ve been reviewing the book Adam and the Genome by biologist Dennis Venema, a theistic evolutionist associated with BioLogos. See “A Professor’s Journey Away from Intelligent Design” for Ann Gauger’s comments on why the topic merits this attention.

At the beginning of this series, we observed that many of the topics covered in Adam and the Genome are not relevant to whether Adam and Eve existed as the progenitors of the human race. Yes, some of the 13 major classes of scientific evidence and arguments discussed by Venema are relevant to the question of a common ancestry linking apes and humans, but the book spends little time saying what that has to do with Bible’s first couple.

So, in retrospect, where does the evidence stand? Here’s a summary: Venema’s main claims in light of the relevant science.

Claim 1: Intermediate whale fossils demonstrate that whales evolved from land mammals.

What does the evidence say? Converting a fully terrestrial mammal to a whale assumes a large number of complex morphological changes. These changes would require numerous mutations to arise. The supposed evolutionary “intermediates” appear only a short period of time before fully aquatic whales appear in the fossil record. There is not enough time in the fossil record for truly aquatic whales to evolve from land mammals via blind evolutionary mechanisms. For more details, please see “Adam and the Genome and Whale Fossils.”

Claim 2: There exists a high degree of genetic similarity between humans and apes.

What does the evidence say? Many studies show that the sequence of amino acids is vital to protein functionality. This strongly suggests functional reasons for the amino acid sequences of human and ape proteins, and shows their similarities can be explained as being due to functional requirements. For more details, please see “Adam and the Genome and Human-Ape Genetic Similarity.”

Claim 3: There exist large-scale genomic similarities between human and ape genomes (known as “synteny”).

What does the evidence say? Many studies have shown that large-scale genomic architecture is vital to genome functionality. This strongly suggests functional reasons for the organization of human and ape genomes, and shows their similarities can be explained as being due to functional requirements. For more details, please see “Adam and the Genome and Synteny.”

Claim 4: There exist shared “nonfunctional” pseudogenes between humans and chimps and other organisms.

What does the evidence say? Much evidence suggests many pseudogenes are functional, and not “nonfunctional” genes. This means they can be explained by common design just as well as by common descent. Moreover, hotspot mutations can explain shared “breakage” mutations in some cases. But perhaps most importantly, we haven’t studied the vast majority of pseudogenes well enough to have determined that they are nonfunctional. Venema assumes they are non-functional when he doesn’t really know that is the case. For more details, please see “Adam and the Genome and ‘Nonfunctional’ Pseudogenes.”

Claim 5: The high degree of human genetic diversity refutes Adam and Eve as the initial parents of humanity.

What does the evidence say? The jury is still out on this one, but serious questions have been raised against Venema’s arguments. Geneticist Richard Buggs evaluated Venema’s arguments and found that they don’t necessarily rule out the possibility that humanity arose from a single pair. Moreover, when Buggs courteously but reasonably requested that Venema provide a scientific citation for his claim that humans evolved from an ancestral population of ~10,000 individuals rather than a short, sharp bottleneck of two parents (Adam and Eve), Venema was unable to provide such a citation, seriously undermining his arguments on this point. Biologist Ann Gauger looked at one of the initially strongest arguments against Adam and Eve from human genetic diversity (HLA genes) and found the evidence is compatible with our descending from an initial couple. ID proponents are actively working on population genetics models and simulations to test these questions. Venema’s suggestions that ID proponents are incompetent or unable to evaluate this evidence are simply false. Two peer-reviewed papers and a book chapter have already been published in the ID-community related to modeling these questions, and early evidence suggests that an initial pair is capable of explaining human genetic diversity. More work is forthcoming, but Venema’s conclusions about Adam and Eve are premature. For more details, please see “Adam and the Genome and Human Genetic Diversity,” “Adam and the Genome and Citation Bluffing,” and “Adam and the Genome and ‘Predetermined Conclusions’.”

Claim 6: Hominid fossils show humans evolved.

What does the evidence say? The fossil evidence does not show the gradual evolution of humans from ape-like precursors. Instead, our genus Homo appears abruptly in the fossil record and is highly distinct from previous ape-like forms, such as the Australopithecines. For more details, please see “Adam and the Genome and Hominid Fossils.”

Claim 7: Neanderthal and Denisovan DNA shows they are related to humans.

What does the evidence say? Yes, there is a high degree of genetic similarity between humans and other members of the genus Homo, and these may very well indicate our relatedness. But this evidence of genetic similarity surprised no one in the Darwinian evolutionist or ID camps. Common design could also explain these similarities. In any case, this evidence is entirely equivocal when it comes to Adam and Eve. For more details, please see “Adam and the Genome and Neanderthal Cave Art.”

Claim 8: Mitochondrial Eve and Y-chromosome Adam probably weren’t an actual couple.

What does the evidence say? The evidence suggests that all humans trace back to a single female and a single male ancestor. Whether the molecular clock evidence suggests these two individuals lived at the same time is another question, although some Darwin skeptics (such as Reasons to Believe) argue that they could have lived contemporaneously. Whether molecular clock data is trustworthy enough to make a precise estimate on these issues is still another matter. For more details, please see “Mitochondrial Eve and Y-Chromosome Adam, and Adam and the Genome.”

Claim 9: Proteins can readily evolve new binding sites, structures, functions, and even folds through blind evolutionary processes — and this refutes arguments for intelligent design.

What does the evidence say? Venema presents three main examples allegedly demonstrating the evolution of a new complex protein and refuting ID:

  • p24-2: Venema presents evidence of a five amino acid difference between p24-2 and another fruit fly gene, Éclair. That’s the raw data. But he presents no evidence showing the differences arose via Darwinian evolution or any other blind mutational mechanism.
  • Nylonase: This is Venema’s centerpiece example of a new gene — allegedly with a new protein fold to boot — evolving spontaneously, via a frameshift mutation. Ann Gauger returned to the original literature on nylonase and thoroughly debunked Venema’s arguments. She has shown that nylonase did NOT arise through a frameshift mutation, but rather, it evolved from a highly similar protein, with a similar folding structure and a similar form of activity. Venema has dramatically overstated or misstated the degree of novelty entailed in the origin of nylonase. When Gauger wrote her rebuttal, Venema did not contest her central points.
  • Lambda phage: Michael Behe reviewed this study when it was first published and, despite Venema’s claims, most likely no new binding site arose and it was only a modification of a pre-existing function. Other elements of this study entail loss of function.

For more details, please see “Adam and the Genome and the Evolution of Novel Proteins.”

Claim 10: Doug Axe’s research published in Journal of Molecular Biology seems to show the difficulty in evolving new protein folds, but criticism of this idea demonstrates otherwise.

What does the evidence say? Venema tries to take Stephen Meyer to task for applying Axe’s research broadly and making an inference that it shows new protein folds are, as a general matter, difficult to evolve. He tries to split Axe and Meyer, implying Axe only applied his results narrowly to the origin of beta lactamase whereas Meyer supposedly misused Axe’s research and misled readers by applying it broadly to the general evolvability of new protein folds. But Axe’s research, which was peer-reviewed, specifically explained and justified why it bore on the unevolvability of proteins in general. Thus, Meyer did not misuse Axe’s paper or its conclusions. Moreover, Axe’s broad conclusions follow other similar technical papers that did similar research, came to similar conclusions about the rarity of functional protein sequences, and applied their results broadly. It is Venema’s accusations against Meyer that are out of step with the literature, not Meyer’s claims. For more details, please see “Adam and the Genome and Doug Axe’s Research on the Evolution of New Protein Folds.” 

Claim 11: The direct templating of RNA and amino acids via biochemical attraction helps explain the evolution of the genetic code.

What does the evidence say? ID proponents Stephen Meyer and Paul Nelson wrote a peer-reviewed technical paper that thoroughly evaluated and critiqued the direct templating model for the origin of the genetic code. Rather than discussing their paper head-on, Venema focuses on a brief treatment of the topic in Meyer’s book Signature in the Cell and only briefly mentions Meyer and Nelson’s technical paper in an endnote buried at the back of the book. In that endnote, Venema fails to address the bulk of Meyer and Nelson’s arguments, and makes an unbacked assertion that doesn’t establish Meyer and Nelson were wrong. For more details, please see “Adam and the Genome and the Evolution of the Genetic Code.”

Claim 12: Whole genome duplication (WGD) events in our genome explain how new genes evolve.

What does the evidence say? At best, the evidence Venema cites explains how genes can be duplicated but the evidence provides no explanation for how gene duplicates might have acquired a new function. This is the key issue regarding gene duplication, and Venema does not address it.  Evolutionary explanations for the origin of new genes cannot simply rely upon duplication, for there must be duplication followed by recruitment to a new function. Venema provides no calculations showing that it is likely that the new genes produced in a WGD event would be recruited to a new function. For more details, please see “Adam and the Genome and Whole Genome Duplication Events.”

Claim 13: Genes can arise “de novo” from non-coding DNA.

What does the evidence say? Venema claims that de novo genes in humans don’t derive from other functional genes but rather from noncoding DNA sequences. He suggests Steve Meyer isn’t aware of this argument even though Meyer discusses the argument in multiple places in Darwin’s Doubt. In any case, there may be functional reasons for similarities between genes and noncoding sequences that don’t imply a gene suddenly sprang into being by blind and unguided mutational processes. Moreover, Venema never provides any calculations to show that the naturalistic accounts of de novo gene origin that he’s promoting are feasible. This is consistent with all other proponents of de novo genes — they never evaluate the feasibility of their highly unlikely evolutionary stories. For more details, please see “Adam and the Genome and the Mysterious Origin of De Novo Genes.”

In sum, Adam and the Genome fails to make a convincing case against Adam and Eve. But perhaps of greater interest, it fails even more so to make a case against intelligent design.

Image: Adam and Eve, Doge’s Palace, Venice, via Wikicommons.