In a previous post, I noted that the theistic evolutionist physicist Stephen Barr has a piece at First Things which greatly overstates the supposed “gradual” nature of human origins. One of Barr’s main sources that he praises in his article is a book by a Catholic theistic evolutionist, Daniel Kuebler, professor of biology at Franciscan University of Steubenville. Barr calls Kuebler’s book, Darwin and Doctrine: The Compatibility of Evolution and Catholicism, “An excellent new book” which explains “the science of evolution, helpfully clearing up common misconceptions along the way.”
Kuebler’s book has many theological aspects which I won’t dare comment upon since I’m not Catholic. However, I can say that a lot of the scientific arguments that Kuebler enlists to advocate for evolution are old-school arguments for that have been dealt with and refuted for years. I’ll review many of these issues below — but because we’ve addressed so many of them multiple times before, much of my response will simply be quoting from or linking to previous articles. And please know that while I’ll show a lot of Kuebler’s argument are flawed, it’s nothing personal. By all accounts Professor Kuebler is a decent person who is seeking truth like the rest of us. But if you’re going to accept evolution, at least do it for good reasons.
Universality of the Genetic Code
Professor Kuebler uses a classical argument for common descent, citing the universality of the genetic code which he calls “probably the best piece of evidence for universal common descent” (p. 107). Here’s what Kuebler writes:
There exists a good deal of circumstantial evidence that all life forms are indeed related via common descent. The most “universal” piece of evidence is the fact that all life forms use basically the same genetic code. (p. 106)
The problem with this argument is that it’s not true. As the NCBI website explains, there are dozens of variants of the genetic code. Kuebler barely gives the slightest hint that these variant genetic codes exist, burying in a footnote the acknowledgment that “There are a few organisms that have slight modifications to the genetic code.” (p. 107)
But of course it is true that the vast majority of organisms do use the same genetic code. Kuebler says there’s no good reason for this, writing:
while the universal genetic code is quite robust, there are a number of other possible genetic codes that would work just as well as the one found in virtually all cells; in fact some alternative versions might work even better. Just like there are many different human languages, most of which function quite well, there could have been many different “languages” of the genetic code. The fact that nearly all organisms share this particular one, even though there are many that would have fit the bill, suggests that the code originated in a common ancestor and was inherited by all subsequent life forms via common descent. (p. 107)
In other words, since there’s no good reason for all these organisms to use the genetic code we use, the explanation must be common ancestry. It’s a classic argument that inefficient and clumsy evolution did it.
But there are very good reasons to use the genetic code found in most life forms. As Jonathan McLatchie explains:
this arrangement is far from arbitrary. Indeed, the genetic code found in nature is exquisitely tuned to protect the cell from the detrimental effects of substitution mutations. The system is so brilliantly set up that codons differing by only a single base either specify the same amino acid, or an amino acid that is a member of a related chemical group. In other words, the structure of the genetic code is set up to mitigate the effects of errors that might be incorporated during translation (which can occur when a codon is translated by an almost-complementary anti-codon).
There are a variety of other special properties about our genetic code which McLatchie documents here, here, here, and here.
“Life’s Solution”
By the way, Kuebler’s citation of the claim that “some alternative versions” of the genetic code “might work even better” is to chapters 1 and 2 of Simon Conway Morris’s book Life’s Solution. It’s a great book but his citation, referencing the work of Steven Freeland and Laurence Hurst, actually shows how efficient the standard genetic code is:
They write: ‘the natural genetic code shows startling [my emphasis] evidence of optimization, two orders of magnitude higher than has been suggested previously. Though the precise quantification used here may be questioned, the overall result seems fairly clear: under our model, of 1 million random variant codes produced, only 1 was better . . . than the natural code- our genetic code is quite literally “1 in a million”.’ (p. 17)
Conway Morris suggests that “there is also a sense that given a world of DNA and amino acids, then perhaps the genetic code we know is more or less an inevitable outcome” (p. 18). I see no evidence from Conway Morris’s book that there are other codes that are remarkably better than the universal code.
Regarding the variant codes, in his paper “On the Origin of the Codes: The Character and Distribution of Variant Genetic Codes is Better Explained by Common Design than Evolutionary Theory,” Winston Ewert found that variant often correlate with the organism’s lifestyle, suggesting that these too are explained by intelligent design:
The near universality of the genetic code is frequently cited as evidence for universal common ancestry. On the other hand, critics of universal common ancestry frequently point to exceptions to the universal code as evidence against it. However, there has never been a comprehensive investigation into the character and distribution of variant genetic codes and their implications for the debate over universal common ancestry. This paper develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery. We found that these two sources of variant codes can be distinguished by considering organismal lifestyle, taxonomic rank, evolutionary feasibility, codon rarity and complexity of distribution. These different approaches to distinguishing the codes give highly correlated results, demonstrating impressive explanatory power for our framework. In contrast, we find that evolutionary theory has difficulty explaining the character and distribution of variant genetic codes.
Thus, to the extent the code is re-used widely in different organisms, or varies in different organisms, it can be explained by intelligent design.
Reusage of Biomolecules and Phylogenetic Trees
Kuebler offers another argument for universal common descent — namely the reusage of the same biomolecules and our ability to construct phylogenetic trees. He writes:
While the genetic code is probably the best piece of evidence for universal common descent, there are other pieces of evidence as well. All cells use double-stranded DNA molecules to store information, they are all bound by similar types of lipid membranes, and they share many of the same basic pathways for producing and using energy in the form of ATP molecules and for performing other key life-sustaining reactions.
Ironically, in my chapter “Universal Common Descent: A Comprehensive Critique” in the volume Theistic Evolution: A Scientific, Philosophical, and Theological Critique, I both anticipated and answered this same line of argument:
Perhaps the most common argument for universal common ancestry encountered by students in college-level biology textbooks is the universality of the genetic code — the claim that all life uses the nucleotide triplets to encode the same amino acids. However, the genetic code isn’t universal; many variants in the genetic code are known among various organisms.
If the universality of the genetic code provides evidence for universal common ancestry, does its non-universality count as evidence against? Whatever the answer, despite the variants the vast majority of organisms do use the same “standard code,” and all life forms employ similar types of biomolecules, such as nucleotides and proteins. Are such widespread biomolecular similarities evidence for common ancestry? A 2010 paper in Nature, “A formal test of the theory of universal common ancestry,” argued yes:
“[T]he ‘universal’ in universal common ancestry is primarily supported by two further lines of evidence: various key commonalities at the molecular level (including fundamental biological polymers, nucleic acid genetic material, L-amino acids, and core metabolism) and the near universality of the genetic code.”
The article’s author, evolutionary biochemist Douglas Theobald, concluded that universal common ancestry is the “best” explanation for these biomolecular similarities. But “best” compared to what? Theobald tested universal common ancestry against the exceedingly unlikely hypothesis that living organisms independently evolved the same biomolecules and sequences by sheer “chance.” Universal common ancestry only appeared compelling because it was being compared to a preposterous null hypothesis. As critics writing in Biology Direct observed:
“Cogniscenti cringed when they saw the Theobald paper, knowing that ‘it is trivial’. It is trivial because the straw man that Theobald attacks in a text largely formulated in convoluted legalese, is that significant sequence similarity might arise by chance as opposed to descent with modification.”
True, universal common ancestry is one possible explanation for genetic similarities — but are there other possible explanations? Indeed. Intelligent agents frequently re-use the same parts in different designs to meet functional requirements, such as re-using wheels on cars and airplanes, or re-using the key computer codes in different versions of Microsoft Windows. As Paul Nelson and Jonathan Wells observe:
“An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently. … If we suppose that an intelligent designer constructed organisms using a common set of polyfunctional genetic modules — just as human designers, for instance, may employ the same transistor or capacitor in a car radio or a computer, devices that are not “homologous” as artifacts — then we can explain why we find the ‘same’ genes expressed in the development of what are very different organisms.”
Thus, common design — the intentional re-use of a common blueprint or components — is a viable explanation for the widespread functional similarities among the biomolecules found in different types of organisms. Universal common ancestry is not the only viable explanation.
(Indeed, contra Theobald’s arguments for universal common ancestry, not all fundamental biomolecules are universal among organisms. As one paper found, “several core components of the bacterial [DNA] replication machinery are unrelated or only distantly related to the functionally equivalent components of the archaeal/eukaryotic replication apparatus,” leading them to suggest “DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.” Even more striking, another paper compared the genomes of 1000 different prokaryotic organisms and found that “of the 1000 genomes available, not a single protein is conserved across all genomes.”)
ID theorists have also recognized that the efficient design of biological molecules and pathways can serve as a superior explanation, compared with common descent, for why they are re-used.
“Reverse Systems Engineering”
Glycolysis is a key and universal metabolic pathway that performs vital functions such as producing energy or helping to synthesize life’s building blocks. Biochemist Emily Reeves and engineer Gerald Fudge published a peer-reviewed study that applied ID-based “reverse systems engineering” to understand why glycolysis works the way it does:
biological systems exhibit features that are traditionally associated with good top-down requirements-driven system engineering practices, such as modularity, optimality, robustness, common protocols, and design reuse.
They concluded that although “the near-uniformity of central metabolism across life has traditionally been attributed solely to universal common descent,” nonetheless “from a systems engineering perspective” this “uniformity might be expected” due to its functional elegance: Glycolysis pathways “maximize thermodynamic efficiency” and use “recyclable waste products” which “simplify maintenance of ecosystem homeostasis.”
In other words, the more we look at biology, the more we realize that there are good reasons why things are designed as they are. Evolutionists like Kuebler stop short of investigating these good design principles that are nearly always built into biology. Instead, they simply assume that common ancestry is the reason for reusage, and miss out on exciting ID engineering-based investigations.