Daniel Stern Cardinale is an evolutionary biologist on faculty at Rutgers University. We have engaged with Stern Cardinale a few times in the past, and he is for the most part one of the more thoughtful critics of intelligent design. In a recent video on his YouTube channel, “Creation Myths,” Stern Cardinale attempts a rebuttal of the argument from irreducible complexity, a concept first coined by Michael Behe and an argument of choice of mine for years.
Stern Cardinale proceeds to offer four alleged counterexamples — that is, empirical observations of irreducibly complex features supposedly evolving through evolution. Stern Cardinale appears to conflate the concept of irreducible complexity with the related concept of the waiting time problem. Typically, when we speak of a system as being irreducibly complex we mean that it is composed of a number of core structural components that cannot be reduced without eliminating the system’s overall function. The waiting time problem is a broader concept that deals with the prohibitive rarity of multiple co-dependent mutations arising by chance in a population. The extent to which this is a challenge to evolution will depend on the population size, generation turnover time, and average mutation rates. Viruses will be able to evolve more complex adaptations than bacteria, and bacteria will be able to evolve more complex adaptations than animals.
Here, I evaluate whether Stern Cardinale’s examples in fact count as reasonable counter-points to irreducibly complex systems.
Evolution of Citrate Metabolism
Stern Cardinale’s first counterexample is Richard Lenski’s famous long-term evolution experiment with Escherichia coli, in which it was observed that, after some 33,000 generations (15 years), bacterial cells evolved the ability to grow on citrate under aerobic conditions.1 Stern Cardinale notes that
that trait involved a number of what the researchers called priming mutations — mutations that were initially neutral. They didn’t do anything, but they were ultimately required for the Cit+ trait. Following those priming mutations, a gene duplication occurred and several additional mutations… All of these changes are required for the novel trait to appear. That’s an irreducibly complex trait. We watched it evolve in the lab.
But E. coli already possesses the ability to grow on citrate under anaerobic conditions, facilitated by a citrate transporter protein encoded by the gene citT. A 2,933 base pair stretch of DNA, containing the citT gene, underwent duplication. The result was that a copy of the hitherto unexpressed citT gene was placed under the control of the promoter of the adjacent gene, rnk, which as a consequence drove expression under aerobic conditions. This is a relatively simple change that does not require multiple co-dependent mutations to bring it about. Indeed, this instance of adaptation does not even require the origin of any novel genes and proteins, or even the modification of existing ones. The citT gene already codes for a citrate transporter which imports citrate into the cell in the absence of oxygen. The duplication event led to a loss of regulation of the citT protein such that it was expressed under both oxygen-rich and oxygen-deficient conditions, rather than in only oxygen-deficient ones.
Furthermore, the ability of the cells to grow on citrate under aerobic conditions was optimized by several other mutations.2 As Behe summarizes:
Even before the critical mutation occurred, a different mutation in a gene for a protein that makes citrate in E. coli degraded the protein’s ability to bind another metabolite, abbreviated NADH, which normally helps regulate its activity. Another, later, mutation to the same gene decreased its activity by about 90 percent. Why were those mutations helpful? As the authors write, ‘When citrate is the sole carbon source, [computer analysis] predicts optimal growth when there is no flux through [the enzyme]. In fact, any [of that enzyme] activity is detrimental.’ And if something is detrimental, random mutation will quickly get rid of it. Further computer analysis by the authors suggested that the citrate mutant would be even more efficient if two other metabolic pathways that were normally turned off were both switched on. They searched and discovered that two regulatory proteins that usually suppress those pathways had been degraded by point mutations; the traffic lights were now stuck on green.3
In other words, these mutations that optimized the ability of the cells to grow on citrate were in fact damaging. Since they supported the present needs of the organism, they were preserved by natural selection. As Behe argues at length in Darwin Devolves, the majority of mutations that are subject to positive selection are damaging rather than constructive, since there are far more ways to acquire an advantage by breaking something than there are ways to do so by building something. Readers may find interesting Behe’s response to Richard Lenski’s review of Darwin Devolves, which you can find here.
One researcher who has studied the evolution of citrate metabolism in E. coli is microbiologist Dr. Scott Minnich, a Senior Fellow with Discovery Institute’s Center for Science and Culture. Minnich’s own investigation into the molecular basis of the acquisition of the Cit+ trait supports Behe’s interpretation of these results rather than Lenski’s — that is, that “no new functional coded element was gained or lost, just copied.”
Lenski’s original paper had suggested that the adaptation process involved three steps — potentiation (involving initial neutral mutations), actualization (the promoter fusion event described above), and refinement (increasing expression of the dctA gene, encoding a transporter that facilitates recovery of lost succinate during citrate import).4 In the view of Lenski and his colleagues, the reason the trait took some 15 years to evolve is because of the need for the initial neutral mutations (“historical contingency”) that by themselves do not promote growth but are necessary for the later actualization event. Minnich’s lab demonstrated that the mutants observed by the Lenski lab could be isolated much more rapidly — within 14 days rather than 15 years (and in as few as a hundred generations rather than 33,000) — and that the length of time it took in Lenski’s experiment more probably reflects an artifact of the experimental conditions than a requirement of evolution.
Evolution of Tetherin Antagonism
Stern Cardinale’s next example is the evolution of tetherin antagonism in HIV-1. Tetherin is a protein that prevents newly formed viruses from escaping from an infected cell. The HIV-1 NL4.3 Vpu TM domain binds to the transmembrane helix of tetherin, ultimately leading to tetherin being disabled. Stern Cardinale cites a paper by Vian and Neil (2010), who “carried out an extensive mutagenesis of the HIV-1 NL4.3 Vpu TM domain to identify three amino acid positions…that are required for tetherin antagonism.”5
This is a particularly weak example, especially given that Stern Cardinale chooses to appeal to a retrovirus, which are particularly fast mutators. It would not be a surprise to me at all if a complex adaptation involving three substitutions arose in retroviruses. Much more interesting would be to see an example in higher life-forms, especially metazoans, which have much lower mutation rates, smaller population sizes, and longer generation turnover times. I am highly skeptical that a complex adaptation involving three co-dependent mutations has occurred among animals.
Furthermore, the authors of the paper cited by Stern Cardinale noted that, whereas mutating two of these three amino acid positions (namely, A14L and W22A) showed a marked defect, the A18L mutant showed only a minor defect. Thus, it is not even the case that all three amino acid positions are crucial for tetherin antagonism.
Evolution of Multicellularity
Cardinale also appeals to the appearance of multicellularity in previously unicellular algae, citing a paper by Herron et al. (2018) — “De novo origins of multicellularity in response to predation.”6 In the study, populations of the unicellular green alga Chlamydomonas reinhardtii were subjected to selective pressure by the introduction of the filter-feeding predator Paramecium tetraurelia. They found that two of the five populations developed multicellular structures. However, the multicellular populations lacked motility and the multicellular structures did not evolve multiple cell types. Moreover, as the authors of the paper note, “The ability of wild-type C. reinhardtii to form palmelloids [i.e. multicellular structures] suggests that the founding population in our experiment already possessed a toolkit for producing multicellular structures.”
While the strains that evolved in the experiment are obligately multicellular (meaning that being composed of multiple cells is an essential and permanent part of their life cycle), the authors suggest that the genetic basis of the evolved multicellularity phenotype “involves the co-option of a previously existing plastic response.” If this is the case, the authors note, “the shift from a primarily unicellular (but facultatively multicellular) to an obligately multicellular life cycle may have required only a change from facultative to obligate expression of the genes involved in palmelloid formation.” In other words, the transition from being able to exist as single-celled organisms, while forming multicellular structures under certain conditions, to being permanently multicellular may have involved a shift from being able to turn the relevant genes on or off to the genes being permanently locked on. See also this short article by Michael Behe where he addresses a similar paper.
Evolution of Placenta in Lizards
Finally, Stern Cardinale also points to the transition in lizards from laying eggs to live birth, citing a paper from 2012 by Blackburn and Flemming.7 Of his four examples, this one is, in my view, the most compelling example of a complex trait. As Stern Cardinale himself notes, however, this case is the only one of his examples that has not been directly observed. Stern Cardinale, therefore, assumes that such a trait arose by unguided processes.
Stern Cardinale anticipates this rejoinder, and responds, “If they say that these lizards, and there’s only a handful of species like this… they just signed up for a species level creation model, since the vast majority of lizards don’t have this ability at all. If they had some remnant of it and they lost it, we would see that in their development. And we don’t.” But Stern Cardinale has created a false dichotomy — either this trait is the product of unguided evolution or you are committed to species-level creation. But this does not follow at all. ID does not even necessarily commit one to a denial of common descent. The core claim of ID is more minimal than that — namely, that undirected processes are inadequate to create complex integrated systems. This leaves open the possibility of some sort of front-loaded design in the ancestral lizard. Even if one postulates that these particular species of lizards were created separately, this does not commit one to positing that every individual species on the planet was independently created. The question comes down to which is of the competing explanations is more ad hoc — that a designer created these species of lizards separately or that this complex feature arose by unguided natural processes.
A Challenge to Daniel Stern Cardinale
I invite Stern Cardinale to attempt to provide a plausible evolutionary explanation of the origins of a complex system such as DNA replication, which in my opinion is one of the strongest examples of irreducible complexity. I give a brief summary of the DNA replisome in this article.
This example represents a particularly strong case for at least two reasons. First, given the primitiveness of the DNA replisome, it is far more difficult to envision any kind of co-optation scenario than it would be for a system that arose much later, such as bacterial flagella. With the flagellum, one can at least point to alternative functions that might be performed by a number of the flagellar components (such as the Type III Secretion System). However, with DNA replication, it is unclear what other systems any of the components might be co-opted from — since any other system would need to have arisen after the origins of DNA replication.
Second, genome duplication is a prerequisite of differential survival, which is necessary for the process of natural selection to even work. Thus, one can hardly appeal to natural selection to account for the origins of DNA replication without assuming the existence of the very thing that one is attempting to explain. It is difficult to envision a viable replication system that is simpler than the DNA replisome. And no, the RNA world thesis isn’t going to work for reasons that I and others have discussed at length elsewhere. Even aside from the inherent instability of RNA, there is a physical limitation to the capability of RNA to self-replicate, since RNA forms complementary base pairs to fold back on itself. This means that part of the molecule no longer presents an exposed strand that can serve as a template for copying.
Irreducible Complexity Remains a Challenge to Evolution
Despite Stern Cardinale’s objections, irreducible complexity remains a formidable challenge to evolutionary theory. To date, nobody has proposed any plausible stepwise pathway to the origin of any of the major irreducibly complex systems that Behe, I, and others, have championed. If Stern Cardinale takes up my challenge above to offer a plausible evolutionary explanation of the origins of the DNA replisome, this will be a significant step towards resolving our concerns.
Notes
- Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature. 2012 Sep 27;489(7417):513-8. doi: 10.1038/nature11514. Epub 2012 Sep 19. PMID: 22992527; PMCID: PMC3461117.
- Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife. 2015; 4:e09696.
- Behe MJ, Darwin Devolves: The New Science About DNA That Challenges Evolution (HarperOne, 2020), 139.
- Blount ZD, Borland CZ, Lenski RE. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):7899-906. doi: 10.1073/pnas.0803151105. Epub 2008 Jun 4. PMID: 18524956; PMCID: PMC2430337.
- Vigan R, Neil SJ. Determinants of tetherin antagonism in the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein. J Virol. 2010 Dec;84(24):12958-70. doi: 10.1128/JVI.01699-10. Epub 2010 Oct 6. PMID: 20926557; PMCID: PMC3004320.
- Herron MD, Borin JM, Boswell JC, Walker J, Chen IK, Knox CA, Boyd M, Rosenzweig F, Ratcliff WC. De novo origins of multicellularity in response to predation. Sci Rep. 2019 Feb 20;9(1):2328. doi: 10.1038/s41598-019-39558-8. PMID: 30787483; PMCID: PMC6382799.
- Blackburn DG, Flemming AF. Invasive implantation and intimate placental associations in a placentotrophic African lizard, Trachylepis ivensi (scincidae). J Morphol. 2012 Feb;273(2):137-59. doi: 10.1002/jmor.11011. Epub 2011 Sep 28. PMID: 21956253.