HUMAN ORIGINS AND JUNK DNA UPDATE

Does the Scientific Evidence Support Evolutionary Models of Human Origins? Casey Luskin June 12, 2023 Author’s note: In a previous post I introduced my paper, “Comparing Contemporary Evangelical Models Regarding Human Origins,” open-access and newly published in the peer-reviewed journal Religions. The paper reviews eight models for reconciling science and Christian theology regarding human origins. Four of those models are evolutionary in nature: (1) the Classical Theistic Evolution/Evolutionary Creationism model, (2) the Homo divinus model, (3) the Genealogical Adam and Eve model, and (4) the Homo heidelbergensis model. And four of those models are considered non-evolutionary: (5) the Unique Origins Design model, (6) the Classical Old Earth Creationist model, (7) the Classical Young Earth Creationist model, and (8) the Old Earth/Recent Humans Hybrid model. The paper goes far afield of intelligent design and gets into some theological territory that is somewhat foreign to me and different from my typical focus on science. But there’s also a lot of science discussed in the paper. In that regard, below I’d like to provide an excerpt from one section of the paper where I discuss how the Theistic Evolution / Evolutionary Creation (TE/EC) model holds up in light of the scientific evidence. Although the material below is framed as a response to the TE/EC model, much of the scientific evidence that is raised is also applicable to assessing any of the four evolutionary models that I assess in the paper. An obvious benefit of [the Theistic Evolution / Evolutionary Creation] model is that it is fully compatible with mainstream evolutionary science. However, in denying the existence of a historical Adam and Eve, it explicitly rejects major traditional theological beliefs about human origins, which will not be acceptable to many seeking to preserve those beliefs (Grudem 2017a, 2017b). Before accepting the TE/EC model, those who value these major traditional theological beliefs may wish to first consider the extent to which scientific evidence against the existence of Adam and Eve and in favor of human evolution is as open and shut as is being claimed. Fossil Evidence First, the fossil record shows a distinct break between the apelike australopithecines, which are supposedly directly ancestral to our genus Homo, and the first humanlike members of the genus Homo (Luskin 2022). Such evidence has led to observations from mainstream evolutionists conceding that there is a “large, unbridged gap” between humanlike members of Homo and the australopithecines (Mayr 2004, p. 198), which required a “genetic revolution” since “no australopithecine species is obviously transitional” (Hawks et al. 2000, p. 4), and implies a “big bang” model of human origins (University of Michigan News Service 2000). While evolutionary paleoanthropologists generally believe that “the transition from Australopithecus to Homo was undoubtedly one of the most critical in its magnitude and consequences,” they admit that “many details of this transition are obscure because of the paucity of the fossil and archaeological records” (Lieberman et al. 2009, p. 1). This lack of fossil evidence for the evolution of the humanlike body plan in the fossil record weakens the necessity of adopting standard evolutionary explanations of human origins. Genetic Evidence Genomic comparisons between humans and chimpanzees are becoming more sophisticated, with recent proposals proposing lower estimates of human–chimp genetic similarity estimates to between 84 percent and 96 percent (Buggs 2018c; Seaman and Buggs 2020). It is also unclear how any percent similarity between human and chimp DNA yields an argument that requires common ancestry (Luskin 2022). Junk DNA genetic arguments for common human–ape ancestry have also come under significant critique in recent years due to the discovery of mass-functionality for non-coding or “junk” DNA in the human genome. A major 2012 Nature paper by the ENCODE consortium reported “biochemical functions for 80%” of the human genome (ENCODE Project Consortium 2012, p. 57). Lead ENCODE scientists predicted that with further research, “80 percent will go to 100” since “almost every nucleotide is associated with a function.” (Yong 2012). In the wake of this research, the journal Science published an article titled “ENCODE Project Writes Eulogy for Junk DNA” which stated that these findings “sound the death knell for the idea that our DNA is mostly littered with useless bases” (Pennisi 2012, p. 1159). Evidence of functions for non-coding DNA has continued to mount at a high pace. A 2021 article in Nature reported that over 130,000 specific “genomic elements, previously called junk DNA” have seen specific functions identified (Gates et al. 2021, p. 215), followed by a paper in Genome Biology and Evolution which concluded, “The days of ‘junk DNA’ are over” (Stitz et al. 2021, p. 11). There is still much we do not understand about the genome and there are many specific genetic elements for which no function has yet been discovered. Nonetheless, this evidence suggests a strong trendline in the research literature away from non-functionality for “junk” DNA. One frequently mentioned example of junk DNA is pseudogenes, which TE/EC advocates commonly cite as “the mutated remains of once-functional genes” (Venema and Falk 2010) that show our common ancestry with apes. Yet, a 2012 paper found pseudogene function is “widespread,” and since “the study of functional pseudogenes is just at the beginning” it predicted “more and more functional pseudogenes will be discovered as novel biological technologies are developed” (Wen et al. 2012, p. 31). Indeed, the literature is now replete with papers reporting functions for pseudogenes (Hirotsune et al. 2003; Pain et al. 2005; Zhang et al. 2006; Tam et al. 2008; Piehler et al. 2008; Poliseno et al. 2010; Muro et al. 2011; Rapicavoli et al. 2013; Ji et al. 2015; Hayashi et al. 2015; Prieto-Godino et al. 2016; Suzuki et al. 2018; Fiddes et al. 2018; Habib et al. 2019), including producing functional RNA transcripts or performing functions without producing any RNA (Poliseno 2012). A 2012 paper notes that although “pseudogenes have long been dismissed as junk DNA,” recent advances have established that “the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions,” concluding that “pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression” (Poliseno 2012, pp. 1, 10). Indeed, many pseudogenes are known to produce proteins, with a study in Nature reporting “more than 200 peptides that are encoded by 140 pseudogenes” (Kim et al. 2014, p. 579). There are good reasons to understand why DNA labeled a “pseudogene” is now turning out to have a function. Pseudogenes are often identified by comparison to some other similar gene sequences encoding a functional protein from which the pseudogene is thought to have been derived and subsequently degenerated. However, regulatory functions of pseudogenes often require them to have some sequence similarity (homology) to their protein-coding counterparts so their RNA transcripts can interact with transcripts from the protein-coding gene, thereby regulating protein production (Salmena et al. 2011). Therefore, the reason our genomes contain sequences that resemble protein-coding-genes but do not produce proteins is not because they are discarded evolutionary “pseudogenes,” but because they are designed that way as important genomic regulatory and control elements. Many papers have criticized the assumption that pseudogenes are functionless junk DNA and now suggest abandoning the term (Pink et al. 2011; Poliseno 2012; Wen et al. 2012; Kovalenko and Patrushev 2018; Troskie et al. 2021). A 2020 paper in Nature Reviews Genetics observes, “Where pseudogenes have been studied directly they are often found to have quantifiable biological roles,” and warns that “the dominant limitation in advancing the investigation of pseudogenes now lies in the trappings of the prevailing mindset that pseudogenic regions are intrinsically non-functional.” It cautions that pseudogene function is “prematurely dismissed” due to “dogma” (Cheetham et al. 2020). There are prominent examples of prematurely dismissing pseudogene function, only to be proven wrong later. During the 2005 Kitzmiller v. Dover trial, biologist Kenneth Miller testified that our beta-globin pseudogene is “broken” because it has “molecular errors that render the gene non-functional,” indicating humans share a common ancestor with apes (Miller 2005, p. 79). Two years later, leading evolution advocate Eugenie Scott claimed this pseudogene “isn’t going to do diddly. It’s just going to sit there” and “not do a thing” (Scott 2007). However, a 2013 study reported that this precise pseudogene is functional (Moleirinho et al. 2013), and a 2021 study found it is “essential” and has “indispensability” for human red blood cell formation (Ma et al. 2021, pp. 478, 490). Endogenous retroviruses (ERVs) are another class of “junk” DNA commonly cited by TE/ECs in favor of human/ape common ancestry. The structure of the arguments here is similar to those used for pseudogenes: ERVs also show widespread evidence of function, particularly gene regulatory roles (Conley et al. 2008; Jacques et al. 2013; Chuong 2018; Robson and Mundlos 2019; Jönsson et al. 2021; Sakashita et al. 2023), and their similarity to viral DNA may exist for functional reasons, as they are involved in immune-functions to repel viral infections (Badarinarayan and Sauter 2021). Again, it is true that there is still much we do not know about junk DNA and there are many specific genetic elements (including pseudogenes and ERVs) for which specific functions have not yet been discovered. However, recent trends in research show that far more functionality is being discovered than was anticipated, leading to the possibility of mass functionality for junk DNA. As a 2023 academic book on RNA states: While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory. MATTICK AND AMARAL 2023, P. VII. If noncoding/junk DNA is in fact functional, then genetic similarities could be the result of common design due to the need to meet similar functional requirements. Even Francis Collins has acknowledged that shared genetic similarity “alone does not, of course, prove a common ancestor” because “such similarities could simply demonstrate that God used successful design principles over and over again” (Collins 2006, p. 134). Population Genetics Third, arguments against Adam and Eve based upon human genetic diversity and population genetics seem to have been undermined by subsequent modeling analyses. One of the first scientific responses to this population-genetics argument against Adam and Eve was published in 2012, when biologist Ann Gauger, a senior fellow with the Discovery Institute (a pro-intelligent-design think tank, where this author also works), reported that genetic diversity in HLA genes — some of the most diverse genes in the human genome — could still be explained if we originated from an initial couple (Gauger et al. 2012, p. 120). After the publication of Adam and the Genome in 2017, biologist Dennis Venema was engaged on the BioLogos discussion forum by Richard Buggs, a geneticist at Queen Mary University London. During the discussion Venema acknowledged that various papers he had cited as having refuted the existence of Adam and Eve had not actually addressed the question of whether humanity descended from an initial couple (Buggs 2017). From this discussion emerged a consensus among various Christian biologists that if an initial pair of humans lived far enough in the past, then modern human genetic diversity could in fact be accounted for by natural biological processes. Eventually, Buggs stated to Venema: “You would do your readers a service if you wrote a blog to tell them now, as far as you are able, that present day genomic diversity in humans does not preclude a bottleneck in the human lineage between approx 700 K and 7myr ago. I think you owe this to them” (Buggs 2018b). (The bottleneck he refers to is the human population being reduced to two individuals — effectively the same as humanity descending from Adam and Eve.) Venema then publicly acknowledged the veracity of Buggs’s critique, replying: “I’ve already agreed with this….You’re welcome to publicize it” (Venema 2018). Buggs later summarized this conversation on his blog with Nature Ecology and Evolution, reporting that the question was no longer whether a historical Adam and Eve could have existed, but rather at what point in time they lived (Buggs 2018a). Gauger along with Ola Hössjer, a professor of mathematics at the University of Stockholm, had already begun a project to address how deep into the past an initial couple had to live in order to account for modern human genetic diversity. They published a series of papers developing and testing a population genetics model which allows for an initial pair of humans to be given “designed variants” of genes representing “primordial diversity” built into the initial genomes of Adam and Eve. Under their model, natural biological processes then govern the subsequent genetic history of the human race. They showed that modern-day human genetic diversity can be explained by a single pair of ancestors — e.g., what one might call Adam and Eve — provided that they lived at least 500,000 years ago (Hössjer et al. 2016a, 2016b; Hössjer and Gauger 2019). S. Joshua Swamidass, a Christian scholar and professor of computational biology at Washington University in St. Louis, performed an analysis that yielded a similar result, finding that Adam and Eve could have lived 495,000 years ago as our sole genetic progenitors (Swamidass 2017). There is another population genetics argument relevant to human origins — but this one is posed as a mathematical challenge to unguided evolutionary models. The MRCA of humans and chimpanzees is said to have lived approximately 4 to 6 million years ago (Wood and Harrison 2011). Though estimates vary, a reasonable accounting proposes that the genetic differences between humans and chimps amount to some “35 million base-pair changes, 5 million indels [sequences of multiple nucleotide bases] in each species, and 689 extra genes in humans” (Cohen 2007). Yet, a population genetics study in the journal Genetics found that if just two specific mutations were required to provide some evolutionary advantage in the line that led to humans, then “this type of change would take >100 million years,” which was determined to be “very unlikely to occur on a reasonable timescale” (Durrett and Schmidt 2008). This “waiting times” problem (Hössjer et al. 2021) suggests there may be far too little time available from the fossil record for standard unguided evolutionary mechanisms to generate observed genetic, morphological, and behavioral differences between humans and chimps. Some have proposed intelligent design as a possible explanation for the rapid appearance of biological information necessary to overcome the waiting times problem and generate these complex traits (Thorvaldsen and Hössjer 2020).