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Questioning Evolutionary Presuppositions about Endogenous Retroviruses
BY ANJEANETTE ROBERTS – DECEMBER 7, 2017
Applying inductive reasoning to comparative genomic analyses is one way scientists search for functional elements within various genomes. A scientist assumes that if the function of a given sequence within a given genome is known and if he finds an identical or similar sequence in another organism’s genome, then he can provisionally assume a similar (if not identical) function in the second organism. Of course, he cannot prove the same function exists in the unknown genome until he designs experiments with proper controls that allow him to actually measure and compare the functions of the similar sequences. But often, especially for multicellular organisms, such an experiment is too complex. So he relies on inductive reasoning to reach some conclusions. This is a key concept in many genomic studies and in Dr. Finlay’s assertion of genetic evidence for common descent.
Virus-Infected Cells, Clonal Expansion, and Common Descent
In his lecture, Dr. Finlay explained how the infection of cells with a type of retrovirus—human T-cell leukemia virus (HTLV)—begins with multiple random insertion events of the HTLV proviral DNA into various sites of the host cell’s chromosomal DNA. Much later, after infection with HTLV, leukemia may develop. When it does, it is observed that every leukemic cell within the infected individual shares the exact same insertion sitefor the HTLV proviral DNA.4 When a retrovirus infects a cell its genomic sequence is inserted into the host cell’s chromosome. So a common shared site of insertion in every leukemic cell indicates that the leukemia results from clonal expansion of one single, HTLV-infected cell and not from multiple independently infected cells. If leukemia arose from multiple independently infected cells, the proviral insertion sites would differ among the host’s leukemic cells. Leukemia, therefore, results from one unique insertion event (among many). This clonal expansion of rogue cells is a well-established hallmark of cancers.
Dr. Finlay took this well-established fact of clonal expansion and applied it to comparative analyses of chromosomal sequences of humans and NHPs. The chromosomes of all hominids are riddled with sequences known as endogenous retroviral (ERV) elements. About 8 percent of the human chromosome is composed of ERV sequences of unknown etiology (origin). ERVs are so named because they share sequence homology and other characteristics with known retroviruses. But unlike modern retroviruses (such as HIV), no human ERV is still functionally infectious. Not only are the genomes riddled with ERVs, but one also finds shared ERV sequences at specific identical insertion sites in the various hominid chromosomes. Since ERVs are no longer infectious and yet occur in identical places in the genomes of hominids, by inference, according to the clonal expansion theory, they are presumably indicative of descent from common forebears. Put another way, for all humans to possess the same set of 400,000 ERV elements “as part of their common genetic endowment, the germ-line cells sustaining the original infections must have been ancestral to us all.”5
And for humans and NHPs to share several thousand chromosomal ERV insertion sites this must reflect a common ancestor that was infected with an ERV progenitor before the various hominids diverged evolutionarily. Like leukemic cells, although the initial viral insertion events were random, the fact that all descendants share identical insertions in their genomes indicates proof of a single infection and insertion event and, therefore, common descent.
Dr. Finlay asserted this as staggering and incontrovertible evidence for common descent; and taken with his presuppositions, he is absolutely correct. However, his presuppositions are many and, although plausible, they may not be as solid as he or other neo-Darwinian evolutionists think.
His presuppositions follow this line of reasoning: (1) ERVs are evolutionary hallmarks of viral infections and insertion events; (2) infection by ERV viral progenitors occurred in gametes or gametic precursors of a common ancestor of hominids; and (3) following infection, ERV progenitor viral sequences were inserted randomly into the genomes of these ancestors and were subsequently passed on to all descendants, including all divergent species that branched off from the ancestors who incurred the initial infectious events. Additionally, he presumes that ERVs are by-and-large nonfunctional within the genomes in which they are found today. As a molecular biologist and virologist I take exception to a few things and think there is room for questioning Dr. Finlay’s presuppositions.
In addressing the first two presuppositions, consider the following. Virus replication is known to be restricted on one level by the types of cells any given virus can infect. This restriction is often mediated at the level of viral entry into the cell by protein receptors on the cell surface. Human retroviruses are known to infect somatic cells, primarily of hematopoietic origin, not gametes or gametic precursors. Gametic cell-types apparently lack the appropriate receptors for viral entry.6
A second obstacle to proviral insertion is raised by the observation that retroviral DNAs of some retroviruses do not integrate into the DNA of quiescent (inactive), nonreplicating cells7—such as gametes.8 Therefore, proviral integration into an ancient gametic chromosome faces two known obstacles: one at viral entry and another at proviral integration. These are nontrivial scientific objections to Dr. Finlay’s first two presuppositions. Nevertheless, if ancient retroviruses were able to infect the gametic precursors of a proposed common ancestor, then the existence of shared ERV sequences at identical sites in all (or almost all) descendants’ genomes would be expected.
Although tantalizing observations of the koala retrovirus (KoRV) activity in captive and wild koalas may shed light on elements of endogenization (establishment of proviral sequences in the germ line), we should resist inferring too much from these observations.9 Recent emergence (estimated date circa 1900) of KoRV may or may not render relevant insight into the presence of shared ERVs in hominid genomes. Like most other retroviruses and ERVs, the origin of KoRV and the closely related gibbon ape leukemia virus (GALV) found in captive gibbons is unknown. These retroviruses utilize a class of cellular receptors for viral entry which results in increased host range (primate and marsupial) and broader cellular tropism (somatic and germ line cells in koalas).10 The greater distribution and shared similarity of the cellular receptors within and across species may be a key factor for the endogenization being observed and, therefore, one must not infer too much from limited data.
Insertion Sites Are Not “Random”
Despite early findings in vitro, retroviral insertion sites are not selected randomly. Various retroviruses have varying degrees of insertion site preferences, some showing site bias and others even demonstrating integration specificity at the primary sequence level. There are a variety of factors now known to effect integration site specificity.11 These include different viral proteins (IN, Gag, U3 LTR), chromatin accessibility (A/T-rich distorted DNA and outwardly facing major grooves), cell-cycle effects (integration in dividing cells occurs at a much higher rate, and increased site specificity is observed in integration in non-dividing cells), and cellular integration co-factors (tethering proteins like LEDGF/p75, gene regulatory elements, and epigenetic marks). Since a range of insertion site specificities and contributing factors exist for the various classes of retroviruses, it is possible that retroviral infections establishing the shared ERV sites in NHP chromosomal segments had even greater specificity for insertion site selection than those actively tested and observed to date.
Furthermore, despite heritability of ERVs at shared insertion sites, absence of specific ERV sequences in some NHP genomes challenges the common descent paradigm. HERV-K GC1 is found in chimps, bonobos, and gorillas, but not in humans.12 PtERV1 is present in chimps and great apes, but not in humans and orangutans.13 As others have noted, these findings undermine the notion that an ancient infection invaded an ancestral primate lineage, since according to phylogenetic analysis of species, great apes (including humans) share a common ancestor with Old World monkeys.14 Another observation of shared NHP ERVs that is contrary to evolutionary predictions involves the divergence of sequences in paired 5’ and 3’ proviral LTRs,15 which accrue differing mutations at similar rates following insertion. Divergence between LTR sequences at a single shared ERV site sometimes varies more significantly in one species than in another, suggesting differences in times of insertion between the two species.16 For example, estimated divergence of chimpanzee 1p31.1a proviral LTRs is 6.5 times greater than that observed in humans. Human 1p31.1a is also dimorphic with solo LTR and provirus, unlike the chimp ortholog. Both of these findings suggest a much more recent integration event in humans than in chimps at orthologous sites.17
Although evolutionary arguments are made to account for these observations,18 independent ERV infection events with similar insertion site specificities offer simpler viable explanations for ERVs that do not track with phylogenetic predictions based on NHP species relatedness. The Reasons to Believe model of common design also offers a simpler explanation for the possibility of multiple ERVs that do not follow primate phylogenetic trees: They serve relevant functions and are not evolutionary artifacts.
Important Sidebar on NHP Genome Analyses
Evolution proponents commonly presuppose that ERVs—along with most other repetitive elements (REs) found in the human genome—are nonfunctional markers of evolutionary processes. In adopting this posture many believe we have sure knowledge for such inductive conclusions. They appeal to whole genome sequencing (WGS) data of human, chimp, gorilla, bonobo, orangutan, Neanderthal, Denisovan, and many others. From these sequences, they highlight data that support their presuppositions and construct various scenarios to account for data that go directly against their predicted model.
These WGS accomplishments are truly remarkable; however we fail to acknowledge that vast troves of information are still uninterpretable and inaccessible. Although it is widely accepted that the human genome sequence was “completed” in 2004, to this day nearly 10 percent of it remains unsequenced because it exists in inaccessible, densely packed heterochromatin (~8 percent) or is replete with repetitive sequences that are not yet possible to assemble (~2 percent).19 The majority of these sequences are simply omitted from genomic comparisons for three reasons:
- The tight association of (constitutive) heterochromatin with its associated proteins makes it inaccessible to current methodologies employed in retrieving chromosomal DNA for analysis.
- Heterochromatin is replete with highly repetitive sequences, as is much of the euchromatin sequenced to date. It is technically very difficult to sequence and accurately align these types of highly repetitive sequences because of the very short “reads” and currently available alignment algorithms.
- The lack of intercellular regulatory access to much of the tightly bound heterochromatin and the basic characteristics of repetitive elements have left many evolutionary theorists arguing for their relative insignificance in function and comparative genomic studies.20
All of these arguments rest primarily on mistaken inferences that these sequences (those inaccessible in heterochromatin and the highly repetitive sequences in euchromatin) are of little to no significance. A critical flaw in this presupposition is a failure to recognize humbly that our efforts at unraveling the complexities of the human genome are still in their infancy.
As with insertion site randomness, more recent scientific findings challenge each of these presuppositions. Genes and regulatory elements have been discovered in heterochromatin. Heterochromatin sequences may in fact have specific developmental (or tissue) roles not captured in snapshots of genomic analyses, which are sometimes performed on immortalized cell-lines rather than on primary, tissue-specific cells.21 Along these lines, information within published genomes may limit our understanding of differences that occur within various tissues, in various stages of development, and under various stresses. Although these variations are unlikely to drastically change primary DNA sequences (unless copy number variations are found to have more significant roles in phenotypic variability at the cellular or organismic level than currently understood), they could certainly contribute to a change in chromosomal architecture and activity. That which is envisioned as fixed may in fact be revealed as having fluidity capable of significant impacts at an individual level. Data collected in the future from transcriptome (RNA molecules) and proteome analyses will help define differences—but with this added data the information to be sorted will grow exponentially.
ERVs and REs Have Significant Function
Researchers have found that REs (like ERVs), once thought to be junk, can be functional.22Some ERVs are transcribed and have specific functions in various cells and tissues. Some REs provide regulatory functions themselves and some affect the proximity of other regulators to specific genes, which also affects expression and function. Additionally REs often occur in long stretches along chromosomes that may provide fluidity for genomic restructuring in complex adaptive situations. In light of these discoveries, it is important to emphasize that additional functions are bound to lie hidden in previously identified ERVs and in ERVs not yet identified.
According to RTB’s creation model, those ERVs or REs held in common with minimal divergence with other NHPs are likely to serve roles common to all. ERVs or REs that differ significantly or are distinctive to humans (or even exclusive to some particular humans) likely contribute to cross-species and interspecies unique attributes.
Other considerations that should not be ruled out in forming presuppositions regarding the presence of shared ERVs in primate genomes depend on the fact that the origins of retroviruses and other viral families are unknown. All viruses depend on living cells in order to replicate. A virus cannot replicate independent from a living cell, which supplies it with energy and mechanisms for replication. The RTB model proposes a Creator who designed with foresight and finesse adaptive mechanisms that would provide organisms the ability to persist and even thrive in conditions of change and stress. Since scientists have discovered function for some ERVs, it is possible that ERVs and transposable elements may be part of these mechanisms.
Evolutionary Presuppositions Need to Change
In light of increasing evidence challenging evolutionary presuppositions, their staying power is quite unfortunate. The most detrimental aspect of accepting the evolutionary explanation of ERVs in human and NHP genomes is that it inhibits scientific inquiry and progress by attributing no other significance to REs and ERV-like elements maintained in NHP genomes than that of evolutionary artifacts. Forcing sequences into a paradigm that renders them insignificant and useful only as evolutionary markers stifles us from probing these sequences for unique, shared, or distinguishing functions. It is in a sense what others have called a classic example of derailing an objective analysis of the data.23
We need to remember (or consider for the first time) that we’ve only just begun to unravel the human genome and all its complexities. It will take decades of dedicated, well-designed, nonpresumptuous research to unpack it. It is no surprise that, as we do, the intricacies and complexities we discover will stretch our imaginations. The intricate networks demonstrate extraordinary orchestration and fine-tuning, which point to incredible, complex design. The greater the complexity and functionality of the human genome, the greater the impedance to plausible neo-Darwinian explanations. Yet discoveries like these, pointing to incredibly intricate and complex designs, are exactly what the RTB creation model predicts. It is surprising that the more we learn about the magnificent orchestration of the diverse symphonies playing inside each cell, the fewer people recognize the obvious themes of a brilliant Composer.24
- Graeme Finlay, “Human Genetics and the Image of God” (lecture, Queen’s Lecture Theatre, Emmanuel College, Cambridge, November 7, 2006). Transcript available at https://www.faraday.st-edmunds.cam.ac.uk/CIS/Finlay/lecture.htm.
- Non-human primates include the non-human members in the taxonomic order Primates (e.g., lemurs, lorises, tarsiers, New World monkeys, Old World monkeys, and apes).
- Nuclear DNA sequences are now available for Neanderthals and Denisovans. Genomic comparisons and arguments pointing to common descent have now been extended to include these extinct hominins as well.
- For a short tutorial of HIV retroviral infection and integration, watch this YouTube video: https://www.youtube.com/watch?v=eS1GODinO8w. Watch from the beginning (0:00) to time signature 2:43.
- Finlay, “Human Genetics.”
- Speculation that HIV may infect spermatozoa exists, but is contrary to current dogma among retrovirologists.
- Debate continues whether retroviral infection and integration occur in quiescent cells. It is an extremely infrequent event if it occurs. If it does occur insertion is less random and appears to be preferentially directed to regions of actively transcribed genes.
- Gametic precursors (i.e., gametogonium and primary gametocytes) replicate DNA during mitosis and meiosis.
- Jon J. Hanger et al., “The Nucleotide Sequence of Koala (Phascolarctos cinereus) Retrovirus: A Novel Type C Endogenous Virus Related to Gibbon Ape Leukemia Virus,” Journal of Virology 74 (May 2000): 4264–72, doi:10.1128/JVI.74.9.4264-4272.2000; Rachael E. Tarlinton, Joanne Meers, and Paul R. Young, “Retroviral Invasion of the Koala Genome,” Nature 442 (July 2006): 79–81, doi:10.1038/nature04841.
- Nidia M. Oliveira, Karen B. Farrell, and Maribeth V. Eiden, “In Vitro Characterization of a Koala Retrovirus,” Journal of Virology 80 (March 2006): 3104–7, doi:10.1128/JVI.80.6.3104-3107.2006.
- Sébastien Desfarges and Angela Ciuffi, “Retroviral Integration Site Selection,” Viruses 2 (January 2010): 111–30, doi:10.3390/v2010111; Heather A. Niederer and
- Charles R. M. Bangham, “Integration Site and Clonal Expansion in Human Chronic Retroviral Infection and Gene Therapy,” Viruses 6 (October 2014): 4140–64, doi:10.3390/v6114140.
- Madalina Barbulescu et al., “A HERV-K Provirus, in Chimpanzees, Bonobos, and Gorillas, but Not Humans,” Current Biology 11 (May 2001): 779–83, doi:10.1016/S0960-9822(01)00227-5.
- Chris T. Yohn et al., “Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans,” PLoS Biology 3 (April 2005): e110, doi:10.1371/journal.pbio.0030110.
- “The Chimp Genome Reveals a Retroviral Invasion in Primate Evolution,” PLoS Biology 3 (April 2005): e126, doi:10.1371/journal.pbio.0030126.
- LTRs are long terminal repeats at the 5’ and 3’ ends of proviral DNA. The 5’ and 3’ LTRs have identical sequences to each other prior to integration.
These divergence rates are normalized for the various interspecies mutation rates for comparison to each other.
- Catriona M. Macfarlane and Richard M. Badge, “Genome-wide Amplification of Proviral Sequences Reveals New Polymorphic HERV-K(HML-2) Proviruses in Humans and Chimpanzees That Are Absent from Genome Assemblies,” Retrovirology 12 (April 2015): id. 35, doi:10.1186/s12977-015-0162-8.
- Macfarlane and Badge, “Genome-wide Amplification of Proviral Sequences”; Desfarges and Ciuffi, “Retroviral Integration Site Selection”; Niederer and Bangham, “Integration Site and Clonal Expansion.”
- Wentian Li and Jan Freudenberg, “Mappability and Read Length,” Frontiers in Genetics 5 (November 2014): 381, doi:10.3389/fgene.2014.00381.
- Insignificant, that is, except in the case of employing repetitive elements as an indication of common ancestry.
- Nehmé Saksouk, Elisabeth Simboeck, and Jérôme Déjardin, “Constitutive Heterochromatin Formation and Transcription in Mammals,” Epigenetics & Chromatin 8 (January 2015): id. 3, doi:10.1186/1756-8935-8-3.
- Graeme Finlay, Stephen Lloyd, Stephen Pattemore, and David Swift, Debating Darwin: Two Debates: Is Darwinism True, and Does It Matter? (Milton Keynes, UK: Paternoster, 2009), 158–60.
- Gerald Rau, Mapping the Origins Debate: Six Models of the Beginning of Everything (Downers Grove: InterVarsity, 2012), 116.
- Romans 1:19–23 (NLT) sheds some light on this lack of recognition: “They know the truth about God because he has made it obvious to them. For ever since the world was created, people have seen the earth and sky. Through everything God made, they can clearly see his invisible qualities—his eternal power and divine nature. So they have no excuse for not knowing God. Yes, they knew God, but they wouldn’t worship him as God or even give him thanks. And they began to think up foolish ideas of what God was like. As a result, their minds became dark and confused. Claiming to be wise, they instead became utter fools. And instead of worshiping the glorious, ever-living God, they worshiped idols made to look like mere people and birds and animals and reptiles.”
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