Parasitic DNA?

Transposable elements have multiple functions that are a problem for evolutionists and point to the Creator

by Harry F. Sanders, III on April 8, 2022
Featured in Answers in Depth
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The genomes of organisms are not only made of protein-coding genes. In fact, protein-coding genes make up only a small percentage of the genome. Most of the genome consists of non-coding sequences, often referred to as “junk DNA.” Transposable elements are part of the non-coding DNA1 and are sometimes referred to as “parasitic DNA.” Transposable elements (TEs)2 are termed parasitic because they can replicate and spread within the genome of an organism.3 Thus some evolutionists have often “blindly and rigidly” accepted the idea that transposable elements are selfish junk.4 But is that narrative true?

Do Humans and Chimps Share “Parasitic DNA”?

One argument commonly associated with the parasitic DNA narrative is that humans and chimps share large quantities of similar DNA sequences, usually termed SINE and LINE elements. Of particular interest are the Alu elements, a type of SINE that is estimated to make up about 11% of the human genome.5 An Alu element is a short sequence of DNA able to migrate throughout the genome. Alu elements are sometimes used to build a phylogenetic tree of humans and their supposed ancestors.6 Further they are commonly used as evidence for evolution in the popular sphere, usually by people with a scientific background such as Francisco Ayala,7 adding to their perceived weight. Ayala argued that the Alu sequences were functionless, and thus could not be part of a designed process.8 Others have argued that Alu elements serve as “molecular fossils,” providing clues to genetic ancestry based on identical insertion points.9

A “Digital Programming System”

Science has proven these arguments wrong. Alu sequences are edited in over 100 million sites spread throughout the genome.10 These editing sites potentially serve as a digital programming system11 with staggering amounts of reprogrammable memory.12 Additionally, there is evidence they are involved in alternative splicing, RNA editing, and translation regulation.13 It has been proposed that Alu-based RNA editing might be used to tell the cell not to translate the edited transcript.14 Further, many Alus serve as enhancers for various genes.15 Many of the enhancements are tissue-specific,16and some are expressed differentially by tissue type.17 The assertion of Alu elements as functionless junk is dead. Ayala was dead wrong.

Further, because Alu elements are functional, evolutionists have pivoted to favoring the second argument: the “similar location” argument. This argument, however, must assume that Alus originated millions of years ago, then spread through transposition throughout the genome. Such an argument effectively assumes what it is trying to prove. If millions of years are not assumed, then the similar location of Alu elements becomes a design argument. Further, the evolutionists admit there are thousands of Alu elements in humans that do not share similar locations with primate Alus, and assume they were post-divergence insertions.18 Worse, Alu elements diverge up to twenty percent from the supposed human consensus sequence, making it questionable as to whether the similarities are truly shared anyway.19 However, if this assumption is false, then similarity of locations of Alus goes out the window as an argument for common ancestry.

As science has advanced, the narrative surrounding TEs has been changing.

However, similar location does not necessarily imply common ancestry, even if millions of years were granted and if every single Alu shared identical sequence and location. Both of those contingencies are false, but even assuming they were true does not necessitate common ancestry. For example, the Alus involved in the digital programming system are much more active in humans than in apes.20 This higher activity cannot be explained by common ancestry but can be explained by a common designer. We are just scratching the surface of Alu elements and other SINEs and LINEs. Undoubtedly, as we learn more about them, further designed differences will become apparent.

Transposable Elements Are Functional

It turns out that the narrative, spun in large part by Richard Dawkins in his book The Selfish Gene, is simply false. Transposable elements may have parasitic elements, but, in general, they are functional. The consensus has changed so much that an article was published in 2007 entitled “The necessary junk: new functions for transposable elements”!21 As science has advanced, the narrative surrounding TEs has been changing. They have begun to be associated with gene regulatory functions.22 This was the view of the discoverer of TE’s Barbara McClintock back in the 1940s and 1950s, but was largely ignored at the time.23 However, more evidence has come to light since then. TEs are associated with transcription regulation in humans.24 TEs are also associated with gene regulatory networks.25 They are also involved in the regulation of genes for cytokine production.26 Transposable elements may not be such parasitic junk after all.

It gets worse for those arguing that transposable elements are parasitic to the genome. Some TEs are associated with genes for sexual development in vivo, helping a developing baby differentiate into a boy or girl.27 When not regulated correctly, TEs cause all manner of developmental defects, from meiosis disruption to abnormal gamete formation.28 Conversely, however, some TEs serve as tissue-specific gene enhancers,29 and some are even species specific!30 Others are involved in activating key proteins in embryonic development.31 Clearly, transposable elements have functions in the genome.

Transposable elements are kept from replicating and spreading freely within the genome by means of epigenetic controls.32 However, TEs also regulate epigenetic changes.33 This creates a sort of circular cycle where epigenetics constrains transposable elements, but the TEs control how much the elements are constrained, which, in turn, decides how the TEs control themselves. These epigenetic impacts go far beyond just controlling TE movements, impacting things like gene transcription,34 expression, and regulation.35

It is important to note here that not all transposable element activity is beneficial. If a transposable element moves and lands within a gene, it will likely make the gene nonfunctional.36 If one were to land in a regulatory sequence, it could harm the function of many genes. There is also a connection between unrepressed TEs and various diseases, like cancer.37

Transposable elements are trending very strongly in the direction of largely functional, precisely what we would expect if the biblical narrative were true. Of course, there are going to be broken things in a fallen and cursed world (Genesis 3). We understand this when operating from a biblical framework; however, the majority of transposable elements appear to be designed and functional, not harmful and parasitic. Transposable elements are not evidence for common descent, but rather common design by God who doesn’t make junk!

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Footnotes

  1. Valer Gotea and Wojciech Makalowski, “Do Transposable Elements Really Contribute to Proteomes?,” TRENDS in Genetics 22, no. 5 (2006): 260–267, https://bioinformatics.uni-muenster.de/publications/papers/TIG-2006-22-260.pdf.
  2. Note that one type of transposable element not covered here are endogenous retroviruses (ERVs). Dr. Andrew Fabich has written an excellent article on the topic, https://answersingenesis.org/biology/microbiology/endogenous-retroviruses-common-ancestry/.
  3. Richard Dawkins, The Selfish Gene, New York: Oxford University Press, 1976.
  4. Margaret G. Kidwell and Damon R. Lisch, “Perspective: Transposable Elements, Parasitic DNA, and Genome Evolution,” International Journal of Organic Evolution 55, no. 1 (2001): 1–24, https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.0014-3820.2001.tb01268.x
  5. Prescott Deininger, “Alu Elements: Know the SINEs,” Genome Biology 12, no. 236 (2011): https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-12-236.
  6. Mark A. Batzer et al., “Alu Elements and Hominid Phylogenetics,” Proceedings of the National Academy of Sciences USA 100, no. 22 (2003): 12787–12791, https://www.pnas.org/content/pnas/100/22/12787.full.pdf.
  7. Ayala is a well-known evolutionary biologist.
  8. Francisco Ayala originally posted on BioLogos website, but his post has been taken down. His comments were reposted by Matthew Cobb, “Francisco Ayala on ‘Signature in the Cell’,” Why Evolution Is True blog, January 7, 2010, https://whyevolutionistrue.com/2010/01/07/francisco-ayala-on-signature-in-the-cell/.
  9. Diane J. Rowold and Rene J. Herrera, “Alu Elements and the Human Genome,” Genetica 108 (2000): 57–72, https://link.springer.com/article/10.1023/A:1004099605261.
  10. Lily Bazak et al., “A-toI RNA Editing Occurs at over a Hundred Million Genomic Sites, Located in a Majority of Human Genes,” Genome Research 24, no. 3 (2014): 365–376, https://genome.cshlp.org/content/24/3/365.full.pdf+html.
  11. Nurit Paz-Yaacov et al., “Adenosine to Inosine RNA Editing Shapes Transcriptome Diversity in Primates,” Proceedings of the National Academy of Sciences USA 107, no. 27 (2010): 12174–12179, https://www.pnas.org/content/107/27/12174.
  12. Sal Cordova, “Some ‘Junk DNA’ May Act as Computer Memory*,” Creation-Evolution Headlines, January 30, 2018, https://crev.info/2018/01/junk-dna-may-act-computer-memory/.
  13. Katharina Strub and Julien Hasler, “Alu Elements as Regulators of Gene Expression,” Nucleic Acids Research 34, no. 19 (2006): 5491–5497, https://academic.oup.com/nar/article/34/19/5491/3112003.
  14. Abram Gabriel et al., “Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome,” Genome Research 14 (2004): 719–1725, https://genome.cshlp.org/content/14/9/1719.full.pdf.
  15. Jing-Dong Han et al., “Evolution of Alu Elements Towards Enhancers,” Cell Reports 7, no 2 (2014): 376–385, https://www.sciencedirect.com/science/article/pii/S2211124714001892.
  16. Xiao-Ou Zhang, Thomas R. Gingeras, and Zhiping Weng, “Genome-Wide Analysis of Polymerase III-Transcribed Alu Elements Suggests Cell-Type-Specific Enhancer Function,” Genome Research 29 (2019): 1402–1414, https://genome.cshlp.org/content/29/9/1402.full.pdf.
  17. Yi Xing et al., “Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues,” PLoS Genetics (2008), https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000225.
  18. Kyudong Han, Yun-Ji Kim, and Jungnam Lee, “Transposable Elements: No More ‘Junk DNA’,” Genomics Information 10, no. 4 (2012): 226–233, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543922/.
  19. International Human Genome Sequencing Consortium, “Initial Sequencing and Analysis of the Human Genome,” Nature 409 (2001): 860–921, https://deepblue.lib.umich.edu/bitstream/handle/2027.42/62798/409860a0.pdf.
  20. Paz-Yaacov et al, 2010.
  21. Fred H. Gage et al., “The Necessary Junk: New Functions for Transposable Elements,” Human Molecular Genetics 16, no. R2 (2007): R159–R167, https://academic.oup.com/hmg/article/16/R2/R159/2356609.
  22. Edward B. Chuong, Nels C. Elde, and Cedric Feschotte, “Regulatory Activities of Transposable Elements: From Conflicts to Benefits,” Nature Reviews Genetics 18, no. 2 (2017): 71–86, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498291/
  23. Barbara McClintock, “Intranuclear Systems Controlling Gene Action and Mutation,” Brookhaven Symposium of Biology (1956): 58–74.
  24. Bartley G. Thornburg, Valer Gotea, and Wojciech Makalowski, “Transposable Elements as a Significant Source of Transcription Regulating Signals,” Gene 365 (2006): 104–110, https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.570.9929&rep=rep1&type=pdf.
  25. Michael P. Snyder et al., “Widespread Contribution of Transposable Elements to the Innovation of Gene Regulatory Networks,” Genome Research 24 (2014): 1963–1976, https://genome.cshlp.org/content/24/12/1963.full.pdf.
  26. Irina A. Udalova et al., “The Role of Transposable Elements in the Regulation of IFN-1 Gene Expression,” Proceedings of the National Academy of Sciences U.S.A. 106, no. 28 (2009): 11564–11569, https://www.pnas.org/content/106/28/11564.
  27. Magali Naville et al., “Sex and the TEs: Transposable Elements in Sexual Development and Function in Animals,” Mobile DNA 10, no. 42 (2019): https://link.springer.com/article/10.1186/s13100-019-0185-0.
  28. Jose L. Garcia-Perez, Ian R. Adams, and Thomas J. Widmann, “The Impact of Transposable Elements on Mammalian Development,” Development 143, no. 22 (2016): 4101–4114, https://journals.biologists.com/dev/article/143/22/4101/47472/The-impact-of-transposable-elements-on-mammalian.
  29. Guillaume Bourque et al. “Evolution of the Mammalian Transcription Factor Binding Repertoire via Transposable Elements,” Genome Research 18 (2008): 1752–1762, https://genome.cshlp.org/content/18/11/1752.full.pdf+html.
  30. Edward B. Chuong et al., “Endogenous Retroviruses Function as Species-Specific Enhancer Elements in the Placenta,” Nature Genetics 45 (2013): 325–329, https://www.nature.com/articles/ng.2553.
  31. Michelle Craig Barton et al., “Foxa1 Functions as a Pioneer Transcription Factor at Transposable Elements to Activate Afp During Differentiation of Embryonic Stem Cells,” Gene Regulation 285, no. 21 (2010): P16135–16144, https://www.jbc.org/article/S0021-9258(20)49426-8/fulltext
  32. Yuh Chwen G. Lee and Jae Young Choi, “Double-Edged Sword: The Evolutionary Consequences of the Epigenetic Silencing of Transposable Elements.” PLoS Genetics (2020): https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008872.
  33. R. Keith Slotkin and Robert Martienssen, “Transposable Elements and Epigenetic Regulation of the Genome,” Nature Reviews Genetics 8 (2007): 272–285, https://image.sciencenet.cn/olddata/kexue.com.cn/upload/blog/file/2008/9/20089370542934.pdf
  34. Hidetoshi Saze et al., “Epigenetic Regulation of Intragenic Transposable Elements Impacts Gene Transcription in Arabidopsis thaliana.”Nucleic Acids Research 43, no. 8 (2015): 3911–3921, https://academic.oup.com/nar/article/43/8/3911/2414390.
  35. Zachary Lippman et al., “Role of Transposable Elements in Heterochromatin and Epigenetic Control,” Nature 430 (2004): 471–476, https://par.nsf.gov/servlets/purl/10027853.
  36. Wei E. Huang et al., “Defensive Function of Transposable Elements in Bacteria,” ACS Synthetic Biology 8, no. 9 (2019): 2141–2151, ttps://pubs.acs.org/doi/full/10.1021/acssynbio.9b00218#.
  37. Guillaume Bourque et al., “Ten Things You Should Know About Transposable Elements,” Genome Biology 19 (2018): https://link.springer.com/article/10.1186/s13059-018-1577-z.

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