October 20, 2021 | Jerry Bergman

Junk DNA Concept Is Mostly Dead

Has the term “Junk DNA” finally been buried for good?
It’s gone from 98.5% to close to zero percent.

 

by Jerry Bergman, PhD

Two new reports proclaim that The days of ‘junk DNA’ are over.” One such statement was made by professors Christoph Grunau and Christoph Grevelding, senior authors of a new research article in Genome Biology and Evolution.

The concept of junk DNA is just what the term implies: DNA that has no function. Scientists originally thought that most of the human genome is is useless or worse. And the original claim was not that a few small sections of DNA were detritus, but 98.5 percent of our genome is junk. Blanco said as recently as 2019 that our DNA

holds the instructions for the proteins that make up and power our bodies. But less than 2 percent of our DNA actually codes for them. The rest — 98.5 percent of DNA sequences — is so-called “junk DNA” that scientists long thought useless.[1]

The concept of junk DNA was already declining years ago. In his 2011 book, The Myth of Junk DNA, Dr Jonathan Wells defined junk DNA as “the non-protein coding portion of DNA” which was used to provide “decisive evidence for Darwinian evolution and against intelligent design, since an intelligent designer would presumably not have filled our genome with so much garbage.”[2]

The notion of junk DNA is “an anti-scientific myth that ignores the evidence, impedes research, and is based more on theological speculation than good science.”

This view was held for many years by many leading proponents of evolution. Grunau and Grevelding write: “When we studied genetics at university in the 1980s, the common doctrine was that the non-protein coding parts of eukaryotic genomes consisted of interspersed, ‘useless’ sequences, often organized in repetitive elements like satellite DNA.”[3] Wells argued that the notion “most of the genome is little more than junk” is “an anti-scientific myth that ignores the evidence, impedes research, and is based more on theological speculation than good science.”[4]

Continued research into noncoding DNA has consistently supported his conclusion. One of the first extensive projects that disproved this claim was an international collaboration of over 400 scientists working with a project called the Encyclopedia of DNA Elements, or ENCODE for short. The consortium looked for function in every letter in the genome and found that, to their surprise, most of the noncoding portions were being transcribed, suggesting that they were doing things. This and other findings led to their reassessment that, though less than two percent of our genome codes for proteins, most of the rest has some function. Specifically, the ENCODE project confirmed that close to 80 percent of the genome has some function, such as gene regulation, scaffolding, protection, or other functions yet to be discovered.

Creationists predict that except for genetic entropy, all DNA will be found to be functional. [Image credit: Illustra Media]

The Amount of Junk DNA Continues to Decline

One of the latest studies by researchers at University of California, Berkeley, and Washington University shows that at least one family of genes called transposons[5] “plays a critical role in viability in the mouse, and perhaps in all mammals. When the researchers knocked out a specific transposon in mice, half their mouse pups died before birth. This is the first example of a piece of ‘junk DNA’ being critical to survival in mammals.”[6] This result was clear evidence for their important function. One of the major causes of differences between mice and men, and all mammals, is gene regulation. And transposons “have the capacity to generate a lot of gene regulatory diversity and could help us to understand species-specific differences in the world.”[7]

Another new study on a large family of repetitive DNA sequences known as W-elements (WEs) found that, far from being “junk,” these base pairs have an enduring influence that facilitate organisms to adapt to its local environment.[8] The study concluded that WEs affect variability or plasticity allowing organisms to adapt. In this particular case, they found that the parasitic flatworm family Schistosomatidae is better able to adapt to its environment using noncoding DNA. A segment that would have been dismissed as junk allows the flatworm to escape host surveillance and colonize new host environments.[9] Understanding this mechanism may help health experts to more effectively contain the parasite.

Of note are the organisms they studied, schistosomes (blood flukes), which are parasitic platyhelminths (flatworms) that causes schistosomiasis (bilharzia or snail fever). This neglected tropical disease infected 61.6 million people in 2014. In terms of human morbidity and mortality, it rivals only malaria. It is the only known trematode that has separate sexes. Furthermore, female sexual maturation depends on constant pairing with the male.[10] All other trematodes are exclusively hermaphroditic, meaning they possess both male and female reproductive organs.

Details of the Research

The schistosome karyotype consists of eight chromosome pairs. Males are homogametic (ZZ) and females are heterogametic (ZW). The nonrecombining portion of the W chromosome is composed mostly of repetitive DNA sequences, the W-elements discussed above. These sequences were assumed to be nonfunctional and female-specific. They were also used as markers to identify the sex of schistosome larvae. A new analysis of W-elements identified 19 different W-element families, varying in copy number from 3 to 450 and found in one or several locations on the W chromosome.

Whether or not these W-elements, or analogous ones, are used in human XY or other chromosomes is unknown. They have, though, been identified on somatic chromosomes. The authors identify some W-elements that produce putative functional RNAs, including microRNAs, small nucleolar RNAs, and self-cleaving ribozymes (hammerhead ribozymes) indicating that these elements can carry genetic information.[11] This research has not identified a function for all “junk DNA,” but this and similar findings has made the research group realize that the trend is clearly in the direction of finding functions in the remainder of DNA still considered junk. Thus, they proclaimed: The days of ‘junk DNA’ are over” (or close to over).*

*Other questions that need to be answered include “are the W-elements also found in other W chromosomes such as those used in birds (in contrast to mammals, male birds are homomorphic (ZZ) and the female heteromorphic (ZW)”? Why in mammals is the female homomorphic (XX) and the male heteromorphic (YY) in contrast to the schistosome karyotype in which males are homogametic (ZZ) and females heterogametic (ZW)? Are the W-elements used in mammal sex chromosomes? Do they exist in a scattered pattern in life, or only in sexually reproducing animals? As the W chromosome produces males in schistosomes, one would expect this to be the case. My supposition is, as more research on the genome used in life is completed, the genome will prove increasingly complex and will look less and less like it evolved from some universal common ancestor, further vindicating the creation worldview. Time will tell, but so far the creation worldview has, indeed, been vindicated by empirical evidence and in-depth analyses.

Summary

As research progresses, more new roles for noncoding DNA have been discovered, and will likely continue to be discovered, for the transcripts once believed to be “junk DNA.”  This research has confirmed predictions by creationists and Intelligent Design supporters that, as research progresses, functions will be found for what was once labeled “junk DNA.”[12]

 

References

[1] Blanco, Daniel Bastardo. 2019. Our Cells Are Filled With ‘Junk DNA’ — Here’s Why We Need It. Discover, August 13.

[2] Wells, Jonathan. 2011. The Myth of Junk DNA. Seattle, WA: Discovery Institute Press. Description in cover page.

[3] McGrath, Casey. 2021. Highlight—“Junk DNA” No More: Repetitive Elements as Vital Sources of Flatworm Variation. Genome Biology and Evolution 13(10): evab217, October. https://doi.org/10.1093/gbe/evab217.

[4] Wells, 2011. Description in cover page.

[5] Bergman, Jerry. 2001. “The Molecular Biology of Genetic Transposition.” CRSQ 38(3):139-150, December.

[6] Sanders, Robert. 2021. So-called junk DNA plays critical role in mammalian development. Berkeley News.

[7] Sanders, Robert. 2021.

[8] McGrath, 2021.

[9] Stitz, Maria, et al. 2021. Satellite-like W-elements: Repetitive, transcribed, and putative mobile genetic factors with potential roles for biology and evolution of Schistosoma mansoni. Genome Biology and Evolution 13(10): evab204. https://doi.org/10.1093/gbe/evab204.

[10] Mone’ H, Boissier J. 2004. Sexual biology of schistosomes. Advanced  Parasitology 57:89–189.  doi: 10.1016/S0065-308X(04)57002-1.

[11] McGrath, 2021.

[12] Bergman, Jerry. 2001. The Functions of Introns: From Junk DNA to Designed DNA. Perspectives on Science and Christian Faith 53(3):170-178, September.

See also: Bergman, Jerry 2020. Jumping Genes: From Genome Havoc to Designed Variety. Another New Discovery of their Function. March 2.


Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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