December 15, 2022 | Jerry Bergman

What Are Introns For?

The origin of introns is a mystery to evolutionists.
They apply Darwin magic, calling it an “evolutionary burst.”

 

 

by Jerry Bergman, PhD

Since the hypothetical first primitive cells did not have the critical important sections of chromosomes called introns, a concern of evolutionists is to explain the origin of these mysterious regions.[1] The facts run counter to their expectations.

History of intron discoveries

Introns were first discovered in 1977 as a result of the observation that the mRNA used to code for proteins was almost always shorter than the DNA from which it had been transcribed.[2] Thus it was realized that something was removed before it was translated into RNA. Early insight on intron function was a result of the finding that many of these non-coding DNA intron sequences are not random base pairs, but have certain features in common with human language.

The finding that introns manifest the same complex patterns of communication found in human speech supports the supposition that they carry important functional information. The fact that a large quantity of cell resources and energy are invested in these structures, especially in the complex intron-splicing mechanism, argues that this non-coding DNA has important biological functions, including a means of facilitating genetic diversification.[3]

What introns do

The many important functions of introns include genomic regulation, to play an essential role in gene-expression regulation, such as mRNA export, enabling alternative splicing, making it possible to generate multiple proteins from a single gene. Some introns, through further processing after they are spliced, encode functional RNA molecules.

One role of introns may be to help ensure that genetic data is processed correctly.[4]  This theory was supported by Shepherd’s analysis of thousands of DNA sequences obtained from the human genome project. He observed that enzymes in the nucleus do not discriminate between exons and introns when they construct messenger RNA from the original DNA template.[5]

The problem of identifying introns was compounded by the discovery that alternative readings of the genetic code exist in which “introns” function as “exons.”[6] Some DNA portions behave as exons when expressed by one pathway, but as introns when expressed by another pathway.  Both pathways can operate simultaneously, resulting in greater protein variety.[7]  For the reason that introns have these paramount roles in the cell, explaining their evolution is critical. As Huff et al. have noted:

The discovery of introns four decades ago was one of the most unexpected findings in molecular biology…. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. …  although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale.”[8]

Origin of introns

Introns appear early in the history of life and no evidence of their evolution was ever found. Evolutionists admit that “Introns are a crucial part of eukaryotic genomes, but their origins are poorly understood.”[9] Initially, scientists conducted the

first large-scale search for intron gains, in some 1,500 pairs of mouse–human orthologs. The results were deeply surprising: no evidence for intron creation was found in either species in 80 million years, a conclusion that was later extended to the entire genome. Subsequent studies found a similar dearth of intron creation among related species in many biologically and phylogenetically diverse eukaryotic lineages.[10]

Because they appear to have been produced at about the same time in history, a new theory has attempted to explain their origin from an evolutionary perspective. The explanation points to introners, a theoretical “intron creator” which involves a type of genetic element that creates copies of itself which inserts into many genes across the genome:

one of several proposed mechanisms for the creation of introns [was] discovered in 2009, as an explanation for the origins of most introns across species. The researchers believe that introners are the only likely explanation for intron burst events, in which thousands of introns show up in a genome seemingly all at once, and they find evidence of this in species across the tree of life…[This study] provides a plausible explanation for the vast majority of origins of introns,” said Russell Corbett-Detig, associate professor of biomolecular engineering and senior author on the study. There’s other mechanisms out there, but this is the only one that I know of that could generate thousands and thousands of introns all at once in the genome. If true, this suggests that we’ve uncovered a core process driving something that’s really special about eukaryotic genomes – we have these introns, [and as a result] we have genomic complexity.[11]

This mechanism implies a haphazard planting of introns in random places in the genome. After admitting that “Large variation in intron numbers exists across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive,” Corbett-Detig et al. added:

Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms.[12]

Convergence and junk theory

Evolutionists assume that  introners have evolved convergently hundreds of times from non-autonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, introners may explain the episodic nature of intron gain across the eukaryotic tree of life.

Introns are non-protein, coding DNA that Darwinists once argued are relics of once-functioning genes or useless “junk” DNA that strongly argued against design. Introns are normally removed to produce RNA by splicing enzymes to allow mRNA (messenger RNA), rRNA (ribosomal RNA), and tRNA (transfer RNA) to carry out their cell functions. To prevent literally destroying the genome, where they splice themselves into the genome must be highly regulated.

Observations do not fit Darwinian expectations

Introner theory postulates at one point in evolution the introners evolved and spread to all life that evolved from this early precursor organism. One major problem with the introner theory is that introns are extremely common in eukaryotes, and are even found in archaebacteria, eubacteria. They are  even found in proteobacteria, specifically in several species of photosynthetic cyanobacteria. A few introns have even been found in animal viruses, mitochondrial DNA, and chloroplast DNA. No evolutionary pattern explains their presence in life. In contrast to the genomes of higher organisms, both viruses and bacteria consists of wall-to-wall genes with comparatively few introns. Both introns in bacteria and mobile introns tend to be self-splicing, negating the need for the complex splicing machinery used by eukaryotes. Furthermore, the amount of non-coding DNA in eukaryotes varies enormously. Some newts have 20 times more DNA than humans, some ferns have 50 times more, and a few amoebas have fully 200 times more than humans.[13]

The base-pair pattern and size of introns varies enormously and the introns of many closely related organisms show little resemblance to each other beyond the fact that they occupy the same positions in the genes.[14] Comparisons of different species also reveal that although the introns, even those of closely related organisms, are “quite often different from each other,” the exons are often “very similar.”[15]  This finding poses major problems for evolution theory.

Conclusions

New UC Santa Cruz research implies that some introns can propagate themselves without killing their hosts. These introns made copies of themselves that insert into many genes across the genome. This haphazard process would, unless some system existed to regulate their implantation, damage the cell often to the point of destroying it. This view by Gozashti et al. supports the position that evolution is a blind, purposeless process except when it facilitates an organism’s ability to pass on its genes. Biologists Ursula Goodenough’s conclusion that some introns are regulatory modules floating in seas of meaningless sequences is a crazy quilt idea.[16]  Professor Raymo concludes that this structure “is not what one would expect of an intelligent designer… but is exactly what one would expect from …” evolution. In other words, the genome, because of all of its “junk” or useless base pairs, shows evidence of chance-driven evolution, not intelligent design. As important functions were discovered for introns, the evolution claim that they were useless remnants of viruses became yet another embarrassment for evolution.

No clear evidence yet exists that introns support an evolutionary origin for the genome. It now appears that problems with non-coding DNA develop only when mutations or other damage to the system occurs. We now know that DNA sequences not only carry information for making proteins, but also play many supportive roles in protein synthesis including manufacturing transfer RNAs that help to assemble amino acids into proteins and rRNA, as well as other forms of RNA.

In the past, evolutionary geneticists were uncertain as to what this apparently superfluous DNA does, and thus referred to introns and other non-coding DNA as “junk.” Evidence is now being accumulated that indicates most all of this DNA is not junk, but rather is critical for life. If functions for most or all of the non-coding DNA are found, Darwinism would be without the raw material needed to produce new genes by mutations that can be selected for evolution to occur. Furthermore, much of this new information on the complexity of the genome elegantly provides evidence for both intelligent design and for the concept of irreducible complexity.

Junkyards do not spontaneously produce functional complex systems when the wind blows. Graphic drawn for Creation-Evolution Headlines by J. Beverly Greene.

References

[1] Roy, Scott. Genome Evolution: Where Do New Introns Come From? Current Biology 22(13):R529-R531, 2012, p. R529.

[2] Watson, J.C., Gilman, M., Witkowski, J., and Zoller, M. Recombinant DNA. W.A. Freeman and Company, New York, 1992.

[3] Raymo, Chet. “Intelligent design does not compute.” The Boston Globe 19 June 2001.

[4] Coghlan, A. Science: The cryptographer who took a crack at ‘junk’ DNA. New Scientist, Issue 1879, p. 15, 26 June 1993.

[5] Coghlan, 1993, p. 15.

[6] Sica, A., Tse-Hua, T., Rice, N., Kretzchmar, M., Ghosh, P., and Young, H.A. The C-rel proto-oncogene product C-rel but not NF-kappa-B binds to the intronic region of the human interferon-gamma gene at a site related to an interferon-stimutable response element. Proceedings of the National Academy of Sciences of the United States 89(5):1740-1744, 1992.

[7] Malkinson, Alvin, and You, M. The Intronic Structure of Cancer Related Genes Regulates Susceptibility to Cancer.  Molecular Carcinogenesis 10:61-65, 1994.

[8] Huff, Jason, et al. Mechanism for DNA transposons to generate introns on genomic scales. Nature 538(7626):533–536, 2016.

[9] Gozashti, Landen, et al. Transposable elements drive intron gain in diverse eukaryotes. PNAS 119(48):e2209766119. https://doi.org/10.1073/pnas.2209766119, 2022.

[10] Roy, 2012, p. R529.

[11] University of California – Santa Cruz. Long-standing genomic mystery about the origins of introns explained in new study. https://phys.org/news/2022-11-long-standing-genomic-mystery-introns.html, 2022. Emphasis added.

[12] Gozashti, Landen, et al. Transposable elements drive intron gain in diverse eukaryotes. PNAS 119(48): e2209766119, 2022.

[13] Clark, David, and Russell, Lonnie. Molecular Biology. Cache River Press, Vienna, Illinois, p. 229, 1997.

[14] Wills, C. Exons, Introns, and Talking Genes; The Science Behind the Human Genome Project. Basic Books, New York, p. 178, 1991.

[15] Wills, 1991, p. 191.

[16] Quoted in Raymo, 2001; see Ref. 3.


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 1,800 college libraries in 27 countries. So far over 80,000 copies of the 60 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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