More Evidence Refutes Myth of Junk DNA

The Junk DNA idea is still dying.
It’s not dead yet but getting there.

 

by Jerry Bergman, PhD

Preface

The headline of a new article in Science News about the findings of a new study announced “A key to the mystery of fast-evolving genes was found in ‘junk DNA’”[i] The details show why some genes rapidly “become crucial because they regulate a type of DNA called heterochromatin. Once considered ‘junk DNA,’ heterochromatin actually performs many important jobs, including acting like a tightly guarded prison: It locks up ‘bad actor’ genes, preventing them from turning on and doing damage.” This new study indicates that what had been called “new genes,” supposedly created by random mutations and favored by natural selection evolution (such as the gene in fish that makes a novel antifreeze), were there all the time.[ii] The existing genes were activated when the conditions were appropriate! If this finding is supported, a favorite evidence of the ability of mutations to evolve new genes that produce new traits will have to be added to the many mistakes and blunders of evolutionists![iii] I will report on this research in a future post.

[i] Brouillette, Monique. 2020. A key to the mystery of fast-evolving genes was found in ‘junk DNA’ Science News. December 3 2020. https://www.sciencenews.org/article/essential-genes-fast-evolution-junk-dna-heterochromatin-genetics
[ii] Kasinathan, B.  et al. Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. Published online November 10, 2020. doi: 10.7554/eLife.63368.
[iii] Bergman, Jerry. 2017. Evolution’s Blunders, Frauds and Forgeries. Atlanta, GA: CMI Publishing.

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Main Article

After the human genome was sequenced, a major conclusion of preliminary research was that over 98 percent of the DNA in our genome is junk – meaning it appeared to lack any function. Science writer Daniel Blanco recalls the feeling at that time in Discover Magazine in August 2019: “Our genetic manual 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]

This widespread view handed evolutionists a golden nugget to augment and reinforce claims of ‘poor design’ in the human body. Some evolutionists keep lists of organs and structures in our genes they claim are useless. If God created us, they reasoned, why would humans have so many examples of bad design? Conversely, evolutionists claimed, this knowledge fits perfectly with evolution. Their conclusion: junk DNA refutes Intelligent Design.[2]

Wikipedia explains the argument from poor design, formally called the dysteleological argument:

if “creation” contains many defects, then design appears an implausible theory for the origin of earthly existence. Proponents most commonly use the argument in a weaker way, however: not with the aim of disproving the existence of God, but rather as a reductio ad absurdum of the well-known argument from design (which suggests that living things appear too well-designed to have originated by chance, and so an intelligent God or gods must have deliberately created them).[3]

An article “produced and financed by the University of Oslo” in April 2020 quoted Professor Glenn-Peter Sætre and concluded the following:

Evolution is a fantastic and exciting process, which has come up with an endless number of creative life forms and shapes. However, there is no reason to believe that an intelligent designer controlled the process. Any poor designer with millions of years available for trying out new solutions could have done a much better job.[4]

Readers are not told that every example used to support the anti-creation position cited in this article has been well-documented as wrong in peer-reviewed scientific literature.[5] Another scientist publishing in Princeton University Press in 2006 opined,

What designer with any competence and with any compassion at all would construct a mode of living and survival that entails so much pain, so much awkwardness, such clumsy reuse of organs and limbs apparently adapted for other purposes? Why force aquatic birds (with wings that don’t work as means to flight but are already readapted for swimming) to “march” for seventy miles from their source of food to their breeding grounds, or to walk on their heels for months in order to protect the egg from touching the ice and immediately freezing? Was it an intelligent designer, or the penguins, who figured out that this was a manageable way to do things, and then did it?[6]

D. Wise made similar “poor-design” claims in 2005 when belief in junk DNA was still strong:

[We] have a philosophic choice between evolution or belief in ID, so called intelligent design. But even a first-year engineering student would be embarrassed to have designed your lower back with the extreme bend that allows you to stand erect even though your pelvis slants forward for knuckle-dragging like all our near relatives. You probably have had braces or wisdom teeth extracted because there are too many teeth for the size of your mouth. Then there are your sinuses, with a flawed drainage system that would provoke laughter from a plumber. Yet evolution provides a ready and rational explanation for all these design failures: by progressive changes into an erect posture, by shortening of a mammalian muzzle into a face, and by expansion of our large brains to crowd the facial bones. So take your choice: Do you prefer evolution or an ID whose letters may as well stand for Incompetent Design?”[7]

Now, though, Wise should be embarrassed by such irresponsible claims. They have all been refuted by the peer-reviewed scientific literature.

Likewise, the oft-stated belief that 98 percent of the human genome is junk would (if true) eloquently support the claim that the dysteleological argument disproves design and forcibly supports the evolutionist position that we are the result, not of design, but of billions of mutations. It would also support the idea that mutation does not overwhelm the organism and cause genetic catastrophe. Why? Well, since 98 percent of all mutations do not affect the genes that make protein, mutations must be tolerated.

Time and more research, however, has not supported these positions.

Things Get More Complicated

Blanco wrote that “the protein-making process is not as straightforward as reading a cooking recipe. Before putting proteins together, DNA gets transcribed into threads of RNA that are chopped and reassembled into smaller pieces.”[8] Did you get that? RNA is chopped up and reassembled into smaller pieces. Assuming this is correct, this means a designed system must make the cuts in the right places at the right time and then reassemble the parts, ensuring they are reassembled in the correct order, and then stitch the sections together. It requires an accurate fine-tuned mechanism to achieve this goal.

The splicing system must be well-designed in order to reassemble the sections correctly. Otherwise the protein will not function properly, or will not function at all, which could be lethal. And this process must be carried out for all, or most, of the 20- to 23-thousand genes that the Human Genome Project estimates exists.[9] The assembly process, therefore, appears to be more complex than the genes themselves. If we estimate that the assembly process requires 10 parts, that would mean that up to 200- to 230-thousand parts would be required for all of the genes.

Blanco continues, writing: “During the chopping, the non-coding stretches — the junk — are discarded, meaning they never even get used to make proteins. Why nature carries so much seemingly unnecessary material in its guidebook is a question that researchers continue to ponder.”[10] He correctly suggests that the intelligent design position might be correct, writing: “The most logical explanation is that this ‘junk DNA’ might not be so useless after all.”[11] This is exactly what research is finding. Specifically, over

the last 10 years, an international team of 442 scientists have assailed 147 different types of cells with 24 types of experiments. Their goal: catalogue every letter (nucleotide) within the genome that does something. The results are published today in 30 papers across three different journals.[12]

These 442 scientists released what they called the Encyclopedia of DNA Elements, or ENCODE. The collaboration researched the function of every letter in the human genome. The results of this massive undertaking rejected the junk DNA claim. But the findings were resisted strenuously by many evolutionists who did not want to lose this important evidence for Darwinism.

What the Junk Does

Here are some of many examples of now ‘ex-junk’ DNA. Some portions contain docking sites where proteins can be attached to regulate genes. So far, more than 70,000 genes called promoters control nearby genes. More than 400,000 examples were found that function to enhance transcription, often influencing genes great distances away from the controlling element. Some non-coding regions affect how DNA is folded and packaged. Other ‘junk’ DNA is transcribed into RNA. Science writer Ed Yong comments, many evolutionists still “maintained that much of these sequences were, indeed, junk.” That had been true for the eight years prior to his article in 2012 about ENCODE. The deniers today, however, are dwindling in number.

This latest study reported on here will push a few more evolutionists to accept the design conclusion. The study supports the picture of a genome that is clearly well-designed, all of it. In 2012, 80 percent of non-coding DNA was found to be transcribed, indicating it has a function. Evolutionists could claim that the remaining 20 percent is junk, allowing them to argue for evolution, however much less confidently. Even in 2012, Ed Yong felt that the remaining 20 percent was probably not junk either. That view is proving correct.[13]

The Remaining “junk” DNA Is Full of Information

A review of a study from November 2019 remarks that it “should not surprise us that even in parts of the genome where we don’t obviously see a ‘functional code’” (speaking of the new type of code discovered) there are functions that are “not like anything we’ve previously considered.” They found portions responsible for “gene spaces” and “spatial compartments” such as genome 3-D shape design. Essentially, the non-coding DNA performs the role of punctuation and formatting of the coding DNA. This discovery is helping to resolve the “longstanding problems of “non‐coding DNA,” “junk DNA,” and “selfish DNA” leading to a new vision of the genome as shaped by DNA sequences.”[14]

In other words, “junk” DNA, among other things, helps regulate the arrangement of information in the genome and the “structurally important elements in forming the correct shape and separation of condensed coding sequences in the genome.”[15] Another finding was that non-coding DNA may have a role in “alternative splicing” – i.e., that a single sequence can “encode” more than one piece of information, depending on what is “reading” it and in which direction it reads it. For instance, “viral genomes are classic examples in which genes read in one direction to produce a given protein overlap with one or more genes read in the opposite direction.”[16] Moore’s article relates another example:

the amino acid Threonine can be coded in eukaryotic DNA in no fewer than four ways: ACT, ACC, ACA or ACG. The third letter is variable and hence “available” for the coding of extra information. This is exactly what happens to produce the “genomic code”, in this case creating a bias for the ACC and ACG forms in warm-blooded organisms.[17]

Moore is speaking of the fact that some amino acids can be coded by multiple codons. In the past, geneticists assumed that it did not matter which one, in this example of four codons for threonine, was used to make protein, but it is now realized that it does matter and this is one more example of why: the protein gets additional information from the type of codon specified. This is another example why mutations, even if they do not change the amino acid in a protein, are mostly deleterious.

Much more could be said about the findings of the study reviewed here, but these few examples will give the reader some insight into the direction research is taking us.

Summary

The genome is not only more complex than we thought a few years ago, it is more complex than we thought it could be. This study has opened the door a little wider to reveal that complexity. More research assuredly will open it even further.

References

[1] Blanco, D,B., Our Cells Are Filled With ‘Junk DNA’ — Here’s Why We Need It, https://www.discovermagazine.com/health/our-cells-are-filled-with-junk-dna-heres-why-we-need-it, August 2019.

[2] Wise, D.U.,  “Intelligent” Design versus Evolution, Science 309(5734):556–557, July 2005.

[3] Argument from poor design. https://en.wikipedia.org/wiki/Argument_from_poor_design, January 2021.

[4] Rosjo, B., Evolutionary flaws disprove the theory of intelligent design: Evolution has produced amazing life forms, but you need look no further than to the human body to find examples of poor construction,  https://partner.sciencenorway.no/evolution-genetics-natural-sciences/evolutionary-flaws-disprove-the-theory-of-intelligent-design/1670232, April 2020.

[5] See Bergman, J., Useless Organs: The Rise and Fall of the Once Major Argument for Evolution, Tulsa, Oklahoma, Bartlett Publishing, 2019, and Bergman, J., The “Poor Design” Argument Against Intelligent Design Falsified, Tulsa, Oklahoma, Bartlett Publishing, 2019.

[6] Levine, G., Darwin Loves You: Natural Selection and the Reenchantment of the World. Princeton, New Jersey, Princeton University Press, 2006, pp. 256-257.

[7] Wise, D., “Intelligent” design versus evolution, Science 309(5734):556-557, August 2005.

[8] Blanco, 2019.

[9] What is a gene?, MedlinePlus, https://medlineplus.gov/genetics/understanding/basics/gene/, September 2020.

[10] Blanco, 2019.

[11] Blanco, 2019.

[12] Yong, E., ENCODE: the rough guide to the human genome, https://www.discovermagazine.com/the-sciences/encode-the-rough-guide-to-the-human-genome#.XVLhe5NKjm3, September 2012.

[13] Moore, A., That “junk” DNA … is full of information! Advanced Science News, https://www.advancedsciencenews.com/that-junk-dna-is-full-of-information/, November 2019.

[14] Bernardi, G., The genomic code: A pervasive encoding/molding of chromatin structures and a solution of the “Non‐Coding DNA” mystery, BioEssays 42(12): 1900106, https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201900106, November 2019.

[15] Moore, 2019.

[16] Moore, 2019.

[17] Moore, 2019.

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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.