Junk DNA Is Slowly Revealing Its Secrets

A CRISPR study found
another important use of
once-labeled “Junk DNA”

by Jerry Bergman, PhD

What is junk DNA? It is the name for nonfunctional DNA. The belief that only a fraction of the human genome could be functional dates back to the late 1940s. The reason for this idea was laboratory evidence showing that the mutation rate in all life, including humans, was very high. If a large fraction of those mutations were deleterious, as the evidence indicated, the mutation load would eventually result in the extinction of all life. Therefore, the mutation load would be intolerable if all the DNA were functional. The conclusion was, a large amount of junk DNA must exist, and mutations in the junk DNA would not adversely affect survival.[1] Only mutations in the functional would be a problem.

This reasoning led to predictions in the late 1940s by one of the founders of population genetics, J.B.S. Haldane, and Nobel laureate Hermann Muller, that only a small percentage of the human genome would contain functional DNA elements (now called genes) that could be damaged by mutation. As most DNA was useless, thus “junk DNA,” most mutations would be in the useless junk DNA.

When the human genome was sequenced, it was found that only about 1 to 2 percent of the human genome codes for proteins. The vast majority (about 98-99 percent) was non-coding DNA.[2] Evolutionists exploited this finding which explained the existing high mutation rate. It also supported the view that, like the evidence of poor design, supported the evolutionary view. Clearly, an intelligent designer would not have designed a genome that was largely useless, or worse. Ruling out a designer opens the door to evolution.

The junk DNA theory is slowly disproved

One important discovery that forced researchers to reassess non-functional DNA came from studies of bacterial genomes. These typically have an extremely high gene density, and only a small percentage of genes were non protein-coding.[3] Soon, important uses were confirmed for the non-protein coding DNA. Noncoding DNA contains many types of regulatory elements, such as promoters, which provide binding sites for the protein machinery that carries out transcription used to make protein. This type of promoter is typically found in front of the gene.

Also found were enhancers, which provide binding sites for proteins to activate transcription. Enhancers were located on the DNA strand in front of, or after, the gene they regulated. Silencers provide binding sites for proteins that repress transcription. Like enhancers, they exist before or after the gene that they control. Insulators provide binding sites for proteins that regulate transcription. Some prevent enhancers from aiding transcription (enhancer-blocker insulators). Others prevent structural changes in the DNA that represses gene activity (barrier insulators). Some insulators even function as both enhancers, blockers, and sometimes also barriers as well!

Numerous other examples exist in genomic research showing specified complexity and design of the genome—characters only explainable by intelligent design, not by evolution. In recent decades geneticists have been uncovering a bewildering level of specified complexity that needs to be explored.

Failures in “Junk DNA” linked to Alzheimer’s Disease

The latest finding is that so-called “junk DNA” contains powerful switches that help to control the brain cells linked to Alzheimer’s disease.[4]  Genetic variants associated with complex traits often lie in enhancers, which function as switches located some distance away from the genes they regulate. Switches and regulators speak of design, not unguided evolutionary processes.

AstroREG is an example of an enhancer gene that regulates human astrocytes (thus the name Astro Regulator). Astrocytes are star-shaped brain cells that provide physical, metabolic, and functional support for neurons. They are crucial regulators, controlling neurotransmitter levels, supplying energy (lactate) to neurons and regulating ion balance. They also influence neuron synaptic strength and repair to keep neurons healthy, and enable efficient neural communication.

By testing nearly 1,000 enhancers identified by the ENCODE project, the researchers found over 150 regulatory interactions of enhancers that regulate the key astrocyte genes that are implicated in Alzheimer’s disease. They were then able to predict regulatory interactions with high specificity. The result was a comprehensive functional map of enhancer-mediated regulation in a key cell type, allowing researchers to better understand both brain function and disease. This knowledge can then be used to predict early onset of Alzheimer’s and lead to potential causes and treatments of this devastating disease-causing, progressive brain disorder that slowly destroys memory and thinking skills. Alzheimer’s is the most common cause of dementia, causing difficulty with daily tasks and changes in mood and behavior. The current theory is that the disease results from amyloid plaques and tau tangles that kill neurons. One summary of the study concluded

that so-called “junk DNA” contains powerful switches that help control brain cells linked to Alzheimer’s disease. By experimentally testing nearly 1,000 DNA switches in human astrocytes, scientists identified around 150 that truly influence gene activity—many tied to known Alzheimer’s risk genes. The findings help explain why many disease-linked genetic changes sit outside genes themselves. The resulting dataset is now being used to train AI systems to predict gene control more accurately.[5]

The technique used at the University of New South Wales, Sydney, to make these discoveries was CRISPR.[6]

Summary

This CRISPR research is only one example of research that leads to better understanding of specified complexity, which is more evidence of intelligent design and less evidence of mutation, natural selection caused evolution. Continued work will no doubt determine more uses for so-called junk DNA until, some researchers conclude, eventually all wrongly-labeled “junk DNA” will be determined to have important functions.

References

[1] Ohno, S., “An argument for the genetic simplicity of man and other mammals,” Journal of Human Evolution 1(6): 651–662, 1972.

[2] “What is noncoding DNA?,” MedlinePlus, https://medlineplus.gov/genetics/understanding/basics/noncodingdna/, 19 January 2021.

[3] Zhao, Z., et al., “Keeping up with the genomes: Efficient learning of our increasing knowledge of the tree of life,”  BMC Bioinformatics 21(1): 412, 21 September 2020.

[4]  University of New South Wales, “The 98% mystery: Scientists just cracked the code on “junk DNA” linked to Alzheimer’s,” ScienceDaily, 19 December 2025.

[5] University of New South Wales, 2025.

[6] Green, N., et al., “CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease,” Nature Neuroscience,

https://www.nature.com/articles/s41593-025-02154-3, 18 December 2025.

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 1,900 publications in 14 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.