The End of the Junk DNA Theory

Posted: December 14, 2011 in Biology Related
Tags: , , , , , , , ,

“When the first molecular geneticists worked out the details of transcription and translation in the 1960s, they never imagined that only 1.5 percent of human DNA encodes protein. What does the “other” 98.5 percent do? It includes viral sequences, sequences that encode RNAs other than mRNA (called noncoding or ncRNAs), introns, promoters and other control sequences, and repeated sequences… Most of the genome is transcribed- it isn’t ‘junk.’”[1] –Dr. Ricki Lewis, Geneticist and Genetic Counselor for CareNet medical Group



“When James Watson and Francis Crick solved the structure of DNA in 1953, Crick formulated the “Central Dogma” of molecular biology, often stated as “DNA makes RNA makes protein makes us.” This implies that mutations in protein-coding DNA provide the raw materials for evolution. In the 1960s, however, biologists discovered that about 98% of our DNA does not code for protein. Some — including Crick — called the non-protein-coding DNA “junk” and attributed it to the accumulation of molecular accidents during evolution.

Since the mid 1990s, some defenders of Darwinian evolution — including Richard Dawkins, Kenneth R. Miller, Douglas J. Futuyma, Michael Shermer, Francis S. Collins, Philip Kitcher, Jerry A. Coyne and John C. Avise — have argued that “junk DNA” provides evidence for Darwinian evolution and against intelligent design. (Intelligent design, or ID, is the view that we can infer from evidence in nature that some features of the world, including some features of living things, are better explained by an intelligent cause than by unguided natural processes.)

By 2007, however, it was clear that most of the mammalian genome is transcribed into non-protein-coding RNA. Since organisms struggling for survival would presumably not invest so much energy in producing junk, this implied that most non-protein-coding DNA is probably not junk after all.

Since then, specific biological functions have been discovered for many non-protein-coding RNAs. Although functions have not yet been identified for many parts of our genome, the list of specific functions for so-called “junk DNA” is already long, and it grows longer every week. Defending Darwinism and criticizing ID on the grounds that most of our genome is junk amounts to a “Darwinof the gaps” argument that has to retreat with each new discovery.”[2] –Jonathan Wells, Molecular and Cellular Biologist

“…molecular taxonomists, who have been drawing up evolutionary histories (‘phylogenies’) for everything, are going to have to undo all their years of ‘junk DNA’-based historical reconstructions and wait for the full implications to emerge before they try again. One of the supposedly ‘knock-down’ arguments that humans have a common ancestor with chimpanzees is shared ‘non-functional’ DNA coding. That argument just got thrown out the window.”[3] Dr. Alex Williams, Botanist and Radioecologist


“‘Junk’ DNA is thought by evolutionists to be useless DNA leftover from past evolutionary permutations. According to the selfish or parasitic DNA theory, this DNA persists only because of its ability to replicate itself, or perhaps because it has randomly mutated into a form advantageous to the cell. The types of junk DNA include introns, pseudogenes, and mobile and repetitive DNAs. But now many of the DNA sequences formerly relegated to the junk pile have begun to obtain new respect for their role in genome structure and function, gene regulation and rapid speciation. On the other hand, there are examples of what seem to be true junk DNAs, sequences that had lost their functions, either to mutational inactivation that could have occurred post-Fall, or by God-ordained time limits set on their functions.

Criteria are presented by which to identify legitimate junk DNA, and to try to decipher the genetic clues of how genomes function now and in the past, when rates of change of genomes may have been very different. The rapid, catastrophic changes in the earth caused by the Flood may also have been mirrored in genomes, as each species had to adapt to post-Flood conditions. A new creationist theory may explain how this rapid diversification came about by the changes caused by repetitive and mobile DNA sequences. The so-called ‘junk’ DNAs that have perplexed creationists and evolutionary scientists alike may be the very elements that can explain the mechanisms by which God is at work in His creation now and in the past.”[4] –Dr. Linda K. Walkup, Biochemist and Molecular Geneticist


“We are now seeing the majority of the rest of the genome is active to some extent… This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed.”[5] –Dr. Tim Hubbard, Head of the Human Genome Analysis


“A number of studies have now confirmed that this “junk DNA” is functional. A 2004 study suggested that this class of DNA, comprising more than 1/3 of mouse DNA, is involved in controlling the complex sequence of events during embryo development. A study in 2009 showed that retro-transposons are located before and after protein coding genes; they do not occur at random. Ones located before the protein-coding genes enable multiple readings for the genes: the genes can produce different proteins using different starting points in the supposedly “junk” DNA. Some enable genes to be ‘read’ in the opposite direction to normal, again producing an entirely different protein. Ones that follow the genes regulate the gene activity, controlling how much of the protein the cell produces. The researchers found some 23,000 such likely regulatory regions in the ‘junk’. Clearly, the idea of junk DNA is junk science. Not only is evolution bad for theology; it’s bad for science as well.”[6] –Dr. Don Batten, Horticulturist and Plant Scientist



“It is hoped that studying the non-coding sequences will lead to a greater understanding of disease processes. The likelihood of developing Type 2 diabetes has already been linked to mutations in non-coding sequences… Unfortunately, for many years this notion that non-coding DNA was not functional (“junk”) actually inhibited science.”[7] -Dr. Georgia Purdom, Molecular Geneticist


“These new discoveries are prompting scientists to think twice about dismissing such a large portion of the genome as nothing but ‘junk.’”[8] Dr. Leslie Pray, Population Geneticist

[1] Lewis, R. (2008) Human Genetics: Concepts and Applications, McGraw-Hill,New York; NY, pp. 208

[2] Wells, J., (October, 2011) “The Receding Myth of ‘Junk DNA,’” Evolution News and Views,

[3] Williams, A., (June 2007) “Astonishing DNA Complexity Uncovered,”

[4] Walkup, L.K., (August 2000) “’Junk’ DNA: Evolutionary Discards or God’s Tools?” Technical Journal, 14(2); pp. 18

[5] (June 2007) “Human Genome Further Unraveled,” BBC News,

[6] Batten, D., “The Lingering Death of Junk DNA,”

[7] Purdom, G., (August 2007) “’Junk’ DNA- Past, Present, and Future,” Answers in Genesis,

[8] Pray, L., (2008) “Transposons, or Jumping Genes: not Junk DNA?” Scitable by Nature Education,


  1. matthew2262 says:

    “What is increasingly seen as the DNA story unfolds is prima facie evidence of intelligent design extending over the whole molecule. What used to be thought of as a prodigious 95 per cent excess of repetitive and useless DNA turns out to be an interactive regulatory network controlling gene expression in the remaining five per cent. Even the humble trinucleotide repeat sequence CAG has been implicated in the pathogenesis of a number of serious neurological diseases. This illustrates the complicity of the simplest codes in the intricate regulatory network, and puts further strain on ideas of the code’s abiotic origin.” Biochemist and head of the Department of Nuclear Medicine and Director of Clinical Research at the Singapore General Hospital, Dr. Aw Swee-Eng. “The Origin of Life; a Critique of Current Scientific Models,”

  2. matthew2262 says:

    “Some junk is worth keeping. Non-coding, or junk, mouse DNA contains vast amounts of information vital to gene function — and those regulatory functions take up much more space on the genome than the all-important coding segments.

    Less than 2 per cent of DNA actually codes for proteins, so the double helix is responsible for a great deal more than making proteins. Some segments are designated enhancers and promoters. These bind transcription factors that allow coding DNA to be read and translated into proteins. Other regions, called insulators, prevent neighbouring genes from being read together accidentally.

    To work out which sections of DNA might contain these segments – collectively known as cis-regulatory elements — Bing Ren at the Ludwig Institute for Cancer Research at the University of California, San Diego and colleagues looked at the genomes of 19 types of mouse tissue.”

  3. matthew2262 says:

    “Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes.”

  4. matthew2262 says:

    “For a long time, DNA with no known purpose in the cell was called junk DNA. As with vestigial structures, the problem was the key word ‘known.’ For thirty years after the elucidation of the structure of DNA and its role in inheritance, little attention was paid to noncoding DNA, and the 90% that does not code for protein, but since the 1980s studies have revealed that at least the vast majority of DNA has a function. While scientific journals started putting ‘junk DNA’ in scare quotes in the middle of the 1990s to indicate that the name was no longer fit, textbooks and popular science writers have been slow to follow suit. The focus on genes as the basis of heredity similarly limited research on factors outside the DNA base sequence that also play a role in inheritance, a field now known as epigenetics.”

    -Gerald Rau (Ph. D., Cornell) Founder and Chief Editor at Professional English International.

    Rau, G., (2012) Mapping the Origins Debate, (Downers Grove, IL: InvterVarsity Press) pp.116

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