Reasons to Believe

“Junk” DNA: An Outdated Concept, Part 1 (of 6)

Recently, I sat in an audience of nearly 500 Christian leaders and listened to a biologist use the presence of Alu elements (a type of so-called “junk DNA”) in the human genome as a “proof” of evolution. Since I’ve always been a skeptical sort—especially when it comes to my own field—I whipped out my laptop and quickly scanned the scientific literature on the topic. Within a few moments, I was asking myself “Why would he choose Alu elements? There’s so much recent information in the scientific literature on functions for these sequences.” I still don’t have a good answer for that question.

This biologist isn’t alone. Many evolutionists use “junk DNA” as evidence for evolution. But, just as he isn’t alone, neither am I. More scientists are beginning to think that “junk DNA” is anything but “junk.” There is a growing acknowledgement that there are just too many important functions associated with these areas of DNA to refer to them as “junk.” Just consider some of these science stories from the past few years:

Even the Wikipedia entry on “junk DNA” has been updated to reflect a more current understanding of the concept. So, how did we even get to the term “junk DNA,” why has it been used as a line of evidence for evolution, and why is that no longer valid?

The History of “Junk DNA”
For many organisms (including humans), the vast majority of DNA in the genome does not contain information that leads directly to the production of proteins. Because they don’t “code” for a protein, these areas of DNA are called noncoding DNA. Scientists have identified a number of noncoding DNA categories, some of which were quickly recognized as possessing function even though they don’t code for a protein. However, some major categories of noncoding DNA were labeled “junk” because researchers truly believed these categories served no function. The label carried with it a connotation of something useless, like waste and rubbish.

This supposed lack of function combined with their consistent placement in the genome led researchers to consider the “junk DNA” as evidence for evolution. Evolutionists claim that the consistent placement proves the genomes were “inherited” from common ancestors. They argue that since these areas of DNA have no function, there is no reason why they need to be in the same place in multiple organisms; they occur in the same place only because the genome was inherited in the evolutionary process.

This argument hinges on the DNA’s lack of function—because once a segment of DNA has function, then its placement in the genome is likely critical to its function. As it happens, scientists steadily and continually report newly discovered functions for supposed “junk” DNA. It looks like using “junk DNA” as an argument for evolution is a thing of the past.

We at RTB like to stay on top of cutting-edge science apologetics. With that in mind, this six-part article series aims to help the term “junk DNA” to the quick demise it deserves. In particular, I will highlight the latest research into the functions of Alu elements—a type of “junk DNA” used by scientists as evidence for evolution.

A Few Key Cell Biology Concepts
Basic cell biology concepts are essential to understanding the functions of Alu elements. Since Alu elements are found exclusively in primates, all our descriptions will be in the context of primate cell biology.

A single cell doesn’t possess the capacity to house an organism’s genome. For example, if the DNA in a single human cell was stretched out to its full length, it would be approximately 2 meters in length. To help the cell accommodate that volume, the DNA is packaged into complexes of DNA and proteins called chromosomes. The number of chromosomes varies from organism to organism. Chimpanzees have 48 chromosomes, humans have 46.

The chromosome’s compact form is created by wrapping a segment of DNA around a group of proteins called histones. This creates a structure known as a nucleosome. Nucleosomes occur at somewhat regular intervals along the DNA, creating the appearance of beads on a string. When a segment of DNA is tightly coiled into a nucleosome, it is generally inaccessible for use by the cell; but researchers are pursuing the possibility that even DNA in the nucleosome may be accessible for some uses in the cell.1

Genes express themselves and exert their influence on a cell through two processes, primarily transcription and translation. Transcription produces a copy of the DNA known as pre-messenger RNA (pre-mRNA). The pre-mRNA contains some information unnecessary for creating a protein, so these areas of the pre-mRNA are removed in a process called splicing. Following splicing and additional chemical modifications, the pre-mRNA is ready to be used for making proteins and is dubbed messenger RNA (mRNA).

The mRNA docks on an organelle in the cell called the ribosome. There, the process of translation occurs. The information in the mRNA is “read” by the ribosome and used to build a protein. Proteins are the workhorse molecules of the cell, conducting most of its activities. Therefore, by serving as the starting point for the production of the cell’s proteins, the genes in the DNA end up controlling most of the activities in the cell.

Researchers now understand that Alu elements play a variety of roles in regulating the expression of the genes in a cell by influencing:

  • the placement of nucleosomes along the DNA;2
  • transcription; and
  • translation.

Over the next several weeks, we will examine these functions in more detail. For now, don’t label that DNA “junk” just yet.

Part 1 | Part 2 | Part 3 | Part 4 | Part 5 | Part 6

Dr. Patricia Fanning

Patricia Fanning is an RNA biochemist with a PhD from North Carolina State University and formerly a consultant for software companies. As a visiting scholar to Reasons To Believe in 2011, she specialized in human embryology and evolutionary development and regularly contributed to RTB’s podcasts and publications.


Subjects: Junk DNA

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Endnotes:

1. Geng Li et al., “Rapid Spontaneous Accessibility of Nucleosomal DNA,” Nature Structural & Molecular Biology 12 (January 2005): 46–53; Geng Li and J. Widom, “Nucleosomes Facilitate Their Own Invasion,” Nature Structural & Molecular Biology 11 (August 2004): 763–69; Miraslov Tomschik, K. van Holde, and J. Zlatanova, “Nucleosome Dynamics as Studied by Single-Pair Fluorescence Resonance Energy Transfer: A Reevaluation,” Journal of Fluorescence 19 (January 2009): 53–62; Feng Cui, M. V. Sirotin, and V. B. Zhurkin, “Impact of Alu Repeats on the Evolution of Human p53 Binding Sites,” Biology Direct 6 (January 6, 2011): 2–20.

2. Yoshiaki Tanaka et al., “Effects of Alu Elements on Global Nucleosome Positioning in the Human Genome,” BMC Genomics 11 (May 17, 2010): 309–19.