Until very recently, one of the strongest arguments for Darwinian evolution and against intelligent design (ID) was the appearance of what many molecular biologists call “junk DNA.” 

The DNA molecule provides instructions that ultimately form the proteins that are the building blocks of life.¹ When the iconic helix-shaped DNA molecule was first characterized by Francis Crick and James Watson in 1953, DNA was thought to have a single function: to build the thousands of different proteins that form the various organs and structures in all life-forms on the planet.² Later the somewhat similar RNA molecule was found to play an intermediary role in protein synthesis.³

Crick went on to enunciate what he modestly called the Central Dogma of molecular biology (yes, the caps go with it!).⁴ It can be stated simply: DNA builds RNA. RNA builds proteins. Proteins build organs and organisms.

Discovering the Junk

However, dogma—central or not—sometimes oversimplifies the complexity of reality. Throughout the latter half of the twentieth century, cell biologists began to discover that much—in fact, most—of the DNA molecule did not participate in the synthesis of proteins. Confronted with this fact and interpreting through the framework of Darwinian evolution, scientists began to view this non-coding DNA as vestiges of lower forms of life whose DNA was altered by mutations in a way that made them useless to their progeny. Hence the name “junk DNA.”

As the percentage of the DNA strand known to code for protein synthesis dwindled to little more than 1 percent,⁵ evolutionary biologists began to mock ID theorists about an Intelligent Designer who “would litter the human genome” with a “hodgepodge of borrowed, copied, mutated, and discarded sequences and comments that has been cobbled together by millions of years of trial and error.”⁶  

Richard Dawkins, a biologist and leader in the New Atheist movement, goes a bit further in his taunting: “It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene—a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something—unless he was deliberately setting out to fool us.”⁷

Junk DNA and Junk Organs

However, recent advances in our ability to “see” the hidden world of coded information and the intricate machinery within a cell is revealing a far different story.

The junk DNA argument is going the way of the older “junk organ” argument, which posited that our bodies contain vestigial organs from long-past ancestors: gills from our fish ancestor (which turned out to be mere skin folds near the ear); the spleen; and, most famously, the appendix. But far from being useless, the appendix is vital in repopulating the intestines with helpful bacteria after an illness, according to Bill Parker, an assistant professor of surgery at Duke University Medical Center.⁸ What were once called junk organs have been shown either not to be organs at all or to, in fact, have functions. 

Fast forward to 2012. A nearly $200-million six-year study called ENCODE concluded that at least 80 percent of the human genome is biochemically functional.⁹ Says molecular biologist Dr. Fuzale Rana: 

Since the initial sequencing of the human genome, many skeptics and evolutionary biologists have asserted that the most compelling evidence for human evolution—and the most potent challenge against intelligent design/creationism—is the vast amount of junk DNA in the human genome. And yet, with the results of the ENCODE Project, these arguments evaporate. We can no longer consider the human genome a vast wasteland of junk, but an elegant system that displays sophistication in its architecture and operation, far beyond what most evolutionary biologists ever imagined.¹⁰

Molecular biologist Dr. Todd Howren agrees: 

Molecular evolution states that the supposed Junk DNA is the leftover DNA from biological experiments, genes that are no longer needed, etc. This leftover DNA is a critical piece of evidence supporting molecular evolution. Because the junk theory provides support to Darwinian origin models, the naturalists are attacking ENCODE’s findings ardently.¹¹

Describing the functions of the non-coding DNA as revealed through the ENCODE project gets very technical very quickly. For the reader interested in understanding these processes, a good place to start is The Myth of Junk DNA by Jonathan Wells.¹² Wells summarizes some of the several hundred studies stemming from this work, all of which point to the functionality of what was once called junk DNA.

Abandoning Darwinism

It would be wrong to imply that the scientists who are discovering functions for non-coding DNA and no longer use the phrase “junk DNA” are giving up on Darwinism altogether. A paradigm shift may indeed be in the making, but powerful dogmas die hard—especially when careers and reputations have been heavily invested in the Darwinian enterprise.

To be sure, other factors are at work in the reticence to abandon the Darwinian paradigm. Some point to the historical tendency of scientists to hold on to a faulty explanatory model until a better one can replace it. Certainly another part of the reluctance to abandon Darwinism lies in the very definition of the word “science.” 

In more recent times, science has been redefined to exclude explanations that suggest non-naturalistic forces may be involved in the natural world. Therefore, if an Intelligent Designer best fits the data at hand, this explanation is labeled “religious” and ruled unscientific. And, because science is viewed as the modern arbiter of truth, design inferences are out-of-bounds in the objective quest for truth (and therefore should only be discussed as a matter of subjective opinion).

Regardless, the term “junk DNA,” like “junk organs,” is no longer an effective argument against intelligent design.