Is Intelligent Design theory a science stopper? The ENCODE project

The Intelligent Design theory of life on Earth has been labeled a “science-stopper” by some who believe in a purely naturalistic evolutionary beginning and development of living organisms. The assertion accuses ID theorists of invoking a supernatural cause to natural processes that are not well understood. Is that true? Ardent atheist Richard Dawkins, wrote in his influential 1976 book The Selfish Gene, that non-coding DNA functioned like a “parasite” within the genome. In the evolutionary process, these useless segments of the genome remained after fulfilling their function, raising the question, according to Dawkins, of why a creator would insert worthless code into a genome. Even Francis Crick, Nobel Prize winner and co-founder of the double helical structure of DNA, in 1980, dismissed most of the genome as “little better than junk”. He continued by predicting that it would be “folly” for scientific researchers to “hunt obsessively” for function for many sections of DNA. [1]

Beginning in 2003, the National Human Genome Research Institute initiated an ambitious project named ENCODE, the Encyclopedia of DNA Elements, with the goal of identifying functional elements in the human genome sequence. The ENCODE project continued where the Human Genome Project left off. The first phase concluded in 2007 and the results of the second phase were released on September 15, 2012 in the form at least 30 papers published in several scientific journals (Nature, Genome Biology, and Genome Research). After $185 million, research by 32 groups involving more than 440 scientists, the consortium has discovered function for roughly 80% of the genome, including more than 70,000 “promoter” regions where proteins bind to control gene expression. They have also identified almost 400,000 “enhancer” regions which regulate expression of distant genes. [2] Researchers mapped more than 4 million regulatory regions where proteins interact with DNA. They performed more than 1,600 sets of experiments, using state of the art DNA sequencing technologies, generated more than 15 trillion bytes of raw data and consumed the equivalent of more than 300 years of computer time for analysis. [3]

The researchers found that, though only a small amount of genome directly manufactures messenger RNA for protein-coding, much of the DNA becomes transcribed into non-coding RNA molecules, some of which regulate gene expression. This critical function can operate to turn on or turn off certain portions of the genome. In the past, these segments were often called DNA deserts or “junk DNA”, because they did not appear to have any useful function. In 2000, when the Human Genome Project presented its first rough draft of the sequence of bases, the initial results seemed to confirm evolutionary theory that perhaps 97 percent of the 3.2 billion bases had no apparent function. About 1.2% of the genome bases were found to be involved in protein-coding, which was somewhat expected. However, the ENCODE project found about 8-9% of the bases were involved in regulation. According to computational biologist and project manager Ewan Birney, “One can use the ENCODE data and come up with a number between 9 and 80 percent” attributable to functional significance. [4] It could take decades to fully analyze and comprehend the raw data, but results at this time clearly indicate that vast portions of DNA previously considered to be useless are indeed useful.

Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute (NHGRI) stated: “"During the early debates about the Human Genome Project, researchers had predicted that only a few percent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong." [3] While naturalistic Darwinian theorists essentially considered these regions to be the molecular equivalent of a human appendix – useless leftovers from our evolutionary past – intelligent design proponents asserted that function could be discovered for most or all of these. So, which theory would have been considered more of a science-stopper just a few years ago? Rather than an alleged God-of-the-gaps, “junk DNA” could logically be considered evolution-of-the-gaps reasoning.

Biochemist Dr. Fazale Rana notes that “researchers are uncovering more and more examples of the functional importance of junk DNA. In light of this ongoing advance, it is becoming harder and harder to maintain that genomes are riddled with useless evolutionary vestiges.” [5] Even more intriguing, the methods of data organization within DNA are uncannily similar to those utilized in digital data storage by humans today. Stephen C. Meyer, PhD, University of Cambridge, noted that the hierarchical layering within the genome allow for vast amounts of data storage: “The functions they perform are so strikingly similar to functions that we’ve designed to solve similar information and storage problems in high tech digital computers.” [6]

Rather than applying the brakes to scientific discovery – a common accusation - belief in God and Christianity in particular was the impetus for the greatest expansion of knowledge and discovery throughout much of history. Of the major world religions, Christianity is based on reason, giving rise to exploration of logical physical laws of the universe and a rational creator. A very short list of scientists who have made critical discoveries while holding to a strong Christian faith were: Johannes Kepler (laws of planetary motion), Isaac Newton (mathematics), Nicholas Copernicus (astronomy), Francis Bacon (experimentation and inductive reasoning), Robert Boyle (gas laws), Michael Faraday (electricity and magnetism), William Kelvin (modern physics), Max Planck (quantum theory), and Gregor Mendel (mathematical foundations of genetics). Some additional 20th century Nobel prize winners in the sciences with a strong faith in God include: Werner Heisenberg, Erwin Schroedinger, Gugleilmo Marconi, and Arno Penzias. [7]

The discovery of function in regions of the human genome that were previously thought to be useless leftovers from our evolutionary past further illustrates the fact that belief in an intelligent creator is not a science-stopper; on the contrary, it provides the philosophical impetus to uncover the intricacies of the creation. Other examples could be cited, such as the big bang theory. Prior to Georges LeMaitre and Albert Einstein’s discoveries that the universe is indeed expanding, the prevailing understanding of the cosmos was that of a steady state, with no discernible beginning. That would have been more of a science-stopper than belief in the Bible, which states the universe had a beginning. Astrophysics caught up with the Bible and now we are witnessing the same phenomenon on the level of molecular biology.

[1] Francis Crick, quoted by Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.
[2] Brendan Maher, “ENCODE: The human encyclopaedia”, Nature, Vol. 489, Issue 7414, 5 Sept 2012.
[3] NIH/National Human Genome Research Institute. “First holistic view of how human genome actually works: ENCODE study produces massive data set.” ScienceDaily, 5 Sep. 2012, Web 28 Dec. 2012.
[4] Stephen S. Hall, “Hidden Treasures in Junk DNA”, Scientific American, 8 Sept 2012.
[5] Fazale Rana, “Gene deserts take the life out of evolution’s best argument”, Reasons to Believe, 6 Apr 2011.
[6] Stephen C. Meyer, quoted by Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.
[7] Tihomir Dimitrov, “50 Nobel Laureates and Other Great Scientists Who Believe in God, 2007.
Daniel James Devine, “Debunking Junk”, World magazine, 6 Oct 2012.