Feedback: Degeneracy Discarded But Design Discovered

I am a Biblical Creationist who happens to teach General College Biology at a local community college. My lectures have always included the standard secular treatment regarding the "redundancy" of the genetic code.

Thank you for your September 16 article “Genetic ‘Degeneracy’ Goes the Way of ‘Junk’ DNA” as I am planning on incorporating the original article you cite [David D’Onofrio and David Abel, “Redundancy of the genetic code enables translational pausing,” Frontiers in Genetics (20 May 2014), doi: 10.3389/fgene.2014.00140. journal.frontiersin.org/Journal/10.3389/fgene.2014.00140/full] into my lectures.

While this is the first time that I have heard of the proposed function for redundancy in the genetic code, others suggest it is old news. Such a suggestion is the topic of the following link:

http://sandwalk.blogspot.com/2014/08/another-stupid-prediction-by.html

I can usually come up with my own response to scathing attacks on Creationist interpretations but I am having a problem in this case. I need help on this one.

Yours in Christ,

T. Z., Colorado, US

Thanks for reading our News to Know columns and for putting the information to use by teaching a broad range of students how to think critically about what they hear. It is always a challenge in articles like these to supply the public with the background research—what’s already known—while communicating what’s new.

For those readers who may not recall the article “TZ” is asking about, “Genetic ‘Degeneracy’ Goes the Way of ‘Junk’ DNA” reports that in addition to dictating amino acid sequences using a series of codons, the protein-coding regions in DNA have embedded in them an additional code! The essence of this code depends on the fact that there are multiple ways to “spell” the “word” (codon) that codes for certain amino acids. In the latest study the authors explain how the second code works and the evidence for their conclusions.

The apparent redundancy of the genetic code . . . has long been called codon “degeneracy”—evidence that the present genetic code is an evolutionary product.

The apparent redundancy of the genetic code, having several codons for the same amino acid, has long been called codon “degeneracy”—evidence that the present genetic code is an evolutionary product.

If “synonymous” codons (meaning they code for the same amino acid) are not redundant, degenerate, and functionally equivalent, but instead have purposeful redundancy in order to provide the building blocks for another code, then the notion that the genetic code is a product of random evolution becomes even more untenable. And if the structure, mechanism, and essential purpose of the secondary code are discovered—as this study suggests—then the observations of science support the fact that life was created by our intelligent Creator. And it is the latter that the study uncovered—not just the way the second code works but also what kinds of instructions it is giving and their vital purpose.

By analyzing data collected by many scientists over time, the authors of the latest study have unraveled the nature and purpose of a previously suspected secondary genetic code superimposed on the primary one. Nothing about this precise, unambiguous, critically important secondary code suggests it is a product of random chance. On the contrary, this study illustrates nothing random about the structure of DNA. DNA is a product of design, not disorder!

As I’m sure you noticed, the article I cited by D’Onofrio and Abel in Frontiers in Genetics is a “review article.” Such reviews of the published literature put together pieces of information reported or suspected by many scientists over a period of time—even decades—sometimes inferring new information and insights from a fresh perspective. Reviews like this are very valuable as they help scientists and the public see the “big picture.” Obviously, the editors of the peer-reviewed journal Frontiers in Genetics thought that “big picture”—in this case a better understanding of a genetic code within a code and the idea that what is still commonly called “degeneracy" is not—was worth publishing. (Perhaps the journal editors failed to consult the Sandwalk blogger who saw nothing new in the study and authored the derisive “Another stupid ‘prediction’ by Intelligent Design Creationists.”)

Additionally, some reviews—like this one—uncover patterns that reveal new information or confirmation of ideas previously only suspected. Through their analysis of three decades of data, D’Onofrio and Abel garner support for conclusions about the actual purpose and function of the superimposed genetic code within a code. Even if some people previously pondered the possibility proposed in the study, explains Answers in Genesis molecular geneticist Dr. Georgia Purdom, that is not the same thing as making a scientific case that such a hypothesis is correct:

I would agree that it has been known for some time that codon usage does slow or pause translation, but I don't believe it's been known that there was a reason for that (folding of proteins). Maybe some people guessed that was the reason,

but there wasn't actually measurable scientific evidence of it. All the critical Sandwalk blog does is link to past papers that show translational slowing/pausing occurs but not why it occurs.

Despite strong suspicion that a second layer of code was present in DNA, the term degeneracy, with its evolutionary implication, has persisted.

Despite strong suspicion that a second layer of code was present in DNA, the term degeneracy, with its evolutionary implication, has persisted. This analysis in Frontiers in Genetics makes a good case for just what that code is doing and why. Biblical creationists understand that the Creator God is the intelligent Designer who is the source of not only the information in the genomes of all kinds of living things but the Author of the very language in the genetic code itself.

God is the Common Designer of all living things. Because all living things reside on the same planet, they have many of the same biochemical needs, and draw from the same basic resources. It is only reasonable that God designed all living things to use the same genetic code, or language. In other words, the nucleotide combinations that stand for amino acids or signals in protein building and even in many regulatory genes are quite consistent across the biological world. That our intelligent Creator would construct a second coded language and superimpose it on the first is a delightfully complex design. Elucidation of what kind of instructions that language is issuing and the reason those instructions are important during protein synthesis is a grand discovery that points to the Author of all genetic codes and information.

That DNA contains a complex multi-level code was not a surprise to biblical creationists, just as the discovery in the ENCODE studies that most so-called “junk” DNA is not a useless evolutionary leftover but has function. The Sandwalk blogger’s argument reminds me of the hue and cry that went up when evidence emerged that most “junk” DNA has some function. Some evolutionary bloggers acted like they’d never considered it junk, while others declared that it was still function-less junk. (As an aside, the existence of some DNA for which we cannot determine a modern function is not proof of an evolutionary history. We may not know the function, or it may have been damaged by mutation, or it may have been switched off through various means.) Read more about this issue in “Junk DNA and ENCODE Revisited.”

Furthermore, if all the information about redundant codons has really been known for 30 years, as the Sandwalk blogger insinuates, why is the term degeneracy still in common use? If this is a beautifully designed, highly functional code, there is nothing “degenerate” about it. Could it be that the evolutionary implications of the word are too convenient and precious to relinquish?

Clearly, most discoveries in science come about through years of incremental efforts on the part of many people. And just as clearly, inconvenient scientific facts are sometimes ignored until they are forced to the surface. (I’m thinking of the fact that the appendix was known to have a role in the immune system for many years while it was still treated as a useless evolutionary vestige by scientists, medical and non-medical alike.) Articles like this one pull together scientific discoveries and draw long overdue conclusions about the big picture. And that makes it news! News that the people—inundated with evolutionary claims conveniently bottled in catchy words (like junk and degeneracy) and cute names for our so-called ancestors (like “Lucy” and “Karabo”)—need to know!