Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

A sampling of new research uncovers more function for junk DNA, undermines one of the best arguments for biological evolution

My wife enjoys shopping at large club stores. I, however, don’t care for them much. Still, from time to time I’ll join Amy on her shopping excursions, usually enticed by the prospects of free food samples. Nothing’s better than walking up and down store aisles greedily ingesting morsels of tasty food on a late Saturday morning, right before lunch.

Club stores offer free bites of food to let the customers know about all the wonderful products that are available. I’m going to follow suit in this article by offering up a sampling of recent discoveries that ascribe function to junk DNA with the hope that you will have an idea of the remarkable advances happening in molecular biology—advances that are eroding support for one of evolution’s best arguments.

Junk DNA and the Case for Biological Evolution
Evolutionary biologists consider the existence of junk DNA as one of the most potent pieces of evidence for biological evolution. According to this view, junk DNA results when biochemical processes and chemical and physical events transform a functional DNA segment into a useless molecular artifact. Such pieces of DNA remain part of an organism’s genome solely because of its attachment to functional DNA. In this way, junk DNA persists from generation to generation.

Evolutionists also highlight the fact that in many instances identical (or nearly identical) segments of junk DNA appear in a wide range of related organisms. Frequently, the identical junk DNA segments reside in corresponding locations in these genomes. Evolutionists take this to indicate that these organisms shared a common ancestor, suggesting that the junk DNA segment arose prior to the time that the organisms diverged from their shared evolutionary ancestor.

The challenge represented by junk DNA takes on a similar logical form to the problem of evil:

• God is all-good.
• God is all-powerful.
• God is all-knowing.
• Junk DNA exists.

For skeptics and atheists, the last statement is incompatible with the first three. Evolutionists ask, “Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?”

Responding to the Junk DNA Challenge
Proponents of intelligent design and creationism respond to this valid objection by highlighting the many recent findings that attribute function to junk DNA. Here is a sample of findings that have been reported during the last few months—just to give you a taste.

SINE DNA

This class of junk DNA belongs to a category of sequences known as transposable elements—pieces of DNA that jump around the genome, or transpose. In the process of moving around the genome, some transposable elements make additional copies of themselves, and therefore increase in number when they transpose. SINES belong to a subclass of transposable elements, called retrotransposons. Molecular biologists believe that these DNA elements duplicate and move around the genome through an RNA intermediate and the activity of reverse transcriptase.

SINES range in size from 100 to 300 base pairs (genetic letters). In primates, the most common SINES are the so-called Alu sequences. In fact, there are about 1.1 million Alu copies in the human genome (roughly 12% of the human genome). Alu sequences contain a segment that the cell’s machinery can use to produce an RNA message. In this way, SINES can duplicate and move around the genome as reverse transcriptase back-converts SINE RNA into DNA.

Previous work has identified a functional role for SINE DNA in gene regulation and stress response. (For discussions about SINE DNA function see my books Who Was Adam? and The Cell’s Design.)

New work has now uncovered a role for a newly discovered subclass of SINE DNA in regulating gene expression during brain development in mammals.

Introns

This class of junk DNA consists of DNA sequences that interrupt the coding region of a gene. The DNA sequences that make up genes in eukaryotes consist of stretches of nucleotides that specify the amino acid sequence of a protein (called exons) interrupted by nucleotide sequences that don’t code for anything (called introns). After the gene is copied into a messenger RNA molecule, the intron sequences are excised and the exons spliced together by a protein-RNA complex known as a spliceosome. Because introns interrupt coding sequences of DNA and are excised by the cell’s machinery, many scientists view these elements as junk DNA.

A recent study, however, indicates that introns do serve a function. It appears that some of these sequences help direct messenger RNA to specific locations in the cell.

Once assembled and processed, messenger RNA migrates from the nucleus of the cell into the cytoplasm. At ribosomes, messenger RNA directs the synthesis of proteins. Once produced, the proteins diffuse away from the ribosomes and begin their work for the cell.

Up until now biochemists thought that before exiting the nucleus, where the splicing and other processing reactions take place, all the introns were removed from the RNA message. But new work indicates this is not the case. Researchers discovered a messenger RNA molecule in the cytoplasm of neurons with an intronic sequence.

This messenger RNA molecule harbors a copy of the information needed to produce a protein component of a channel complex that permits the flux of calcium ions across the membranes of the dendrites. This process is essential for nerve transmission. It appears as if this intron helps direct the messenger RNA to the appropriate location in the dendrites where it then directs the production of the proteins that will eventually form the calcium ion channel.

This newly discovered regulatory mechanism may well be a general strategy that helps dictate gene expression in neurons and maybe other cell types as well.

These two advances give a sampling of flavors for the numerous discoveries that have been published in the last few months assigning function to so-called junk DNA. I could continue, but I don’t want to overdo it. After all, consuming too many samples can ruin Saturday’s lunch out.

Next week, I’ll resume the sampling by describing another newly recognized function for a class of junk DNA known as pseudogenes. I hope you’re hungry for more.

by Jeff Zweerink

Do graphite whiskers in meteorites require shaving dark energy out of cosmological models?

Consider a familiar scenario. Your child lies on the couch acting unusually calm. You touch your their forehead and it feels warm. The insta-thermometer gives a reading of 101.2^oF from the child’s ear. The traditional thermometer in the mouth gives a reading of 101.4^oF. Without question, your child has a fever.

But does your conclusion change if you discover that the batteries in your insta-thermometer are dying?

Graphite whiskers may represent dying batteries among the evidence for dark energy in the universe. Astronomers use the brightness of Type Ia supernovae to measure the expansion rate of the universe. Because these supernovae each emit the same amount of light (after some straightforward calibrations), astronomers use the measured brightness to determine the distance to each galaxy containing the supernova. Comparing the distance with the redshift provides the expansion history of the universe. Because distant supernovae have appeared dimmer than expected, astronomers concluded that dark energy pervades the universe, causing its expansion to accelerate for the last 5 billion years.

One alternative explanation is that a “grey dust,” proposed to populate intergalactic space, absorbs the supernovae light in a way that mimics the effects of dark energy. By carefully analyzing the oldest remnants of the early solar system—namely carbonaceous chondrite meteorites—scientists from the Carnegie Institution have discovered one potential grey dust candidate. Specifically, the researchers found graphite whiskers in three different parts of the meteorite (see here).

Graphite absorbs light that is characteristic of distant supernovae very efficiently. Thus, if enough graphite whiskers were ejected from star-forming nebulae and/or supernovae out into the intergalactic medium, they might explain the dimness of Type Ia supernovae without needing to invoke dark energy. Much work remains to check the validity of this explanation, but finding the graphite whiskers was a critical first step.

In the bigger picture, the possibility of these results removing the necessity of dark energy remains small. Type Ia supernovae are not the only indicators of dark energy. Data from both the WMAP and the SDSS both provide compelling evidence for dark energy, independent of the supernovae data.

Dark energy stands as the strongest single piece of evidence for fine-tuning in the universe—evidence that effectively argues for the intervention of a supernatural Designer. While scientists may have discovered some dying batteries (the graphite whiskers), rather than shaving dark energy out of the cosmological models, this phenomenon remains charged for the long haul.

Kenneth Richard Samples

I once heard a scientist say the following:

Only scientists are qualified to speak about matters of science.

Understood in a general sense, this point seems reasonable. For example, for a person to comment intelligently about a field of study one would expect that person to be adequately acquainted with that particular discipline. Since the various fields of science are highly specialized, rigorous training is often required to obtain a mastery of a given scientific discipline. This is, of course, why RTB employs highly trained scientists to work on the scholar team of a science apologetics organization.

However, as I pointed out in part one of this series, to assert that only scientists can speak intelligently about science ignores the reality that the scientific enterprise itself involves many assumptions that are not technically part of the natural sciences.

Some of these philosophical presuppositions foundational to the study of science include: (1) the existence of an objectively real cosmos; (2) the comprehensibility of that cosmos; (3) the general reliability of sense perception and human rationality; (4) the uniformity of the laws of nature; and (5) the validity of mathematics and logic.

Given these philosophical assumptions, philosophers of science potentially have much to say of vital importance concerning the nature of the scientific enterprise. In addition, mathematicians and logicians can authoritatively comment on scientific matters. In fact, the scientific enterprise is directly dependent upon the soundness of mathematics and logic.

When I listen to my scientifically trained friends at RTB talk about their fields, I note how the claims of science often come down to the issue of who has the best argument. Whose model best explains the data? Whose model has the superior explanatory power? These are specifically issues of logic and argumentation.

Even Charles Darwin’s theory of evolution was essentially an inference to the best explanation type of logical argument. Deciding whether some form of creationism or naturalistic evolution is best supported by the scientific data involves something like an abductive form of logical reasoning.

Could not logicians appropriately comment about the arguments made by scientists without themselves being formally trained in a given scientific discipline? Of course they can!

Could not lawyers, familiar with the use of arguments and evidence, also carefully evaluate scientists’ conclusions and conceivably add something significant? Yes.

Good science involves very specialized learning. But it also involves careful thinking. When it comes to thinking, some nonscientists can indeed speak intelligently to important aspects of science.

In the next installment of this series I will raise the issue as to whether theology has anything of importance to contribute to matters of science.

Additional Resources:
- For a detailed discussion of inference to the best explanation and abduction, see pages 39-54 of my new book A World of Difference: Putting Christian Truth-Claims to the Worldview Test.
- For a legal expert’s analysis of Darwinian evolution, see Philip E. Johnson, Darwin on Trial.
- For an introduction to the philosophy of science from a Christian perspective, see Del Ratzsch, Science & Its Limits: The Natural Sciences in Christian Perspective.
- For an essay on science’s relationship to historic Christianity, see chapter 14 of my book Without a Doubt: Answering the 20 Toughest Faith Questions.