The Method Behind the Madness: New Function Ascribed to Junk DNA

The Method Behind the Madness: New Function Ascribed to Junk DNA

Though this be madness,
Yet, there is method in’t.
           Hamlet, act 2, scene 2

Polonius thinks that Hamlet has gone mad. But as he listens to Hamlet’s speech, he is convinced that underlying the prince of Denmark’s insanity resides some method—a cleverness and order. He just can’t quite figure out what Hamlet is up to.


Oxytrichia Reproduction and Growth

This single-celled ciliate displays a complex reproductive process and life cycle. Oxytrichia possesses three nuclei: two micronuclei and one macronucleus. The large nucleus controls the metabolic activity of the cell during its vegetative state and also directs asexual reproduction. On the other hand, the micronuclei are quiescent during this life cycle stage.

Scarcity of food triggers Oxytrichia cells to engage in sexual reproduction. This is a highly involved process that centers on the micronuclei. During conjugation, two cells bind to each other and a portion of the cells fuse, permitting the exchange of genetic information between the conjugants.

This exchange begins when the micronuclei undergo several rounds of specialized division (called meiosis). The result is the generation of gametes (sex cells). One is a migratory nucleus and the other one stationary. The two conjugants exchange their migratory nuclei. The migratory and stationary nuclei then fuse. After the fusion event, the resulting zygote in each cell divides two times to produce four identical nuclei. One of them dissolves, two become the new micronuclei, and the fourth transforms into the macronucleus.


For years evolutionary biologists viewed junk DNA as a type of biomolecular madness, the result of chaotic biochemical processes that converted functional DNA to useless junk.1

Yet, intelligent design proponents and creationists have long maintained that if life stems from the work of a mind—a Creator—then junk DNA will possess functional utility.

Not until a few years ago were scientists able to identify the exact role that junk DNA played. As I discuss in The Cell’s Design, researchers have now discovered function for a number of different types of junk DNA. And a recent study helps reveal even more of the intelligent method in the biomolecular madness. Scientists have learned that a class of junk DNA called transposons play a central role in the genome rearrangement that takes place during the development of a single-celled organism called Oxytrichia.

Transposons are pieces of DNA that can move around a cell’s genome. For some types of transposons, the process is mediated by enzymes called transposases. Some genomes harbor a large number of transposons. Because of their prevalence most scientists view these DNA elements as junk. Others hold an even lower opinion of transposons, referring to them as parasitic or selfish DNA. This moniker appears to be well-deserved because the mobile pieces of DNA indiscriminately insert themselves throughout the genome, potentially disrupting genes and other critical regions.

But the latest research is beginning to change scientists’ opinion. Though it seems like transposons cannot possibly serve any useful role, better understanding of their activity reveals a “method to the madness.” Their ability to move around the genome allows for the extensive genome rearrangement and reduction that takes place in Oxytrichia after sexual reproduction occurs and the organism transitions into the vegetative stage of its life cycle.


Changes in the Oxytrichia Genome

Once a new macronucleus forms after the conjugation process is complete, its genome undergoes extensive rearrangement and reduction in size (by about 95%). This reduction process generates smaller nanochromosomes. The rearrangement and reduction is mediated by transposons and enzymes called transposases. The transposon movement causes extensive chromosome fragmentation. During this process noncoding DNA between genes and within genes is destroyed. So, too, are the transposons themselves. Remaining sequences of DNA harboring genes are fused together in a highly precise and reproducible manner to generate the nanochromosomes.

Once the genome rearrangement and reduction process is completed, the cell enters into the vegetative state and the macronucleus directs the cell’s activity.


As the authors of the paper point out, “These transposons might not merely be parasitic invaders that reduce the fitness or have little phenotypic effect but instead mutualists directly contributing a useful function to the organism.”3

The recognition of transposon utility in Oxytrichia opens up the possibility that these so-called parasitic pieces of DNA may demonstrate widespread usefulness across the biological realm. This new insight also weakens the best argument for biological evolution and common descent. That argument states that if a Creator existed he would not purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related organisms.

This discovery explains why identical junk DNA sequences occur in corresponding regions of the genomes of related organisms. The precise location of junk DNA sequences may well be critical for these DNA elements to operate properly.

When it comes to junk DNA, there really does appear to be a method to the madness. As scientists continue to discover usefulness for junk DNA, they see in that method less madness and more genius.

  1. Edward E. Max, “Plagiarized Errors and Molecular Genetics,” Talk Origins Archive,, accessed December 13, 2009.
  2. Mariusz Nowacki, et al., “A Functional Role for Transposases in a Large Eukaryotic Genome,” Science 324 (2009): 935-38.
  3. Mariusz Nowacki, et al., 935-38.