Fruit Fly Genome Studies Confirm That There Is Little “Junk DNA”

Creationists and ID advocates predict little junk DNA in nature, and studies confirm that prediction.

Creationists and Intelligent Design advocates long ago predicted that the more we learn about genetics, the more we will see that there is very little “junk DNA” in nature. About a year ago, I discussed the first results that came from project ENCODE. Those results indicate that there is very little DNA in the human genome that is not used by the cell, indicating that there is very little “junk DNA” in people. Not surprisingly, as the genomes of other organisms are studied, we are finding that they also have very little “junk DNA.”

To understand what fruit flies are telling us about “junk DNA,” you need to understand the term “transcription” as it applies to genetics. The information in DNA is stored in a code, which must be read and translated in order for it to turn into something useful for the cell. It turns out that the cell has an elegant mechanism to do this, and that mechanism can be described in two phases: transcription and translation. In transcription, the code is copied and then transported out of the nucleus of the cell and to the protein-making factories in the cell. At that point, the protein-making factories perform translation, where the code is translated into proteins that perform all sorts of vital functions for the cell.

Since transcription requires a large amount of energy and resources, it is assumed that a cell won’t perform transcription on any portion of DNA that isn’t used by the cell. Thus, by seeing what portions of DNA are transcribed, we can see what portion of the genome is functional. Just as the entire collection of DNA is called a “genome,” the entire collection of transcribed DNA is called the “transcriptome.”

With that background, you can now understand what studies of the fruit fly transcriptome have told us about “junk DNA.”

An article in the journal Nature reviewed three recent papers that report on studies of the fruit fly transcriptome. Here is one of the conclusions the author reaches:1

This comprehensive view of the fly transcriptome reveals that some 75% of the organism’s genome is transcribed at one stage or another — in line with the widespread transcription observed in other species.

In other words, these studies show that three-fourths of the fruit fly’s genome is transcribed. Thus, a minimum of three-fourths of the fruit fly’s genome is functional.

Why do I say this is a minimum figure? Because as detailed and impressive as these studies were, they could not possibly have caught all the functional DNA. Remember, DNA is used throughout the entire life of the organism. That includes development, maturity, reproduction, and even the process of dying. The study that forms the backbone of this analysis looked at fruit flies in 30 different developmental stages.2 That’s a lot, but it doesn’t capture all stages of a fruit fly’s life. Thus, it is very possible that this study missed DNA that is functional only during a narrow window of the fruit fly’s lifespan.

In addition, one of the other studies examined 25 different fruit fly cell lines. So instead of looking at different stages of development, it looked at cells that originally came from 25 different flies. Interestingly enough, it found that of the known genes, only 64% were expressed in at least one of the cell lines, and only 21% were expressed in all the cell lines.3 What does this tell us? It tells us that while one individual uses certain parts of its DNA, another individual uses different parts of its DNA. So unless we study a large range of individuals, we are probably not catching all the functional parts of the genome.

In the end, then, the 75% figure discussed in the review article is a lower limit. Most likely, significantly more than 75% of the fruit fly genome is transcribed, indicating that there is very little “junk DNA” in a fruit fly. This is exactly what you would expect if the fruit fly genome is the result of design, and it is not what you expect if the genome is the result of random mutations acted on by natural selection!


1. Eileen E. M. Furlong, “A Fly in the Face of Genomics,” Nature 471:458-459, 2011.
Return to Text

2. Brenton R. Graveley, et al., “The developmental transcriptome of Drosophila melanogaster,” Nature 471:473-479, 2011.
Return to Text

3. Cherbas L, et al., “The transcriptional diversity of 25 Drosophila cell lines.,” Genome Research 21(2):301-314, 2011
Return to Text


  1. shevrae April 21, 2011 8:18 am

    I remember learning about “junk DNA” in high school and as a biochemistry major in the 1990s – sadly, these new developments will probably take 20 years (at least) to filter down to high school biology classes. That’s one of my favorite things about homeschooling – I can work hard to make sure my kids have the most up to date information because I’m not assuming that someone else is doing it.

    • jlwile April 21, 2011 10:13 am

      Shevrae, that is so true. In fact, this is one of the many reasons science education is superior in a homeschooling environment. You are not constrained to wait on the textbooks to catch up to the latest in science.