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Friday, April 25, 2014

Time to Redefine the Concept of a Gene?

Posted by jlwile on September 10, 2012

The basic unit of heredity (the gene) has been defined as a stretch of DNA that codes for a protein. In plants, animals, and people, genes are made of introns and exons. The ENCODE results suggest this definition might need to be changed. (Click for credit)

As I posted previously, a huge leap in our understanding of human genetics recently occurred due to the massive results of project ENCODE. In short, the data produced by this project show that at least 80.4% of the human genome (almost certainly more) has at least one biochemical function. As the journal Science declared:1

This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases.

Not only have the results of ENCODE destroyed the idea that the human genome is mostly junk, it has prompted some to suggest that we must now rethink the definition of the term “gene.” Why? Let’s start with the current definition. Right now, a gene is defined as a section of DNA that tells the cell how to make a specific protein. In plants, animals, and people, genes are composed of exons and introns. In order for the cell to use the gene, it is copied by a molecule called RNA, and that copy is called the RNA transcript. Before the protein is made, the RNA transcript is edited so that the copies of the introns are removed. As a result, when it comes to making a protein, the cell uses only the exons in the gene.

By today’s definition, genes make up only about 3% of the human genome. The problem is that the ENCODE project has shown that a minimum of 74.7% of the human genome produces RNA transcripts!2 Now the process of making an RNA transcript, called “transcription,” takes a lot of energy and requires a lot of cellular resources. It is absurd to think that the cell would invest energy and resources to read sections of DNA that don’t have a function.

In addition, the data in reference (2) demonstrate that many RNA transcripts go to specific regions in the cell, indicating that they are performing a specific function. Since there is so much DNA that does not fit the definition of “gene” but seems to be performing functions in the cell, scientists probably need to redefine what a gene is. Alternatively, scientists could come up with another term that applies to the sections of DNA which make an RNA transcript but don’t end up producing a protein.

There is another reason that prompts some to reconsider the concept of a gene: alternative splicing. The ENCODE data show that this is significantly more important than most scientists ever imagined.

I have talked about alternative splicing before (here and here). For many years, evolutionists tried to convince us that introns were junk DNA. Remember, after a gene is copied in transcription, the RNA transcript is edited to remove the introns. Only then is the RNA transcript used by the cell to make a protein. According to evolutionists, then, the introns were junk that had to be removed before the gene could do its job. Creationists, of course, refused to believe such nonsense, and they were eventually demonstrated by the data to be correct.

We now know that the introns serve an incredibly important purpose. They split up the exons into smaller units of information, and those smaller units can be combined in different ways, producing different proteins. That’s what alternative splicing is, and it allows DNA to store information in an incredibly efficient way. As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins!

While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25.

Based on these results, it seems clear that the RNA transcripts are the real carriers of genetic information. This is why some members of the ENCODE team are arguing that an RNA transcript, not a gene, should be considered the fundamental unit of inheritance. We’ll see how that argument plays out. For right now, I think everyone can agree with Jason Lieb, an ENCODE team member who is quoted in reference (1) as saying:

What we found is how beautifully complex the biology really is.

Indeed. The biology is beautiful and complex, because it was designed by an all-powerful Creator.


1. Elizabeth Pennisi, “ENCODE Project Writes Eulogy for Junk DNA,” Sience 337:1159-1161, 2012.
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2. Sarah Djebali, et. al.,”Landscape of transcription in human cells,” Nature 489:101-108, 2012. (Available online)
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6 Responses to “Time to Redefine the Concept of a Gene?”
  1. Jason says:

    Wow, great article Dr Wile. Thanks for simplifying this for us.

  2. Inazuma says:

    Amazing. I hope we never fully understand God’s creation because it’s way too much fun to discover how awesome the world is!

    Here’s to complexity!

  3. Jacob says:

    The first time I read this post, my mind was blown away! Had to go back two times over! I’m glad I’m not God, because I am way too unintelligent to create life… or anything else for that matter!

    Thanks for posting this, Dr. Wile, and I can’t wait to see what comes next of ENCODE’s results!

  4. Eric H. says:

    Excellent article Dr Wile. Please keep them coming! I think I’ve read mostly all your blog posts for the last year or so. Psalm 33:8-9,
    “Let all the earth fear the LORD;
    let all the people of the world revere him.
    For he spoke, and it came to be;
    he commanded, and it stood firm.” Foundation of modern science, anyone? It is becoming more and more obvious that God formed us in the womb and is upholding us and all of creation by the power of his WORD, every moment, every day, and is becoming apparent that it is by the vastly complicated information(word) in the genome! I always wondered how God was currently forming us in the womb, since he said he completely finished his creation long ago, but now I understand! Has it ever been easier to believe that God is the creator of the universe and all life? If discoveries keep going at this rate, you would think that atheistic evolution would be a relic of the past soon enough, as obsolete as spontaneous generation! I sure hope so!

  5. jlwile says:

    Thanks, Jacob. I agree that God’s handiwork is mind-blowing!

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