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Thursday, November 27, 2014

Despite Their Protests, Evolutionist Do Depend on “Junk DNA,” and LOTS of It!

Posted by jlwile on October 8, 2011

As important functions are found for more and more junk DNA, some evolutionists are trying to claim it is not all that important to evolution.

Once Susumu Ohno coined the term “junk DNA” and called it the remains of extinct genes1, junk DNA started to become the darling of the evolutionary community. First, it was seen as an effective argument against creationism or intelligent design. After all, why would the Creator put so much useless DNA into His creation? More importantly, however, it was considered an integral component of evolution. After all, evolution requires that genetic mutations acted on by natural selection produced genes with novel functions. However, it is difficult to expect that to work when the mutations occur in genes that the organism needs. Thus, one of the major mechanisms of genetic evolution involves gene duplication. In this view, a gene is duplicated, and one copy continues to produce the protein it always produced, while the other is free to mutate wildly. Waving the magic wand of time, the evolutionist then says that a large number of these mutating copies will become useless junk, but a small number of them will develop into novel genes. As you can see, then, junk DNA is integral to evolution, and according to evolution, most organisms should have a lot of it.


This, of course, is why Dr. Jerry Coyne says the following in his book, Why Evolution Is True:2,

When a trait is no longer used, or becomes reduced, the genes that make it don’t instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA. From this we can make a prediction. We expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed. In other words, there should be vestigial genes…Our genome—and that of other species—are truly well populated graveyards of dead genes.

Unfortunately for evolutionists, function is routinely being found for this supposed “junk DNA.” As a result, some evolutionists have realized that they need to back away from the claim that junk DNA is integral to the process of evolution.

For example, Dr. Larry Moran has tried to rewrite the history of evolutionary thought. In discussing Dr. Jonathan Wells’s book The Myth of Junk DNA. He writes:

The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a “pillar” of support for evolution. That’s hard to do when their understanding of evolution is so flawed that they don’t see the difference between “Darwinism” and evolution by random genetic drift. Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. (emphasis his)

Not surprisingly, its Moran’s statement that is 100% false, and its falsehood can be demonstrated quite clearly simply by reading a recent paper written by two young-earth creationists and published in a secular, peer-reviewed scientific journal. —Sigh— Yes, both creationists and intelligent design advocates write papers about evolution that are published in the secular, peer-reviewed literature. Anyone who says otherwise spends little time reading such literature.

This particular paper was written by Chase W. Nelson and world-renowned geneticist J.C. Sanford. They examined the program Avida, which attempts to simulate evolution using “digital organisms.” In the digital world of Avida, the organisms are replicating “creatures” whose “DNA” is composed of strings of computer instructions. As these creatures replicate, mutations change those instructions. Avida has shown that over time, these mutations (acted on by a digital form of natural selection) produce creatures that can perform new logic operations, which would be the digital equivalent of new biological characteristics. In other words, Avida produces a digital simulation of evolution using strings of computer instructions as DNA and logic operations as biological traits. It is considered the gold standard when it comes to digital simulations of evolution.

The problem that Nelson and Sanford point out in their excellent paper3 is that Avida uses only high-impact mutational events – events that produce a lot of fitness very quickly. However, such high-impact mutational events are extremely rare in nature. To be more realistic, the authors conclude, Avida should use digital mutation events that are more like real-life mutational events when it comes to their effect on the fitness of the organism. When the authors do this, they find that Avida is unable to produce new logic operations. In other words, when you make the simulation more realistic, you no longer see the evolution of new traits. This, of course, is precisely what creationism predicts, but it is not all that surprising. As I have already pointed out, the longest-running experiment on evolution shows that the changes mutations can make in the genome are extremely limited.

What I found interesting was another point they make in their paper. They say that an integral part of the Avida program is…wait for it…junk DNA:

The ancestral genome devotes about 15 instructions to the essential replication code, while the remaining 85 positions are occupied by benign no-operation instructions, analogous to inert “junk DNA” that can be used as raw material for evolutionary tinkering.

Now remember, Moran claims that a large amount of junk DNA is not a pillar of support for evolution. Contrary to that assertion, the standard digital simulation of evolution starts out with a genome that is 85% junk DNA. I don’t know about Moran, but to me, a genome that is 85% junk does, indeed, represent a genome with “huge amounts” of junk DNA, and that is the beginning assumption of the standard computer simulation of evolution. As this makes clear, a vast amount of junk DNA in most creatures’ genomes is an integral component of evolutionary theory, and like most things, the more we learn about genetics, the more we realize how wrong that integral component is.

REFERENCES

1. Susumu Ohno, “So Much ‘Junk’ DNA in Our Genome,” Evolution of Genetic Systems. Brookhaven symposia in biology, 23:366-370, 1972.
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2. Jerry A. Coyne, Why Evolution Is True, Viking, 2009, pp 66-67
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3. Chase W Nelson and John C Sanford, “The effects of low-impact mutations in digital organisms,” Theoretical Biology and Medical Modeling, 8:9, 2011 (Available online)
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Comments

11 Responses to “Despite Their Protests, Evolutionist Do Depend on “Junk DNA,” and LOTS of It!”
  1. Sean says:

    Great job taking a prediction from WEIT and turning it on its head.

  2. Evan Arcadi says:

    Great post. This is a little off topic but I recently heard an atheist refer to wisdom teeth as “caveman teeth” and I was wondering how to respond to that statement without backsliding.

  3. jlwile says:

    Evan, the atheist needs to keep up with the scientific literature! There was a time when evolutionists thought that wisdom teeth were leftover vestiges of evolution. However, even as far back as 1985, people who studied the issue understood that this was not the case. Wisdom teeth are a modern phenomenon, resulting from modern humans’ dietary changes as well as mutations. Here is a detailed article that the atheist should read in order to keep his or her information up to date.

  4. JL says:

    Thanks for the information about wisdom teeth! Oral surgeons have made a lot of money off my older children’s wisdom teeth based upon the threat of later infections, and I haven’t been able to get a good answer to why they’re a problem now when people have been surviving to old age for thousands of years without oral surgeons. Now I can be more proactive about decision-making for when the younger ones get to that stage.

  5. Josiah says:

    I agree that vast quantities of Junk DNA (which is properly junk, not just “non coding”) are required for evolution, and that there doesn’t seem to be much of it left.

    However I am surprised at you for taking your evidence from a computer simulation of the process. Especially since, as you note elsewhere in the post, the simulation isn’t a very close match to what is observed in the real world.

  6. jlwile says:

    Josiah, I think you misunderstand the point of the post. As I said, the computer model results aren’t surprising. When the model is forced to be realistic, it gives the same results as the longest-running evolution experiment. The point of the post was to show that when evolutionists are forced to provide a mechanism for evolution (after all, you can’t have a computer simulation without a mechanism), the mechanism involves an enormous amount of junk DNA. Thus, contrary to the claims of people like Dr. Moran, lots of junk DNA remains a pillar of support for evolution.

  7. Vivielle says:

    Evolution in general makes me want to ask an evolutionary biologist what the difference is between the theory of evolution and spontaneous generation… I’ve always been curious to know what the response would be to that.

  8. jlwile says:

    Vivielle, the first thing most evolutionists would say is that the origin of life is a question that is separate from evolution. This is untrue, but many evolutionists are forced to believe this. They have to set up this false distinction, because all available evidence points against the idea that life can appear by naturalistic means. Thus, they need to divorce evolution from the origin of life.

    Second, the idea of spontaneous generation deals with a fully-functional organism arising at once from something that is not alive. Maggots come from decaying meat, eels come from the muck at the bottom of the river, and microorganisms come from broths of nutrients. In each case, an organism appears fully-functional and in a short amount of time from something that is dead. It was also assumed to happen over and over again. In naturalistic origin-of-life scenarios, the living organism is produced stepwise by natural processes over millions or billions of years. In this scenario, only one organism was produced, or at most, only a few.

  9. Scott says:

    Jay, I really enjoy following your blog. I wanted to send you an e-mail, but I can’t figure out how, so I am using this forum. I read an interesting article the other day and wanted to share it with you. You may have seen it, but, if you haven’t, I think you will enjoy it.
    http://www.internetmonk.com/archive/five-things-science-cannot-prove-but-are-necessary-for-science-to-work

    Thanks for your ministry!

  10. Vivielle says:

    Interestingly, in my bio classes I’ve never heard a professor divorce evolution from the origins of life…The iron-sulfur world and the prebiotic soup theories spring to mind. (And yes, I did have a moment or two of thinking that they were spoofing themselves when they started talking about those theories.)

    I guess that’s why I’ve always wondered what they’d say about the two theories. Thanks for your explanation! My goal is to someday be brave enough to ask one of my bio professors that question.

  11. jlwile says:

    Thanks for your kind words, Scott, and thanks for the link as well! I had not read that article before. Webmonk has commented here a couple of times, though.

    You can contact me privately by going to the contact form on my home page.

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