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"Junk" DNA is not really junk (Talk.Origins)

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Response Article
This article ("Junk" DNA is not really junk (Talk.Origins)) is a response to a rebuttal of a creationist claim published by Talk.Origins Archive under the title Index to Creationist Claims.

Claim CB130:

So-called junk DNA is not really junk. Functions have been found for noncoding DNA which was previously thought to be junk, and we cannot be sure that the rest of the junk DNA is not functional as well.

Source: Behe, Michael J., 2003. A functional pseudogene?: An open letter to Nature.

CreationWiki response: (Talk.Origins quotes in blue)

It has long been known that some noncoding DNA has important functions. (This was known even before the phrase "junk DNA" was coined.) However, there is good evidence that much DNA has no function:

While it is true that noncoding DNA is long known to have important function, that does not really affect the claim.

Sections of DNA can be cut out or replaced with randomized sequences with no apparent effect on the organism (Nóbrega et al. 2004).

While this is a useful test, it can only determine if there is an active use for the "junk" DNA. For example, in a computer data center, one could cut out the entire backup system and replace it with randomized computers and it would have no apparent effect on the datacenter -- that is until a restoration was needed.

Likewise, in the creationist model, many regions of DNA are for adaptive purposes, and are not activated except in specific environments where they are needed. If this is indeed the case (and there is evidence that it is), this indicates design on quite a grand scale. If it can be shown that there exist adaptations within an organism for environments which the organism has never experienced that can be easily switched on reliably by the organism itself, that is significant evidence for design. The problem being that it is difficult to determine for certain the complete natural history of an organism and what proteins it had needed in the past.

In addition, modern experiments have shown that DNA can in fact spontaneously revert mutations back to the original coding. This indicates that there may be a repository that genes can use to verify the validity of their coding. In computers, memory cells can contain hamming codes which are extra memory cells to verify the integrity of other cells. This is not the same as a backup copy, and instead are parity bits -- so an observer not aware of the coding would not necessarily be able to make out what it means. Cells apparently have some sort of mechanism like this in order to be able to revert mutations, and therefore it is not unreasonable to think that some of this "junk" DNA is in fact some sort of parity mechanism for other coding regions.

Likewise, transposons have often been looked at as parasitic elements of DNA. This is based on the assumption of a static genome. In the creationist model, transposons are part of the genome's mechanism for organizing itself. Evolutionists agree with the transposon's role in speciation, but most still view them as only occurring by non-adaptive mechanisms, where there adaptiveness is a happenstance that is selected for, not a design quality. In the creationist model (and some new evolutionary models, too), transposons are part of a designed adaptive process to help the genome reconfigure itself in response to environmental stress. It's interesting that this was first proposed by Barbara McClintock, who first discovered transposable elements in the genome. However, the idea of a genome that could modify itself was an anathema to the idea of a naturalistic origin of the genome, and therefore work in this area until recently has been based on the assumption that these are parasitic elements.

Now, creationists agree with evolutionists that some parts of the genome have been deactivated due to mutation, and no longer play any role in the organism. This is due to the fall. The idea that all organisms should be perfectly designed (argument from natural evil) is one commonly used against the idea of creation. However, while this might be true for a pre-fall creation, it is not true for a post-fall creation. There is indeed degradation that has occurred from the fall.

Some sections of DNA are corrupted copies of functional coding DNA, but mutations in them, such as stop codons early in the sequence, show that they cannot have retained the same function as the coding copy.

The idea that they are corrupted is an assumption. They are obviously not the same, but the reasons why are not necessarily known. These could at one point have been active, but been deactivated by a control mechanism. They could also be used to verify the integrity of the original. The fact that biologists have not found a use for these does not mean that they are non-functional. Our knowledge of biochemistry, while great, is still in its infancy.

The fugu fish has a genome that is about one third as large as its close relatives.

Again, this means little unless we know why the fugu fish's genome is smaller.

Mutations in functional regions of DNA show evidence of selection -- nonsilent changes occur less often that one would expect by chance. In other sections of DNA, there is no evidence that any changes are selected against.

This would be true as well if these were adaptive mechanisms. A flaw in a backup system does not degrade the running operation of a computer facility. Selection is based simply on an organism's current capacity to reproduce. Natural selection cannot act on adaptive mechanisms until after they are needed.

Related References

Creationist Resources

Secular Resources

  • A 21st Century View of evolution by James Shapiro (Journal of Biological Physics 28(4):745-764)
  • See also reference list for Genetic Variability by Design above