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A Rational Look at Christianity; Basing Reason in Truth

Flat Earth Thinking
Why does About.com maintain their belief that "junk DNA" proves evolution?

About.com's atheism and agnosticism pages has an article (or at least it did as of the time of the posting of this essay) in their section of Evolution FAQ entitled "Is Evolution Science? Junk DNA". It first describes "junk DNA" as follows:

Junk DNA are basically pieces of DNA that have no function (or in some cases, such as introns, they produce no protein but may be involved in regulation of the gene). When the DNA is transcribed, these pieces of DNA either do not get transcribed at all or are only partially transcribed, with no final result (i.e., a functional protein) being produced. You can cut out or modify most of this junk DNA without affecting the organism.

Supposing that it is true that "junk" DNA exists, what does it prove? Well, to About.com's Atheism/Agnosticism editors, it must prove that evolution happened.

"It is hard enough to explain (if you don't accept evolution) why some functional pieces of DNA show great similarities. It is pretty much impossible to rationally explain why nonfunctional DNA, erroneous DNA, would be very similar between different species. Why would genetic code that doesn't do anything and which clearly appears to be the result of mutations be similar, or in many cases identical, between different organisms? The only explanation that makes any sense is if this DNA was inherited from a common ancestor. Homologies between junk DNA are probably the most powerful of the homology evidence for common descent, as common descent is the only rational explanation for them."

While I personally think that their logic falls well short of convincing, and while I certainly don't feel compelled to agree with the first sentence at all, there is another and greater problem with this approach: there may not be any "junk DNA" at all.

Consider, for example, the following from the BBC in an article entitled "'Junk' throws up precious secret" dated May 12, 2004:

"A collection of mystery DNA segments, which seem to be critical for the survival of many animals, are causing great interest among scientists. Researchers inspecting the genetic code of rats, mice and humans were surprised to find they shared many identical chunks of apparently 'junk' DNA. This implies the code is so vital that even 75 million years of evolution in these mammals could not tinker with it. But what the DNA does, and how, is a puzzle, the journal Science reports.

Before scientists began laboriously mapping several animal life-codes, they had a rather narrow opinion about which parts of the genome were important. According to the traditional viewpoint, the really crucial things were genes, which code for proteins - the 'building blocks of life'. A few other sections that regulate gene function were also considered useful. But the new findings suggest this interpretation was somewhat wanting.

* * *

Professor Chris Ponting, from the UK Medical Research Council's Functional Genetics Unit, told BBC News Online: 'Amazingly, there were calls from some sections to only map the bits of genome that coded for protein - mapping the rest was thought to be a waste of time. It is very lucky that entire genomes were mapped, as this work is showing.' He added: 'I think other bits of 'junk' DNA will turn out not to be junk. I think this is the tip of the iceberg, and that there will be many more similar findings.'"

Will there be similar findings? Consider the following from the Reasons to Believe e-Newsletter dated August 20, 2004:

Evolutionary biologists maintain that junk DNA provides incontrovertible evidence for evolution. This study demonstrates that one class of non-coding DNA, endogenous retroviruses, plays an important role in protecting the cell from retroviral infections. The functional importance of junk DNA indicates that careful planning by an Intelligent Designer, rather than undirected, random biochemical events, shaped the genomes of organisms.

Theodora Hatziioannou et al., “Retrovirus Resistance Factors Ref1 and Lv1are Species-Specific Variants of TRIM5,” Proceedings of the National Academy of Sciences, USA 101 (2004): 10774-10779.

This study is not unique. An example of the scope of the recent discoveries regarding the use of DNA previously identified as "junk" can be found in "Junk DNA", By Jaan Suurkula M.D.:

In June 2004 a team at Harvard Medical School (HMS) reported, that they have, in a yeast, found a "Junk DNA" gene that regulates the activity of nearby genes. While common genes work by giving rise to proteins, this gene works by just being switched on. Then it blocks the activity of an adjacent gene.

* * *

Some studies have found that noncoding DNA plays a vital role in the regulation of gene expression during development (Ting SJ. 1995. A binary model of repetitive DNA sequence in Caenorhabditis elegans. DNA Cell Biol. 14: 83-85.). . . (List of studies omitted.)

Over 700 studies have demonstrated the role of non-coding DNA as enhancers for transcription of proximal genes. (List of studies omitted.)

Over 60 studies have demonstrated the role of non-coding DNA as silencers for suppression of transcription of proximal genes.(List of studies omitted.)

Some studies indicate that non-coding DNA regulate translation of proteins.(List of studies omitted.)

I took the liberty of removing the references that are found in the text of the webpage to some of the individual studies. Anyone interested is, of course, free to go to the webpage and peruse them.

What is Dr. Suurkula's conclusion?

The idea that a major part of our DNA is "garbage" ignored the fact that a key feature of biological organisms is optimal energy expenditure. To carry enormous amounts of unnecessary molecules is contrary to this fundamental energy saving feature of biological organisms. Increasing evidence are now indicating many important functions of this DNA, including various regulatory roles.

This means that this so-called non-coding DNA influences the behavior of the genes, the "coding DNA", in important ways. Still there is very little knowledge about the relationship between non-coding DNA and the DNA of genes.

Thus, there is a continuing progression of research that is determining more and more that "junk" DNA is far from junk--rather, it is a vital part of the DNA structure in many animals. What does this mean for About.com's FAQ answer? Well, to begin with, they acknowledge in their definition of "junk" DNA that it may serve some function. To the extent that it does, that admission destroys the argument that "it is pretty much impossible to rationally explain why nonfunctional DNA, erroneous DNA, would be very similar between different species." Maybe, but since it has a function, the argument doesn't apply, does it? Of course not. And since it is appearing more and more likely that the DNA previously thought of as "junk" has some functions (even though we may not yet be able to identify them), the idea that "junk" DNA proves evolution is fading fast.

The idea that the cell contains "junk" DNA that is being copied only because it is evolutionary in nature is day-by-day being proven to be overstated. As more and more evidence comes in, it appears that the amount of "junk" DNA has been greatly overstated. The argument that 97% of the DNA in the cell is "junk" and therefore proves evolution ought to be discarded as "flat earth" thinking.

For more on this issue, I recommend reading "When Junk DNA isn't Junk," from the author of (and CADRE member) Evidence for God from Science.

3 comments:

Here are two articles from the American Scientific Affiliation that may be relevent:

http://www.asa3.org/ASA/PSCF/2001/PSCF9-01Bergman.pdf
http://www.asa3.org/ASA/PSCF/2003/PSCF9-03Collins.pdf

The second one is by the director of the Human Genome project and he says:

"I have been troubled for a long time about the way in which we dismissed about 95% of the genome as being junk because we didn’t know what its function was. We did not think it had one because we had not discovered one yet. I found it quite gratifying to discover that when you have the whole genome in front of you, it is pretty clear that a lot of the stuff we call "junk" has the fingerprints of being a DNA sequence that is actually doing something, at least, judging by the way evolution has treated it. So I think we should probably remove the term “junk” from the genome. At least most of it looks like it may very well have some kind of function."

Good articles. I also received the following in a new e-Newsletter from Reasons to Believe.

Evolutionary biologists maintain that junk DNA provides incontrovertible evidence for evolution. This study demonstrates that one class of noncoding DNA, endogenous retroviruses, plays an important role in protecting the cell from retroviral infections. The functional importance of junk DNA indicates that careful planning by an Intelligent Designer, rather than undirected random biochemical events, shaped the genomes of organisms.

Mannuela Muraet al., “Late Viral Interference Induced by Transdominant Gag of an Endogenous Retrovirus,” Proceedings of the National Academy of Sciences, USA 101 (2004): 11117-11122.

I cannot tell from the blurb whether this is the same study or a new study.

Still another resource from Reasons to Believe mentioned in the same newsletter:

http://www.reasons.org/resources/fff/2000issue03/index.shtml?main#junk_dna

Yet Another Use for “Junk” DNA
By Fuz Rana, Ph.D.

A team of scientists from Case Western Reserve (CWRU) School of Medicine in Cleveland, Ohio, has developed convincing circumstantial evidence for yet another function for so-called “junk” DNA.1,2 Critical to this discovery was the sequence data recently made available by the Human Genome Project.

===snip===

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