Archive for May 27th, 2007

Genetics: Alternate Reading Frames May Be Common, Science, Uncategorized, Unexplained Artifact | Posted by Chris Parker
May 27 2007

In “The Inspiration of the Scriptures Scientifically Demonstrated, Ivan Panin, writes about a numeric phenomenon in the Bible that would be virtually impossible to recreate even with modern computers and which he believed “scientifically” demonstrated that the scriptures were “inspired”. 

Dr. Jeffrey B. Satinover, in “Proof of the Divine Authorship of the Bible”, found numerical patterns in the Bible using a computer which puzzled referees for “Statistical Journal”, which published the article.

Could the same thing be true for our genetic code and DNA? In the case of the Bible, letters are also numbers in the original Greek and Hebrew. In the case of DNA, it is a made up of four letters.

What if within the coding a pattern was found that was so complex it would be virtually impossible for it to have arisen by chance? Proof of divine authorship of life?…

Commentary by“Imagine a book written in a language where there were no spaces, and every word was three letters long. Now imagine that you could get one story by starting at the first letter, and a different story by starting at the second letter, and another by starting at the third letter.

That’s the situation with some genes in the genetic code. DNA can code for one protein in the first reading frame, but a different protein in an alternate reading frame. Since the DNA language has three nucleotide “letters” per codon “word,” and since the opposite strand has three more reading frames, there are potentially six reading frames per gene. How commonly are alternate reading frames used by an organism?

A paper in PLoS Computational Biology hints that there may be widespread examples of alternate reading frames (ARFs) in mammalian genomes. ARFs were thought to be rare in eukaryotes. An international team, using new statistical techniques, found 40 cases in the human genome, but says that this may be a significant underestimate, since their analysis was very conservative. Their author’s summary asks and answers why these alternate reading frames were not found before:

A textbook human gene encodes a protein using a single reading frame. Alternative splicing brings some variation to that picture, but the notion of a single reading frame remains. Although this is true for most of our genes, there are exceptions. Like viral counterparts, some eukaryotic genes produce structurally unrelated proteins from overlapping reading frames. The examples are spectacular (G-protein alpha subunit [Gnas1] or INK4a tumor suppressor), but scarce.  

The scarcity is anthropogenic in origin: we simply do not believe that dual-coding genes can occur in eukaryotes. To challenge this assumption, we performed the first genome-wide scan for mammalian genes containing alternative reading frames located out of frame relative to the annotated protein-coding region.

Using a newly developed statistical framework, we identified 40 such genes. Because our approach is very conservative, this number is likely a significant underestimate, and future studies will identify more alternative reading frame-containing genes with fascinating biology.

“They said there was an almost zero probability these ARFs were due to chance: in fact, one section of the paper is subtitled, “Dual Coding Is Virtually Impossible by Chance.” 

 Finding so many ARFs was surprising, they said, because maintaining ARFs by natural selection is “costly” – i.e., mutations in one reading frame could disable the information in the alternate frame.Often, the proteins that result from alternate reading frames are related to the same function or process in the cell. The researchers compared the well-known ARFs between humans, mice and some other mammals and found them to be highly conserved (i.e., unevolved).

1Chung, Wadhawan, Szklarczyk, Pond, and Nekrutenko, “A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes,” Public Library of Science: Computational Biology May 18, 2007.

Try writing a message that could be read three different ways depending on which letter was the starting point. It is extremely difficult. If this turns out to be a common mechanism in genetics, it reveals an astonishing level of intelligent design. How, and why, would a blind process do such a thing? Notice how geneticists were not even looking for this amount of complexity because they did not believe it was possible.

This technique of “data compression” could expand the functional information of the genome significantly. ARF! The hunt is on. Sic the design community on this fascinating puzzle. They won’t be tied up and muzzled from announcing the return of the Master to biology.



‘Junk’ DNA Now Looks Like Powerful Regulator, Researcher Finds

Church of Darwin,, Science, Uncategorized | Posted by Chris Parker
May 27 2007

Famous Atheist Dawkins Snidely Chides Creationists About Imperfect “Junk DNA”.“…And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA. …

Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2% – considerably less than the proportion of my hard disc that I have ever used since I bought it.” – Richard Dawkins, “The Information Challenge.” the skeptic. 18,4. Autumn 1998

William A. Dembski predicted in 1998 that Doubters Like Dawkins Would Prove to be As Wrong About “Non_Coding DNA As They Were About Everything Else

But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.”

Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA.

If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function.

For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.”

Design encourages scientists to look for function where evolution discourages it. Subsequent ID theorists repeated this ID prediction that functionality would be found in agenic or “Junk” DNA.


“…a certain amount of hubris* was required for anyone to call any part of the genome ‘junk’” Francis Collins (2006)

Click Here to Read:’Junk’ DNA now looks like powerful regulator