Creation Moment 11/8/2020 - Destruction of the Junk DNA MYTH

 For the wisdom of this world is foolishness with God. 1 Corinthians 3:19

"Imagine everyone’s surprise when scientists announced that there were only about 23,000 (or fewer) genes in the more than 3 billion nucleotides of the human genome. This meant that less than 2% of the human genome coded for proteins! 

 

What was the rest of that huge collection of noncoding nucleotides doing? 

 

This finding seemed to indicate that the vast majority of the human DNA had no apparent function. According to Ewan Birney, head of

the European Bioinformatics Institute in Cambridge, England, people always knew that there must be some regulation of the genes, but even if the useful information were doubled, compared to the amount in the genes, that would only result in 8-9% functional information at most among the 3.2 billion nucleotides.

 

There were two responses possible to this astonishing discovery. 

---One was to declare that the human genome was full of “junk DNA.”  According to this point of view, the genome was obviously the product of long periods when DNA which had been originally useful, was now broken so that other sequences had to take over control.  Huge areas of repeat sequences seemed to confirm the idea of useless DNA. The human genome was declared to be stark confirmation of the reality of evolution and a rejection of creation. What creator would leave so much junk lying around? And this is how junk DNA with no function came to be equated with arguments for evolution. 

---Another group asked what the rest of the genome was doing. Were these lengthy sequences functional, and if so, what were they actually doing?

The initial ENCODE report was interesting enough to encourage the U.S. based National Human Genome Research Institute to fund a study of the whole human genome. As a result, in 2012, a new larger ENCODE consortium published its results. In summary they found that:

The vast desert regions have now been populated with hundreds of thousands of features that contribute to gene regulation. And every cell type uses different combinations and permutations of these features to generate its unique biology.

This was a major bombshell to come out of the ENCODE II study. Actually, the result had been hinted at in the first report, namely a repudiation of the concept of “junk DNA.” Many biologists were deeply incensed at the suggestion that: “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside the well-studied protein-coding regions.”

.....the person who became best known for his attacks on ENCODE was Dan Graur. Concerning the 80% functional claim of the consortium for the human genome, Dan Graur and colleagues declared:

Progress in understanding the functional significance of DNA sequences can only be achieved by not ignoring evolutionary principles.

As an alternative, Graur and his friends argued for a 10% functional proportion in the genome.Their article was provocatively entitled: “On the immortality of television sets: ‘Function’ in the human genome according to the evolution-free gospel of ENCODE.”

 .....in their reply, however, the ENCODE II consortium referred to another bombshell connected to their report: the fact that since 2005, important genetic markers connected with specific diseases, had increasingly been identified in the noncoding part of the genome (that is, the part not connected with genes, supposedly representing junk DNA). The consortium used Genome Wide Association Studies (GWAS) in part to make these identifications. Meanwhile, progress in the ability to obtain sequences of entire genomes from more and more people developed. Specialists began to look for unique markers in people with a specific disease (or condition) compared to others who lacked this trait. And surprise, surprise:

More recently, genome-wide association studies have indicated that a majority of trait-associated loci [locations], including ones that contribute to human diseases and susceptibility, also lie outside the protein-coding regions. These findings suggest that the noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse regulatory and other functions.”

The scientists had discovered that a great deal of important activity was going on in noncoding regions of the genome. If markers of disease are found not connected to genes, it must mean that something important is going on in these noncoding regions. If the area were unimportant, a change in the DNA order of nucleotides there would not matter one way or the other. But it obviously did matter.

 ENCODE III added to the evidence for function in non-coding DNA with newly discovered regulatory sequences such as a “class of

functional sequence elements not previously recognized by ENCODE.”  The result of this discovery alone is: “These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RNA binding proteins.” Similarly, they declare: “ENCODE III data increased the number of annotated cis-regulatory elements by nearly 22% compared with ENCODE II.” CEH