Defining the “Junk” Genes That Separate Chimps and Humans

Defining the differences . . . assuming the reasons

We have been hearing for years that chimp and human DNA is 98.5% identical, as if that proves our common ancestry. Later we learned that “junk DNA” serving a regulatory function is likely responsible for many of the differences. A new study from Georgia Tech biologist John McDonald’s team has examined such “junk DNA” in detail and correlated its presence with differences in gene expression.

McDonald writes, “Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more that 98.5% identical at protein-coding loci.” Acknowledging the enormous difference between humans and chimpanzees, he adds, “This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the species.” In his study, he sought confirmation that “the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with extensive insertion and deletion (INDEL) variation between the two species.”1

The team was able to use the improved quality of chimp genomic information now available. They identified 26,509 INDELs, each a large sequence (80 to 12,000 base pairs long) present in either chimp or human DNA but not both. Of these the majority consisted of large repeated transposable elements. Furthermore, there were significantly more regulatory sequences in human DNA. Most importantly, the majority of identifiable differences in gene expression did correlate with the presence of such regulatory sequences. They concluded that these pieces of regulatory DNA arose from mutations after divergence from the common ancestor and were the differences on which natural selection operated to produce humans and chimps, acting as a significant “driving force behind human regulatory evolution.”2

“Transposable elements were once considered ‘junk DNA’ with little or no function. Now it appears that they may be one of the major reasons why we are so different from chimpanzees.”

“Transposable elements were once considered ‘junk DNA’ with little or no function. Now it appears that they may be one of the major reasons why we are so different from chimpanzees,” McDonald explains. “Our findings are generally consistent with the notion that the morphological and behavioral differences between humans and chimpanzees are predominately due to differences in the regulation of genes rather than to differences in the sequence of the genes themselves.”

So have these researchers proven that humans and chimps share a common ancestor? No, not at all. They simply assume such evolution as a fact. Even the vocabulary used to describe the differences as insertions and deletions reflects the evolutionary assumption.

Their analysis suggests that many genetic differences detectable with present technology consist of certain genes being switched on or off. (See How Genomes are Sequenced and Why it Matters: Implications for Studies in Comparative Genomics of Humans and Chimpanzees for a thorough explanation of the way genomes are actually compared to learn how many more differences get overlooked due to the practical limits of sequencing technology.)

Many people mistakenly think that such research puts to rest the creationist assertion that one kind of organism cannot acquire the genetic information to become another kind of organism. After all, they think, evolving seems merely a matter of flipping switches. What they fail to see is that all of these regulatory sequences—both the sequences themselves and their placement—are information also, information that would have to be acquired to change kinds. Furthermore, the source of the original information—both the protein-coding genes and the regulatory DNA—cannot be explained by evolution.

Determining the genetic basis for many differences between humans and chimps does not explain the origin of those differences or prove our divergence from a common ancestor. What humans and chimps do share is a common Designer. God used many similar bits of genetic information to produce anatomical features needed in similar sorts of organisms. God created each kind of organism and equipped each with the DNA information to reproduce after its kind. We know from the book of Genesis that God did not use one organism as raw material for the next but instead spoke each into existence over the course of a few days. Chimpanzees and human beings were each created on the sixth day. And human beings have a spiritual nature chimps have never had and will never have. Ancestral biology cannot explain even the origin of the information for physical and cognitive differences, much less the spiritual differences. The Bible, however, does.

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  1. Nalini Polavarapu, Gaurav Arora, Vinay K. Mittal, and John F. McDonald, “Characterization and Potential Functional Significance of Human-chimpanzee Large INDEL Variation,” Mobile DNA 2, no. 13: doi:10.1186/1759-8753-2-13.
  2. Ibid.


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