If ENCODE is right Darwinism is wrong

[Stu]

Junk DNA: Darwinists Say They Are "Largely Free from Assumptions or Hypotheses"

According to a recent Science Daily news item, Oxford University researchers say that only 8.2% of our DNA is likely to be functional. The rest is "junk."

The 8.2% figure contradicts the conclusions of the ENCODE Project (for "Encyclopedia of DNA Elements"), which was established after the Human Genome Project to make sense of our newly sequenced DNA. In September 2012, the results from over a thousand experiments -- involving dozens of laboratories and hundreds of scientists on three continents, published almost simultaneously in dozens of articles in five different journals -- provided evidence that 80% or more of our DNA is functional.

The results were consistent with The Myth of Junk DNA, which I published in 2011. But the ENCODE research had been going on for about five years. Why were the articles published almost simultaneously? Perhaps because the authors wanted to present a united front against the reaction they anticipated from "junk DNA" advocates. And what a reaction they got! Darwinists Larry Moran, Nick Matzke, and P.Z. Myers (among others) lit up the blogosphere with their denunciations.

Near the heart of the controversy is the definition of "function." The ENCODE researchers defined function biochemically: A DNA segment is functional if it "participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type." The Darwinists define function in terms of evolutionary theory: A DNA segment is functional if it is subject to natural selection.

The Oxford researchers took the evolutionary approach. To determine what percentage of human DNA is subject to selection, they compared published sequences from humans, mice, rats, cattle, dogs, horses, guinea pigs, rabbits, bushbabies, pandas and rhinos. One of the researchers, Gerton Lunter, explained: "Throughout the evolution of these species from their common ancestors, mutations arise in the DNA and natural selection counteracts these changes to keep useful DNA sequences intact." The researchers looked for places in the DNA where insertions and deletions were far apart, reasoning that the intervening DNA sequence was constrained by purifying selection because it was biologically functional. They found that about 8.2% of our DNA is constrained in this way, and thus likely to be functional (though less than 2% of our DNA is protein-coding). They concluded that DNA that differed substantially among the species they studied -- DNA that was non-conserved -- had not been subject to purifying selection and was thus non-functional.

But while sequence conservation may imply function, non-conservation does not imply non-function -- as biologists have long recognized. Indeed, to whatever extent DNA differences play a role in distinguishing different species, non-conserved sequences must be functional.

Furthermore, biologists now know that as much as 30% of the protein-coding DNA in every organism consists of "orphan genes" that bear little or no similarity to DNA sequences in other organisms. While the functions of most orphan proteins are not yet known, few people would be so foolhardy as to suggest that they are non-functional. Yet in a search for evolutionary constraint such as the Oxford researchers used, these protein-coding regions would be judged non-functional.

Why do Darwinists find evolutionary speculation more reliable than biochemical experimentation? A clue might be found in a presentation given by Dan Graur at the 2013 meeting of the Society for Molecular Biology and Evolution in Chicago. As Graur -- a vocal, even nasty, opponent of ENCODE -- reasoned in his presentation:

"If the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all DNA, or as much as possible, is expected to exhibit function. If ENCODE is right, then Evolution is wrong."

So while the definition of "function" is close to the heart of the controversy, adherence to Darwinian evolution is even closer. And it seems that adherence to Darwinism has a way of blinding people to the assumptions they make. Perhaps this is why Gerton Lunter, quoted above about the role of evolutionary theory in the Oxford study, told Science Daily that "our approach is largely free from assumptions or hypotheses."

[melanie]

Interesting read, thanks Stu.
It has been said that assumption is the mother of all screw-ups.

[Ivellious]

The problem with the 80% figure cited by ENCODE and, subsequently, the media, is that most people don't actually understand what it means. Their extremely broad definition of "functional" includes and part of DNA that is ever transcribed. Even if the byproduct of that transcription does literally nothing (and thus has no function), the ENCODE definition of "function" included it.

The biological science community was upset at this wording/defining of "function" because, in simple terms, ENCODE was counting DNA as "functional" even if its transcribed byproduct did nothing after being transcribed. Even if they didn't intend to, their wording gave the impression that they were saying most or all of our DNA actually did anything related to proteins or gene regulation, which is totally untrue. Plus, the research methodology used by ENCODE focused on large scale projects. Instead of investigating certain segments of DNA specifically, they studied massive amounts of DNA at a time. It took less time to study the genomes they looked at, but in turn opened the research to lots of false positives, which likely inflated their percentage in the process.

The ENCODE researchers tried to make a splash in the media by using a definition of "functional" that they knew would catch the media's attention, and it it unintentionally made the ID community jump on their research as proof of the demise of evolution...which is laughable if you actually understand the scientific implications of what they were trying to say. The good news for the ID crowd is that most people simply don't, which is why you see the above article claiming victory over an issue of semantics.