Skeptics of ENCODE’s Discovery of Function

In 1972, geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in reference to  pseudogenes but the meaning expanded to non-coding DNA as well. Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Out of a span of 30 years or so, scientists didn’t do much research on what was considered “fossil remains” of DNA.  Then a group of scientists called, ENCODE discovered something very interesting in 2007. DNA is transcribed into RNA!

Ewan Birney, a coordinator of ENCODE said, “The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.” 

Then on September 5, 2012, the guardian reports…

“Long stretches of DNA previously dismissed as “junk” are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists’ understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.”

80 percent of the genome is now regarded to having function which is a major shift considering most of it was considered junk. The discovery has caused quite a stir with those who advocate “junk DNA” being necessary for evolution (having a critical role in ensuring the survival of biological lineages) while using it for evidence against creationism or intelligent design.

P.Z Meyers has been a skeptic of ENCODE and a huge advocate of junk DNA, (but admires their work) here he writes the following in his blog called, “The ENCODE Delusion.” 

“The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.”

“That isn’t function. (says PZ Myers) That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.”

Nick Matzke in Panda’s Thumb, reiterates what Myers spewed out…

“The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.”

“However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”.

“People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.”

ENCODE defines function by activity meaning, the transcription into RNA which makes 80% of our DNA functional which is a perfectly logical conclusion. However, PZ Myers suggests in his sarcasm…”Oh, jeez, straining over definitions—ultimately, what he ends up doing is redefining “functional” to not mean functional at all, but to mean simply anything that their set of biochemical assays can measure.” 

ID proponent and scientist says…”Non-protein-coding DNA even provides spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals.”  –Biologist Jonathan Wells.

Skeptics of ENCODE, are just one angry bunch of men because one of their weapons they have used for many years is being taken away from them as a result of better science. There is nothing to suggest that the majority of scientists even agree with them just rumblings on facebook and twitter. That is not to say the majority in the science community is always right, (many times they are wrong concerning evolution) but they have always advocated the majority to creationists as being logically conclusive and right in science. But we know that is nothing more than a straw man’s argument along with circular reasoning.

How Richard Dawkins Fights For Evolution

One has observe it in the pages of research, now one has observed it in the realm of debate. Back in 2009, Richard Dawkins thought he was putting it to the creationists and the modern intelligent design movement with his argument about junk DNA.

Here is what he says in his book, The Greatest Show on Earth (pp. 332-333)…

“It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene — a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something — unless he was deliberately setting out to fool us.”

Now here, Dawkins believes that pseudogenes are genetic relics that have lost their original protein-coding function which had been possessed by some ancestral creature. Thus, Dawkins contends that pseudogenes provide convincing evidence for evolutionary history rather than an intelligent designer namely, God!

Then Dawkins goes on to say in his book…

“Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes…useful for. . . embarrassing creationists.”

Dawkins statement was embarrassing not creationists but rather the ENCODE project which back in 2007, two years before his book was published…was the remarkable and unexpected discovery (by evolutionists but predicted by creationists and proponents of intelligent design) that vast regions of non-coding DNA (formerly known as junk) were transcribed into RNA, This included what? Yes! This included a significant amount of pseudogenes!

There were other papers also being published that Dawkins failed to accept at the time like Balakirev and Ayala who wrote two papers back in 2003 and 2004 (here and here) on discovering functions with pseudogenes.

The two papers talk about pseudogenes being involved with gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity.

“Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over non-synonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles.”

The modern Intelligent Design Movement had also predicted function in junk DNA even though it was the prevailing viewpoint in evolutionary theory to oppose it…Here is their trailer about this very subject…

Even this gal in her youtube  program, “Ask A Biologist” who is very smart also predicts function with junk DNA…

So there was research refuting one of Dawkins arguments against creationism and yet he decided to try to stick it us.  Ok, fast-forward to 2012…

Wait a minute! Dawkins not only acknowledges that what was considered junk DNA, does in fact have function like pseudogenes and that but evolution predicted it all along….lol My question to Richard Dawkins is when and why he changed his mind? I know why he hasn’t admitted his mistake because he doesn’t want to look weak in front of creationists and his choir. But the reality of it is in black and white.

So this is how Richard Dawkins fights for evolution, he is not totally honest with the public about his position. One has to keep in mind, many of them use a similar slant for debate. I have never seen a top-notch creation scientist debate like Richard Dawkins does and that is because they are honest! It’s not like creation scientists don’t make mistakes, they are human too which is something Richard Dawkins should think of himself, human who makes mistakes! He is wrong about evolution!