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.

Nick Matzke Expels Caroline Crocker

Can the politically appointed and self-imposed establishment tolerate scientists who doubt various theories in evolution? It became a hot topic in 2008, when a documentary with a well-known movie star (Bein Stein) called, “Expelled” became the number one topic in the blogosphere before its release and then many months thereafter when it was released to the public. Nick Matzke is a cult follower of evolution.

Who is Nick Matzke? For those who are not familiar with him, he worked for the NCSE (National Center For Science which is a special interest group) as a Public Information Project Director while playing an important role in the Kitzmiller v. Dover Area School District trial.

Thus, Matzke often times likes to use the bumper sticker phrase or word when one doubts evolution as “anti-science” but this of course is an over simplification on the matter which is nothing more than inventing a straw man.  No skeptic of evolution is against things like computer science or rocket science or adult stem cell research which is only part of many great things in science!

Nick Matzke goes after Caroline in a cult-like way using a quote from another website, in UC he writes and then quotes in the comment section…

Following the evidence wherever it leads, eh? Caroline Crocker’s record does not suggest that she is any good at doing this. Instead she just brazenly repeats the crudest creationist arguments. Documentation:

“In the above-mentioned article in the Washington Post, Crocker is described teaching her students a laundry list of discredited Creationist arguments. In a video on the Coral Ridge Ministries site, several of Crocker’s slides are shown. Though it’s not known whether Crocker used the same slides while teaching at George Mason, the Washington Post article provides evidence that they were part of her Northern Virginia Community College lectures. Her use of these slides suggests that Crocker shows either a shocking ignorance of evolutionary science, or a rather shameless willingness to distort the evidence.”

The following are just a small sample of her erroneous and clearly creationist claims:

* Archeopteryx [sic] is a bird (like an Ostrich), not a reptobird
* Only one complete fossil, and has been questioned as a fraud

One can tell Caroline Crocker wasn’t teaching creationism at a government University, all this accusation is implying is that she is a creationist because she is skeptical about Archeopteryx. Then the accusation uses the typical argument about consensus among scientists which somehow helps proves that Archeopteryx is a transitional form. Let’s use a more certainty in science and that is physics. Nothing is more absolute than physics, right? It holds the most certainty in science, right? Many things in the physical world relies on the constancy of this value. Yet, Einstein’s theory of relativity, nothing can exceed the speed of light as measured in a vacuum is being challenged. Experiments are being conducted in order to make an attempt to overturn it!

CERN researchers have claimed that have done just that, Neutrinos which are a subatomic particle that has the least resistance of any particle known to man because it has very little mass was claimed to have gone faster than the speed of light! Now let’s take Nick’s argument and ask, how can one question a well-establish fact like Einstein’s theory of relativity and not be labeled as “anti-science” or a “creationist”? Why can physics be questioned or challenged and not theories within Darwinian evolution? These things only happen in cults. They have some sort of dogma that they believe in and in order to rescue it from criticism that might result in a conversion against them, they guard it like a holy grail.

Scientists have never observed a living Archeopteryx and therefore have used massive amounts of inferences due to their own bias or a particular framework which thus opens it up to more criticism as a result of using speculation than with the certainty of physics. Caroline Crocker responded to the accusations by saying…

“Dr. Crocker was summoned by her department head, accused of teaching creationism despite a singular lack of written even one complaint, and told she had to be disciplined. He immediately removed her from lecturing, even though this was against policy listed in the Faculty Handbook. In fact, she was told to sign up to teach extra lab classes without delay. Many students complained because they had signed up specifically for her lecture class. The short-notice replacement teacher was struggling and not covering the material that was necessary for them to do well in the lab and in future classes.

“The sole reason for Dr. Crocker’s removal from the classroom was a single lecture that was not even delivered that semester, where she suggested that the theory of evolution may not have all the answers and may, in fact, have been rendered out-of-date by current scientific knowledge. Faculty and staff members confirmed that this was the only issue.”

“Finally, the writer of this article complains that many of Dr. Crocker’s arguments were “creationist.” Perhaps he does not appreciate what the word “creationist” means. It is someone who considers a religious book to have scientific authority. It is not someone who sees scientific problems with scientific theories! Her questions about the theory of evolution were as a result of seeing that science has advanced beyond the explanatory reach of this theory. In addition, the writer should be aware that calling scientific arguments “creationist” does not address the validity of the arguments. It is merely an ad hominem attack that does not require response.”

How something relativity simple can change a person’s life! In this case, Caroline’s life. Those like Nick Matzke are cult followers of evolution, which is why they treat certain scientists as prophets, which is why evolution is reverend to them like a religion rather than a scientific prospective or theory which in turn is why a requirement of membership is involved, nowhere in any other area of science does this happen as physics was a great example of that!

Nick Matzke Makes Common Accusation Against ID

Most liberals with a particular agenda are relentless in their quest to accuse others for the purpose of stereotyping them which they consider a much easier way of disqualifying their opposition.  Now there are flaws in the modern intelligent design movement which has been pointed in here. We also have observed the modern intelligent design movement trying to distant themselves many times  from creationism as pointed out in here. Nick Matzke using some sort of conspiracy style in his writing in which he claims to be collecting evidence and then showing it in Pandas Thumb, calling ID proponents, young earth creationists…

He writes…

“There was a huge stink raised over the alleged inappropriateness of linking ID to creationism. After much argument the anti-linkage people more or less conceded that there were some good reasons to link ID to a somewhat generic definition of creationism (relying on special creation), but still protested loudly about how inappropriate it was to make the linkage, because most people (allegedly) would assume that creationism = young-earth creationism, and linking ID to young-earth creationism was oh-so-wildly unfair.

Well, it’s now a week later, and, what do you know, but right there on the latest blogpost on William Dembski’s Uncommon Descent is a big fat advertisement for a straight-up young-earth creationist conference.”

There are different groups of people who are in the modern intelligent design movement. Dr. Dean Kenyon doesn’t represent everyone in ID. In fact, there are atheists and agnostics who have a connection in some particular way with the organization and yet, ID proponents will not throw out their membership per say because of their views about the supernatural. Most ID proponents don’t believe in the earth being six thousand years old, rather they accept the evolutionary viewpoint when it comes to the age of the earth.

ID can be compared to something like the 12 steps which has been used by the US government for rehab, the higher power is never defined to any particulars, it could be yourself, it could be the supernatural like God, it could be the devil, or any other religion or non-religion. It’s similar to how the modern intelligent design movement is run today.

Just like Dawkins who uses Fox News to promote his books, William Dembski uses various conferences to promote ID. He writes in Uncommon Decent“For the record, just because various non-ID conferences and events are reported here at UD (e.g., creationist, atheist, or theistic evolutionist) does not constitute an endorsement of those events.

Nor does the appearance of an ID proponent at such events constitute complicity with the positions of the organizers. I myself have appeared at atheist (World Skeptics Congress), theistic evolutionist (Templeton conferences), and young-earth creationist (local gatherings here in Texas) events. I believe in getting the word out about ID and, frankly, am happy to have the opportunity to address people on the other side of these issues.”

Nick Matzke like many liberals with an agenda hammer time and time again lame accusations towards a group of people in whom they disagree with, thinking this has won the debate when in fact it shows how much dislike they have for people in general whom they disagree with which provides no real evidence for their position! If Nick Matzke was able to produce proof that leading figures in ID like William Dembski were embracing not just attending some young earth creationism conference or skeptics conference, then it would be another story.