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.

Scientists Claim: They Performed Evolution

Geneticists are in the process of engineering molecules which is great science, but when scientists alter molecules which is not found in nature, are they performing evolution which is a mindless unguided process or intelligent design? Is there any evidence for evolution in the experiment?

The abstract in the paper goes like this…

“Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution. It involves the storage and propagation of molecular information and the refinement of that information through experience and differential survival. Heretofore, the only molecules known to be capable of undergoing Darwinian evolution were RNA and DNA, the genetic molecules of biology. But on page 341 of this issue, Pinheiro et al. (1) expand the palette considerably.”

“They report six alternative genetic polymers that can be used to store and propagate information; one of these was made to undergo Darwinian evolution in response to imposed selection constraints. The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself. “

Here the paper uses circular reasoning, “Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution.” There was no observation of nature selecting the defined structures nor the targets, nor the aptamers! It was an international team of scientists who did the selecting! Not only that but their altered molecules “remains relatively inefficient.” unnatural or designed by scientists are poor polymerase substrates at full substitution.

Molecular memory is not a demonstration of evolution rather it’s an assumption of the data.  Scientists invented their own selection strategy which they call  “compartmentalized self-tagging.”  

The conclusion of the paper says…

“Our work establishes strategies for the replication and evolution of synthetic genetic polymers not found in nature, providing a route to novel sequence space. The capacity of synthetic polymers for both heredity and evolution also shows that DNA and RNA are not functionally unique as genetic materials.”

“The methodologies developed herein are readily applied to other nucleic acid architectures and have the potential to enable the replication of genetic polymers of increasingly divergent chemistry, structural motifs, and physicochemical properties, as shown here by the acid resistance of HNA aptamers (fig. S17). Thus, aspects of the correlations between chemical structure, evolvability, and phenotypic diversity may become amenable to systematic study. Such “synthetic genetics” — that is, the exploration of the informational, structural, and catalytic potential of synthetic genetic polymers — should advance our understanding of the parameters of chemical information encoding and provide a source of ligands, catalysts, and nanostructures with tailor-made chemistries for applications in biotechnology and medicine.”

Other media makes wild claims that this experiment produces a more understanding about the origin of life which is nothing more than presupposes the existence of DNA. Because without DNA along with its specified information, and proteins to build DNA, nothing happens! Unless scientists are observing this in nature without their tinkering around, this is not evolution rather they are tinkering with something that was intelligently designed by God.  Even if evolution was true, just because it was done in a lab, doesn’t mean nature does it and altering molecules in a lab is not a demonstration on how evolution works rather just like evolution itself, it’s a man-made up story about the experiment.

The Cell’s Importance Of Optimizing And Repair

A car gasoline engine cannot be bigger and faster while getting better gas mileage than smaller cars. A computer cannot run more components without using more electricity. Thus, it is not always possible to have all the elements of a product be ideal.  Recent recent research shows a unique combination of the two.

The title of the PNAS paper says the “Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.”  There are competing forces the paper admits, “Translation of the ancient and universal genetic code into protein on ribosomes requires precise mRNA decoding by aminoacyl-tRNAs (aa-tRNAs) and rapid formation of nascent peptide chains.”   Accuracy and speed are required for the cell to survive and since this is the case with the limitations of time and space, how do they work together for the benefit of the cell?

When it comes to the transfer of  RNA, the  anticodon must find the right codon within a certain time frame. The article says  in regards to this, “Codon reading by aa-tRNAs ultimately relies on the specificity of cognate in relation to noncognate codon–anticodon interactions, but two ribosome-dependent specificity enhancements greatly improve mRNA decoding.”

There is not one but incredibly two well-designed mechanisms that act like an editor whose job is to proofread to make sure the job is done right, ” “the ribosome enhances the accuracy of codon reading by a twostep mechanism in which initial codon selection by a tRNA is followed by a proofreading step.”  The speed is accomplished by the tRNA matching up initially with its cognate, but “editors” in the ribosome during translation clean up any mistakes.

Then the authors looked for optimizing by examining the “maximal possible discrimination between a cognate and a noncognate codon–anticodon interaction: the ‘d value’,”  Just tentative numbers, further study is required for a better conclusion. Not surprisingly, the article then gives credit to evolution where it says, “Finally, we propose that quantitative estimates of the d values of the genetic code in conjunction with the remarkably simple efficiency-accuracy trade-off revealed by the present experiments will clarify how the accuracy in living cells has been evolutionarily tuned for maximal fitness of growing bacteria.”

It really doesn’t explain evolution other than the authors believe in it rather this is amazing observational science. Darwinism actually hinders the science with a better understanding that comes from  intelligent design. The designs we see in nature come from a mind not a non-thinking process. These designs are highly advanced and require much study for us mere humans to understand.

New Scenarios Proposed For Fundamental Problem

Non-living chemicals emerging into living cells are not being observed in nature but evolution requires such an observation like that to occur and scientists are down to creating a story about RNA. Two recent studies have surfaced in this area. The first is an RNA reactor being a precursor for life.

Physorg tells the story…

“Nobody knows quite how life originated on Earth, but most scientists agree that living cells did not abruptly appear from nonliving cells in a single step. Instead, there were probably a series of pre-cellular life forms that arose from nonliving chemicals and eventually led to a living cell, one that could undergo metabolism and reproduce. One of the most well-known theories of pre-cellular life is the RNA world theory, which proposes that life based on RNA predates current life, which is based on DNA, RNA, and proteins.”

“But recently, scientists have been wondering what may have preceded RNA. In a new study, a team of scientists from Germany has suggested that the ability to self-replicate may have first emerged in the form of an RNA reactor, which they show can transmit information.”

From an evolutionary standpoint, these scientists admit they have no clue on how non-living chemicals supposedly became a living cell. In the article it contains a display of weak information being transferred in RNA strands, but the text is vague about the definition of information which is vital for every living cell.  We know when a computer is built where the information comes from which wasn’t a by-product of mere survival of random sequences. Even if there was some hypothetical meaningful use of “information” in this particular scenario, it would be quickly lost in an “error catastrophe” without accurate replication.

There wasn’t much hype with this particular scenario as though it was going to solve the fundamental problem, rather it was viewed as another angle for them to explore. Two chinese scientists offer up their scenario on the origin of life in PLoS One.

“It is now widely accepted that at an early stage in the evolution of life an RNA world arose, in which RNAs both served as the genetic material and catalyzed diverse biochemical reactions. Then, proteins have gradually replaced RNAs because of their superior catalytic properties in catalysis over time. Therefore, it is important to investigate how primitive functional proteins emerged from RNA world [sic], which can shed light on the evolutionary pathway of life from RNA world to the modern world.”

“In this work, we proposed that the emergence of most primitive functional proteins are assisted by the early primitive nucleotide cofactors, while only a minority are induced directly by RNAs based on the analysis of RNA-protein complexes. Furthermore, the present findings have significant implication [sic] for exploring the composition of primitive RNA, i.e., adenine base as principal building blocks.”

Admitting its a fundamental problem concerning the origin of life, they confined themselves by bowing to the most widely accepted scenario out there. Their experiment consisted of searching a database for existing RNA-binding proteins in living cells that they targeted as possibly “primitive”.  Since polypeptide chains do not naturally form from amino acids in water (and even if they did, are unlikely to be functional), any results from a dubious method are likely to remain dubious.

Their scenario makes quite a leap from the fact that ATP, NAD, FAD, and more all contain adenine. “Considering the notion that early cofactors are vestiges of RNA world, we thus believed that adenine base should be included in the original composition of primitive RNA,” they said. There is a reason why they had made such a leap from fact, you see in order to believe that the building blocks of RNA, the bases A, G, C, and U, formed naturally and available on an early prebiotic Earth. But that has a fundamental problem too, while some of these bases have been found in meteorites (A, G), no one has been able to cook up cytosine (C) in a plausible early earth. So they focus on adenine which could come from space which is quite a leap.

NASA which mission to the moon was changed to a plan for a $800 million asteroid sample-return mission called OSIRIS-REx, which stands for Origins, Spectral Interpretation, Resource Identification, Security-Regolith Explorer. If this mission is ever followed through on, it will no doubt give evolutionary scientists more material to invent new scenarios in order to explain a fundamental problem.

This is where people’s tax money is going, scientists providing pseudo-scientific props for their materialist world views. Science is considered a representative of knowledge, did anybody see any knowledge going on in these articles? Just because it makes in a peer-review science journal doesn’t make it science. Using scenarios is not science. Busy work is not science. Merely using words like arose and emerged is also not science. Suggestive phraseology like “RNA world” and “building blocks of life” is not science either rather knowledge is supposed to be justified true belief!