The Encode Project

Our Take on the ENCODE Project. 

Here's what we think about the Encyclopedia of DNA Elements (ENCODE).

One of our readers, Joseph, found January's Web Site of the Month column “fascinating,” and wished we would do an article on the ENCODE Project. The Science Against Evolution Genie will grant his wish - right after this short comment.

Reviewed websites are selected because they merit mention—even if we don't agree with them. We try to present the issues as honestly as possible, and sometimes we do that by reviewing websites with opinions we don't share. Since we don't necessarily endorse or agree with the content of websites reviewed, Joseph wanted to know what we think about the ENCODE Project.

The ENCODE Project

Here’s the abstract of the main article in the peer-reviewed professional journal, Nature, describing the results of the ENCODE Project.


The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

They studied “the human genome.” In case you don’t know what a genome is,

The genome is the entire set of genetic instructions found in a cell. In humans, the genome consists of 23 pairs of chromosomes, found in the nucleus, as well as some DNA molecules found in the cells' mitochondria. Each set of 23 chromosomes contains approximately 3.1 billion bases of DNA sequence. 

The genome is the genetic information that the human body uses to build all the cells it is made up of.

The purpose of the study was not to prove evolution. It was biomedical research. They were trying to figure out what each part of the human genome does, and how it is related to disease. Evolution was not discussed because it was taken for granted by the study authors.

The article itself is pretty boring, and is not very quotable. It is mostly a lot of stuff about mapping where various things are found on the DNA molecule. The comments about the article are more pertinent to evolution than the article itself. Before addressing those comments, let’s make an analogy between DNA and Egyptian hieroglyphics.

Decoding Names and Proteins

The Rosetta Stone contains writing in Egyptian hieroglyphs, Demotic script, and Ancient Greek. Archeologists assumed that the hieroglyphs said the same thing as the Greek inscription. Since the names "Ptolemaios" and "Kleopatra" appeared in multiple places in the Greek, Jean-François Champollion looked for them in the hieroglyphics, and found them.

Suppose you don’t know anything about the Russian language, but discovered a bi-lingual document in Russian and English discussing the Soviet Leaders Сталин (Stalin), Ленин (Lenin), and Никита Хрущев (Nikita Khrushchev). Knowing how the names are pronounced, you could start to figure out how Cyrillic letters are pronounced. That’s how Champollion figured out how to pronounce hieroglyphics. But knowing what the hieroglyphics sound like is just the beginning. He still had to figure out what the sounds that weren’t names meant. That took longer.

When the DNA structure was first analyzed, nobody knew what the DNA did. The first thing they discovered was that portions of the DNA molecule caused proteins to be produced. (They “coded for proteins” in genetic jargon.) Until recently, scientists were unable to figure out what the rest of the DNA molecule did. All they knew was,

More than 98% of the human genome does not encode protein sequences, including most sequences within introns and most intergenic DNA. 

Arrogantly, they thought that if they didn’t understand what it did, it must not do anything. It must be random “junk” left behind by evolution. If Champollion had been as arrogant, he would have thought that all the hieroglyphics that weren’t names were just junk doodles, and would not have discovered what they meant.

Not Junk

The ENCODE Project has now been able to assign biochemical functions for 80% of the genome, so that 80% of the human genome clearly isn’t “junk.” As time goes by, we expect the purpose for the remaining 20% will be found, too.

The Evolution Connection

You might be wondering why an article about biomedical research, which has no creationist agenda, would be so controversial in the evolutionary community. It is because this biomedical research strikes at the heart of an evolutionary assumption that has been around at least since 1986, and probably much longer.

In 1986, the famous militant evolutionist, Richard Dawkins, challenged William Paley’s long-standing watchmaker analogy. (In 1802, Paley argued that if a pocket watch is found on a heath, it is most reasonable to assume that someone dropped it and that it was made by one or more watchmakers, and not by natural forces.) In his book, The Blind Watchmaker, Dawkins wrote,

"Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind’s eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker."

This has become a fundamental tenant among evolutionists. Evolution must have no goal in mind because a goal implies intention, intention implies design, design implies intelligence, and intelligence implies a deity.

The problem for evolutionists is that studies of living things have produced an insurmountable mountain of evidence that life could not have evolved by chance. The probability of chance producing living things so well designed is just too small. So, ten years after The Blind Watchmaker, Dawkins wrote Climbing Mount Improbable, in which he introduced a new class of objects.

"I shall call them designoid (pronounced ‘design-oid’ not ‘dezziggnoid’)… Designoid objects look designed, so much so that some people — probably, alas, most people — think that they are designed. These people are wrong."

He admits that living things clearly appear to have been designed; but he claims that is just an illusion. Although he admits they certainly appear to be designed, he claims they weren’t really designed for no other reason than that he doesn’t believe in a designer. He sees the evidence, but can’t accept the logical conclusion.

Because of the theological implications, it is vitally important to evolutionists that no hint of purpose be admitted in evolution. This brings us back to the idea of “junk DNA.”

Junk DNA

Dawkins believes that the god he doesn’t believe in would not create any junk DNA. That is, if DNA was designed on purpose, there would not be any unnecessary parts. Unnecessary parts just drive up the cost.

In 2015, Ford produced 2,613,162 cars.  None of them came with fuzzy dice hanging from the rear view mirror. Fuzzy dice serve no purpose. If you want fuzzy dice, you have to spend $4 to $12 dollars of your own money to get them. If Ford bought fuzzy dice wholesale at a deep discount of $1 per pair, and put them in every car sold, it would have reduced Ford’s profit by more than 2.5 million dollars. Smart designers don’t add things that don’t have a function. Functionless cosmetic features are added only if it is believed that their beauty will increase the number of units sold.

Dawkins’ point, accepted by most evolutionists, is that if the human genome were designed on purpose, it would not be 2% useful parts that code for proteins and 98% random junk that doesn’t do anything. Therefore, DNA must be the result of purposeless accidents filtered by natural selection.

The ENCODE Project found functions for at least 80% of the human genome, and the possibility that the remaining 20% has functionality that hasn’t been understood yet. If the human genome is lean and mean, with no unnecessary extra baggage, then it must be the product of conscious design.

The Broken Clock

The other problem evolutionists have with the ENCODE Project is that their findings break the molecular clock. It used to be thought that the "junk" regions, which were previously believed to have no function, could accumulate mutations which would not be removed by natural selection because they don't affect the viability of the organism. Therefore, they believed they could determine how long it could have been since two “closely related” organisms diverged from their imaginary common ancestor by counting the number of differences in the junk DNA and dividing by an average mutation rate. (The mutation rate was based on the differences in DNA of species which were “known” to have diverged after a “known” number of years.)

If the junk regions really do have functionality, as the ENCODE Project has discovered, then accumulated differences aren’t immune to “negative selection” (to use jargon the ENCODE Project uses). Therefore, the accumulated differences can’t be used as an evolutionary clock.

They Still Believe

Despite this, it is clear from their report that the authors of the ENCODE Project still believe in evolution. Their paper is full of sentences like this one:

Our data show that global patterns of modification are highly variable across cell types, in accordance with changes in transcriptional activity.

“Global patterns of modification” implies evolution. They assume that some creatures are more recently evolved, and are the result of modification of the DNA of a more primitive creature. They recognize that the amount of evolution is “highly variable across cell types.” In other words, they believe that certain parts of the DNA molecule have evolved a lot, and other parts have not evolved very much. (This also invalidates the notion of the molecular clock.) They explain this away by saying it is the result of “changes in transcriptional activity.” They expect you to accept this explanation without question, so they offer no proof that it is true.

I Didn’t Know the Gun Was Loaded

The authors of the paper seem clueless as to the obvious damage this report does to the theory of evolution. They believe completely in evolution, so it apparently never occurred to them that their discovery of functionality in junk DNA absolutely refutes Dawkins’ position. They just innocently presented their data showing conclusively that they have found purpose for 80% of the human genome and did not prepare any defense for the attacks they would get from evolutionists who fear that creationists can use this to their advantage.

Astute evolutionists, like Steven Pelech, immediately recognized the vulnerability of the theory of evolution to creationists in light of this information, and used this defense:

"There appears to be strong evolutionary pressure in multicellular organisms to retain excess baggage so as to simply make sure that the important parts are retained. There are countless cases of this ranging from the extensive remodelling of embryos during early development, to the hundreds of thousands of superfluous phosphorylation sites in the proteins encoded by the human genome. At the levels of gross anatomy down to the molecular, there are so many examples of inefficiencies in biology."

Even though the researchers found that 80% of DNA wasn’t really junk, and isn’t unnecessary “excess baggage,” Pelech says that retention of unnecessary excess baggage really is necessary to “make sure that the important parts are retained.” He thinks that the way embryos develop is inefficient, as if he knows a more efficient way to create offspring.

The Inefficiency Defense

Pelech insists that there are many examples of inefficiencies in biology - an argument that optical engineers just can’t see. Here’s why:

You’ve probably heard more than one evolutionist say that the human eye is inefficient, claiming that the human retina is installed backwards. Just in case you haven’t, here’s an example of the argument from poor design.

The structure of humans' eyes (as well as those of all vertebrates). The retina is 'inside out'. The nerves and blood vessels lie on the surface of the retina instead of behind it as is the case in many invertebrate species. This arrangement forces a number of complex adaptations and gives mammals a blind spot.

It should come as no surprise to you that the bigger a telescope is, the more sensitive it is. The telescope on the front of the infrared air-to-air missile I helped design in the 1970’s was about three inches in diameter. It could barely see as well as a human eye. There was no way I could shrink the telescope down to the size of the pupil of a human eye. Hawk, owl, and eagle eyes are even smaller than human eyes, but clearly have good enough sensitivity to see small rodents from high in the sky. Don’t talk to me about “inefficiencies in biology” and claim that eyes are badly designed.

The Bottom Line

The less “junk” there is, the more evidence there is for design. That’s why the discoveries of genetic research in general, and the ENCODE project in particular, are so damaging to the theory of evolution.

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