ENCODE and the Dark Matter of the Genome, Part One

I’m so excited to be writing a blog on the new research published by ENCODE on “junk” DNA! In fact, as I looked over the material I decided I should devote two blogs to the topic. Part one will cover what ENCODE found and why it’s important. In part two, I’ll discuss opposition to the research findings by many evolutionists.

ENCODE is an acronym for ENCyclopedia Of DNA Elements. The ENCODE project is devoted to essentially making sense of the human genome. The sequence of the human genome was completed in 2000, but all it gave us was the order of the individual components, called bases or nucleotides, in the DNA (which is an amazing feat!). We still didn’t know the function of many of those components. Of course, some genes (packets of information in the DNA for making proteins) were known, but that only accounted for about two percent of the human genome. What about the other 98 percent?

For many years even prior to 2000, that 98 percent was affectionately called “junk” DNA. It was assumed to be an evolutionary wasteland of sequences that were discarded as we climbed the “tree of life” from a single-celled organism to human. However, when it was discovered that humans, as the most complex organism on the planet, only have about 20,000 genes and they are similar to genes in many other organisms, scientists knew they had to look elsewhere for the differences.

In 2007 the ENCODE project released a multitude of papers explaining their findings from analyzing just one percent of the human genome (mostly the “junk”). One of the scientists involved in the research said, “We are now seeing the majority of the rest of the genome is active to some extent.”1 This was a surprising finding for supposed “junk”! Fortunately, this prompted more extensive research of the remaining 99 percent of the genome over the last five years.

Last week, over 400 scientists in 32 different laboratories released their findings in 30 papers published in several different scientific journals. The sheer volume of information is amazing, consisting of hundreds of terabytes of data! ENCODE estimates that 80 percent of the genome is functional in the sense that it has “specific biochemical activity.” So much for it being “junk” DNA! Mark Gerstein, an ENCODE researcher said, “It is like opening a wiring closet and seeing a hairball of wires. We tried to unravel this hairball and make it interpretable.”2

Most of the function is believed to be regulatory. In the simplest terms, the “junk” DNA is telling the genes when to produce their product (the protein) and when not to. The goal is to eventually figure out the function of each and every one of our three billion bases of DNA! ENCODE researcher Tom Gingeras said, “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more.”3 ENCODE only studied 147 cell types, and considering the human body has a few thousand cell types, Ewan Birney, ENCODE’s Lead Analysis Coordinator, said, “It’s likely that 80 percent will got to 100 percent.”4 I think we really need to come up with an alternative name for “junk” DNA!

The ENCODE findings will likely have significant impact on disease diagnosis and treatment (in the future). For many years we have known that certain variations in the DNA code (called single nucleotide polymorphisms, SNPs) are associated with risks for disease or with the disease itself. But 90 percent of those variations fall outside of genes (in the “junk” DNA), so up to this point no one really knew how that variation was causing the disease. The ENCODE study found that 60 percent of these variations fall in regions that affect the activity of genes. I have a couple friends that suffer from Crohn’s disease, and the ENCODE study found five variations in Crohn’s patients related to a specific factor that Crohn’s researchers weren’t even looking at. Of course, translating the basic lab science to clinical applications and treatments will take time, but it puts us one step closer in our battle against disease in this sin-cursed world.

A third phase of the ENCODE project is now beginning to further refine exactly what all the “junk” DNA is doing. Ewan Birney stated, “We are the most complex things we know about. It’s not surprising that the manual is huge. I think it’s going to take this century to fill in all the details.”5 Or will it take longer? Geneticist Rick Myers stated, “We’re far from finished. You might argue that this could go on forever.”6 Agreed! I couldn’t help but think of the following verses as I read through the ENCODE findings.

For You formed my inward parts;
You covered me in my mother’s womb.
I will praise You, for I am fearfully and wonderfully made;
Marvelous are Your works,
And that my soul knows very well. (Psalm 139:13–14)

• ENCODE Project
• Nature ENCODE

Be sure to come back next Tuesday when I will discuss the negative reactions of many evolutionists to the ENCODE findings.

Keep fighting the good fight of the faith!