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Junk Dna Research Paper

Evolutionary Worldview Inhibited Study of Junk DNA

For many years the notion that non-coding DNA was not functional (“junk”) actually inhibited science. Many scientists didn’t spend their time studying it because of their evolutionary presuppositions that it was worthless DNA.

No “Junk” DNA

In contrast to the secularist view that expected “junk” to clutter the genome after eons of time, creationists had predicted that the all-wise Creator had designed amazing, functional complexity into DNA.

Interbreeding Not Possible Because of “Junk” DNA

“Junk” DNA can be responsible for rendering two otherwise closely related species unable to interbreed. Exactly why the created kinds have fractured into many incompatible species has only been answered indirectly by creationists, who point to the speciating effects of genetics and geography.

Articles About “Junk” DNA

  • Magazine Department Article

    Junk Science

    Jan. 1, 2013 from Answers Magazine

    The evolutionary assumption that 98% of human DNA is "junk" actually inhibited our understanding of the human genome.

  • Unnecessary DNA

    Sept. 8, 2007

    How can rats, mice, and humans share so many identical DNA sequences? Look inside!

  • Neutral DNA

    July 14, 2007

    DNA elements sometimes confer neither benefits nor disadvantages.

  • Vestigial Genes?

    Aug. 5, 2006

    Scientists have found supposedly worthless DNA. What are these pseudogenes and what do they mean?

  • Semi-TechnicalResearch Paper

    Pseudogene Function: More Evidence

    Aug. 1, 2003, pp. 15–18

    According to standard evolutionary thinking, pseudogenes are simply disabled copies of genes.

  • TechnicalResearch Paper

    ‘Junk’ DNA: Evolutionary Discards or God’s Tools?

    Aug. 1, 2000, pp. 18–30

    That functions are being found for junk DNAs fits in well with creation science. But evolutionary theory is being adjusted again to accommodate the data.

The new result “is a stunning resource,” said Dr. Lander, who was not involved in the research that produced it but was a leader in the Human Genome Project. “My head explodes at the amount of data.”

The discoveries were published on Wednesday in six papers in the journal Nature and in 24 papers in and Genome Biology. In addition, The Journal of Biological Chemistry is publishing six review articles, and is publishing yet another article.

Human DNA is “a lot more active than we expected, and there are a lot more things happening than we expected,” said Ewan Birney of the European Molecular Biology Laboratory-European Bioinformatics Institute, a lead researcher on the project.

In one of the Nature papers, researchers link the gene switches to a range of human diseases — , , , , — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a researcher for the project, called Encode, for Encyclopedia of DNA Elements.

And that, said Dr. Bradley Bernstein, an Encode researcher at , “is a really big deal.” He added, “I don’t think anyone predicted that would be the case.”

The discoveries also can reveal which genetic changes are important in cancer, and why. As they began determining the DNA sequences of cancer cells, researchers realized that most of the thousands of DNA changes in cancer cells were not in genes; they were in the dark matter. The challenge is to figure out which of those changes are driving the cancer’s growth.

“These papers are very significant,” said Dr. Mark A. Rubin, a genomics researcher at Weill Cornell Medical College. Dr. Rubin, who was not part of the Encode project, added, “They will definitely have an impact on our medical research on cancer.”

In prostate cancer, for example, his group found mutations in important genes that are not readily attacked by drugs. But Encode, by showing which regions of the dark matter control those genes, gives another way to attack them: target those controlling switches.

Dr. Rubin, who also used the Google Maps analogy, explained: “Now you can follow the roads and see the traffic circulation. That’s exactly the same way we will use these data in cancer research.” Encode provides a road map with traffic patterns for alternate ways to go after cancer genes, he said.

Dr. Bernstein said, “This is a resource, like the human genome, that will drive science forward.”

The system, though, is stunningly complex, with many redundancies. Just the idea of so many switches was almost incomprehensible, Dr. Bernstein said.

There also is a sort of DNA wiring system that is almost inconceivably intricate.

“It is like opening a wiring closet and seeing a of wires,” said Mark Gerstein, an Encode researcher from Yale. “We tried to unravel this hairball and make it interpretable.”

There is another sort of hairball as well: the complex three-dimensional structure of DNA. Human DNA is such a long strand — about 10 feet of DNA stuffed into a microscopic nucleus of a cell — that it fits only because it is tightly wound and coiled around itself. When they looked at the three-dimensional structure — the hairball — Encode researchers discovered that small segments of dark-matter DNA are often quite close to genes they control. In the past, when they analyzed only the uncoiled length of DNA, those controlling regions appeared to be far from the genes they affect.

The project began in 2003, as researchers began to appreciate how little they knew about human DNA. In recent years, some began to find switches in the 99 percent of human DNA that is not genes, but they could not fully characterize or explain what a vast majority of it was doing.

The thought before the start of the project, said Thomas Gingeras, an Encode researcher from Cold Spring Harbor Laboratory, was that only 5 to 10 percent of the DNA in a human being was actually being used.

The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”

By the time the National Human Genome Research Institute, part of the , embarked on Encode, major advances in DNA sequencing and computational biology had made it conceivable to try to understand the dark matter of human DNA. Even so, the analysis was daunting — the researchers generated 15 trillion bytes of raw data. Analyzing the data required the equivalent of more than 300 years of computer time.

Just organizing the researchers and coordinating the work was a huge undertaking. Dr. Gerstein, one of the project’s leaders, has produced a diagram of the authors with their connections to one another. It looks nearly as complicated as the wiring diagram for the human DNA switches. Now that part of the work is done, and the hundreds of authors have written their papers.

“There is literally a flotilla of papers,” Dr. Gerstein said. But, he added, more work has yet to be done — there are still parts of the genome that have not been figured out.

That, though, is for the next stage of Encode.

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