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Sunday, September 09, 2012

Washington Post: "‘Junk DNA’ concept debunked by new analysis of human genome"

The Washington Post is a highly respected newspaper read by millions. It is very influential, especially among politicians in Washington.

Here's what David Brown and Hristio Boytchev published a few days ago:
‘Junk DNA’ concept debunked by new analysis of human genome
Most of a person’s genetic risk for common diseases such as diabetes, asthma and hardening of the arteries appears to lie in the shadowy part of the human genome once disparaged as “junk DNA.”

Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades.

Those are among the key insights of a nine-year project to study the 97 percent of the human genome that’s not, strictly speaking, made up of genes.

The Encyclopedia of DNA Elements Project, nicknamed Encode, is the most comprehensive effort to make sense of the totality of the 3 billion nucleotides that are packed into our cells.

The project’s chief discovery is the identification of about 4 million sites involved in regulating gene activity. Previously, only a few thousand such sites were known. In all, at least 80 percent of the genome appears to be active at least sometime in our lives. Further research may reveal that virtually all of the DNA passed down from generation to generation has been kept for a reason.

“This concept of ‘junk DNA’ is really not accurate. It is an outdated metaphor,” said Richard Myers of the HudsonAlpha Institute for Biotechnology in Alabama.

Myers is one of the leaders of the project, involving more than 400 scientists at 32 institutions.

Another Encode leader, Ewan Birney of the European Bioinformatics Institute in Britain, said: “The genome is just alive with stuff. We just really didn’t realize that beforehand.”

“What I am sure of is that this is the science for this century,” he said. “In this century, we will be working out how humans are made from this instruction manual.”
This is wrong. Most of our genome is still junk in spite of what the ENCODE Consortium says.

Who is Richard Myers and where did he get the idea that the concept of junk DNA is an outdated metaphor? Does he have an explanation for all the evidence his statement refutes?

Here's the important question. Who is going to take responsibility for this PR fiasco?


  1. NY Times is on the bandwagon too:

    The article is being promoted by the Richard Dawkins Foundation for Science and Reason:

    From the article: "Now scientists have discovered a vital clue to unraveling these riddles. The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches."

  2. This will need to be debunked with data since the PR battle is clearly already lost. Someone will have to engineer an organism with all the junk deleted and demonstrate that nothing happens. Could be a good synthetic life project for the Venter Institute.

    1. Someone will have to engineer an organism with all the junk deleted and demonstrate that nothing happens.

      They already did the megabase deletion mouse. If that doesn't stop the hype, whay will?

    2. Someone will have to engineer an organism with all the junk deleted and demonstrate that nothing happens.

      Some intelligent fishy scientists did that one hundred million years ago when they created the pufferfish. It didn't work. The creationists simply claimed that the pufferfish species with the small genome would never survive because all the deleted DNA was essential for future evolution (as God intended).

      So the fishy scientists released the genetically modified pufferfish into the wild knowing that one hundred million years later intelligent beings would be able to refute the creationists.

      That didn't work either. Even the non-creationist scientists ignored the result.

  3. Oh, the New Scientists has declared the death of Junk DNA:

    The leading theory, although this has been on shaky ground for a while now, has been that the non-coding, junk DNA didn't really do anything at all. But this idea has finally been laid to rest by the new findings of a massive research effort.

    Who says junk DNA is bad for you?

  4. "This is wrong. Most of our genome is still junk in spite of what the ENCODE Consortium says."

    Why? Because you don't want it to be so? Because there are methodological problems? Because the data has been misinterpreted?

  5. I see many of you here like the idea of junk DNA. It mus be that since you don't have to explain junk you don't have to admit you actually can't explain this mystery DNA. What's next? Junk brain? Do you have an explanation as to why we only use a certain portion of our brain's capacity? I don't think so. So are you going to call the part of the brain we never get to use "junk brain," or is that there is something about what we are and in the way we operate we don't know much about and we like to pretend is irrelevant because it conflicts with our evolutionary beliefs?

    Once you admit there is no such thing as junk DNA or junk brain, you have to also admit there is some serious programming going on here. We're talking information, codes, memory space, bio-software and controlled functionality. That kind of puts a dagger into random gradualism, doesn't it. That also kills the idea that some kind of supernatural god created stuff on a whim and for no good reason, if there was something left of that to kill.

    As for Richard Dawkins, what a character this guy is, a few years ago he and Ken Miller were saying that "junk DNA" made sense from an evolutionary point of view and it was held by them to be the poster child for bad design. The same Dawkins is now rushing to proudly promote on his foundation website the reality of the fact that there is no such thing as "junk DNA" as if he was saying that all along. This is the same individual who had repeatedly called people did not believe what he believed idiots, insane and wicked. What should we do now with the fact that he is switching away from his beliefs as evidence proves him and his neo-Darwinism constantly wrong? Whose the insane and the wicked one now?

    There is no such thing as "junk DNA." In order to cover up for our ignorance, our dominant ego tends to put labels on things we don't understand and than we pretend we know what we are talking about because, you see, we are scientists, and who is to doubt our expertise in things we claim without any proof or reason we know everything there is to know about.

  6. Why are they all still wrong, Why is the junk still junk? Care to tell us why you believe that?

  7. @Paul Greene - You're the man.

    @Diogenes - Regarding the megabase deletion mouse, they deleted 1,234 kilobases out of 3,200,000, or roughly .03%. How exactly does this 'prove' that the 98% of DNA that doesn't synthesize proteins is 'junk', and thereby disprove 9 years of research done by scientists from all over the world?
    I would love to see an attempt to 'debunk' this; that is, make a creature with DNA that had maybe 5% of the data that the natural creature from which it was created possessed (not this junk where you use 99.07% of the original creature's DNA and declare it a 'gene desert', like with the megabase deletion mouse). I think the result would easily put the concept of 'junk' DNA to rest.

    1. @Charles Loggins,

      How exactly does this 'prove' that the 98% of DNA that doesn't synthesize proteins is 'junk', and thereby disprove 9 years of research done by scientists from all over the world?

      40 years of research from scientists all over the world has established beyond doubt that more than 50% of our genome is junk.

      What discoveries in the past 9 years has refuted all that work? I'm not aware of any research that establishes a function for a substantial fraction of the defective transposons in our genome and I'm not aware of any research showing that a substantial fraction of long introns has a function.

      The mouse deletion experiments deliberately targeted regions of the genome that were supposed to have functional conserved RNAs.

  8. I refer to the 9 years of research performed by ENCODE, which was unable to be completed until the human genome was completely sequenced in 2003. While I'm sure the last 50 years of research have been of great use, it seems logical to assume that research recently completed, using new technology, AND using information that wasn't available until 9 years ago, might yield new information that makes us question what we had assumed from the information we had available 41 years before that. Our scientific body of knowledge is constantly evolving, and to adhere to old ideas because they support a belief you hold regarding how we were created is ridiculous...

    1. The sequence of the human genome confirmed that only a small percentage consisted of genes and most was bits and pieces of defective transposons. None of the subsequent work by The ENCODE consortium changed that view. Instead, it provided further confirmatiom of the basic biochemistry of DNA protein interactions and abortive transcription start sites.

      None of the work by the ENCODE consortium changed our view of genetic load nor did it have any effect on our understanding of the so-called "C-value" paradox. (Think of the onion test.)

      Furthermore, you over-estimate the importance or the human genome sequence. Large parts of the human genome were sequenced in the 1990s, including one entire chromosome. We knew how the human genome was organized back in the 1980s. In fact, we had a broad outline in the 1970s - an outline that turned out to be correct except that we underestimated the sizes of introns.

  9. Paul Green, "Bio-software" and all that other currently untestable stuff, beyond grasping at straws and a bit wacky to say the least.

    Laurance, you're an embarrassment to science. You're grumpy, old, and set in your ways. You're as bad as a fundamentalist christian.

    If fifty years of research into DNA using terribly outdated techniques and equipment that left much to be desired, while using only portions of genomes which hadn't been fully sequenced constitutes irrefutable proof, you might as well give up science and switch to believing in some super natural wizard that created the everything in 7 days on a whim and simply tossed in the universe to give us something pretty to stare at.