One Giant Leap for Human Genomics Science and Business

9/26/12

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by Drs Eric Schadt and Rui Chang in a recent Science article.

Another major impact of the ENCODE Consortium’s work will come from the management model it used to generate these results. Just as the Space Race required a large and far-flung group of scientific collaborators, the ENCODE Consortium had to find ways to manage over 440 strong-willed individuals in a highly collaborative endeavor—more people than the vast majority of biomedical organizations have.

How did they accomplish this?

We can see hints in one of the key results reported by the ENCODE Consortium-that 80% of the genome has a specific biochemical function. One of the reasons for emphasizing this number is very pragmatic and very human.

Dr. Ewan Birney, associate director of the European Bioinformatics Institute (EBI) and one of the project’s members wrote in a blog post, “we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best conveys the difference between a genome made mostly of dead wood and one that is alive with activity.”

The ENCODE Consortium could recognize all the work and all the collaborators involved in the entire project, not just those working on the ‘important’ parts. And no one felt that helping anyone else was going to hurt their own chances of getting published.

Scientific research is often a zero-sum game full of competition that works against collaboration. Seeking non-zero sum solutions not only helped solve the complex conundrum of managing over 440 people, it can also be seen in one of the truly innovative aspects of the entire project—the very open nature of the simultaneously published work.

It will take some time to digest this huge amount of work. Although almost all of the documents are free to read — an important innovation of the digital age — we are talking about several hundred of pages of dense reading.

But Nature has a very nice explorer that lets us all see which papers touch which topics.

Never in scientific history has so much data from so many papers with so many collaborators in so many locations been published simultaneously in so many journals. And it is available to all, not just a scientific elite.

Large collaborative research projects may never be the same. Small research projects can now leverage the huge amount of data from the ENCODE Consortium to explore new areas. Novel ideas can be explored by non-scientists who will now access this tremendous horde of information for free.

Fifty years ago this week, President John F. Kennedy committed the US to putting a man on the Moon by the end of a decade. The resulting Apollo program accomplished that goal both ahead of schedule and under budget.

At its peak that public-private partnership not only changed our fundamental understanding of the universe, it employed over 400,000 people at all levels of our economy (from the seamstresses at the Playtex corporation who made the spacesuits to the engineers, designers and marketers at GM and Boeing who created the amazing lunar rover). By one estimate it turned a $100 billion investment of tax dollars into $1.5 trillion in new wealth, setting the stage for the IT revolution that powered our economy for decades after Apollo ended.

We now stand on the verge of an abundant future, fueled by the technologies driving Space-X, Planetary Resources, Blue Origin and others into novel explorations of space, all based on the foundation created by NASA more than 50 years ago.

The results of the Human Genome Project are biology’s Sputnik. The ENCODE Consortium’s data and tools are the biological equivalent of Neil Armstrong’s first steps on the Moon.

There can be no doubt that these data and tools will also lead to a newer and deeper understanding of life on Earth, powering a new cycle of wealth creation in ways now unimaginable.

The data and analysis tools are now free for anyone to examine and use. Got a bright idea? Get to work.

Becky Drees is the chief scientific officer at Seattle-based Spiral Genetics. Follow @

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  • http://twitter.com/rbgayle Richard Gayle

    Just to get things started – there is a marvelous interview with John Stamatoyannopoulos in the latest NCI Bulletin discussing the ENCODE Consortium’s work. http://www.cancer.gov/ncicancerbulletin/091812/page5

  • http://twitter.com/jamesian Sally James

    Helpful and comprehensive context for how to see this. I’m not sure the general public has ever found a core analogy for epigenetics. But I like “Sputnick of biology” comment.

    • http://twitter.com/rbgayle Richard Gayle

      Epigenetics is such a great example of the divide between the rapid changes in biology and the public’s general knowledge. Most have absolutely no idea what we mean. And putting together a narrative they can understand without a lot of jargon is really hard.

      We’ve seen similar with ‘junk DNA’, the Central Dogma and so much else. Things are just changing so fast, almost too rapidly for the public to keep up, straining our use of metaphor and analogy to explain.

  • http://twitter.com/rbgayle Richard Gayle

    Here is an interesting video on ENCODE, narrated by Tim Minchin, which is both engagingly and maddeningly simplistic. http://youtu.be/TwXXgEz9o4w

  • http://twitter.com/rbgayle Richard Gayle

    The NIH just announced $31 million in new grants for ENCODE, with an emphasis on increasing the different cell types and examining mice in greater detail. John Stamatoyannopoulos, at the University of Washington will map chromatin structure in the human and mouse genomes. http://www.genome.gov/27550184

  • http://www.facebook.com/mark.e.minie Mark Edward Minie

    Here are two other really excellent videos on epigenetics-

    One from NOVA with Neil deGrasse Tyson
    NOVA | Epigenetics
    http://youtu.be/avWwfuJYnnI

    and another from the always entertaining SciShow with Hank!
    Epigenetics
    http://youtu.be/kp1bZEUgqVI

  • http://www.facebook.com/mark.e.minie Mark Edward Minie

    On a slightly different note, ENCODE is already having an impact on the legal system :)

    Forensic Law Turns to ENCODE:
    Privacy advocates are arguing that collecting genetic data upon arrest is an invasion of privacy, given recent evidence that 80 percent of the human genome is functional.
    http://the-scientist.com/2012/09/25/forensic-law-turns-to-epigenetics/

    • http://twitter.com/rbgayle Richard Gayle

      This is actually an interesting case. The parts of the genome used for genetic fingerprinting have held up to legal scrutiny because, while they could identify a suspect, the regions themselves had no function and thus could not invade the privacy of the innocent. This legal argument allows them to collect DNA from anyone they arrest, etc. Because the DNA sequences ere really only good for identification. But now that many of them may be involved in function, it now becomes an invasion of privacy to take from innocent people. This’ll keep lawyers on retainer for some time.

  • user0


    National Human Genome Institute’s (NHGI’s)” should be “National Human Genome Research Institute’s (NHGRI’s)”