Time magazine's top 10 discoveries of the year: fooled by Craig Venter

So Time magazine has a list of its choices for "top 10 scientific discoveries of the year". We all love these top-10 lists - they're fun. But they made a huge error on one of them, so I'll make a small, probably futile, effort to correct it here.

Their #2 discovery is "Human mapped", which refers to Craig Venter's publishing his own genome. I blogged about this before, pointing out that PLoS Biology was lowering their standards by publishing that paper, which had virtually no novel scientific content. But Time reports breathlessly that the publication was "the first such genome ever published" of " all the DNA in both sets of chromosomes inherited from each of his [Venter's] parents." But was it?

No - of course it wasn't. If the Time reporter (Krista Mahr) had actually read the paper rather than the press releases, she'd have learned that the paper describes just one set of chromosomes - not two. In fact, Craig published a mishmash of his chromosomes, with bits and pieces of each chromosome merged together in a mosaic. (This is exactly what we did in the original human genome papers, by the way.) The only slight contribution of this year's paper was to fill in some of the gaps, and in some cases to separate the haplotypes (the two chromosomes) enough that, as I wrote in my original blog, they could claim that blocks of 200,000 bases on average came from a single chromosome. What does that mean? It means that in in the genome they published, each chromosome is a composite sequence containing many bits and pieces of both the parental chromosomes. For chromosome 1 there are over 1000 of these chunks, for example, and there is no information (in Venter's paper) about which chunk comes from which parent.

Furthermore, because Venter and colleagues didn't sequence his parents, they have no idea which parent any chunk came from. In other words, Venter did not publish his entire diploid genome: that would imply he published two copies of each chromosome, one from his mother and one from his father. Am I being clear here? Time magazine got this wrong, as did some of the original press reports.

Having worked with Craig for years and observed much of the press hullaballoo that he works so hard to generate, I'm not surprised that Time got this wrong. Craig is the main source of the misinformation: if you go to his institute's website today, as I did, the front page has a big image of a human karyotype (showing two copies of each chromsome), with the text below saying "New individual human diploid sequence." Sure sounds like there are two sequences for each chromosome, doesn't it? And the front page also has a link to a press release about the paper titled, "First individual diploid huma genome published by researchers at J. Craig Venter Institute." The press release goes on to refer to "six billion base pairs from the genome of one person." It also says that "the publicly funded genome ... is a composite version," implying that Craig's is not.

Obviously the Time reporter is reading the press releases: if you go to PLoS Biology and look at the paper, the second sentence of the article says that the genome comprises 2,810 million bases. If anyone is counting, that's just under 3 billion, not 6 billion. The paper also makes it clear that Craig's parents were not sequenced, so there is no way to tell which parts of any chromosome came from which parent.

Clearly Craig is trying to re-write scientific history by press release, and he might even get away with it. I claim that it is scientifically dishonest for him to have these misleading statements on his institute's website. If Time magazine were to look at the actual scientific paper, they'd realize that this item on their top 10 list is sloppy journalism, and an unfortunate mistake.

Let's be clear here: the Venter Institute's own press release says
"Independent sequence and assembly of the six billion base pairs from the genome of one person..."
but the paper reports 2.81 billion bases. That's not six billion. And that is misleading. I think we can get the public excited about science without lying to them - and it's too bad that it succeeded (this time) in getting Time magazine to report a "discovery" that didn't happen.

1 comment:

  1. Looking through the entire list, most of them seemed to be culled from, at best, headlines in the popular press, and maybe 2 could possibly have some impact on life on earth. Here is the last one, for example:
    #10. Real-Life Kryptonite
    In April, geologists in Serbia dug up a white, powdery mineral that they weren't sure what to make of. They turned it over to Chris Stanley, a mineralologist at London's Natural History Museum, who discovered that it had the same chemistry — sodium lithium boron silicate hydroxide — as the fictional kryptonite, the green glowing rock that, aside from Lois Lane, is Superman's only weakness. Its chemical make-up was revealed in the 2006 film Superman Returns in which villain Lex Luthor writes the formula on a box of rocks he steals from a museum. The real-life substance will be called jadarite, after the area of Serbia in which it was discovered. It can't be called kryptonite, alas, because krypton, the gas, is already a real element."

    If this is in the top 10, our sicentists are really wasting their time!


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