Wednesday, May 28, 2008

Genomics By Press Release Award #2: Lieden Leiden University and the First "Female" Genome

Ooh. Ahh. That is what we should all be saying as it has been announced that the first "female" genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman's genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that thethere is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports ""No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.") This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say
“If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.
I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say
Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings
And for this, Lieden University is becoming the recipient of my second "Genomics By Press Release Award." (see my first one here, where interestingly, the discussion of sequencing a woman's genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

13 comments:

  1. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say: "If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist"

    While I agree that science by press release is deplorable, I don't really get the problem with stressing that Kriek is a clinical geneticist. I don't think they are trying to claim that clinical geneticists are better than bioinformaticians, etc. but rather just stressing that, like Venter and Watson before her, she is capable of understanding her genome sequence (well, to the limited level that anyone can at this point).

    What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

    Probably not any more than a genetic counselor or bioinformatician, but understanding genetics mades her more qualified than a typical priest or ethicist :-)

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  2. Well, they did no say "As a clinical geneticist she is poised to help understand the implications .."

    THey implied more, that clinical geneticists were somehow the holy grail of interpreting the human genome data. That is what I did not likel

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  3. It's Leiden, not Lieden.

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  4. "The problem is that the is no there there yet."

    Is this a direct translation from the Dutch?;)

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  5. Thanks Adrian ... just a rapid typing error ... Although now you have me wondering how to say "there is no there there" in other languages

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  6. Yes, Leiden has pulled a stunt, but it is a stunt that comments on other stunts of equally dubious merit--sequencing Venter and Watson. What were they trying to achieve, some kind of immortality? Is that science?

    If you are going to sample a population, you don't go out and handpick a few "prime" (and male) examples.

    So Leiden has countered stunt science with stunt science. That ought to be enough to force biology to put an end to this nonsense and implement a valid program.

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  7. Yes, it is true that this is stunt upon stunt (ooh -- the stunted science award .. that could be my next thing).

    But do not count on scientists changing any time in the future. We live in an age where evidence is no longer considered necessary for any activity. So why should scientists stick to those icky things involving data and evidence and papers.

    I do agree that it would be nice to have an actual random sampling of the population. But having a few self-chosed genomes is not a bad thing per se, it just should be viewed as a biased sampling.

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  8. You are quite prepared to tolerate biased sampling?

    Historically, stunts and counter-stunts are part of (but just part of) the way science progresses in fact. Scientists like to think science is a nice clean respectable process, but it isn't. In some cases stunt counters stunt until the discipline decides it is time to get serious.

    August Weismann's cutting the tails off mice was a stunt to provoke neo-Lamarckians into try to prove "induction from the environment". He meant it as a provocation (stunt) and it was taken as such. I read the Leiden news release in the same way. They know they're provoking. The appropriate response is to say: "Okay, we get the point. Let's put Venter and Watson's DNA sequences in the Stunt Science Museum and start over, without biased sampling.

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  9. I am of course prepared to tolerate biased sampling. That is what most of the data that has been collected in all fields starts out as. Plants and animals from a couple of islands, for example. Bacteria found inside the colon of a few people. Stars found in just the Milky Way. Etc. If I was reviewing a grant proposal, I would ask for unbiased sampling. But that does not mean biased sampling is bad per se. And just as a lot was learned from naturalists trips to selected islands,we will likely learn a good deal from Venter and Watson's and the clinical geneticist's genomes.

    And I am not immune to stunted science. Just wait until next

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  10. Perhaps the press release should have said "If anyone couple properly consider the irrelevance of making a big deal about a female genome that is simply a male genome without a Y chromosome, it is a clinical geneticist."

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  11. Of course a female genome is more than just a male genome without a Y chromosome. It's about time they sequenced the genome of a true diploid and not another one of you pitiful hemizygotes.

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  12. I guess we will have to wait and see ... one of these days someone will sequence what they think is the genome of a XX or XY and it will turn out that the phenotype will be different from the genotype ... For now I am sure they do a little screening in advance in most cases but in the future, sequencing will be cheaper than Karyotyping.

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