Mike the Mad Biologist

Why Are We Duplicating Genome Efforts?

Posted by Mike on September 28, 2010
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ctd05
SEQUENCE GENOMES!!!

Proflikesubstance has a very good post about PR announcements in science, which stems from the duplicated sequencing of the cacao and Tasmanian Devil genomes. What struck me is this bit:

What also seems ridiculous to me is that there are TWO groups sequencing either of these genomes. I can understand the race for the human genome and maybe even things like fruit fly and Arabidopsis, but since when did the Tasmanian devil fan club go all cut throat? And I like chocolate as much as the next person, but two genome sequences*? It’s hard to tell whether this is competition or lack of communication, but either way it seems like a giant FAIL to commit the duplicated resources. If it’s the former it’s just stupid and if the latter maybe it’s time to think about a mechanism by which people could list what genomes are being sequenced…


(An aside: NIAID does require confirmation that genomes aren’t being sequenced elsewhere, but I don’t know about other funding agencies).

I can sort of understand why Mars wants to sequence the cacao genome: it appears, in part, to be an attempt to lock down the data (and thanks for collaborating in this USDA!). Sleazy, but understandable.

What I do not get at all is the duplication of efforts on the Tasmanian Devil genome. Look, the whole contagious cancer thing is pretty dreadful–and could be scientifically useful. But do we need two genomes? Especially when it seems these are competitive projects, not coordinated ones (i.e., a Hundred* Tazzy genome project done by multiple groups could be very interesting).

I find it hard to believe that the funders are happy with this. So, does anybody know how this came about? Was the original group not moving fast enough? Did the Sanger group decide to use a different technology platform?

Regardless, I agree with proflikesubstance: there’s too much to be done to waste capacity like this (even if the limited capacity is analytical, not pushing data out of the machines).

*Are there even 1,000 Tasmanian Devils left?

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Comments

  1. #1 Kevin
    September 28, 2010

    I can see why there’s consternation at this, but I think we need two devil genomes about as much as we need one, which is to say: not much. I’m not saying it’s useless science – I actually think categorizing a lot of species is a good thing, but if you can justify spending the money for one group to get the sequence, why not spend it for two to compete and get the best data?

    Having no competition for obscure organism genomes seems like a recipe for fraud/misuse of resources. At least this way we have independent verification.

  2. #2 Kaleberg
    September 28, 2010

    It sounds like a lot of groups have been ramping up sequencing capacity and are thrashing around looking for good stuff to sequence. The Tasmanian devil is about as isolated a marsupial as one is likely to find living, so it is definitely worth a look for the same reason it makes sense to sequence genomes for blind cave fish or Hawaiian flightless geese. The problem is that most of the labs are using the same sequencing technologies and produce the same level of good results. Ideally, there would be a centralized plan to avoid duplication of effort. Astronomers produce a plan every decade with hoped for high priority telescopes and space probes ranked for budgeting, but their costs are astronomical in comparison with modern genome sequencing costs. Maybe the problem is that no one puts out a PR release saying that they are seriously proposing to sequence X well before they start, and if anyone else is doing so they can toss a coin for the privilege.

  3. #3 mike shupp
    September 29, 2010

    I can’t think of a better way to show that these new gene mapping tools work and are being operated properly than by running comparisons. Which means doing two sequences (or more!) now and then on similar or the same species.

    Think of it as training costs, guys.

  4. #4 Prof-like Substance
    September 29, 2010

    I can’t think of a better way to show that these new gene mapping tools work and are being operated properly than by running comparisons. Which means doing two sequences (or more!) now and then on similar or the same species.

    If this were a coordinated effort with directly comparable results, maybe this would be true. But neither this or the cocao effort were attempts to make use out of having two sequences. In the end, multiple genomes might make the data better, but so much better that it is worth the duplication? Probably not when the alternative could have been some experimental or functional comparisons using transcript data (which would also improve the genome sequence)

  5. #5 robotkid
    November 4, 2010

    I have do say, as much as I’m not a big fan of “science via press-release”, I have minimal sympathy for crocodile tears shed over loosing the race to be first in a high-profile, low-innovation consortium project. From the Science article “the assembly went better than we could have imagined”, i.e., anyone with the right resources could have done it just as well. It’s virtually impossible to get involved in one of these without KNOWING that there is competition and duplication of effort, what with all these big sequencing centers itching to get some flashy return on their infrastructure investment.

    So the real question isn’t why are funding agencies funding duplicate science, as it is why aren’t they funding innovative, hypothesis-driven science? Consortium projects are boku expensive. . ..