Birney thinks the Onion Test is silly.

A few people have wondered what Ewan Birney, lead coordinator of ENCODE, would have to say about the Onion Test.

Well, here’s what he had to say on Twitter.

It’s hard to tell from this dodge, but I suppose the suggestions here are that a) the fact that humans have more DNA than pufferfishes is easy to account for because we’re more complex, but b) testing this logic by pointing out that even the smallest salamander genome is 4x larger than ours is silly.

Also, onions (and most salamanders) aren’t polyploid — it’s one of the reasons I chose them for the initial comparison. It didn’t have to be onions, of course. There is no relationship between genome size and organism complexity, which we’ve known for 60 years.

I would still like Birney to answer the question. How is it that humans “need” 100% of their non-coding DNA, but a pufferfish does fine with 1/10 as much whereas a salamander has at least 4x as much? It hardly seems silly to me to ask this very, very basic question about genome evolution.


5 comments to Birney thinks the Onion Test is silly.

  • sparc

    If he considers polyploidy for genome size differences he can’t be a biologist. Where has he been since 2007? ENSEMBL was not only critisized in the blogosphere and has been critisism in peer reviewed journals (e.g. on dark matter transcripts). However, without the hype ENCODE is stirring up.
    I guess one of the problems that cause situations like this is the different speed of tecnolgical and scientific development. Of course it is interesting how different parts of the genome interact with each other and how phenotypes are regulated. Howver, such research, especially if hundreds of people and millions of dollars are involved, doesn’t ask proper questions. Otherwise you would have to accept hypotheses like “everything relates to everything or at least to something. Besides such fig question big science is free of hypotheses. It collects data because it can. One day, of course, Big Science has to publish to maintain Big Science big. And to make it even bigger it has to publish as much data as possible which has the nice side effect that the hollowness of at least some of Big Science claims (in the case of ENCODE surely the 80% of the genome is functional claim) can be hidden from the public and (more importantly) the funding agencies. Still, there is hope that it becomes obvious to them that the Emporer is naked or at least not fully dressed.
    cross posted at Sandwalk
     

      (Quote)

  • John Harshman

    I was just talking about this very thing with some friends at a meeting (North American Ornithological Conference in Vancouver), that avian phylogenetics is currently drowning in data, and that high-throughput sequencing has exceeded our capacity to analyze what we have, with the result that among other things there seems to be a current slowdown in publications.

    One problem with the ENCODE case is that people who work exclusively with model organisms (and <i>H. sapiens</i> is the extreme example of a model organism) often don’t consider the value of comparative data. Phylogenetic context is crucial. And thus in the current case their failure to think about the implications of onions, fugu, and so on for their hypotheses is a big problem.

      (Quote)

  • gillt

    Maybe salamanders require greater regulatory plasticity than humans. Maybe they’re lineage fell under greater environmental stress, which lead to retrotransposon expansion which lead to heritable variation on which selection could act and speciation could take place. Within genus genome size differences is a poorly understood question, I think, for many species. 

      (Quote)

  • Wait– didn’t Birney just admit, in the Tweet above, that at least 7/8 of the human genome must be NON-functional? Re: fugu?  Where’d his 80% go? *flushing sound*

      (Quote)

  • M

    At AIG Dr. Georgia Purdom has written two essays on ENCODE and junk DNA.
    I think her example opposing the onion test is weird and not useful for the argument she was trying to make.

      (Quote)

Leave a Reply

 

 

 

You can use these HTML tags

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>

*