Friday, November 10, 2006

Sea Urchin Genome and the Ridiculous Evolutionary Claims of Genome Researchers

All I can say is "AAAAARGH"

A sea urchin genome has been sequenced and there are some really interesting findings that have been reported based on analysis of the genome. For example, there appears to have been a large expansion of genes involved in the innate immune system in the species sequenced, Strongylocentrotus purpuratus.

All the good science aside, what most struck me were some of the ridiculous quotes attributed to some of the researchers in this project in stories and press releases. For example, in an article on MSNBC, George Weinstock says
“The sea urchin is surprisingly similar to humans,"
"Sea urchins don't look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do."
Apparently, George was glossing over the reason this organism was chosen for sequencing in the first place. If you go to the NHGRIs web site you can get the white paper written that led to the selection of this species for sequencing. Perhaps the most important reason is that evolutionarily the sea urchin is closer to humans than fruit flies are. Therefore, it should only be a surprise to someone who does not know the evolutionary position of this species.

Perhaps even more appalling is the discussion of the apparent large number of genes for light sensory systems in this species. Again, Weinstock is quoted:
“There is not a lot of light at the bottom of the ocean, so it is not clear what they might be ‘seeing,'" Weinstock said. "This is certainly an area that will be studied intensively as a result of the genome project.”
I can only view this as some sort of joke. First of all, blind cavefish still have the genes for light perception even though they do not see. This is because it takes time for such genes to disappear. Second, apparently George has never really thought about where this species of sea urchin is found. It is found in the intertidal zone -- hardly the dark depths of the ocean. I could go on and on but I will just get more annoyed. In this case, Weinstock has proven that many Genome Scientists are almost completely clueless about the organisms they are working on. Which is a shame. Becuase sea urchins are fascinating creatures and the fact that they are more closely related to humans than are most other invertebrates is one of the main reasons they have been a focus on so much research up until now. Oh well ...


  1. I'll agree - many of the people who work on the sequencing side of things are really interested in improving and speeding up the sequencing pipelines. Their involvement after the publishing of the genomes is extremely limited. That's not surprising, though, considering that the genome center is currently sequencing everything from cows to aphids to bacterial species.

    Weinstock was the right person to talk to about the sequencing process, but certainly not the best person to explain the importance of sea urchins.

  2. Well, I guess I would disagree somewhat, as someone who has run dozens of genome projects. I only took projects on if I was personally interested in the science. I guess the difference is I was only a faculty member at TIGR - I did not run the whole place. But I could easily have taken on lots of projects that I had no direct interest in in order to keep paying my salary but I just avoided them. Instead, I was more selective and much happier for it. I got to sequence two organisms that I did experimental work on as part of my thesis (Chlorobium tepidum and Haloferax volcanii) as well as lots of organisms of direct interest to my studies of the evolution of DNA repair (e.g., Deinococcus radiodurans). I guess I never liked the model of "lets sequence everything we can get monye for" but in the end, the sequencing centers are like big drug dealers. They have to keep the machines running and they will take whatever they can.

  3. This argument predates genomics. When I was in grad school (clears throat) there was a lot of huffing from old school parasitologists about these molecular biologists coming into the field who couldn't tell a tsetse fly from a tapeworm. And that was when you could spend your whole Ph.D. sequencing one gene.

  4. Andy - I agree. The genomics folks seem to have missed out on all the previous controversies. They seem to think they are the first to study evolution and organismal biology. I won't even get started about how some of them think they are the first to deal with polymorphisms ...

  5. Some other blogs about the Sea Urchin genome:

  6. While I agree that George is not the best person to talk about the ecology of the sea urchin, I think there are more complicated aspects of his comments than are being addressed here. [In the interests of full disclosure, I was one of the many co-authors of the urchin genome paper.]

    An interesting point is that tunicates (aka urochordates, more specifically Ciona spp.) share fewer homologous genes with humans than urchins do. The cnidarian Nematostella vectensis has about the same number of best reciprocal blast hits with humans as Ciona does. Perhaps the more pertinent question is why do fruit flies share so few?

    As for light sensing, sea urchins have _more_ opsins than humans. I think what is surprising is not that homolgous genes exist, but that so little is known about sea urchin senses that we were surprised to find so many.

  7. OK I do agree with Jed on some things. I was mostly just poking fun at George at little bit when I wrote this. I have known him for many years and think he is generally very very good. I just thought some of his quotes were way off base and wanted to use them to talk about evolution. As for the # of shared genes between species, this is a frequently misleading statistic in my mind. For example, as we talked about in my Tetrahymena genome paper, Tetrahymena shares more genes with humans than yeast shares with humans despite humans being closer to yeast. The number of shared genes is dependent on common ancestry as well as the amount of gene loss and other events. So shared genes is not a good metric for evolutionary relatedness.

    Fruit flies probably share so few because (1) they have undergone gene loss and (2) they evolve very rapidly and homologs are harder to identify. In fact, some people think they are a bad model system due to their high rates of evolution (note - I disagree with this --- I think they are a great model system).

  8. "the sequencing centers are like big drug dealers"?????

    Remind me to send sequence files out to collaborators in little baggies :)

  9. OK - maybe a bad choice of analogies there. The sequencing centers have a supply of something (sequencing lanes) and need to keep up demand. Which reminded me of drug dealers. But I am sure there are better analogies. Maybe the sequencing centers are like farmers. Is that better?


Storify of Day 1 of "An open digital global south meeting" at #UCDavis

I made a Storify of Tweets and some pictures from the "An open digital Global South" meeting that I am a co-organizer of. This was...