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Is this thing still on?

::cough cough::

It’s kind of dusty in here… 😉

Hi all, I know this site has been pretty dead for a long time. I hadn’t stopped writing, but a lot of that writing was re-directed into a series of scientific papers, now published. My plan is to post a series of postson these papers, but I’ve had a lot of plans to start writing again, and most of them have come to nothing, so until that happens:

Let me leave you with a couple of fun things. I’ve just returned from the 53rd Annual Maize Genetics Conference. As usual it was loads of fun, and I learned about a lot of cool new science and mouthwateringly useful data sets. For an overview of the science and good times check out Biofortified’s coverage of the conference (with photos!). Both Karl and Anastasia were diligently blogging and tweeting the whole conference while I was walking around in a daze all weekend. Anastasia also introduced the official maize research blog. Which I think has a lot of potential, but could definitely benefit from more contributions from maize geneticists… you know who you are.

Finally, one of the most enjoyable things for me to use this space for has been to tear about bad logic and poor science journalism. In this case (written by Lee Dye over at ABC news) though, it’s like shooting fish in a barrel:

“Until now, it was not known that the evolutionary process took place over many generations.”

That gem of a sentence is talking about research conducted by Doug and Pam Soltis, two awesome researchers at Florida. (They studying whole genome duplications, like I do, but in different species with different methods than I do. A significant fraction of the papers I had to read to get ready for my qualifying exam came from their lab.) Exciting science. Frighteningly bad journalism.


  1. Grandma Beth says:

    Glad you’re writing again in J&TGC. Always enjoy!

  2. Kurt Kiesling says:

    Hope to see you active soon — enjoy your commentary.

  3. Richard says:

    Hi James. Looking forward to future posts about biotech specifically, and agriculture in general. I belong to an agchem trade group in Sacramento and I am always search for more information about plant engineering, crop protection tools and fertilizers. I’m sure we can have a useful back-and-forth once you are up and running again.

  4. Kurt Kiesling says:

    Hope we’ll see you posting again soon. I’m not trained in your field, but curiosity got me to look up Whole Genome Duplication, and I have a question. The article I read about it indicated that after duplication, fractionation takes over and eventually many of the duplicated genes are lost, most likely due to a lack of selection (one gene is enough — the duplicate is redundant). I assume duplication is a very rare event, so why was there selection for the “duplicated” organism over the original unduplicated one?

    1. James says:

      Hi Kurt,

      Well the first part of the answer is that, in plants, whole genome duplications aren’t all that rare. In many cases you’ll see essentially the same species growing in the same ecological niche as a diploid (unduplicated) and tetraploid (doubled genome).

      But when it comes to polyploids are sometimes so successful and go on to be the ancestors of many more species, no one knows for sure, although there are a number of hypotheses out there.

      1) sometimes rather than doubling the genome of a single species, whole genome duplication is the result of combining the genomes of two closely related species into a single organism (allopolyploidy). This could potentially be a mechanism to “lock in” a form of hybrid vigor, giving the resulting species a competitive advantage over either of its parents.

      2) Polyploids may be more tolerant of environmental stressed than unduplicated species. We know that the percent of plants which are duplicated increases farther away fro the equator in cooler climates. So some people think during big climate shifts or extinction events, polyploids are more likely to survive than their unduplicated relatives. (And there may be a cluster of polyploidies in different plant families around 65 million years ago right when the dinosaurs were dying out).

      3) Creating duplicate copies of every gene creates the opportunity for one copy to specialize in new functions while the second one continues to carry out its ancestral role. Essentially polyploidies might enable the evolution of new traits which either give a species a competitive advantage in its existing niche, or allow it to exploit a whole new one. And once more, if you look at the family tree of plants you can link polyploidies to a number of major morphological innovations, like the nitrogen fixing nodules of the legumes and the heavily altered flowers of the grasses relative to other monocots.

      The 3rd is my personal favorite, but it is very difficult to prove any of these ideas.

      You know, with some pictures and links to sources I might even be able to clean this comment up into a post of its own. Thanks for getting me thinking about it!


      1. Kurt Kiesling says:

        Good logical response. Interesting how theories all carry some flaws — nature always has the upper hand in the long run. I’m wondering if there is some “practical” potential from the phenomena of gene doubling and fractionation. Lets say doubling offers some advantage resulting in selection and the elimination of the undoubled variety. Fractionation takes over and eliminates duplicate genes which did not result in any of the “advantage”. After enough time (ie 65 million years), would the remaining doubled genes offer some insight on genes or gene combinations critical for high vigor or survivability during stress?

        1. James says:

          It’s a good question and I don’t have a solid answer. Before I joined my current lab, they did some interesting work with retained duplicate genes in arabidopsis from a ~25 million year old tetraploidy with large and conserved promoter sequences, and these genes did, in fact, turn out to be biased toward genes whose expression responds to environmental stresses:

          Freeling M, Rapaka L, Lyons E, Pedersen B, and Thomas BC. 2007. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell 19: 1441-1457.

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