Author Archives: T. Ryan Gregory

Genome Biology and Evolution.

Posted on by

The online journal Genome Biology and Evolution is now publishing its initial set of articles, so be sure to have a look and watch for some good stuff in the future.

I notice that there’s a paper on mammalian genome sizes planned for the first issue. It looks interesting, though I note the following intriguing quotes:

“The evolutionary patterning of genome architecture by nonadaptive forces is supported by population-genetic theory, estimates of the relative power of the major forces of evolution, and comparative analyses of whole-genome sequences. Nevertheless, some biologists still adhere to the idea that even the most arcane aspects of genome evolution, including expansions of genome size by mobile-element proliferation, are direct products of natural selection (e.g., Gregory 2005; Kirschner and Gerhart 2005; Caporale 2006)”.

“our results challenge the notion that genome size reflects a finely tuned structural determinant of the adaptive phenotypes of organisms (Cavalier-Smith 1978; Hughes and Hughes 1995; Gregory 2005).”

Readers of this blog can probably answer the issue of whether I believe all aspects of genome expansion are adaptive.

__________
Update:
I have looked at the article in more detail, and it is indeed interesting. However, as is common with this kind of analysis, there are some questions. Here are the species they examined to claim that no reductions in genome sizes occurred in plants or invertebrates:

Plants — Arabidopsis thaliana (thale cress, genome size 125Mb, one of the smallest in plants), Populus trichocarpa (cottonwood, 500Mb), and Oryza sativa (rice, 420Mb). The average genome size for flowering plants is 6,400Mb based on more than 4,000 species, ranging from around 60Mb to 124,000Mb.

Invertebrates — Strongylocentrotus purporatus (sea urchin, 870Mb), Anopheles gambiae (mosquito, 280Mb), Drosophila melanogaster (vinegar fly, 175Mb), Caenorhabditis elegans (nematode, 100Mb), Ciona intestinalis (tunicate, 195Mb), and Daphnia pulex (water flea, 230Mb). I would not want to suggest a mean genome size for “invertebrates”, but I can say that even in mosquitoes they range at least 8-fold.

If people who work on genome size do not immediately accept the population size explanation for differences among taxa, it’s not because they don’t understand the argument. It’s because the data are based on a tiny and non-random subsample of genomes, and because predictions don’t seem to be upheld when we examine genome sizes. Being miscited doesn’t help.

Funding for research in Canada round-up

Posted on by

For incisive commentary on the topic of science policy in Canada, I direct you to Rob Annan’s excellent blog over at Don’t Leave Canada Behind. Most recently, he provides a response to a rather misplaced critique of Canadian researchers by Michael Bliss in the National Post.

Just to clarify, we’re not just asking for more money. We’re responding to several major policy issues that are going to affect Canadian research across the nation:

1) Cuts to the three granting agencies.
2) Lack of support for Genome Canada.
3) Cutting the MSc scholarship to 1 year.
4) A focus on few, very large scholarships instead of supporting established labs.
5) Investment in buildings rather than people.
6) Dismissal of the science advisor.
7) Decisions about what kinds of research will be funded based on short-term returns.
8) An emphasis on applied studies at the expense of basic science.

Emerging Leaders of the Americas.

Posted on by

Just got this through email.

Emerging Leaders in the Americas Program (ELAP)

At the Summit of the Americas in Trinidad and Tobago, Prime Minister Stephen Harper announced that Canada will allocate $18 million over the next four years for a new scholarship program. The Emerging Leaders in the Americas Program (ELAP) will award up to 1600 new scholarships for Latin American and Caribbean students to pursue studies or research in Canada.

The ELAP will support human capital development and a new generation of leaders in the Americas while strengthening linkages between Canadian institutions and those in the region.

The first round of ELAP scholarships is now underway for study or research commencing in the Fall of 2009. The deadline for applications from Canadian post-secondary institutions is June 29, 2009 .

Program Description

The scholarships will be facilitated through inter-institutional exchange agreements and will provide students with the opportunity to undertake study or research at Canadian universities and colleges. Recipients will remain students of their home institutions during this exchange. In addition, the ELAP will offer a study tour component to selected students to expose them to Canadian governance, business and civil society in key priority areas.

I am all for supporting students from Latin America and the Caribbean (two of my first grad students were originally from S. America). However, two issues:

  • “Recipients will remain students of their home institutions during this exchange.” So, we don’t get supervisor credit (co-supervisor would be fine, however.)
  • “Key priority areas”. We know what that means, and it ain’t basic science.

50!

Posted on by

I received notification today that the most recent article from my lab has been accepted by BioScience. I am feeling a bit sentimental about it because this marks my 50th peer-reviewed paper. It’s also something new for me, a study on grad student conceptions of evolution. I have now officially been all over the map — experimental, comparative, synthetic, reviews, methods, and educational. Thanks to all my colleagues and students who have been co-authors to date!

In which Dr. Eisen gets scooped.

Posted on by

Jonathan Eisen, of Tree of Life, has an excellent feature called the “Overselling Genomics Award”. Here, I am gonna scoop him and hand out something similar, at least based on the heading.

A genome may reduce your carbon footprint

This somewhat rhetorical title must excite many scientists, particularly those with ongoing research on biomass, feedstock development, and lignocellulosic breakdown/fermention. With the costs of sequencing rapidly decreasing, and with the infrastructure now developed for almost anyone with access to a computer to cheaply store, access, and analyze sequence information, emphasis will increasingly be placed on ways to apply genome data to real world problems such as reducing dependency on fossil fuel. For the efficient production of bioenergy, this may be accomplished through development of improved feedstocks. This article will consider more closely the impact of very cheap sequence data (approximately 1USD per genome) on improvement of switchgrass (Panicum virgatum L.), a perennial grass well suited to biomass production.

Wow, $1 per genome? That would be sweet!

Evolver Zone.

Posted on by

Readers of this blog will soon notice some changes. This is because the Evolver Zone site has now been launched, and Genomicron will be fit within it. For now, it will remain a separate blog at this same location, but the look will be updated shortly. Meanwhile, have a look at the resource of multimedia and information about software, databases, journals, and web links at Evolver Zone (www.evolverzone.com).

Agaporomorphus colberti.

Posted on by

Quentin Wheeler and Kelly Miller have named a beetle after faux-blowhard Stephen Colbert.

Agaporomorphus colberti

This might be pretty cool, if not for the following issues:

1) This was done explicitly to get publicity.
2) It has already been done. (A spider was named after Colbert last year).
3) Apparently without intending to be ironic, Wheeler has also named species after Bush, Cheney, and Rumsfeld.

I absolutely support the need to gain attention for the importance of taxonomy. I also think the tradition of naming species in honour of individuals is amusing. Heck, I’m still waiting to have something with my name attached to it. But I’m not sure that naming species after people willy nilly just because they might bring attention is very dignified. On the other hand, maybe Wheeler thinks Colbert is right wing (apparently his illusion is effective among conservatives) such that there’s no inconsistency there.