Field of Science

Promoting Plants at the Expense of Fungi?

Ryan Gregory, over at Genomicron, found an interesting tidbit on the Discovery Channel website entitled Plants and Animals: Long-Lost Relatives?. He is surprised to read that
"organisms such as fungi should be given a demotion — placed further from animals on the tree — while green plants should get a leg up."
This is the case, apparently according to a recently-published paper from John Stiller at East Carolina University.

Gregory is (rightfully) annoyed at the suggestion of any group "getting "demoted" one way or another because this idea of rank (was) should have been abandoned 150 years ago." and that was the main point of his post. Ryan has been (again, rightfully) critical of science reporting and this doozey has all of the right parts, as detailed in his Anatomy of a bad science story.

However, there have been a series of comments about the veracity of the Stiller paper, so I thought I would make a few of my own here. First of all, it should be duly noted that the paper in question, Plastid endosymbiosis, genome evolution and the origin of green plants, is explicitly labelled as "Opinion"; this is on top of the fact that it is published in the review journal TRENDS in Plant Science—not a primary research venue. Neither of these facts are damning to the work, but they certainly suggest caution in reporting the findings.

Second, it is fair to say that this hypothesis (wrongly called "Stiller's theory" by the Discovery story) is way out of the mainstream of current thought. Again, this alone should neither preclude the publication nor, by itself, lend it to immediate scorn. It's great to see such examples of how science works in the marketplace of ideas. But we all know that just because something gets published, does not mean it's right.

In any case, there are two main components that Stiller argues in this paper:
  1. that the "Plantae" [Viridiplantae (green algae & land plants), Rhodphyta (red algae) and Glaucocystophyta] are not a monophyletic group, and
  2. that the Viridiplantae are more closely related to animals than are fungi.
The data on "Plantae" monophyly are certainly not so compelling as to rule out other possible answers. But recent work (here and here) is increasingly providing support for this relationship. Stiller has been a long-standing contributor to the literature on non-monophyly of green+red algae. I have worked on some of the same molecules that he has (i.e., RNA pol II) and he might have a point for there not being strong support in favor of "Plantae". However, I don't think that there is an alternative that garners anywhere near the consistent support that "Plantae" gets in multigene trees.

The data on the sisterhood of animals and fungi grouping to the exclusion of plants (e.g., Viridiplantae) is about as solid as deep relationships among eukaryotes can be. A nice summary of these results was recently presented in PLoS Genetics. Since the paper is Open Access, I won't repeat the findings here (full disclosure: although I am not an author of this paper, I do collaborate with them). Suffice it to say that there is not even a hint of evidence that Viridiplantae is closer to animals that are fungi as suggested by Stiller. Note also that these authors are not particularly bullish on "Plantae" either.

Stiller cites the presence of certain enzymes and protein domains in both plants and animals (apparently absent in the fungi) as evidence for a closer relationship of plants to animals. But the problem is that such things only have to be lost once in the fungal lineage (if they have been lost at all) to make these cases complete non-sequiturs. To explain why plants don't fit in with animals, Stiller would rather invoke some sort of bias in the data. Although such biases may exist, I am very cautious about invoking an entire reworking of the tree based on them.

Stiller ends with four "Future Perspectives" of which I find the following most telling:
"There should be no a priori assumption that the strongest tree-building signal in a given data set reflects evolutionary history rather than bias in the data."
I'll file that in the category of "Things that make you say Hmmm".

Favorite Science Blogs

As ususal, I am late to the party where everyone is discussing their favorite science blogs. This was a no-RSVP-required affair that The Scientist has been hosting under the banner of "Vote for your favorite life science blogs". Most of my favorites are listed in the "Other Interesting Blogs" on the left of my blog. I actually use this list as my major navigation tool for blog-visiting. Of these, here are my most frequently-visited (and therefore most favorite):

Daily (or throughout the day):

Sandwalk. Bravo, Larry!
Pharyngula. Does PZ sleep?
Tree of Life. Jonathan says things that I wish I would have said (& some I'm glad I didn't).
FemaleScienceProfessor. Wow. FSP is anonymous and it really works!

Slightly less than daily:

Fungal Genomes & Comparative Genomics
Scientia Natura
The Evilutionary Biologist
The Loom

More than weekly:
all the rest.

My New Device

Yes, it's as cool as it seems. My wife got me an iPhone for my birthday this year! How am I so lucky? Although I was excited about it from the start, I let it sit unopened for a couple of weeks while I figured out whether I was really prepared to pay for it. My cell phone was with Verizon, so to activate the iPhone required me to switch to ATT (@ $60/month) and start another 2-year contract. And that's on top of the device buy-in (which was purchased prior to the $200 price cut). Anyway, it's out of the box now and I am really enjoying it. I recieved and sent multiple emails today while stolling across campus. My iCal is seamlessly synched between my laptop (MacBook Pro) and my iPhone, which means that I don't have to lug my laptop around so much. Sorry if this post seems like advocacy, but sometimes you just have to let out the joy! Back to science shortly...

Joe Biden on Science Funding

Iowa is a great place to be if you are at all interested in national politics. Case in point: last Thursday I found myself in the same place as presidential hopeful Joe Biden. He was at the University Bookstore signing copies of his book, "Promises to Keep: On Life and Politics". The line wasn't very long, and I consider Joe to be one of my top three candidates this year. So I ponied up the $27 to buy a copy so that I could get him to sign it and throw a few questions at him.

I introduced myself as a Biology Professor and asked him about his thoughts on basic science funding. Without hesitation, he said that he would support a doubling of the NIH and NSF budgets. When I asked if I could post that comment on my blog, Biden agreed. He also was keenly aware that the although funding for both has increased in recent years under the current administration, it has not been effective at increasing basic science. I don't know how much of that was just telling me what I wanted to hear, but I was pleased.

He signed my book "Keep the faith. Keep on teaching" I don't know about the former....

On a related topic, check out the following link that matches your views to those of the current presidential candidates.

Sexy Fungi

I just found out that ASM Press has recently published a new book entitled "Sex in Fungi: Molecular Determination and Evolutionary Implications", (Editors: J. Heitman, J.W. Kronstad, J.W. Taylor, & L. A. Casselton; ISBN: 978-1-55581-421-2). My Department colleague, David Soll, who wrote a chapter on mating type switching in Candida, let me borrow his copy for the weekend. It looks really great.

The release of this book is good timing for me, too. I have a recently-funded project in my lab to study the evolution of sex and meiosis in diverse fungi. A postdoctoral position is available in my lab immediately to work on this project. Send me an email if you are interested in hearing more.

Thomas "Vandy" Vanderford, PhD

Belated, but sincere, congratulations to Vandy on the successful defense of his PhD thesis on August 13th. His dissertation is entitled "Adaptation of a diverse SIVsm population to natural and non-natural hosts". Vandy was a student in the Population Biology, Ecology & Evolution (PBEE) program at Emory University and he was jointly supervised by myself and Silvija Straprans. Even though I moved from Emory to Iowa in 2003, Vandy continued to work with me on the evolutionary aspects of his research on SIV. To make things happen, he travelled mutiple times to Iowa City and I went to Atlanta a few times, too.

Vandy gave a clear talk which was followed by some questions by the audience and commitee members. His post-seminar defense was rather short--his committee didn't even grill him! What a lucky guy. Afterwards, Vandy was treated to a reception hosted by the Vaccine Center (where Silvija's lab was located--she is now at Merck). After the festivities, Vandy and I spent the remaining afternoon celebrating over a few beers (picture above taken at that time) while listening to The Raconteurs. Later, accompanied by Vandy's girlfriend, Mitzi (who drove) we had dinner and a few more beers at the Brick Store Pub. I'm proud to add Vandy to my list of PhD grads. Congratulations, Dr. Vanderford!