Evolution of Eukaryotes—Early or Late?

It was inevitable. In this week's Science magazine there is a Letter by Martin, Dagan, Koonin, Dipippo, Gogarten and Lake. They forcefully deconstruct a paper, "Genomics and the Irreducible Nature of Eukaryote Cell" that Kurland, Collins and Penny published last year in Science. There was some popular press that followed the original publication.

The Kurland et al. article did not—by far—represent the consensus view of scientists working on eukaryotic origins. However, this paper has, until now, gone without much challenge in the literature (although it shows 11 citations at ISI).

Kurland et al. argued for the (early) emergence of eukaryotes prior to prokaryotes:

"...we favor the idea that the host that acquired the mitochondrial endosymbiont was a unicellular eukaryote predator, a raptor. The emergence of unicellular raptors would have had a major ecological impact on the evolution of the gentler descendants of the common ancestor. These may have responded with several adaptive strategies: They might outproduce the raptors by rapid growth or hide from raptors by adapting to extreme environments. Thus, the hypothetical eukaryote raptors may have driven the evolution of their autotrophic, heterotrophic, and saprotrophic cousins in a reductive mode that put a premium on the relatively fast-growing, streamlined cell types we call prokaryotes."

In essence, complex eukaryotes came first, followed by prokaryotes which evolved by reduction. In today's letter, Martin et al. point out that this is a re-clothed view of eukaryotic evolution that was popular in the early 1980s. At the time, this idea was mostly centered on the origin and evolution of introns, which were assumed by some to be responsible for building the ancestral set of protein-coding genes by exon shuffling (the introns-early view); to be true, massive intron loss must have characterized the (reductive) evolution of prokaryotes. This scenario has since been thoroughly debunked. Although Kurland et al.'s hypothesis includes more than introns, it suffers from the same problems that led to the demise of introns-early.

In their response, Kurland, Collins and Penny insist that:

"...cellular and molecular biology, especially genomics, reveals signs of an ancient complexity of the eukaryotic cell. This new information was not available to older hypotheses for eukaryote origins..."

I don't find Kurland et al.'s arguments any more compelling than when I first encountered them almost twenty years ago. However, it's great to see these important questions being discussed on the pages on Science.

Picture and caption from MSNBC (Lesley Joan Collins/Science).
"This illustration shows a single-celled predator (colored brown), swallowing up much smaller and less complex single-celled bacteria (yellow and green). Researchers say such a predatory eukaryote, nicknamed "Fred the Raptor," would have had "a major ecological impact" during the early stages of cellular evolution."

1000 visitors in 1 month!

Just a quick post to commemorate my ~1000th visitor. Since I put up the counter a few days into my blog-adventure, I probably missed a few hits (including those initial ones dropping in following PZ's peer pressure post). Thanks for stopping in--it's been a fun first month. I hope that I can keep it up...

Image of Giardia from Kingdom Protista.

The Origins of Genome Architecture

I was really excited to find in my mail yesterday a copy of Michael Lynch's new book, The Origins of Genome Architecture, just-published by Sinauer. This book represents a synthetic detailing of Mike's ideas about evolutionary principles that underlie the origin and diversification of genomes. It is very likely to become a classic in evolutionary biology. Last year, Mike published a seminal paper entitled The origins of eukaryotic gene structure in Molecular Biology & Evolution that is a precis of sorts on this topic. I am generally a big fan of his ideas, although they are not without detractors.

In full-disclosure mode, I should point out that I provided some comments to Mike on one of the chapters, resulting in the complementary book (thanks, Mike & Sinauer!). However, I have not yet had the opportunity to consider the whole book. I'll need to add it to my ever-lengthening list!

Good Lab Webpages?!

Pimm has been looking for examples of good lab webpages. Although my lab's webpage is functional, it is certainly in need of a facelift (note, for example, the 2004 copyright date on the home page). I'm especially concerned given that the websites of many of my friends and colleagues have been listed: I clearly need to keep up with the Redfield's, Kissinger’s, Leander's, Roger's , Archibald's, Waller's, and Patterson's labs! Perhaps some (non-human) organism pictures would help....

Evolution for Everyone

This afternoon, I picked up a copy of David Sloan Wilson's (DSW) new book, Evolution for Everyone. I have been looking forward to reading it ever since I heard about it a year or so ago. The idea that DSW puts forward is that evolutionary thinking can illuminate many subjects, not just those in biology. In the opening chapter, DSW refers to himself as an "evolutionist" as opposed to an "evolutionary biologist": although he is a certainly a biologist, he uses evolutionary thinking to consider a whole variety of problems not exclusive to biology.

In putting his efforts where his mouth (or keyboard) is, DSW has also organized what sounds like a really exciting program at Binghamton University called Evolutionary Studies (EvoS). The program is described in some detail in his recent paper in PLoS Biology, Evolution for Everyone: How to Increase Acceptance of, Interest in, and Knowledge about Evolution.

Along with a thoughtful review from one of my favorite science writers, Natalie Angier, the New York Times has made the first chapter available online. A review that recently appeared in the New Scientist said:

"DO WE need another popular book on evolution? That 54 per cent of adults in the US believe we did not evolve from earlier species is reason enough, but David Sloan Wilson's book also has much to teach those of us who are already convinced. His aim is to show that evolution can transform our basic understanding of everyday life. We have no problem believing in the physical sciences, he says, because we are so used to them in our lives - when we drive cars or build bridges, for example. Evolution is different, yet without it we can't understand medicine, politics, economics, art and, yes, religion. With a clear passion for the subject, Wilson shows that understanding evolution is easy, even intuitive - it really is for everyone. If only everyone would read his book."

I'm only three chapters into the book so far, but I'm already really enjoying it; I'll report more later. In the meantime, if anyone has comments on the book (or article), please leave them.

Hello (I Love You) from "The Last Mimzy"

This American Life

This is a bit off-topic, but I haven't posted to my blog for a while (sorry). Anyway, on my way into the office this afternoon, I was listening to "This American Life" on my local NPR station, WSUI. For those of you that don't know about this show, give it a listen. I also was reminded that the show has now been ported to TV (Showtime, that is). The first episode is available for free viewing; it definitely does the radio show proud.

Dark Matter between students and mentors

I don't have alot to say about this yet, but there is a new film called Dark Matter that recently won the Alfred P. Sloan Prize for science films at this year's Sundance Film Festival. It's based on a tragic story that happened here at the University of Iowa in 1991. Gang Lu, a physics PhD student shot and killed five people (including his advisor), seriously injured another and then killed himself. It's a harrowing case of conflict between mentor and student gone terribly wrong. There is an interesting article in the New York Times today about the new film and some of the realities of mentoring. I don't think that the film has screened in Iowa City yet, but I assume it will soon.

Image from the Dark Matter wikipedia site.

"fundamentally, the involvement of silent mutations in disease undermines the neutral theory of molecular evolution"

The claim, quoted above, comes from a recent article in SEED magazine, entitled The Sound of Silence by Lindsay Borthwick. I had forgotten about the article after initially seething over it a few weeks ago. However, I was reminded of it by noticing that Larry Moran has performed a proper debunking of the article over on his blog, Sandwalk.

Just because some synonymous (aka "silent") substitutions have some selective value (and they do: we have known this for many years!), this does not mean that all such substitutions do. "Fundamental" impacts should be just that and not just some hot air to get attention and a good title. The new study that demonstrates translational slow-down caused by synonymous differences is really interesting, but I'd bet more than a few beers that these kind of effects are the exception, rather than the rule. In evolution, we are interested in both exceptions and rules. But often the former illuminate the latter, rather than cause us to throw out the baby with the bathwater. SEED should do better than this if its going to have any future on my coffee table.

(image from the SEED webpage)

Parenting without believing

Even though it's only been a few days for me here, I will go ahead and "out" myself as a non-believer. That won't come as a huge surprise to many, perhaps. I'm not planning to get into philisophical issues here, but as a parent and a general member of society, there are some important practical things to deal with. Both parenting and religion are among my "approved" topics for this blog...

So when I was asked by a colleague to write a short review on the upcoming book Parenting Beyond Belief for the Iowa Secularists newsletter, I was delighted to oblige. Although I haven't yet completed the book (and the review!), I am already in a position to reccommend it to parents like myself. It is a series of essays from a wide variety of folks on a diverse set of topics. The website says:

"Parenting Beyond Belief is the first comprehensive parenting book by a major publisher on raising children without religion"

So far, my favorite essays are by Penn Jillette (of Penn & Teller), Julia Sweeney (formerly, of SNL) and Richard Dawkins (most recently, of The God Delusion). The latter is a reprint of my favorite piece from A Devil's Chaplain, called Good And Bad Reasons For Believing. This is an open letter that Dawkins wrote to his 10-year-old daughter on the nature of evidence and belief. I am moved everytime I read it.

Since I'll retain copyright on the review, I'll also publish it here when its done. I had better finish the book now...