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...

Favorite Popular Science Book #2

Another great "popular" evolution book is Steve Jones' "retelling" of The Origin of Species, called Darwin's Ghost (in the UK it was called Almost Like a Whale). As with Dr. Tatiana, I have used this book with success for teaching in both undergraduate (introductory Evolution) and graduate (Molecular Evolution) courses. It's a highly engaging introdution to evolution--I found it to be particulary good for those students who are somewhat knowledgable in genetics and molecular biology, but who have little or no background in evolution (I would get some of these students in my ME course that I, sadly, no longer teach). The basic idea is that Jones keeps Darwin's chapters and topics intact, but he re-writes them to include up-to-date material that reflect today's science (or at least 1999's). I don't know if it's in the works, but perhaps a revision would be in order...

Bdelloid Rotifers-Ancient Asexuals?

It appears that I started this blog just in time: in a paper just-out today in PLoS Biology, entitled Independently Evolving Species in Asexual Bdelloid Rotifers Fontaneto et al. describe their recent results on the "scandalous" bdelloid rotifers:

"The evolution of distinct species has often been considered a property solely of sexually reproducing organisms. In fact, however, there is little evidence as to whether asexual groups do or do not diversify into species. We show that a famous group of asexual animals, the bdelloid rotifers, has diversified into distinct species broadly equivalent to those found in sexual groups. We surveyed diversity within a single clade, the genus Rotaria, from a range of habitats worldwide, using DNA sequences and measurements of jaw morphology from scanning electron microscopy. New statistical methods for the combined analysis of morphology and DNA sequence data confirmed two fundamental properties of species, namely, independent evolution and ecological divergence by natural selection. The two properties did not always coincide to define unambiguous species groups, but this finding is common in sexual groups as well. The results show that sex is not a necessary condition for speciation. The methods offer the potential for increasing our understanding of the nature of species boundaries across a wide range of organisms."

In other words, these data suggest that bdelloids seem to evolve just like "normal" sexual eukaryotic species. Hmm...if it quacks like a duck...

The article is accompanied by a commentary entitled Who Needs Sex (or Males) Anyway? by Liza Gross and the study has already been picked up by the media, including this story on Science Daily.

Thanks to Coturnix for the lead. Thanks also to David Mark Welch & Matthew Meselson for the image: see Meselson's website for the legend.

New Layout

Some of the initial correspondents have noted how difficult the dark background is for them to read, so I have switched to another template. Please let me know if this is better or worse. I'm one of these guys who uses white backgrounds on my power-point slides, but I am always jealous of those who can use black backgrounds and pull it off effectively.I guess it's different for blogs, where it is mostly text and you have to be able to read all of the words.

Dr. Tatiana Rules!

I'm going to take advantage of my newbie blogger status and mention a book that everyone should read. Really! It's Dr. Tatiana's Sex Advice to All Creation. The Definitive Guide to the Evolutionary Biology of Sex, by Oliva Judson. This is simply a fantastic book about the evolution of sex. I have now used it for two classes. The first was a graduate seminar where I used it to whet the appetite of the grad students for the primary literature (even though it is a "popular" science book, it is very well referenced). I am currently using it for my freshman seminar course "Sex: why we do it", where it is not only a great introduction to the evolution of sex, but also to evolution itself.

For those that already have made Dr. Tatiana's acquaintance, who is your favorite correspondent?

What will go here?

I probably should have thought about this some more before jumping into the deep end, but here's some of what you might find me blogging about in the near future:

Origin and Evolution of Sex. When did meiosis evolve and from what processes did it derive? Is DNA repair the original function of meiotic recombination? Are there any bona fide ancient asexual eukaryotes? If so, how do they persist?

Early Eukaryotic Evolution. What are the evolutionary relationships among the major lineages of eukaryotes? (& what are the major lineages of eukaryotes?) Can the answers provide some hints about the origin of novel features in eukaryotic cells?

Introns. What is the evolutionary history of eukaryotic gene structure? Have spliceosomal introns been mostly gained or lost during eukaryotic evolution? How? Why?

Evolution Teaching. What can be done to ameliorate the pitiful level of evolutionary knowledge in students (and the public) at all levels in the US? What information do parents and teachers need to communicate the fascinating science of evolutionary biology?

Other stuff relating to politics, religion (or lack thereof), parenting, lab management, professor-dom and other life-pusuits...

My First Post

Here it is, the end of Spring Break. While I have a dozen other things to do, I have (finally!) set up my own blog. I am hoping that this will be as fun as it looks. I have been lurking on others' blogs for awhile and it's time for me to add a few cents of my own.