30 May 2011

Mapping fitness: ribozymes, landscapes, and Seattle

ResearchBlogging.orgA few months ago, we were looking at the concept of a fitness landscape and how new technologies are creating opportunities for biologists to look in detail at relationships between genetics and fitness. The first post discussed the concepts of a fitness landscapes and adaptive walks, with some focus on the limitations of the metaphor. The second post summarized some recent work on bacterial fitness and mutation rates, with the concept of a fitness landscape as a theme, and the third post reviewed another recent paper, one that described techniques for studying fitness landscapes in detail by linking protein function (which can be screened and/or selected) and genetic information. Here we'll look at yet another approach to the problem, in which the subject of the analysis is not an organism (as in the first paper) or a protein (as in the second paper) but an RNA molecule.

21 May 2011

New reading on "junk DNA"

John Farrell runs an interesting blog at Forbes.com, and he regularly discusses genetics, design, and other topics of interest around here. His latest points to work by Larry Moran and Ryan Gregory, both of whom have debunked some of the "junk DNA" misinformation concocted by design theorists, then looks at some interesting new blogging from one Stanley Rice. It's interesting stuff.

Casey Luskin shows up in the comments. Nothing new there. Run over and check it out.

15 May 2011

Alu need to know about parasitic DNA: telling the whole story about Alu elements and "design"

So, Alu elements are mobile DNA modules that can exert diverse influences on genomes and the organisms harboring them. They can affect genome function in constructive ways, by altering gene expression or supporting chromosome structure. And they can be damaging, even deadly. There are more than a million of them in the human genome, and we don't know what each one does. But, as I explained in the first post in this series, we do know that they can play both helpful and harmful roles, in the same way that other kinds of parasites can be good, bad, or indifferent.

Alu elements and other genome-wide repeats are a big problem for intelligent design (ID) theorists of some stripes. Any ID proponent who claims that genomes are carefully-designed, well-optimized systems must deal with the reality of the enormous numbers of mobile elements in (for example) the human genome. Now, I can think of various ways such an ID theorist might discuss Alu elements. She could propose that all of their characteristics (including their mobility) are part of their design, such that they can bring new design features quickly into being; she could propose that their mobility is a "bug" rather than a "feature," and perhaps speculate on how things went wrong; she could postulate that the damage caused by their expression and their mobility is being misattributed to the genome when it is instead caused by some other external process. (Or she could say, "We're still working on that one.")

13 May 2011

Exploring the protein universe: a response to Doug Axe

One of the goals of the intelligent design (ID) movement is to show that evolution cannot be random and/or unguided, and one way to demonstrate this is to show that an evolutionary transition is impossibly unlikely without guidance or intervention. Michael Behe has attempted to do this, without success. And Doug Axe, the director of Biologic Institute, is working on a similar problem. Axe's work (most recently with a colleague, Ann Gauger) aims (in part, at least) to show that evolutionary transitions at the level of protein structure and function are so fantastically improbable that they could not have occurred "randomly."

Recently, Axe has been writing on this issue. First, he and Gauger just published some experimental results in the ID journal BIO-Complexity. Second, Axe wrote a blog post at the Biologic site in which he defends his approach against critics like Art Hunt and me. Here are some comments on both.

01 May 2011

How do fish adapt to life in hydrogen sulfide?

To find out, and to read some of the best recent blogging on evolution, visit the new Carnival of Evolution, 35th Edition, at Lab Rat. And go to the official carnival page to learn more about the Carnival of Evolution and perhaps to sign up as a future host.