HENRY

Nature announces the ENCODE project (ENCyclopedia Of DNA Elements) which is a pilot program to investigate the functional elements in 1% of the human genome:

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function

The full-text of the article is available: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, and Nature has more information, including a rather cool poster (PDF!)

Update: Genomicron has yet more details.

One of Darwin’s pet examples of sexual selection were the Diving Beetles, where he argued that the male and female members of the same species co-evolved their mating techniques (i.e. males with large suction cups to hold the females).

However, it appears that this is more of an inter-sex arms race, where the females develop modifications of their dorsal surface to hinder the male suction cups:

To trace the evolutionary history of sex-specific characters in diving beetles, we used the recently revised genus Acilius which contains 13 extant species distributed over the Northern Hemisphere. The genus is characterized by having dense macropunctures on the dorsal surfaces, females with prominent, setose furrows on the elytra, and males with broadly expanded protarsi equipped ventrally with three large and many minute suction cups. These structures even attracted the attention of Charles Darwin, who regarded the setose female furrows in Acilius as an example of an aid for males to better grip females during mating. However, it is clear from basic physical laws and simple experiments, that the mechanically working male suction cups function best on smooth surfaces where complete contact around their circumference enables attachment.

Continued at Phylogeny of Diving Beetles Reveals a Coevolutionary Arms Race between the Sexes.

The always wonderful bibliodyssey has posted some beautiful simian pictures from Johann Baptist von Spix’s 1823 book, Simiarum et Vespertilionum Brasiliensium Species Novae.

Finally! a real competitor to John Frum - Prince Philip:

Legend had it that there was a clutch of villages on the island of Tanna in Vanuatu which - as bizarre as it may seem - worshipped Prince Philip as a god.

How and why they had chosen the Duke of Edinburgh, I had no idea. I fully expected the story to be either false, or wildly exaggerated.

(thanks Rob!)

Sean Carroll reviews the latest insult to intelligence from Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism

The continuing futile attacks by evolution’s opponents reminds me of another legendary confrontation, that between Arthur and the Black Knight in the movie Monty Python and the Holy Grail. The Black Knight, like evolution’s challengers, continues to fight even as each of his limbs is hacked off, one by one. The “no transitional fossils” argument and the “designed genes” model have been cut clean off, the courts have debunked the “ID is science” claim, and the nonsense here about the edge of evolution is quickly sliced to pieces by well-established biochemistry. The knights of ID may profess these blows are “but a scratch” or “just a flesh wound,” but the argument for design has no scientific leg to stand on.

Sorry - been lazy recently, here’s a roundup of interesting stuff:

Ancient DNA work into woolly mammoths shows that they experienced a fairly drastic population bottleneck:

“In combination with the results on other species, a picture is emerging of extinction not as a sudden event at the end of the last ice age, but as a piecemeal process over tens of thousands of years involving progressive loss of genetic diversity,” said Dr. Ian Barnes, of Royal Holloway, University of London. “For the mammoth, this seems much more likely to have been driven by environmental rather than human causes, even if humans might have been responsible for killing off the small, terminal populations that were left.”

The paper is in this month’s Current Biology: Genetic Structure and Extinction of the Woolly Mammoth, Mammuthus primigenius(doi)

Next, some archaeologists have found what appears to be the oldest known jewelry. The 13 shells covered in ochre, were found in Morocco, and are a staggering 82,000 years old. National Geographic has more details.

Finally, Deric Bownds over at Mind Blog talks about some new research into the fascinating Synesthesia:

Synesthesia, in which letters or numbers elicit color perception, could be due to increased brain connectivity between relevant regions, or due to failure to inhibit feedback in cortical circuits. Diffusion tensor imaging now provides evidence for increased connectivity in word processing and binding regions of the brain.

A forthcoming paper by Andrew Whiten and associates follows up on their previous work which identified a number cultural traits in chimpanzees. This new work introduced a number of new food extraction and tool use behaviors into experimental populations. In a number of sites, the new behaviors spread throughout the population, and even jumped between a few groups within eyesight of each other.

This is very cool - it’s more strong evidence of cultural traditions in chimpanzees, and very indicative of social learning and some form of cultural evolution.

The abstract (doi) says:

Field reports provide increasing evidence for local behavioral traditions among fish, birds, and mammals. These findings are significant for evolutionary biology because social learning affords faster adaptation than genetic change and has generated new (cultural) forms of evolution. Orangutan and chimpanzee field studies suggest that like humans, these apes are distinctive among animals in each exhibiting over 30 local traditions. However, direct evidence is lacking in apes and, with the exception of vocal dialects, in animals generally for the intergroup transmission that would allow innovations to spread widely and become evolutionarily significant phenomena.

Here, we provide robust experimental evidence that alternative foraging techniques seeded in different groups of chimpanzees spread differentially not only within groups but serially across two further groups with substantial fidelity. Combining these results with those from recent social-diffusion studies in two larger groups
offers the first experimental evidence that a nonhuman species can sustain unique local cultures, each constituted by multiple traditions. The convergence of these results with those from the wild implies a richness in chimpanzees’ capacity for culture, a richness that parsimony suggests was shared with our common ancestor.