Martin Rundqvist reviews the History Channel documentary, "Journey to 10,000 BC." The doc focuses on "Clovis-era North American archaeology and paleontology."

Overall, the film has very poor visuals. It looks cheap, it's repetitive and it conveys a lot of wordless errors. We get endless ugly machinima-level computer animation combined with bluescreened live actors who interact with beasties that aren't visible to them. There are many cloned copies of each digital being, with jerky movements that Harryhausen wouldn't have accepted 40 years ago.

The date is such an interesting one, as indicated by the (now) two film attempts. I'd really like to see someone do a good documentary or book about it. Rundqvist does write that the academics in the film do a good job. It's an exciting time for that subject, with new genetic and archaeological discoveries every few months.

Massimo Pigliucci describes the agenda for the upcoming Altenberg meeting, attempting to hash out the place of some recent developments in evolutionary theory:

The basic idea is that there have been some interesting empirical discoveries, as well as the articulation of some new concepts, subsequently to the Modern Synthesis, that one needs to explicitly integrate with the standard ideas about natural selection, common descent, population genetics and statistical genetics (nowadays known as evolutionary quantitative genetics). Some of these empirical discoveries include (but are not limited to) the existence of molecular buffering systems (like the so-called “heat shock response”) that may act as “capacitors” (i.e., facilitators) of bursts of phenotypic evolution, and the increasing evidence of the role of epigenetic (i.e., non-genetic) inheritance systems (this has nothing to do with Lamarckism, by the way). Some of the new concepts that have arisen since the MS include (but again are not limited to) the idea of “evolvability” (that different lineages have different propensities to evolve novel structures or functions), complexity theory (which opens the possibility of natural sources of organic complexity other than natural selection), and “accommodation” (a developmental process that may facilitate the coordinated appearance of complex traits in short evolutionary periods).

It's interesting that there is so much public access to what is essentially a small private conference (via Pharyngula).

Genetic Future comments on news from the Wellcome Trust Sanger Institute:

At the current rate (which is rapidly increasing) the Sanger is churning out more DNA sequence every two minutes than was generated by the entire research community from 1982-1987. This obscene rate of data generation has been enabled by the development of next-generation DNA sequencing platforms, which can each churn out one human genome equivalent in less than a week.

Sorry to those hitting the site from old permalinks ending with a ".w" extension; I'm working on a rewrite rule to handle those now. In the meantime, all these pages are there, with the supported ".html" extension.

Paleolithic multimedia?

A trained vocalist was sent through the caves testing different sounds and pitches in various locations. Spots of maximum resonance, or places where the voice was most amplified and clear, were noted in each section and later laid over a map of the cave drawings.

The vast majority of the paintings, up to 90 percent in some cases, were located directly at, or very near, the spots where the acoustics were the absolute best, they found.

The work is by Iegor Reznikoff, no publication yet.

DavidB at Gene Expression continues his wonderful series on Sewall Wright with a detailed post on the population genetics of migration.

Gary Marcus contributes an article to the Huffington Post, reflecting on the new Louisiana creationism law:

At this point, 30 years after the Nobel Laureate Daniel Kahneman and his late collaborator Amos Tversky started documenting a rash of fallacies in human reasoning, the idea that the human mind would be "perfect in His image" is as outdated (and narcissistic) as the idea that the solar system would revolve around the planet earth.

Marcus' new book is Kluge: The Haphazard Construction of the Human Mind. I'll be reviewing it here in the next few weeks.

R. Ford Denison:

In A Study in Scarlet, [Holmes] expresses the opinion that it makes no practical difference whether the sun orbits the earth or vice versa. Yet, in The Musgrave Ritual, it turns out that incorrect theories make incorrect predictions.

The dialogue that ensues is classic.

Molly Moore of the Washington Post turns in a nice report on the problems facing Lascaux, about which I wrote earlier this year:

"Microbiologists and geologists say we have to observe and understand what's happening first, that we can't disturb the cave. They don't agree with the treatment," [Marie-Anne] Sire said. "Other groups say the risk is too big to watch and take no action."

According to the article, Lascaux II, the reproduction cave for tourists, is also facing trouble: the works are fading.

On Monday's "NewsHour", PBS ran an interview with archaeologist Dennis Jenkins, who worked on the Paisley Caves human-DNA-containing scat.

DENNIS JENKINS: We were looking and hoping, of course, to find spear points, evidence of their technology. Instead, what we found was the perfect human signature, their coprolites. It was, if you will, the perfect artifact.

LEE HOCHBERG: Coprolites are an archeology term for fossilized feces. Jenkins says they're from humans, and they're more than 14,000 years old.

DENNIS JENKINS: So this was the evidence we had dug all summer to get to.

There's some critical discussion of the find, also; seems like a nice story.

There was also a History Channel show entirely devoted to scat the other night. It was a pretty good show, considering... There was lots of woolly mammoth poop. And it's being rebroadcast this Saturday (7/5)

That "celebrity chimpanzee" that caused all the trouble three years ago is now on the loose in the hills outside LA.

There have been scattered reports of missing chickens and garden hoses turned on in the vicinity of the hunt -- but no solid evidence that Moe is to blame.

"They've positioned people about every 300 feet in cars. Their job is to keep a lookout and see if they can see movement anywhere. Thank goodness for people willing to do this," LaDonna Davis said. "A lot of people on horseback have offered their services, a lot of hikers."

He's been in a shelter for ten years, after several biting incidents. It was in that shelter in 2005 that the owner, St. James Davis, was brutally injured by other chimpanzees:

The 65-year-old former NASCAR driver lost all of his fingers, an eye, his nose, parts of his cheek and lips, and pieces of his torso to attacking chimpanzees in 2005. The animals pounced after apparently becoming jealous that Davis was preparing to present a birthday cake to Moe at their refuge.

The story is tasteful enough not to mention the chimpanzees tearing off testicles. I, however, am not. Chimps are not pets.

Wired's Brandon Keim covers a new study by Susan Goldin-Meadow, which shows a conflict between linguistic and gestural communication strategies:

"This may reflect the real thought that comes before language," said study co-author Susan Goldin-Meadow, a University of Chicago psychologist. "It seems pretty natural."

Goldin-Meadow's team asked forty people -- ten speakers apiece of English, Mandarin Chinese and Spanish, each of which follows the SVO order, and ten speakers of Turkish, which follows an SOV order -- to describe a series of simple actions, such as a girl turning a knob, with gestures.

Regardless of their native language, the subjects almost universally preceded object with verb: girl knob turns.
"We expected that the language they spoke would influence the language of their gestures, but it didn't," said Goldin-Meadow.

They propose the "meaning" of the study is that the gestural strategy here reflects the actual structure of symbolic communication in the brain. In that view, the linguistic version is a language-specific translation of the brain's version.

Carl Zimmer has moved his blog, The Loom, to Discover magazine's stable of blogs.

This is a press release from CNRS:

A complete mandible of Homo erectus was discovered at the Thomas I quarry in Casablanca by a French-Moroccan team co-led by Jean-Paul Raynal, CNRS senior researcher at the PACEA[1] laboratory (CNRS/Université Bordeaux 1/ Ministry of Culture and Communication). This mandible is the oldest human fossil uncovered from scientific excavations in Morocco. The discovery will help better define northern Africa's possible role in first populating southern Europe.

A Homo erectus half-jaw had already been found at the Thomas I quarry in 1969, but it was a chance discovery and therefore with no archeological context. This is not the case for the fossil discovered May 15, 2008, whose characteristics are very similar to those of the half-jaw found in 1969. The morphology of these remains is different from the three mandibles found at the Tighenif site in Algeria that were used, in 1963, to define the North African variety of Homo erectus, known as Homo mauritanicus, dated to 700,000 B.C.

The mandible from the Thomas I quarry was found in a layer below one where the team has previously found four human teeth (three premolars and one incisor) from Homo erectus, one of which was dated to 500,000 B.C. The human remains were grouped with carved stone tools characteristic of the Acheulian[2] civilization and numerous animal remains (baboons, gazelles, equines, bears, rhinoceroses, and elephants), as well as large numbers of small mammals, which point to a slightly older time frame. Several dating methods are being used to refine the chronology.

And now, you know as much as I do.

Reuters is reporting on a Middle Pleistocene find from Serbia:

The fragment of a lower jaw, complete with three teeth, was discovered in a small cave in the Sicevo gorge in south Serbia.

"It is a pre-Neanderthal jaw that we believe is between 130,000 to 250,000 years old," said Belgrade University archaeology professor Dusan Mihailovic, head of the team studying the jaw.

Sounds cool, but there's little in the way of relevant detail.

Note to self: If the skull-shaped death whistle has lain silent for seven or more centuries don't create an exact replica and blow into it.

Daniel Macarthur, of Genetic Future, reviews the amount of information required to store genomic information. Naturally, you'd probably think it was around 12 billion bits (2 bits per base pair), but sequencing technologies and the availability of references from other people make things a little more complicated.

This interesting quote about the raw image files generated by the Illumina platform presents some of the range of complications:

Almost as soon as these images are generated they are fed into an algorithm that processes them, creating a set of text files containing the sequence of each of the fragments. The image files are then almost always discarded. Why are they discarded? Because, as you will see in a minute, storing the raw image data from each run in even a moderate-scale sequencing facility quickly becomes prohibitively expensive - in fact, several people have suggested to me that it would be cheaper to just repeat the sequencing than to store these data long-term.

An accurate read requires lots of redundant bits, which adds up to lots and lots of data storage. If these are winnowed down to a real "best" sequence, then you're back to 12 billion bits (=1.5 gigabytes), more or less. Of course, most of that sequence is redundant and may be significantly compressed. And if you compare with a reference sequence, really a small amount of information is sufficient to distinguish your genome compared to the reference. Anyway, all this is explained at the link.