john hawks weblog

A concise 4-paragraph article by Mathieu Schuster and colleagues reports on dune deposits that show the Sahara formed during the Late Miocene.

After the mid-Holocene humid period (6000 years ago), arid conditions developed throughout North Africa, culminating in the formation of the Sahara, which is the largest warm-climate desert on Earth (9,000,000 km2). However, earlier desert recurrences in the region are also documented. Direct evidence for eolian deposition is given by thermoluminescence dating for the Late Pleistocene; e.g., in Mauritania [25 to 15 thousand years ago (ka)] (1) or in Tunisia (86 ka) (2). The latter is currently considered as the oldest terrestrial record for desert conditions in the Sahara (2), even if firm evidence exists for a pre-Quaternary Great Western Sand Sea in Algeria (3). Some earlier arid episodes (Miocene-Pliocene) were also suggested by marine records off West Africa (4); but until now, no contemporary in situ eolian deposits were known in the Sahara region. In the northern Chad Basin, we recently identified and dated widespread outcrops of eolian dune deposits that are distributed over an area more than 2000 km². Our results testify that the onset of recurrent desert conditions in the Sahara started at least 7 million years ago (5-7) (Schuster et al. 2006:821).

The desert comes and goes, expanding and contracting -- and those vacillations are recorded by this earliest evidence, also:

In the Toros Menalla region, these eolian sandstones are conformably overlain by a horizon bearing abundant vertebrates fossils, including Sahelanthropus tchadensis, the earliest known Hominid [sic] (5, 7). In this horizon, named the Anthracotheriid Unit, biostratigraphic correlation of the mammalian fauna indicates an age of 7 Ma (5–7).

Now, this isn't news (which I'm sure Science didn't bother to check) since Vignaud and colleagues (2002) published the same evidence, complete with the wind direction chart:

The lower part of the section (at least 4 m thick) is composed of fine to very fine white sands, poorly cemented, and is mainly constituted by numerous quartz grains, without matrix. The grains are well sorted, well rounded, matt and frosted, and are strong evidence for aeolian modelling. The foreset laminations (avalanche laminations in front of the aeolian dune) represent a typically aeolian deposit. These sands show cross-beddings that progressively decrease in size from the bottom (1 - 2 m) to the top (20 cm). This facies exhibits typical alternations of grain-fall and grain-flow laminations, characteristic of aeolian dune deposits. Our interpretation is confirmed by frequent wind ripples at the foot of the fossil dunes, whose crests are perpendicular to the direction of dune progradation. These fossil dunes are, to our knowledge, the oldest evidence for desert conditions in the southern Sahara area (Vignaud et al. 2002:152).

I guess this is the science journal equivalent of getting "punk'd" -- "Ha ha! You published what we printed four years ago!"

I opened up the Vignaud paper to double-check the paleoenvironment in the fossil-bearing layer. From the faunal list, they conclude this:

The oldest known East African hominids (Ororrin [sic], Ardipithecus) are contemporary with faunas associated with wooded environments. Younger australopithecines lived in a wider range of habitats. In contrast, the TM 266 vertebrate fauna contemporary of the Toros-Menalla hominid suggests a mosaic of environments from gallery forest at the edge of a lake area to a dominance of large savannah and grassland. Determining the precise habitat of the TM 266 hominid locality among the mosaic of environments available to it constitutes a research challenge to be met by further laboratory and field studies currently in progress (Vignaud et al. 2002:155).

They (Vignaud et al. 2002) interpreted the succession of dune and lacustrine deposits to mean that the hominids lived in a mosaic environment near sandy desert, but locally including marshy/swampy, lake, and gallery forest. An alternative interpretation might be that the desert really receded (or disappeared) during the later time period when the hominids were there. In either case, the paleoenvironment is interesting, because it means that the Sahelanthropus-like primates colonized (and possibly repeatedly recolonized) areas that were periodically dune desert (and therefore probably not habitable by large primates). This may not mean much in terms of locomotion -- the hominid-bearing unit is clearly water-rich, and we can't refute the idea that the surroundings were as woodland-like as those preserved in the Late Miocene Middle Awash localities.

But I think it is a good hypothesis that all of these apes (or hominids) were very cosmopolitan compared to extant chimpanzees and gorillas. The question is whether their actual dispersal abilities were different from chimpanzees. Prehistorically, genetics would seem to indicate that chimpanzees had long-distance dispersal; the only fossil evidence of chimpanzees has been found in a region that historically did not support chimpanzees; and they today successfully utilize relatively open savanna at the eastern end of their range.

So it is by no means obvious that the cosmopolitan nature of these Late Miocene lineages would have required a specialized terrestrial adaptation -- at least not beyond the specialization of knuckle-walking. So why become bipeds?

References:

Schuster M et al. 2006. The age of the Sahara Desert. Science 311:821. Full text (subscription)

Vignaud P et al. 2002. Geology and paleontology of the Upper Miocene Toros-Menalla hominid locality, Chad. Full text (subscription)

"We're going to arm you with Christian Patriot missiles," Ham, 54, recently told the 1,200 adults gathered at Calvary Temple here in northern New Jersey. It was a Friday night, the kickoff of a heavily advertised weekend conference sponsored by Ham's ministry, Answers in Genesis.

There has been a lot of attention this week to the congregations that are observing Darwin Day, as a recognition that evolution and religion are not in conflict.

The LA Times has an article profiling Ken Ham, who would be on the, um, other side of this issue.

A former high-school biology teacher, Ham travels the nation training children as young as 5 to challenge science orthodoxy. He doesn't engage in the political and legal fights that have erupted over the teaching of evolution. His strategy is more subtle: He aims to give people who trust the biblical account of creation the confidence to defend their views -- aggressively.

He urges students to offer creationist critiques of their textbooks, parents to take on science museum docents, professionals to raise the subject with colleagues. If Ham has done his job well, his acolytes will ask enough pointed questions -- and set forth enough persuasive arguments -- to shake the doctrine of Darwin.

The article reports on one of these training sessions. Here's the part excerpted by Ann Althouse:

Evangelist Ken Ham smiled at the 2,300 elementary students packed into pews, their faces rapt. With dinosaur puppets and silly cartoons, he was training them to reject much of geology, paleontology and evolutionary biology as a sinister tangle of lies.

"Boys and girls," Ham said. If a teacher so much as mentions evolution, or the Big Bang, or an era when dinosaurs ruled the Earth, "you put your hand up and you say, 'Excuse me, were you there?' Can you remember that?"

The children roared their assent.

"Sometimes people will answer, 'No, but you weren't there either,' " Ham told them. "Then you say, 'No, I wasn't, but I know someone who was, and I have his book about the history of the world.' " He waved his Bible in the air.

"Who's the only one who's always been there?" Ham asked.

"God!" the boys and girls shouted.

"Who's the only one who knows everything?"

"God!"

"So who should you always trust, God or the scientists?"

The children answered with a thundering: "God!"

I notice the annual budget of Answers in Genesis ($15 million) is almost enough to sequence the genome of another mammal species -- every one of which shows 3 billion or so marks of evolution.

We need to get more fossils into schools.

I was reading The Scientist because RPM sent me to this article, titled "The Human Genome Project +5".

And yet the last five years, in Olson's view, have been "a period of a great grinding of gears, kind of shifting of gears." In the terms of the science historian Thomas Kuhn, it's been "a period of consolidation and more normal science." Others, such as Sydney Brenner of the Salk Institute, the Nobel Prize-winning pioneer of the worm, Caenorhabditis elegans, go further, worrying that the genome sequence and the growing lists of sequences and proteins and protein interactions and functional elements don't get very deep into such core problems of biology as the operations of the cell, of development from egg to adult, or the problem of consciousness. "We've become very geno-centric," says Brenner. "The cell must become the focus."

I would say this is pretty much correct -- there has been a long period of normal science in genetics lately, with new findings pretty much following one after another. There have been no revolutions coming out of the HGP.

But I think this scale of examination is a bit misleading. The HGP opened the deep end of the data pool, and we are still swimming in the toddler tank.

Consider what is happening in terms of new data:

One of the most dramatic efforts to push genomics into the realm of complex, multi-genic diseases is the five-year, $138 million haplotype map (HapMap) project, involving samples donated by Japanese, Han Chinese, Yoruba, and Americans of European descent. The project takes advantage of the fact that the millions of single nucleotide polymorphisms (SNPs) found in at least one percent of humans tend to pass between generations in blocks of DNA called haplotypes. The project announced its Phase 1 analysis in October 2005, and said that the analysis of Phase 2, already completed, would be published in 2006. Despite successes, such as using HapMap data to pinpoint a gene for macular degeneration, there remains controversy over HapMap's reach into domains such as rearrangements like deletions and reversals, or the numerous rare mutations that may be involved in diseases.

The minor variations are of central interest to Bentley of Solexa, who has specialized in rare variations. The HapMap, he says, has limitations, capturing only common variations in three target populations, missing the rare mutations. But it may provide a quick way to find more disease genes. Still, in three to five years, he says, the new sequencing machines should open the option of going after virtually all the many genes involved in a disease like diabetes. To be sure, the multiple sequences of patients and "controls" will have to square with what HapMap has found. "Everything that a HapMap captures should also be captured by a technology that aims to do better." Bentley, an early proponent, calls the HapMap "a real benchmark."

There seems to be a "Moore's law" for genome sequencing:

The workhorses of the 2001 human drafts have kept doubling their throughput about every 22 months over 15 years. In September, 454 reported that, in a single run, its system did a shotgun sequence and assembly of the microbe, Mycoplasma genitalium, in four hours. Claire Fraser's team at the Institute for Genomic Research took three months to work out Mycoplasma's sequence in 1995.

And there are gene expression microarrays and microRNA assays, as described in the article. For people who want to know about gene activity at every stage of life, in every type of cell, and in response to every external stimulus, the tools are in place to figure those things out.

As for myself, I think the accumulating data will have some revolutionary effects. These won't be in genetics itself -- I think the paradigms in place now in terms of gene interactions and regulation are very powerful. No doubt some new twists in gene sequence and function will be found, but I would guess that the current picture will expand rather than being overthrown.

But for other fields, I think genetics has some revolutionary power. Obviously genomic medicine has the potential to radically change the way we approach chronic conditions. And metagenomics is already changing the way biologists study microbial communities in all kinds of environments. It wouldn't surprise me if scientists working in places like the Foja Mountains work with DNA tag samples before they do traditional taxonomy on new species.

What will happen to anthropology as a result of the HapMap? There are surprises in store...

This is an old paper by Peter and Rosemary Grant, from 2002:

Unpredictable Evolution in a 30-Year Study of Darwin's Finches

Peter R. Grant and B. Rosemary Grant

Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001, Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.

It seems like the purpose of the paper is to demonstrate the fluctuating evolution of the finches in response to environmental change. But I was drawn to it by the demonstration of biased gene flow from one species to the other:

The proportionally greater gene flow from G. fortis to G. scandens than vice versa has an ecological explanation. Adult sex ratios of G. scandens became male biased after 1983 (Fig. 4C) as a result of heavy mortality of the socially subordinate females. High mortality was caused by the decline of their principal dry-season food, Opuntia cactus seeds and flowers; rampantly growing vines smothered the bushes (16). G. fortis, more dependent on small seeds of several other plant species, retained a sex ratio close to 1:1 (Fig. 4C). Thus, when breeding resumed in 1987 after 2 years of drought, competition among females for mates was greater in G. fortis than in G. scandens. All 23 G. scandens females paired with G. scandens males, but two of 115 G. fortis females paired interspecifically. All their F1 offspring later bred with G. scandens (43) because choice of mates is largely determined by a sexual imprinting-like process on paternal song (42).

They conclude that this hybridization had an introgressive effect, acting in the same direction as selection for beak shape during the early 1990's, but continuing throughout the decade while there was little evidence for selection. There was little or no fitness loss to interspecific hybrids.

The case is distinctive because the effects of introgression on the characters of beak size and shape are consistently large enough to be measured each generation. This despite the fact that the proportion of F₁ hybrids and first-generation backcrosses in the G. scandens population was never greater than 20 percent.

References:

Grant PR, Grant BR. 2002. Unpredictable evolution in a 30-year study of Darwin's finches. Science 296:707-711. Full text (subscription)

You've probably seen the story about the Foja Mountains in Papua New Guinea. Here are a couple of paragraphs:

JAKARTA, Indonesia - Describing it as the discovery of a "Lost World," conservation groups and Indonesia on Tuesday said an expedition to one of Asia's most isolated jungles had found several dozen new species of frogs, butterflies, flowers and birds.

"It's as close to the Garden of Eden as you're going to find on Earth," Bruce Beehler, a Conservation International scientist who led the expedition, said in a statement.

OK, so is it the "Lost World" or the "Garden of Eden"? Let's get this straight.

I say, it's the Garden of Eden if it has unicorns, and the Lost World if it has dinosaurs. Gretchen says it depends how bloodthirsty the animals are.

The AP is reporting on a new cave art find in France.

PARIS - Cave drawings thought to be older than those in the famed caves of Lascaux have been discovered in a grotto in western France, officials from the Charente region said Sunday.

A first analysis by officials from the office of cultural affairs suggests the drawings were made some 25,000 years ago, Henri de Marcellus, mayor of the town of Vilhonneur where the cave is located, told France-Info radio.

No details or pictures. The BBC has some quotes from the discoverer:

Gerard Jourdy, 63, said he found human and animal remains in the chamber in the Vilhonneur forest, in caves once used to dispose of animal carcasses.

The paintings included a hand in cobalt blue, he told AFP news agency.

The discovery was made in November, but kept secret while initial examinations were carried out.

Mr Jourdy also said he saw a sculpture of a face made from a stalactite - which would be a scientific first for the era, but experts were dubious about this claim, AFP says.

"In a small chamber I found the bones of two hyenas - complete skeletons, which is rare. And I saw human bones amid the debris - tibias, vertebrae and shoulder-blades," he told the news agency.

"Then in the bigger chamber there was this hand - very beautiful, very delicate. There was just the one in cobalt blue. When you come into the chamber it is like it is greeting you. It's incredible."

I wonder if those bones are really human. I guess we'll find out.

UPDATE (2/6/06): The New York Times has a short item including this:

Michel Bilaud, the governor of the department of Charente, expressed doubt about the art. "There are traces of human occupation," he said. "There are bones, and there are lines on the wall. There is a print of a hand. But for the rest, it is just marks. There is nothing figurative."

For those interested in the sociological side of neuroscience, GameSpot has a quick review of mirror neurons and their relevance to video games.

Neuroscience and video games. What do they have to do with each other? Aside from whatever research went into crafting games like Psi-Ops and Psychonauts, it doesn't seem like the two subjects have much in common. Sure, neuroscience is the study of the brain, and despite what everyone tells you, you do use your brain when you're playing video games. But what are the chances that the latest neuroscientific research is going to be of any interest to the game industry? Well, if you've been following the (relatively) recent work on mirror neurons, then you would realize that neuroscience is about to have a huge impact--if not on video games, then on the discussions we have about them--for a long time to come.

The emphasis on the article is the possible long-term effects of violent video games on violent crime rates. To that end, it discusses the possible effects of mirror neurons in familiarizing people with experiences that they do not themselves actually do, as well as "super mirror" neurons that may regulate those perceptions.

We can tell if someone is watching a television by the way that person is facing it--even if we can't see or hear if the television is even on. It also means that we can experience the mental states associated with actions without ever having to perform those actions. In video games, in particular, it's like we're automatically empathizing with what is happening on the screen as if we were the video game characters ourselves. If you've ever had a particularly heart-palpitating race in Burnout, surely you can relate.

"We can tell if someone is watching a television..." certainly gives a hint about the evolutionary history of the mirror neurons, but they are strange beasts.

I was just discussing with someone today the merits of taking an old idea and giving it a new name, and now I find out from the NY Times just what a good strategy it can be:

It may seem odd that scientists in the Internet age spend years on a line of research, even bet their careers on it, without having first determined that their mountain had not already been climbed. But Dr. Stigler said that scientists often are ignorant of the work being done by others in their field, and searches of scientific literature can be hard to conduct. Web search engines, for example, look for words, not ideas, and Dr. Vohra said he discovered that every researcher who had made his discovery had given it a different name and description.

In 1957, for example, a statistician named James Hanna called his theorem Bayesian Regret. He had been preceded by David Blackwell, also a statistician, who called his theorem Controlled Random Walks. Other, later papers had titles like "On Pseudo Games," "How to Play an Unknown Game," "Universal Coding" and "Universal Portfolios," Dr. Vohra said, adding, "It's not obvious how you do a literature search for this result."

The idea in question is that random stock buyers can outperform professionals with a simple buy-and-hold strategy. I especially like "Bayesian Regret"; it looks like somebody's dissertation title.

There's always this;

For example, there is the oft-told story about Larry Shepp, a famous mathematician at Rutgers University. Dr. Shepp, when told that a piece of work he thought was his discovery actually duplicated another mathematician's breakthrough, replied: "Yes, but when I discovered it, it stayed discovered."

That's my favorite line from this article in the Economist about Bayesian logic.

From Wikipedia, a short introduction to Bayesian logic:

For example, Laplace estimated the mass of Saturn using Bayesian methods. However, on the frequency interpretation of probability the laws of probability cannot be applied to this problem. This is because the mass of Saturn isn't a well defined random experiment or sample. From what population is the mass of Saturn taken? In what sense is Saturn picked at random from that population? Similarly, when comparing two hypotheses and using the same information, frequency methods would typically result in the rejection or non-rejection of the original hypothesis with a particular degree of confidence, while Bayesian methods would yield statements that one hypothesis was more probable than the other or that the expected loss associated with one was less than the expected loss of the other.

The Economist article is a good short introduction to what Bayesian logic is, and it follows some interesting research that indicates that human minds are especially good at it:

Dr Griffiths and Dr Tenenbaum conducted their experiment by giving individual nuggets of information to each of the participants in their study (of which they had, in an ironically frequentist way of doing things, a total of 350), and asking them to draw a general conclusion. For example, many of the participants were told the amount of money that a film had supposedly earned since its release, and asked to estimate what its total "gross" would be, even though they were not told for how long it had been on release so far.

Besides the returns on films, the participants were asked about things as diverse as the number of lines in a poem (given how far into the poem a single line is), the time it takes to bake a cake (given how long it has already been in the oven), and the total length of the term that would be served by an American congressman (given how long he has already been in the House of Representatives). All of these things have well-established probability distributions, and all of them, together with three other items on the list -- an individual's lifespan given his current age, the run-time of a film, and the amount of time spent on hold in a telephone queuing system -- were predicted accurately by the participants from lone pieces of data.

By "accurately", they appear to mean that the prior distribution was reconstructable from the responses of the 350 people, not that every person guessed the right answer.

The "forever" line comes from this passage:

There were only two exceptions, and both proved the general rule, though in different ways. Some 52% of people predicted that a marriage would last forever when told how long it had already lasted. As the authors report, "this accurately reflects the proportion of marriages that end in divorce", so the participants had clearly got the right idea. But they had got the detail wrong. Even the best marriages do not last forever. Somebody dies. And "forever" is not a mathematically tractable quantity, so Dr Griffiths and Dr Tenenbaum abandoned their analysis of this set of data.

Personally, I think it's romantic that 52 percent of people predicted that marriage would last forever!

I suppose that helps to underlie the last two paragraphs:

How the priors are themselves constructed in the mind has yet to be investigated in detail. Obviously they are learned by experience, but the exact process is not properly understood. Indeed, some people suspect that the parsimony of Bayesian reasoning leads occasionally to it going spectacularly awry, with whatever process it is that forms the priors getting further and further off-track rather than converging on the correct distribution.

That might explain the emergence of superstitious behaviour, with an accidental correlation or two being misinterpreted by the brain as causal. A frequentist way of doing things would reduce the risk of that happening. But by the time the frequentist had enough data to draw a conclusion, he might already be dead.

Which may help to explain why it takes a certain size and structure of population to develop science -- probably including writing, so it's harder to ignore information that someone else collects.

Anyway, read the article to find out the problem people had guessing the length of the reigns of Egyptian Pharaohs.

An upcoming paper in Journal of Human Evolution by O. F. Huffman and colleagues reports on a possible location for the Mojokerto skull. A 1994 paper by Carl Swisher and colleagues dated rock from the supposed site to 1.81 million years ago.

This paper finds that the real site is a bit above that dated horizon. The abstract:

The fossil calvaria known as the Mojokerto child's skull was discovered in 1936, but uncertainties have persisted about its paleoenvironmental context and geological age because of difficulties in relocating the discovery site. Past relocation efforts were hindered by inaccuracies in old base maps, intensive post-1930s agricultural terracing, and new tree and brush growth. Fortunately geologic cross sections and site photographs from 1936-1938 -- not fully utilized in past relocation fieldwork -- closely circumscribe site geography and geology. These documents match the conditions at just one sandstone outcrop. It is situated on the southern margin of a topographic nose at the upper end of a 18 m-wide gully (0663760 m E, 9183430 m N, UTM Zone 49M), 15 m southeast of the Kumai et al. (1985) relocation. The relocated discovery bed is 3.3 m of fossiliferous pebbly sandstone, a river-channel deposit cut into tuffaceous mudstone. The sandstone and mudstone beds correspond to original site descriptions. Pebbly sandstone is also found within the skull.

The calvaria is well-preserved and taphonomically similar to large and fragile specimens found among several hundred vertebrate fossils excavated from the sandstone in 2001-2002. Since no well-preserved fossils were found intact at the surface of the sandstone, the good condition of the Mojokerto skull suggests that it was buried fully when discovered. The relocated hominin bed is the uppermost fluvial sandstone of a marine-deltaic sequence in the upper Pucangan Formation. The Mojokerto child probably died along the ancient seacoast, judging from the large extent of the deltaic facies and evidence that the calvaria experienced minimal transport. The relocated discovery bed is 20 m stratigraphically above the horizon from which the widely cited 1.81 +- 0.04 Ma ⁴⁰Ar³⁹Ar date for the skull (Swisher et al., 1994, Science 263, 1118) was obtained. Additional field and laboratory results will be required to determine the skull's age.

The paper gives a good history of attempts to find the original excavation site. An interesting heterogeneity of the matrix fill inside the skull (assessed by CT) also factors in the story.

After a long discussion of the complexities in dating the site, they conclude:

In summary, additional field and analytical results are needed to date the Mojokerto fossil more exactly than latest Pliocene or early-mid Pleistocene in age. The 0.3 Ma difference between the ⁴⁰Ar/³⁹Ar and fission-track age determinations must be resolved. For any of these radioisotopic dates to be considered other than a maximum age, better evidence must be advanced to show that the dated material was erupted shortly before deposition at Perning. Additional paleontological and magnetostratigraphic control and radioisotopic dating would seem to be required. Geochronological conclusions have to be evaluated further in terms of the potential for temporal stratigraphic breaks in the section, rates of deposition, and the regional stratigraphic (including sequence stratigraphic) context.

I don't suppose there will ever be a very good date for the specimen. But it's impressive the amount of work there has been on it in the past several years.

References:

Huffman OF, Zaim Y, Kappelman J, Ruez DR Jr, de Vos J, Rizal Y, Aziz F, Hertler C. 2006. Relocation of the 1936 Mojokerto skull discovery site near Perning, East Java. J Hum Evol (in press). DOI

Swisher CC 3rd, Curtis GH, Jacob T, Getty AG, Suprijo A, Widiasmoro. 1994. Age of the earliest known hominids in Java, Indonesia. Science 263:1118-1121. PubMed