Saturday, February 17, 2007


Birth rate, competition are major players in hominid extinctions

Modern human mothers are probably happy that they typically have one, maybe two babies at a time, but for early hominids, low birth numbers combined with competition often spelled extinction.

"The lineages of primates have some traits that make it hard for them to respond to rapid perturbations in the environment," says Dr. Nina G. Jablonski [1], professor of anthropology and department head at Penn State. "Through time we see a lot of lineages become extinct when environments where the species are found become highly seasonal or unpredictable."

Primates evolved in the Paleocene and Eocene when worldwide climate was less seasonal. The beneficial environment allowed primates to evolve as relatively brainy animals that reproduce slowly. However, when climate changed so that tropical forests shrunk and the environment became patchy, many species including primate species became extinct.

"While past primate populations moved with the forest, early hominid cultures 2.5 million years ago show signs of the ability to live in marginal areas and live on more dynamic, seasonal landscapes," Jablonski told attendees on February 16 2007 at the annual meeting of the American Association for the Advancement of Science/AAAS in San Francisco.

Through time, the human lineage evolved to fill a wide variety of ecological niches, but those species that filled narrow environments, were less able to withstand the effects of climate change. Paranthropus boisei, a Pleistocene hominid, thrived around 2.5 million years ago, but disappears from the fossil record a million years ago. Paranthropus boisei became extinct when it was unable to compete with other mammals.

A specialized feeder, Paranthropus boisei dined on hard objects like seeds, tubers and bones. While it had a variety of food sources, they all required the crunching, grinding force of its teeth. Unfortunately, bush pigs and hyenas had great grinding and crushing teeth, too, and went after the same food. Paranthropus could not compete because it produced one offspring a year at most, while the others had large litters and could increase their populations at a much faster rate. Paranthropus simply could not compete reproductively and could not alter its choice of food.

"We find that the early members of the genus Homo who succeeded were super ecological opportunists," says Jablonski. "They would eat vegetation and scavenge, kill small animals and forage."

Cultural adaptations helped these opportunists to take advantage of whatever food was available. But culture did not seem to help the Neandertal (alt. Neanderthal). Tremendously successful from about 200 to 50 thousand years ago, they suffered a gradual decrease and extinction from about 30 to 26 thousand years ago.

"Neandertal was extremely adept culturally," says Jablonski. "They had big brains, a wide variety of tools and were extremely successful as active, aggressive hunters of large game. We see evidence of hunting, kill sites, butchery and even herding off cliffs. We find thrusting spears and butchering knives."

The Neandertal encountered increasing environmental seasonality with longer cold seasons and shorter periods of warm weather. Leading up to and during the last glacial maximum about 18,000 years ago, the grassy plains disappeared, taking with them the animals that relied on large expanses of grass for grazing. These animals were the prime food source for Neandertal.

At the same time, modern Homo sapiens experienced the same reduction in large animal game, but switched to also fishing, snaring small mammals like rabbits and capturing turtles and birds.

"Rather than being a specialized large mammal predator, modern humans would eat anything they could get their hands on. They eked out a living even if it meant eating grasshoppers or whatever," says Jablonski. "Even with this, modern humans barely hung on from 12 to 16,000 years ago.

"Why did Neandertal not adapt culturally?" she asks. "Why did they not start eating bunnies? They did begin fishing."

Jablonski believes that competition from modern humans was already too strong. The environment was marginal and modern humans were already foraging and small-animal collecting.

"I think they were out-competed at the very end," says Jablonski. "Modern humans simply did it better, more nimbly."

She adds that modern humans may have had storage capabilities that Neandertal did not. There is evidence that modern humans did have the capacity to store food and water in the late Pleistocene. No evidence exists that Neandertal could store either.

Both Neandertal and modern humans suffered from the primate curses of single births widely spaced. For Neandertal, cultural adaptation was not sufficient to overcome and compete with modern humans, just as Paranthropus boisei could not compete with the likes of bush pigs and hyenas.

" Can we, today, control our cultural behavior to ensure our environmental success,” says Jablonski. "Can we control growth and population density, or come up with new technology to overcome the problems we will face from the global climate change we have created?"

"We clearly have the cultural ability to do either," says the Penn State researcher. "But both require forethought and planning to face the demographic and climate change. A degree of honesty, our species is not known for." [Primatology]

Source: Penn State University PR Friday, February 16, 2007

[Neandertals, Neanderthals]


[1] A Conversation With Nina G. Jablonski
Always Revealing, Human Skin Is an Anthropologist's Map
Published January 9, 2007 in the International Herald Tribune and The New York Times

...QUESTION: You made news in 2004 when you discovered the world's oldest chimpanzee fossil [2]. These were chimp teeth about a half-million years old. Where did you find them?

JABLONSKI: In a drawer at the National Museum of Kenya in Nairobi.

I was rummaging through this bag labeled "fossil monkeys" and I saw it. "This doesn't look like monkey," I thought. It turned out they were from an early chimp. That find proved important because there had been no chimpanzee this old in the fossil record. By analyzing it, we've learned that chimpanzees in their current form have probably existed for longer than previously thought. (Laughs) Since my find, people have been rummaging through dusty museum drawers everywhere!


[2] First fossil chimpanzee
Sally McBrearty and Nina G. Jablonski

Nature 437, 105-108 (1 September 2005) | doi:10.1038/nature04008; Received 31 January 2005; ; Accepted 4 July 2005

There are thousands of fossils of hominins, but no fossil chimpanzee has yet been reported. The chimpanzee (Pan) is the closest living relative to humans. Chimpanzee populations today are confined to wooded West and central Africa, whereas most hominin fossil sites occur in the semi-arid East African Rift Valley. This situation has fuelled speculation regarding causes for the divergence of the human and chimpanzee lineages five to eight million years ago. Some investigators have invoked a shift from wooded to savannah vegetation in East Africa, driven by climate change, to explain the apparent separation between chimpanzee and human ancestral populations and the origin of the unique hominin locomotor adaptation, bipedalism. The Rift Valley itself functions as an obstacle to chimpanzee occupation in some scenarios. Here we report the first fossil chimpanzee. These fossils, from the Kapthurin Formation, Kenya, show that representatives of Pan were present in the East African Rift Valley during the Middle Pleistocene, where they were contemporary with an extinct species of Homo. Habitats suitable for both hominins and chimpanzees were clearly present there during this period, and the Rift Valley did not present an impenetrable barrier to chimpanzee occupation.


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Evidence of a Nonconscious Sibling Detection Mechanism (+ Podcast)

Fundamental theories in evolutionary biology have long proposed that biological kinship is the foundation of the family unit. It not only creates the sense of altruism that exists among genetically related family members, but also establishes boundaries regarding sexual relations within the nuclear family. Questions have persisted, however, regarding the means by which humans recognize family members - particularly siblings - as close genetic relatives.

A team of researchers at the University of California, Santa Barbara, has found evidence of a nonconscious mechanism in the human brain that identifies genetic siblings on the basis of cues that guided our hunter-gatherer ancestors. Their findings will be published in the February 15 2007 issue of the science journal Nature [1].

In a study involving more than 600 test subjects, the researchers found that people felt more altruistic toward individuals this mechanism recognized as siblings, and, at the same time, felt a greater aversion to engaging in incestuous sexual relations with them.

"The old thinking was that Darwinism applied to humans physically, but not socially. Now we see the evolution of a mechanism that finely regulates important aspects of human social behavior," said John Tooby, professor of anthropology and co-director of the Center for Evolutionary Psychology at UCSB. He completed the study with Leda Cosmides, professor of psychology and also co-director of the Center for Evolutionary Psychology, and Debra Lieberman, a former student at the center and now a professor of psychology at the University of Hawaii. Mechanisms such as the one identified in the current study have been found in many species, he added, but their existence in humans had been a matter of controversy.

According to the researchers, the development of altruism between siblings is a result of natural selection, as are their aversions to sexual relations with one another and their aversion to sexual relations among siblings in general. The study's findings indicate these sensibilities are not primarily a result of socialization by parents or peers, but of motivational systems that evolved to respond to cues of genetic relatedness.

The question the researchers sought to answer was how siblings recognize their close genetic matches. Drawing on the socioecology of ancestral human foragers they found the answer in a set of cues that enable humans to identify their brothers and sisters as siblings. For older siblings, what the researchers refer to as "maternal perinatal association" - seeing their mothers care for infant siblings - activates the mechanism in the brain, which, in turn, increases feelings of both altruism and sexual aversion toward younger brothers and sisters.

This cue, however, is unavailable to younger siblings whose birth order precludes the opportunity of watching their mothers care for older brothers and sisters. For these siblings, the mechanism is triggered by the amount of time they live together as a family during the period from the younger siblings' infancy through adolescence. The researchers found that this "co-residence" regulates sibling altruism and sexual aversion toward adopted and step-siblings as well - individuals whom the subjects consciously believe to be genetically unrelated. "This shows that the mechanism operates independently of our beliefs about kinship," Cosmides said. "The cues regulate sibling altruism and sexual aversion, no matter what we believe."

The discovery of a mechanism designed to make family relationships non-erotic casts doubt on Sigmund Freud's view that family members are the first and most powerful objects of sexual desire, say the authors. It also helps to settle a long-running debate in anthropology about whether family relationships are socially created purely by culture, or whether evolved mechanisms in the brain play a role.

The results of the study could also have implications for health care professionals such as psychiatrists and psychologists who treat victims of incest and those who commit it.

"The theory gives a means of identifying who might be at risk," said Tooby. "Siblings who have lived separately for long periods of time have not been exposed to the cues the brain uses to determine who is a sibling. This may offer an explanation as to why someone might have an inclination toward incest." It also suggests, he says, ways of building families that would be more strongly and reliably linked together by bonds of affection.

Source: University of California PR "UCSB Study on Sibling Detection Mechanism Highlighted in 'Nature'" February 15, 2007


[1] Based on:

The architecture of human kin detection
Debra Lieberman, John Tooby, and Leda Cosmides
Nature 445, 727-731 (15 February 2007) | doi:10.1038/nature05510; Received 22 July 2006; Accepted 5 December 2006

Evolved mechanisms for assessing genetic relatedness have been found in many species, but their existence in humans has been a matter of controversy. Here we report three converging lines of evidence, drawn from siblings, that support the hypothesis that kin detection mechanisms exist in humans. These operate by computing, for each familiar individual, a unitary regulatory variable (the kinship index) that corresponds to a pairwise estimate of genetic relatedness between self and other. The cues that the system uses were identified by quantitatively matching individual exposure to potential cues of relatedness to variation in three outputs relevant to the system's evolved functions: sibling altruism, aversion to personally engaging in sibling incest, and moral opposition to third party sibling incest. As predicted, the kin detection system uses two distinct, ancestrally valid cues to compute relatedness: the familiar other's perinatal association with the individual's biological mother, and duration of sibling coresidence.


John Tooby and Leda Cosmides are authors of "Evolutionary Psychology: A Primer"

Listen to related Nature podcast on "HIV's Achilles heel, probing protein regulation, avoiding incest (with Debra Lieberman), the soppy side of science, new diabetes genes, and the darkest galaxies in the universe."


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Friday, February 16, 2007


The Nature of 'Regressive Evolution' in Cavefish Untangled

"Regressive evolution," or the reduction of traits over time, is the result of either natural selection or genetic drift, according to a study on cavefish by researchers at New York University's Department of Biology, the University of California at Berkeley's Department of Integrative Biology, and the Harvard Medical School.

Previously, scientists could not determine which forces contributed to regressive evolution in cave-adapted species, and many doubt the role of natural selection in this process. Darwin himself, who famously questioned the role of natural selection in eye loss in cave fishes, said, "As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse."

A Blind Mexican Cave Tetra, along with its eyed surface relatives.

The research appears in the most recent issue of the journal Current Biology [A].

[Image: New York University]

Cave adaptations have evolved in many species independently, and each cave species can be considered a replicate of the same evolutionary experiment that asks how species change in perpetual darkness. This makes cavefish a rich source for the examination of the evolutionary process.

In this study, the researchers examined the genetic basis of regressive evolution in the eyes and pigmentation of Mexican cavefish. To do so, they mapped the quantitative trait loci (QTL) determining differences in eye and lens sizes as well as the melanophore - or pigment cell - number between cave and surface fish. These QTL represent genes where new mutations arose in cave populations. To better understand the genetic basis for regressive evolution, they focused on two alternative explanations for regression: natural selection, in which beneficial DNA mutations become more common over time, and genetic drift, in which the frequencies of these mutations can rise or fall over time due solely to statistical variation.

Their results suggested that eyes and pigmentation regressed through different mechanisms. Mutations in cave populations that affected eye or lens size invariably caused size reductions. This observation is consistent with evolution by natural selection and inconsistent with evolution by genetic drift. By contrast, mutations in cave populations that affected pigmentation sometimes caused increases instead of decreases in pigment cell density, consistent with evolution by random processes and genetic drift.

Allaying Darwin's doubts about the role of natural selection in eye loss, the researchers suggest that the high metabolic cost of maintaining the retina is the source of selection against eyes in the cave. By contrast, no such great cost is associated with pigmentation - thus, the two traits regress for different reasons.

Source: New York University Thursday, Feb 15, 2007 (N-280, 2006-07)


[A] Based on the Current Biology paper:

Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus

Meredith Protas, Melissa Conrad, Joshua B. Gross, Clifford Tabin, and Richard Borowsky
Current Biology

The evolutionary forces driving the reduction of eyes and pigmentation in cave-adapted animals are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes: "As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse" [1]. We studied the genetics of eye and pigmentation regression in the Mexican cave tetra, Astyanax mexicanus, by mapping and quantitative trait loci (QTL) analysis. We also mapped QTL for the putatively constructive traits of jaw size, tooth number, and numbers of taste buds. The data suggest that eyes and pigmentation regressed through different mechanisms. Cave alleles at every eye or lens QTL we detected caused size reductions, consistent with evolution by natural selection but not with drift. QTL polarities for melanophore number were mixed, however, consistent with genetic drift. Arguments against a role for selection in the regression of cave-fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment. Regression can be caused either by selection or drift.

[1] Darwin, Charles. (1859). On the Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life (London: John Murray).

[2] Culver, D.C. (1982). Cave Life: Evolution and Ecology (Cambridge, MA: Harvard University Press).

[3] Eigenmann, C.H. (1909). Cave Vertebrates of America: A Study in Degenerative Evolution (Washington, D.C.: Carnegie Institution of Washington).

See Richard Borowsky's webpage The Evolutionary Biology of Cave Fishes


Also see:

Embryonic Lens Prompts Eye Development
Elizabeth Pennisi
Science 28 July 2000: 522
DOI: 10.1126/science.289.5479.522b

A blind cave fish is providing new insight into how eyes come to be. In work reported on page 631 [B], two developmental biologists show that the lens plays a leading role in eye development in this fish. If it doesn't form properly, the researchers found, the embryo will not go on to make the cornea and other eye structures.

A copy of the above is available from

..The Maryland team has been studying the fish, which is called Astyanax mexicanus, for the past 6 years. Several dozen isolated populations of the species exist in northeastern Mexico, with some living in surface ponds and streams and others in caves and underground waterways. Over the past million years or so, the eyes of the underground fish have degenerated to varying degrees, while the surface fish have retained their large eyes.

To begin to understand this difference, Jeffery and Yamamoto first monitored eye development in the blind fish. They observed a precursor lens and the rudiments of the optic cup forming during the embryo's first 24 hours. But soon afterward, they found, the cells in the embryonic lens underwent programmed cell death. Other eye structures, such as the cornea and the iris, never appeared, and the retina never developed distinct, organized layers, as it does in normal eyes. The eyeball gradually sank back into the socket and was covered by a flap of skin.

Because eye development seemed to progress normally until the lens degenerated, Jeffery and Yamamoto wondered whether this disintegration was triggered by a signal from the embryo or from the lens itself. To find out, Yamamoto removed the embryonic lens from one eye of a blind cave fish embryo and replaced it with a lens from a surface fish embryo. He also did the opposite experiment, replacing the lens of an embryonic surface fish with one from a cave fish embryo. In all cases, he labeled the transplanted tissue with dye so he could track what happened to it. "It's not a complicated experiment, but it really [was] very elucidative," says Mathers.

In both types of transplants, the lens behaved as if it were still in its original embryo. The one from the cave fish degenerated, even though it was in an environment conducive to further development, whereas the lens from the surface fish thrived in the cave fish embryo and the eye differentiated, forming a cornea, anterior chamber, and iris. These results show that "the lens plays a central role" in determining whether the eye develops, comments David Beebe, a developmental biologist at Washington University School of Medicine in St. Louis. Jeffery doesn't know, however, whether the fish can actually see, as a vision test is quite difficult to devise..

[B] Related paper:

Central Role for the Lens in Cave Fish Eye Degeneration
Yoshiyuki Yamamoto, William R. Jeffery

Science 28 July 2000:
Vol. 289. no. 5479, pp. 631 - 633
DOI: 10.1126/science.289.5479.631

Astyanax mexicanus is a teleost with eyed surface-dwelling and eyeless cave-dwelling forms. Eye formation is initiated in cave fish embryos, but the eye subsequently arrests and degenerates. The surface fish lens stimulates growth and development after transplantation into the cave fish optic cup, restoring optic tissues lost during cave fish evolution. Conversely, eye growth and development are retarded following transplantation of a surface fish lens into a cave fish optic cup or lens extirpation. These results show that evolutionary changes in an inductive signal from the lens are involved in cave fish eye degeneration.


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Thursday, February 15, 2007


DNA method gives new perspective on the Mysteries of Nature

What caused the extinction of the mammoth [2] while other ice age mammals like the musk ox survived to present day? A new scientific methodological approach to detect genetic material will help researchers to solve the many mysteries of the past.

"I’m confident that the new methodological approach will be of great importance to molecular biology", says Professor Eske Willerslev at the Centre for Ancient Genetics, University of Copenhagen. One of his PhD students recently came up with a brilliant idea enabling researchers to get a full view of total ecosystems or populations dating thousands of years back in time. What usually has taken the DNA-researchers several years of laboratory work can now be done in just a few hours.

The automation of a long research process

Professor Eske Willerslev and his team find DNA traces of ancient life in areas where the ground is permanently frozen like in Siberia or Alaska. Here, inside the frozen ground, the team is able to find ancient DNA material from animals and plants that used to live in the area thousands of years ago. In order to detect the types of DNA material in a sample, the researchers normally use a DNA primer - a kind of 'fishing hook' attached to a specific piece of DNA. That particular piece of DNA is then being multiplied, cloned and sequenced (see "DNA Sequencing") which makes it possible for the researchers to identify it. However, this procedure is slow, and it takes years just to identify a fraction of the most common animals and plants available from the many DNA samples.

The technology

A new sequencing machine capable of interpreting millions of pieces of DNA in just a few hours was recently introduced. The machine alone brought in a revolution to the field, but has certain disadvantages and shortcomings. Firstly, an analysis made by the machine is quite expensive. Each analysis costs approximately DKK 45,000 and although the machine reads extensive amounts of DNA material, the cost is still considerable to a research project. Secondly, a vital problem arises when researchers try to benefit from the machine's enormous capacity by analysing samples from multiple locations or specimens in a single run in order to reduce costs. The machine simply cannot separate more than 16 samples from each other.

Eske Willerslev went to check out the machine for himself at the Danish Cattle Research Centre in Foulum - the only place in Denmark, which operates the new sequencing machine. He realised to his great disappointment that the researchers at the University of Copenhagen could not make use of the machine for their respective projects due to the disadvantages mentioned above.

A simple but brilliant idea!

Then Jonas Binladen, a PhD student from his team, came up with a simple but brilliant idea: By attaching a 'finger-print' to the tagged primers ('fishing hooks' used to amplify DNA from each sample), one should - in theory - be able to localise each of the million sequences produced in each run, to its original sample or specimen. By making it possible to process amplification products from multiple samples or specimens in the same run, the team could make use of the machine's great capacity.

The research team now wanted to test the idea. And it really did work! The results are now being published in the scientific web magazine PLoS ONE Publication [1].

According to Eske Willerslev, the new approach have great scientific potentials:

"Today, when using conventional methods to detect ancient DNA, we are only able to test a limited number of samples providing us with a somewhat random image of life in the past. Due to this new method, our knowledge will be put into a whole new perspective. For instance, finding out if species became endangered due to a dramatic change in the climate or if the decline in numbers started many years earlier than we originally thought or estimated".

Source: University of Copenhagen PR 15 February 2007


[1] Based on:

Binladen J, Gilbert MTP, Bollback JP, Panitz F,
Bendixen C, et al. (2007) The Use of Coded PCR Primers Enables
High-Throughput Sequencing of Multiple Homolog Amplification Products
by 454 Parallel Sequencing. PLoS ONE 2(2): e197.



The invention of the Genome Sequence 20TM DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.


We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20TM DNA Sequencing System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced back to its individual source through 5' tag-analysis.


We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate less than 0.4%). Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5' primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.


[2] Excerpt from "Supernova Explosion May Have Caused Mammoth Extinction"

A distant supernova that exploded 41,000 years ago may have led to the extinction of the mammoth, according to research conducted by nuclear scientist Richard Firestone of the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab).

Firestone, who collaborated with Arizona geologist Allen West on this study, unveiled this theory September 24, 2005 at the 2nd International Conference "The World of Elephants" in Hot Springs, South Dakota (see "Evidence of a Catastrophic Impact Event at the End of the Clovis Era"). Their theory joins the list of possible culprits responsible for the demise of mammoths, which last roamed North America roughly 13,000 years ago. Scientists have long eyed climate change, disease, or intensive hunting by humans as likely suspects.

Now, a supernova may join the lineup. Firestone and West believe that debris from a supernova explosion coalesced into low-density, comet-like objects that wreaked havoc on the solar system long ago. One such comet may have hit North America 13,000 years ago, unleashing a cataclysmic event that killed off the vast majority of mammoths and many other large North American mammals. They found evidence of this impact layer at several archaeological sites throughout North America where Clovis hunting artifacts and human-butchered mammoths have been unearthed. It has long been established that human activity ceased at these sites about 13,000 years ago, which is roughly the same time that mammoths disappeared.

They also found evidence of the supernova explosion's initial shockwave: 34,000-year-old mammoth tusks that are peppered with tiny impact craters apparently produced by iron-rich grains traveling at an estimated 10,000 kilometers per second. These grains may have been emitted from a supernova that exploded roughly 7,000 years earlier and about 250 light years from Earth.

"Our research indicates that a 10-kilometer-wide comet, which may have been composed from the remnants of a supernova explosion, could have hit North America 13,000 years ago," says Firestone. "This event was preceded by an intense blast of iron-rich grains that impacted the planet roughly 34,000 years ago."

Source: Berkeley Lab PR September 23, 2005


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Ancient Chimpanzee Tools fuel Evolutionary Debate (Video)

Researchers have found evidence that chimpanzees from West Africa were cracking nuts with stone tools before the advent of agriculture, thousands of years ago. The result suggests chimpanzees developed this behaviour on their own, or even that stone tool use was a trait inherited from our common ancestor.

Julio Mercader, Christophe Boesch and colleagues found the stones at the Noulo site in Cote d'Ivoire, the only known prehistoric chimpanzee settlement. The stones they excavated show the hallmarks of use as tools for smashing nuts when compared to ancient human or modern chimpanzee stone tools. Also, they found several types of starch grains on the stones; part of the residue derived from cracking local nuts.

The tools are 4300 years old, which, in human terms, corresponds to the Later Stone Age.

Image caption: Examples of some of the stones that were excavated. Analysis shows they were used by chimpanzees some 4,300 years ago to crack nuts. (Credit: University of Calgary)

Before this study [1], chimpanzees were first observed using stone tools in the 19th century. Now, thanks to this new archaeological find, tool use by chimpanzees has been pushed back thousands of years. The authors suggest this type of tool use could have originated with our common ancestor, instead of arising independently among hominins and chimpanzees or through imitation of humans by chimpanzees.

This study confirmed that chimpanzees and human ancestors share for thousands of years several cultural attributes once thought exclusive of humanity, including transport of raw materials across the landscape; selection and curation of raw materials for a specific type of work and projected usage; habitual reoccupation of sites where garbage and debris accumulate; and the use of locally available resources. Nut cracking behaviour in chimpanzees is transmitted socially, and the new discoveries presented in this study shows that such behaviour has been transmitted over the course of many chimpanzee generations. Chimpanzee prehistory has deep roots!

The study of our living closest relative, the chimpanzee, constantly highlights new aspects of human evolution, and a better protection of this endangered species will guarantee that we can continue uncovering new facets of our past. Relevant finds come from all parts of the African continent, including the rainforest, and not just the classical east African homeland.

Source: Max Planck Institute for Evolutionary Anthropology - "The Chimpanzee Stone Age" February 13th, 2007

[Primatology, Archaeology]


Video of chimpanzees using stone tools to crack nuts:


[1] Julio Mercader, Huw Barton, Jason Gillespie, Jack Harris, Steven Kuhn, Robert Tyler, and Christophe Boesch

4300-year-old chimpanzee sites and the origins of percussive stone technology.

Published online before print February 20, 2007
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0607909104

Archaeological research in the African rainforest reveals unexpected results in the search for the origins of hominoid technology. The ancient Panin sites from Cote d'Ivoire constitute the only evidence of prehistoric ape behavior known to date anywhere in the world. Recent archaeological work has yielded behaviorally modified stones, dated by chronometric means to 4,300 years of age, lodging starch residue suggestive of prehistoric dietary practices by ancient chimpanzees. The "Chimpanzee Stone Age" pre-dates the advent of settled farming villages in this part of the African rainforest and suggests that percussive material culture could have been inherited from an common human-chimpanzee clade, rather than invented by hominins, or have arisen by imitation, or resulted from independent technological convergence.

Also see:

Excavation of a Chimpanzee Stone Tool Site in the African Rainforest
Julio Mercader, Melissa Panger, Christophe Boesch

24 May 2002:
Vol. 296. no. 5572, pp. 1452 - 1455
DOI: 10.1126/science.1070268

Chimpanzees from the Tai forest of Cote d'Ivoire produce unintentional flaked stone assemblages at nut-cracking sites, leaving behind a record of tool use and plant consumption that is recoverable with archaeological methods. About 40 kilograms of nutshell and 4 kilograms of stone were excavated at the Panda 100 site. The data unearthed show that chimpanzees transported stones from outcrops and soils to focal points, where they used them as hammers to process foodstuff. The repeated use of activity areas led to refuse accumulation and site formation. The implications of these data for the interpretation of the earliest hominin archaeological record are explored.


Recent posts include:

"Anthropologist confirms 'Hobbit' a separate species (+ BBC Video)"

"Study revises understanding of primate origins"

"Humans and Chimps: Close But Not That Close.."

"What Makes Us Different? (TIME Magazine)"

"Evolution of primate gene expression (Nature Reviews Genetics)"

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Wednesday, February 14, 2007


Antibiotic Resistance - Evolution by Any Other Name

An open access article from PLoS Biology:

Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word

Citation: Antonovics J, Abbate JL, Baker CH, Daley D, Hood ME, et al. (2007) Evolution by Any Other Name: Antibiotic Resistance and Avoidance of the E-Word. PLoS Biol 5(2): e30 doi:10.1371/journal.pbio.0050030

Published February 13, 2007

The increase in resistance of human pathogens to antimicrobial agents is one of the best-documented examples of evolution in action at the present time, and because it has direct life-and-death consequences, it provides the strongest rationale for teaching evolutionary biology as a rigorous science in high school biology curricula, universities, and medical schools. In spite of the importance of antimicrobial resistance, we show that the actual word "evolution" is rarely used in the papers describing this research. Instead, antimicrobial resistance is said to "emerge," "arise," or "spread" rather than "evolve." Moreover, we show that the failure to use the word "evolution" by the scientific community may have a direct impact on the public perception of the importance of evolutionary biology in our everyday lives.

To establish whether the word "evolution" is used with different frequency by evolutionary biologists versus researchers in the medical fields, we searched scientific journals published since 2000 for research papers and reviews dealing with antimicrobial resistance. To find these papers, we used standard search engines and databases to identify papers with "antimicrobial resistance" or "antibiotic resistance" (or with names of specific antibiotics) in the titles or abstract. We deliberately did not include the word "evolution" in the searches, so as not to bias our findings in favor of articles with this word. However, we chose for further analysis only those articles that were obviously describing the evolution of antimicrobial resistance, and excluded those that described, for example, the biochemical basis of resistance or the pharmacology of antimicrobial agents. The articles were chosen in an unbiased manner by several readers who each independently read the first papers they found that met these criteria. We compared 15 articles that were primarily published in evolutionary journals (such as Evolution, Genetics, and Proceedings of the Royal Society of London Series B) with 15 articles that were published in primarily medical journals (such as The Lancet, The New England Journal of Medicine, and The Journal of Antimicrobial Chemotherapy). (A list of the papers and articles that are the basis of the results reported here is available in Text S1.)

Each reader then read the articles in their entirety. In each paper we explicitly noted and counted the words or phrases (see below) that were used to describe the evolutionary process, in order to obtain the proportion of times that the actual word "evolution" (or its lexemes such as "evolutionary" or "evolving") was used when reference was being made to the evolutionary process. Although we deliberately read equal numbers of articles in the two types of journals, we actually found that by far the majority of publications on the evolution of antibiotic resistance are in the medical field, and not in academic evolutionary biology or genetics journals. The evolution of antibiotic resistance, while critically important from a medical viewpoint, is no longer in and of itself a novel finding in evolutionary biology.

The results of our survey showed a huge disparity in word use between the evolutionary biology and biomedical research literature (Figure 1). In research reports in journals with primarily evolutionary or genetic content, the word "evolution" was used 65.8% of the time to describe evolutionary processes (range 10%-94%, mode 50%-60%, from a total of 632 phrases referring to evolution). However, in research reports in the biomedical literature, the word "evolution" was used only 2.7% of the time (range 0%-75%, mode 0%-10%, from a total of 292 phrases referring to evolution), a highly significant difference (chi-square, p less than 0.001). Indeed, whereas all the articles in the evolutionary genetics journals used the word "evolution," ten out of 15 of the articles in the biomedical literature failed to do so completely. Instead, 60.0% of the time antimicrobial resistance was described as "emerging," "spreading," or "increasing" (range 0%-86%, mode 30%-40%); in contrast, these words were used only 7.5% of the time in the evolutionary literature (range 0%-25%, mode 0%-10%). Other nontechnical words describing the evolutionary process included "develop," "acquire," "appear," "trend," "become common," "improve," and "arise." Inclusion of technical words relating to evolution (e.g., "selection," "differential fitness," "genetic change," or "adaptation") did not substantially alter the picture: in evolutionary journals, evolution-related words were used 79.1% of the time that there was an opportunity to use them (range 26%-98%, mode 50%-60%), whereas in biomedical journals they were used only 17.8% of the time (range 0%-92%, mode 0%-10%).

How the Evolutionary Process is described in Evolutionary Journals compared with Biomedical Journals

Figure 1. Frequency of Use of Words to Describe the Evolutionary Process in Evolutionary Journals versus Biomedical Journals

The left-hand pair of bars show percentage use of the word "evolution," and the right-hand pair of bars show percentage use of the words "emerge," "arise," or "increase." Data shown are unweighted means and standard errors, based on 15 papers in evolution or genetics journals and 15 papers in biomedical journals.

In spite of the disparity in word use, we found that the papers in the medical literature generally included professional and competent descriptions of evolutionary processes. At times words such as "develop" or "acquire" did creep in, but egregiously misleading phrases were relatively rare. For example, once we found the wording "bacteria had learned to resist antibiotics" and at another time "the activity of antimicrobial agents had decreased" (which, if read literally, implies that the antimicrobials themselves were changing rather than that the pathogens were evolving). But these were exceptions.

In reading these papers, we found no evidence that deliberate efforts were being made by medical researchers to deny that evolutionary processes were involved in the increase of antibiotic resistance. The frequent use of the term "emergence" rather than "evolution" seemed more to be the result of a simplified phraseology that has "emerged and spread" out of habit and repeated usage. It may also be that many nonprofessional evolutionary biologists consider "evolution" to be a rather nonspecific word meaning "gradual change," and that "emergence" more explicitly incorporates the component aspects of the evolutionary process, namely, mutation, recombination, and/or horizontal transfer of resistance. The word "spread" may, similarly, appear to incorporate the component processes of transmission, horizontal transfer, and increase in allele frequency. While these processes are recognized by professional evolutionary biologists as important aspects of evolutionary change, biomedical researchers may have the sense that the word "evolution" is itself too imprecise. Indeed, evolutionary biologists are sometimes accused of focusing too much attention on "change in gene frequency" rather than on the origin of variants by mutation and recombination, or on the consequences of changes in allele frequency for numerical abundance and distribution.

There is also the possibility that the failure to use the word "evolution" may reflect the mistaken sense that evolution implies processes that are long past, slow, and imperceptible. This is more worrying, as it fails to acknowledge the importance of evolution as a powerful force in present-day populations of all organisms, and not only microbes.

A critical question is whether avoidance of the word "evolution" has had an impact on the public perception of science. To investigate this, we examined whether the use of the term "evolution" in the scientific literature affects the use of this word in the popular press, i.e., whether there is evidence for "cultural inheritance" of word use. We searched articles on antimicrobial resistance in national media outlets, such as The New York Times, The Washington Post, Fox News, and the BBC (Text S1). Our results showed that the proportion of times the word "evolution" was used in a popular article was highly correlated with how often it was used in the original scientific paper to which the popular article referred (Figure 2). This clearly shows that the public is more likely to be exposed to the idea of evolution and its real-world consequences if the word "evolution" is also being used in the technical literature.

Comparing use of the word evolution in popular press articles about antimicrobial resistance with their corresponding research article.

Figure 2. Use of "Evolution" in Popular Articles Based on Research Papers

This graph shows the relationship between the frequency of use of the word "evolution" in popular press articles addressing antimicrobial resistance and the frequency of its use in the corresponding research article. Most of the articles included were in the biomedical literature (Text S1). The point at the origin represents nine pairs for which "evolution" was mentioned neither in the scientific nor in the popular version. The regression is highly significant (d.f. = 21, p less than 0.0001, beta = 0.76; weighted arcsine square root transformed; points and fitted line in figure represent untransformed data).

We wondered whether these patterns were changing, so we carried out a survey of the use of the word "evolution" from 1991 to 2005 in the titles and abstracts of papers published in 14 scientific journals, as well as in the titles of proposals funded by both the US National Science Foundation (Division of Environmental Biology) and the US National Institutes of Health (National Institute of General Medical Sciences). The results showed that the use of the word "evolution" was actually increasing in all fields of biology, with the greatest relative increases in the areas of general science and medicine (Figure 3). This reflects the growing importance of evolutionary concepts in the biomedical field, and highlights even more the strange rarity with which the word "evolution" is used in the biomedical literature dealing with antimicrobial resistance. It has been repeatedly rumored (and reiterated by one of the reviewers of this article) that both the National Institutes of Health and the National Science Foundation have in the past actively discouraged the use of the word "evolution" in titles or abstracts of proposals so as to avoid controversy. Indeed, we were told by one researcher that in the title of one proposal, the authors were urged to change the phrase "the evolution of sex" to the more arcanely eloquent wording "the advantage of bi-parental genomic recombination."

Use of the word Evolution in Scientific Journals changes over time (Evolution Research: John Latter / Jorolat)

Figure 3. Change over Time in the Frequency of Use of the Word "Evolution" in Journals and Grant Proposals

This figure shows change in the frequency of use of the word "evolution" in (A) paper titles and abstracts for journals classified by type and (B) titles of funded research proposals classified by US federal granting agency. Note that the data for general science journals and medical journals are shown at 10 and 100 times their values, respectively. Analysis of covariance (log of arcsine square root transformed data) showed that the rate of increase of use of the word "evolution" was significantly greater in the journal categories of general science and medical than in the evolutionary category (p less than 0.002). Journal classification was as follows: evolutionary journals: Evolution, Genetics, Heredity, Journal of Evolutionary Biology, Journal of Molecular Evolution, Molecular Biology and Evolution; general science journals: Nature, Nature Genetics, and Science; medical journals: BMJ, Clinical Infectious Diseases, JAMA, The Lancet, and The New England Journal of Medicine. Funding data are from the online data retrieval systems of the National Science Foundation (Division of Environmental Biology) (NSF [DEB]) and National Institutes of Health (National Institute of General Medical Sciences) (NIH [GMS]).

Nowadays, medical researchers are increasingly realizing that evolutionary processes are involved in immediate threats associated with not only antibiotic resistance but also emerging diseases [1,2]. The evolution of antimicrobial resistance has resulted in 2- to 3-fold increases in mortality of hospitalized patients, has increased the length of hospital stays, and has dramatically increased the costs of treatment [3,4]. It is doubtful that the theory of gravity (a force that can neither be seen nor touched, and for which physicists have no agreed upon explanation) would be so readily accepted by the public were it not for the fact that ignoring it can have lethal results. This brief survey shows that by explicitly using evolutionary terminology, biomedical researchers could greatly help convey to the layperson that evolution is not a topic to be innocuously relegated to the armchair confines of political or religious debate. Like gravity, evolution is an everyday process that directly impacts our health and well-being, and promoting rather than obscuring this fact should be an essential activity of all researchers.

Supporting Information

Text S1. Accessory Materials


We wish to thank Dr. Mark Courtney of the National Science Foundation for help with accessing and collating the word-use data for National Science Foundation grants.


1. Culotta E, Pennisi E (2005) Breakthrough of the year: Evolution in action. Science 310: 1878-1879.
2. Nesse RM, Stearns SC, Omenn GS (2006) Medicine needs evolution. Science 311: 1071.
3. Schwaber MJ, Navon-Venezia S, Kaye KS, Ben-Ami R, Schwartz D, et al. (2006) Clinical and economic impact of bacteremia with extended-spectrum-beta-lactamase-producing Enterobacteriaceae. Antimicrob Agents Chemother 50: 1257-1262.
4. Carmeli Y, Mozaffari E (2006) Health and economic outcomes of vancomycin-resistant enterococci. Arch Int Med 162: 2223-2228.


Recent posts include:

"Horizontal gene transfer adds to speed and complexity of evolution"

"How 'DNA parasites' can increase spread of antibiotic resistance"


Current related paper:

Nature Reviews Microbiology 5, 175-186 (March 2007) | doi:10.1038/nrmicro1614

The antibiotic resistome: the nexus of chemical and genetic diversity

Gerard D. Wright


Over the millennia, microorganisms have evolved evasion strategies to overcome a myriad of chemical and environmental challenges, including antimicrobial drugs. Even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Moreover, the potential problem of the widespread distribution of antibiotic resistant bacteria was recognized by scientists and healthcare specialists from the initial use of these drugs. Why is resistance inevitable and where does it come from? Understanding the molecular diversity that underlies resistance will inform our use of these drugs and guide efforts to develop new efficacious antibiotics.

See "The Microbial "Resistome""

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Tuesday, February 13, 2007


Intelligent Design - Fighting to keep Darwin in the classroom

New journal Outreach and Education in Evolution will arm educators for battle with creationists:

Nearly a century ago, John Scopes [1] was found guilty of violating a Tennessee statute when he taught evolution in his classroom. Though an appeals court later reversed his conviction on a technicality, the law lingered on the books, joined by later laws promoting "scientific creationism," and, most recently, "intelligent design." The battle to keep religiously based explanations of the history of life - especially human life - out of the science curriculum continues unabated. And though a number of educational institutions and organizations have had notable success in combating intelligent design in the classroom, what is needed now is a fresh source of evolution materials and anti-creationism ammunition for our school teachers on the front lines of this ongoing battle. Today, on Charles Darwin's 198th birthday, Springer announces plans for a new journal which will do just that.

A father-and-son team - a world-renowned evolutionary biologist and a highly skilled and sophisticated science high school teacher - have decided it's time to help science educators fight back against the strong pressure creationists are exerting on public education. In the new journal Outreach and Education in Evolution, to be published by Springer starting in March 2008, editors-in-chief Niles and Greg Eldredge intend to fill the gap between scientific literature and curriculum materials normally available to educators and students.

Niles Eldredge has been a paleontologist on the curatorial staff of the American Museum of Natural History (AMNH) since 1969. His theory of "punctuated equilibria" (co-authored with Stephen jay Gould - an SJG Official Archive is under development) is a milestone in contemporary evolutionary biology. He has combated the creationist movement through lectures, articles and books and is the curator responsible for the content of the major exhibition Darwin which opened at the AMNH in New York in November 2005, drawing in over 500,000 visitors. Greg Eldredge has a Masters Degree in Education and has been a New York City school teacher for the past three years. He is a co-author of the children's book The Fossil Factory. The two are supported by an international editorial board, made up of some of the most renowned scientists in the field.

Niles and Greg Eldredge are in agreement: "Evolution remains the central unifying idea in biology and yet is still a source of contention and confusion in the classroom. In Outreach and Education in Evolution, we'll cover the gamut, from molecules to ecosystems and from ‘intelligent design' to natural selection. We aim to make a big difference in evolutionary education."

Amelia McNamara, Vice President, Publishing, Life Sciences and Biomedicine at Springer, said, "Springer stands behind evolutionary theory as a fundamental component of modern science education, especially now since the 'intelligent design' advocates have made worrying attempts to promote their views in public schools. We are committed to helping educators teach Darwin's theory to students at all levels. Outreach and Education in Evolution will provide them with the tools they need."

Outreach and Education in Evolution, a traditional peer-reviewed journal with non-traditional features, will address these concerns. Each quarterly issue will feature peer-reviewed articles on evolution, "letters from the trenches," interviews with prominent scientists and educators, lesson plans, critical essays, cartoons, puzzles, reviews on evolution in the media (books, movies, museum openings and exhibitions) and more. The full-color online edition will offer added value, for example chat rooms, teaching resources and blogging opportunities. In addition, Springer has committed up to 10,000 US dollars annually in grants and prizes for the best paper, the best lesson plan, etc. The journal, aimed at members of the educational, museum, and scientific community involved in the teaching of evolutionary theory, will be available at a very affordable price.

Kathleen K. Smith, Director, National Evolutionary Synthesis Center, said, "As an official partner of Outreach and Education in Evolution, NESCENT is pleased to support this important endeavor. Focusing on the issues and challenges surrounding evolution education, it will provide a much needed resource for teachers presenting this important but often poorly understood subject. I believe that it will fill a valuable niche."

Douglas J. Futuyma, Distinguished Professor at Stony Brook University and President of the American Institute of Biological Sciences, added, "Increasing public understanding of science is of utmost importance. This is most urgently required with respect to evolution, which commands acceptance by less than half the American public. Springer's new journal is very timely and indeed well overdue. It is sure to play a major role in science education in the United States and beyond."

Telmo Pievani, Professor of Philosophy of Science at the University of Milan, Italy, said, "Outreach and Education in Evolution is absolutely opportune in its mission. It is much needed today for European audiences as well, where some conservative and religious leaders have grasped the political power of the tricky ideas of 'intelligent design.' For such a project, education is the main pathway."

Springer is the second-largest publisher worldwide in the science, technology, and medicine (STM) sector. Springer is part of Springer Science+Business Media, one of the world's leading suppliers of scientific and specialist literature. The group publishes over 1,700 journals and more than 5,500 new books a year, as well as the largest STM eBook Collection worldwide. Springer has operations in over 20 countries in Europe, the USA, and Asia, and some 5,000 employees.

The editors-in-chief, Niles Eldredge and Greg Eldredge, are available for interviews.

Source: Springer Press Release (Adapted) - "Fighting to keep Darwin in the classroom" Heidelberg/New York, 12 February 2007


[1] See Tennessee vs. John Scopes: The "Monkey Trial" 1925, The Butler Act, Film footage from the actual Trial, and the 2006 video Scopes Monkey Trial: Context for Controversy from Penn State.

From Clarence Seward Darrow's "The Story of my Life" (1932), Chapter 29, The Evolution Case:

In less than a year after the ending of the Loeb-Leopold case, a most uncommon series of events brought me into even wider notice than any that had happened before. I cannot say that in this case I had nothing to do with the immediate cause of all this publicity. For the first, the last, the only time in my life, I volunteered my services in a case; it was in the Scopes case in Tennessee that I did this, because I really wanted to take part in it.

...The little town of Dayton, Tennessee, had never been heard of very far away from home. A boy, twenty-one years old, had come from Kentucky and applied for a position as teacher in the high school. His name was John T. Scopes. And he was destined to be famous. He was a modest, studious, conscientious lad. His father was a locomotive engineer and formerly a member of the American Railway Union. For his membership in this organization he had been placed on the blacklist, and after the strike he went to Kentucky to look for a job. He was a man of courage and independence, and brought up his family to have their own opinions and to stand by them.

John was a good teacher. He had the respect of the whole town of Dayton and the affection of his pupils. Among other subjects, he taught biology; the work furnished as a textbook was "Hunter's Biology." It seems strange that the Dayton school board did not adopt the first and second chapters of Genesis as a modern textbook on biology. Anyhow, Scopes told the little boys and girls that the origin of life was in the slime and ooze of the sea; that life developed from a germ, and gradually grew and changed until it reached the various forms of the life of to-day.

For this he was indicted for the crime of teaching the truth. John T. Scopes was not the first man indicted for this most heinous offense. So far as I know, he was the last, up to the present time...

[Source: Project Gutenberg of Australia]


'Inherit the Wind' (Spencer Tracy) Creationism v Evolution film/video excerpt (9 mins) - "That rock is not more than 6,000 years old":


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