Saturday, November 18, 2006


Regeneration: Scientist regrow chicken wing

Chop off a salamander's leg and a brand new one will sprout in no time. But most animals have lost the ability to replace missing limbs. Now, a research team at the Salk Institute for Biological Studies has been able to regenerate a wing in a chick embryo - a species not known to be able to regrow limbs - suggesting that the potential for such regeneration exists innately in all vertebrates, including humans.

Their study, published in the advance online edition of the journal Genes and Development on November 17, demonstrates that vertebrate regeneration is under the control of the powerful Wnt signaling system: Activating it overcomes the mysterious barrier to regeneration in animals like chicks that can't normally replace missing limbs while inactivating it in animals known to be able to regenerate their limbs (frogs, zebrafish, and salamanders) shuts down their ability to replace missing legs and tails.

'In this simple experiment, we removed part of the chick embryo's wing, activated Wnt signaling, and got the whole limb back - a beautiful and perfect wing,' said the lead author, Juan Carlos Izpisua Belmonte (homepage), Ph.D., a professor in the Gene Expression Laboratory. 'By changing the expression of a few genes, you can change the ability of a vertebrate to regenerate their limbs, rebuilding blood vessels, bone, muscles, and skin - everything that is needed.'

This new discovery 'opens up an entirely new area of research,' Belmonte says. 'Even though certain animals have lost their ability to regenerate limbs during evolution, conserved genetic machinery may still be present, and can be put to work again,' he said.

Continued at "Regeneration: Scientist regrow chicken wing" [Wingless, Science]

Based on the Genes and Development paper "Wnt/beta-catenin signaling regulates vertebrate limb regeneration":

The cellular and molecular bases allowing tissue regeneration are not well understood. By performing gain- and loss-of-function experiments of specific members of the Wnt pathway during appendage regeneration, we demonstrate that this pathway is not only necessary for regeneration to occur, but it is also able to promote regeneration in axolotl, Xenopus, and zebrafish. Furthermore, we show that changes in the spatiotemporal distribution of beta-catenin in the developing chick embryo elicit apical ectodermal ridge and limb regeneration in an organism previously thought not to regenerate. Our studies may provide valuable insights toward a better understanding of adult tissue regeneration.

Also see "Birds that make teeth (Press Release + Summary)":

Gone does not necessarily mean forgotten, especially in biology. A recent finding by researchers at the University of Wisconsin, Madison, and colleagues from the University of Manchester have found new evidence that the ability to form previously lost organs - in this case, teeth - can be maintained millions of years after the last known ancestor possessed them.

Books on Evolution from the Science and Evolution Bookshop: UK | US

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Intelligent Design Defended by Unsolved Genetic Puzzle

McLean, Virginia. - A distinguished Christian professor of science and religion defended Intelligent Design by presenting an unsolved genetic puzzle on Thursday during a three-day apologetics conference at McLean Bible Church.

Dr. Paul Nelson (info), a Biola (Note 1) professor and apologist, approached the heavily debated theory of Intelligent Design from a biological angle. He set out on an intense 45-minute session entitled "Intelligent Design in Three Easy Steps" to argue that science supports the idea that an intelligent being designed the universe.

...For most of the evening, Nelson used specific examples of genes, enzymes, proteins, and cells with a focus on ORFan (open reading frame) genes, which are sequences of DNA that codes for protein.

Nelson looked at a pattern in biology that pointed strongly to design and challenged Darwin’s theory of common descent. Darwin said that if there were systems in nature that could not be arrived at by some gradual means or process then his theory could be reasonably doubted; the evolution theory requires gradual steps in biological developments.

To challenge Darwin's theory of evolution and defend I.D., Nelson focused on the growing discovery of new ORFan genes that are not in the GenBank database.

Full article at "Intelligent Design Defended by Unsolved Genetic Puzzle"

Paul Nelson co-authored "Homology:
A Concept in Crisis
" with Jonathan Wells (Note 2):

Before Darwin, homology was defined morphologically and explained by reference to ideal archetypes -- that is, to intelligent design. Darwin reformulated biology in naturalistic* rather than teleological terms, and explained homology as the result of descent with modification from a common ancestor. Descent with modification, however, renders design unnecessary only if it is due entirely to naturalistic mechanisms. Two such mechanisms have been proposed, genetic programs and developmental pathways, but neither one fits the evidence. Without an empirically demonstrated naturalistic mechanism to account for homology, design remains a possibility which can only be excluded on the basis of questionable philosophical assumptions.

*In this article, "naturalism" and "naturalistic" refer to the philosophical doctrine that nature is the whole of reality, and that intelligent causation does not qualify as a scientific explanation.

Featured Book: "Three Views on Creation and Evolution (Counterpoints: Exploring Theology" by Paul Nelson, Robert C. Newman, Howard J. Van Till (Amazon UK | US)

Note 1: Biola University is a private Christian university founded in 1908 and located in Southern California.

Note 2: See an earlier post "'The Politically Incorrect Guide to Darwinism and Intelligent Design': Scientist Exposes Evolution's Weaknesses" (Amazon UK | US)

Books on Creationism from the Science and Evolution Bookshop: UK | US

Books on Intelligent Design from the Science and Evolution Bookshop: UK | US

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Homosexuality: Gay animals come out of the closet?

From male killer whales that ride the dorsal fin of another male to female bonobos that rub their genitals together, the animal kingdom tolerates all kinds of lifestyles.

A first-ever museum display, 'Against Nature?,' which opened last month at the University of Oslo's Natural History Museum in Norway, presents 51 species of animals exhibiting homosexuality.

'Homosexuality has been observed in more than 1,500 species, and the phenomenon has been well described for 500 of them,' said Petter Bockman, project coordinator of the exhibition.

Continued at "Homosexuality: Gay animals out of the closet?"

An earlier post on this topic follows:

From The Economist (UK), Saturday, October 28, 2006: Norway - What is taught in a country's schools reveals much about the national psyche. The Norwegian curriculum requires that all 14-year-olds learn about homosexuality. Assisting with this education, the Natural History Museum at the University of Oslo has just opened an exhibition of gay animals.

"Against Nature?" (5 webpages) does not tell zoologists anything new. Homosexuality has been recorded in some 1,500 species so far, and been well documented in about a third of these cases; it has been known since the time of Aristotle, who thought he witnessed two male hyenas having sex with one another. But the exhibition's purpose is not to educate zoologists. It is to persuade the public that, as there are gay whales and worms, gay humans do not disturb the natural order. [Homosexual, Lifestyle]

Books on Evolution and Homosexuality from the Science and Evolution Bookshop: UK | US

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Friday, November 17, 2006


Does Natural Selection Drive The Evolution Of Cancer?

The dynamics of evolution are fully in play within the environment of a tumor (tumour), just as they are in forests and meadows, oceans and streams. This is the view of researchers in an emerging cross-disciplinary field that brings the thinking of ecologists and evolutionary biologists to bear on cancer biology.

Insights from their work may have profound implications for understanding why current cancer therapies often fail and how radically new therapies might be devised.

A review by researchers at The Wistar Institute of current research in this new field, published online November 16, will appear in the December issue of the journal Nature Reviews Cancer.

Continued at "Does Natural Selection Drive The Evolution Of Cancer?" [Therapy]

Based on the Nature Reviews Cancer paper "Cancer as an evolutionary and ecological process" by Carlo C. Maley (homepage) et. al


Neoplasms are microcosms of evolution. Within a neoplasm, a mosaic of mutant cells compete for space and resources, evade predation by the immune system and can even cooperate to disperse and colonize new organs. The evolution of neoplastic cells explains both why we get cancer and why it has been so difficult to cure. The tools of evolutionary biology and ecology are providing new insights into neoplastic progression and the clinical control of cancer.

Featured Books "Cancer: The Evolutionary Legacy" By M.F. Greaves (Amazon UK | US)

And "Evolution of Cancer" by Shinichi Okuyama, Hitoshi Mishina (Amazon UK | US)

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Emotion influences learning, memory - and evolution

From the Daily Princetonian*: Emotion shapes nearly every aspect of human activity - from learning to memory to decision-making - and even influences evolution, University of Southern California neuroscience professor Antonio Damasio (homepage) said in a lecture in McCosh 50 Thursday night.

'Emotion, whichever way you look at it ... is involved in homeostasis,' he said, and 'the business of running our life.'

Damasio's talk focused on the processes involved in triggering and experiencing emotions and feelings.

Though Sigmund Freud and William James investigated the science of emotion more than 100 years ago, such research had largely been abandoned by the turn of the 20th century, he said.

In the past 10 years, however, significant progress has been made in identifying what Damasio termed the 'body loop' theory of emotion production.

Continued at "Emotion influences learning,memory - and evolution"

Opening paragraph of Damasio's 2001 Nature paper "Fundamental feelings":

The groundwork for the science of emotion was laid down most auspiciously over a century ago, but neuroscience has given the problem a resolute cold shoulder until recently. By the time that Charles Darwin had remarked on the continuity of emotional phenomena from non-human species to humans; William James had proposed an insightful mechanism for its production; Sigmund Freud had noted the central role of emotions in psychopathological states; and Charles Sherrington had begun the physiological investigation of the neural circuits involved in emotion, one might have expected neuroscience to be poised for an all-out attack on the problem. It is not usually appreciated that the probable cause of the neglect of the topic was the improper distinction between the concepts of emotion and feelings.

Featured Book: "Descartes' Error: Emotion, Reason and the Human Brain" (Amazon UK | US)

Books on 'Social and Emotional Intelligence' from the Science and Evolution Bookshop: UK | US

See "Daniel Goleman's 'Social Intelligence': Is it More Useful than IQ? (Audio)"

*The Daily Princetonian, nicknamed the 'Prince,' was the second college newspaper in America to publish daily. The paper, founded in 1876 as a biweekly publication named The Princetonian, became The Daily Princetonian in 1892 when it became a daily newspaper.

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Videos of bizarre life around deep-sea gas vents

From the associated post "Voyage reveals bizarre life around deep-sea gas seeps (Video)":

"An international team led by scientists from the United States and New Zealand have observed, for the first time, the bizarre deep-sea communities living around methane seeps off New Zealand's east coast.":

A recent post on extremophile life "Bacteria using radiated water for food live two miles down":

Researchers have discovered an isolated, self-sustaining, bacterial community living under extreme conditions almost two miles deep beneath the surface in a South African gold mine. It is the first microbial community demonstrated to be exclusively dependent on geologically produced sulfur and hydrogen and one of the few ecosystems found on Earth that does not depend on energy from the Sun in any way. The discovery, appearing in the October 20 issue of the journal Science, raises the possibility that similar bacteria could live beneath the surface of other worlds, such as Mars or Jupiter's moon Europa.

"These bacteria are truly unique, in the purest sense of the word," said lead author Li-Hung Lin (homepage), now at National Taiwan University, who performed many of the analyses as a doctoral student at Princeton and as a postdoctoral researcher at the Carnegie Institution's Geophysical Laboratory. [More]

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Evolution's 'Driving Force' Shifts Based on Behavior, Study Says

From National Geographic News: Brown anole lizards on tiny islands in the Bahamas were enjoying the good life, untroubled by a lizard predator found on larger islands nearby.

But all that changed when biologist Jonathan Losos of Harvard University in Cambridge, Massachusetts, appeared on the scene.

Losos's team experimentally introduced predatory curly-tail lizards onto six islands where the ground-dwelling anoles had been living free of predators, sparking a see-saw year of natural selection.

For the smaller anole lizards, a trait that was advantageous in November - six months after the introduction - had become a liability by May.

...The evolutionary experiment, reported in tomorrow's issue of the journal Science, reveals that, even though evolution can seem like a slow process, its driving force - natural selection - can shift like the wind.

...The study also supports a somewhat controversial idea in biology: Animals' behavior in response to environmental change can spur evolutionary adaptations.

"In most cases in evolutionary biology, you have to look back and speculate what might have happened," Cameron Ghalambor said.

"[Losos's study] captures the changes as they occur. We're getting a window into what is actually happening in the very early stages of evolutionary change."

The new perspective may help biologists better understand evolution in the lizard genus Anolis, which contains about 400 species including the brown anole.

A number of Anolis species are tree-dwellers with small hind limbs.

Losos says that at least some of this diversity may be the result of a process similar to the one his team observed.


Based on the Science paper:

Rapid Temporal Reversal in Predator-Driven Natural Selection

Jonathan B. Losos, Thomas W. Schoener, R. Brian Langerhans, David A. Spiller

Science 17 November 2006:
Vol. 314. no. 5802, p. 1111
DOI: 10.1126/science.1133584

As the environment changes, will species be able to adapt? By conducting experiments in natural environments, biologists can study how evolutionary processes such as natural selection operate through time. We predicted that the introduction of a terrestrial predator would first select for longer-legged lizards, which are faster, but as the lizards shifted onto high twigs to avoid the predator, selection would reverse toward favoring the shorter-legged individuals better able to locomote there. Our experimental studies on 12 islets confirmed these predictions within a single generation, thus demonstrating the rapidity with which evolutionary forces can change during times of environmental flux.

Read Jonathan Losos' paper "Adaptation and speciation in Greater Antillean anoles" (Open Access/Free)

Opening paragraph

This section first reviews the evidence that both speciation and adaptation played important roles in anole diversification, focusing primarily on the anoles of the Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico). It then addresses the extent to which the two processes are intimately linked. The theory of adaptive speciation presents one mechanism by which the two processes might occur in an integrated fashion, but there are other possibilities. In part this requires a discussion of what constitutes a species of Anolis, so that it is possible to recognize when two lineages have diverged to the level of different species. Finally, this section addresses some exciting new developments that affect our understanding of the processes important in anole adaptive radiation.


Featured Book "Anolis Lizards of the Caribbean: Ecology, Evolution and Plate Tectonics" (Amazon UK | US)

Books on 'Diversity and Evolution' from the Science and Evolution Bookshop: UK | US

See "Model of an Internal Evolutionary Mechanism" (Draft)

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Thursday, November 16, 2006


Selecting life: Scientists find new way to search for origin of life

Washington, D.C. - Over the last half century, researchers have found that mineral surfaces may have played critical roles organizing, or activating, molecules that would become essential ingredients to all life--such as amino acids (the building blocks of proteins) and nucleic acids (the essence of DNA). But which of the countless possible combinations of biomolecules and mineral surfaces were key to this evolution? This vexing question has stumped scientists for years because of the sheer volume of possibilities. Now an interdisciplinary team of researchers led by Robert Hazen (homepage), of the Carnegie Institution's Geophysical Laboratory and former president of the Mineralogical Society of America, has developed new protocols and procedures for adapting DNA microarray technology to rapidly identify promising molecule/mineral pairs.

Hazen's Presidential Address in the November/December issue of American Mineralogist describes this work. It sets out a first-of-its-kind comprehensive survey into research that has identified processes by which minerals may have prompted the transition from a geochemical world to a biological one almost four billion years ago.

Continued at "Selecting life: Scientists find new way to search for origin of life"

Based on "Mineral surfaces and the prebiotic selection and organization of biomolecules" (Abstract available under 'Presidential Address' - 2nd entry in the left-hand column).

Books on the Origin of Life from the Science and Evolution Bookshop: UK | US

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The Mars Phoenix Lander: Piercing Together Life's Potential

Carol Stoker, a planetary scientist at NASA's Ames Research Center, is a team member for the upcoming Phoenix Lander (website). This mission, launching in 2007, aims to land in the high northern latitudes of Mars to search for frozen water and any indications of past habitable conditions. In this interview with Astrobiology Magazine's Leslie Mullen, Stoker describes what Phoenix can expect to find when it lands on the northern plains of Mars, and why astrobiologists have high hopes for finding the signs of life there.

Astrobiology Magazine (AM): You've outlined three things that any place on Mars would need to be considered habitable: liquid water, an energy source, and the chemical building blocks of life.

Carol Stoker (CS) : That strategy for assessing the habitability of a site was laid out by MEPAG: the Mars Exploration and Payload Analysis Group. They've developed a program for the exploration of Mars over the next decade, and they appointed a committee to devise a strategy for the astrobiology field laboratory. That's the mission after Mars Science Laboratory which is supposed to try to detect life. The committee recommended how to pick a landing site for that mission, and also what are the precursor things that need to be done before you can fly a mission to look for life..."

Continued at "The Mars Phoenix Lander: Piercing Together Life's Potential"


Mission Overview from NASA:

Launch: August, 2007
Arrival: May 25, 2008


The Phoenix mission is the first chosen for NASA's Scout program, an initiative for smaller, lower-cost, competed spacecraft. Named for the resilient mythological bird, Phoenix uses a lander that was intended for use by 2001's Mars Surveyor lander prior to its cancellation. It also carries a complex suite of instruments that are improved variations of those that flew on the lost Mars Polar Lander.

In the continuing pursuit of water on Mars, the poles are a good place to probe, as water ice is found there. Phoenix will land on the icy northern pole of Mars between 65 and 75-north latitude. During the course of the 150 Martian day mission, Phoenix will deploy its robotic arm and dig trenches up to half a meter (1.6 feet) into the layers of water ice. These layers, thought to be affected by seasonal climate changes, could contain organic compounds that are necessary for life.

To analyze soil samples collected by the robotic arm, Phoenix will carry an "oven" and a "portable laboratory." Selected samples will be heated to release volatiles that can be examined for their chemical composition and other characteristics.

Imaging technology inherited from both the Pathfinder and Mars Exploration Rover missions will also be implemented in Phoenix's stereo camera, located on its 2-meter (6.6-foot) mast. The camera's two "eyes" will reveal a high-resolution perspective of the landing site's geology, and will also provide range maps that will enable the team to choose ideal digging locations. Multi-spectral capability will enable the identification of local minerals.

To update our understanding of martian atmospheric processes, Phoenix will also scan the martian atmosphere up to 20 kilometers (12.4 miles) in altitude, obtaining data about the formation, duration and movement of clouds, fog, and dust plumes. It will also carry temperature and pressure sensors.


Other posts include:

"Earth-like planets may be more common than once thought"


Books on Astrobiology from the Science and Evolution Bookshop: UK | US

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Wednesday, November 15, 2006


Research News: Neanderthal Genome Sequencing Yields Surprising Results

The veil of mystery surrounding our extinct hominid cousins, the Neanderthals, has been at least partially lifted to reveal surprising results. Scientists with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and the Joint Genome Institute (JGI) have sequenced genomic DNA from fossilized Neanderthal bones. Their results show that the genomes of modern humans and Neanderthals are at least 99.5-percent identical, but despite this genetic similarity, and despite the two species having cohabitated the same geographic region for thousands of years, there is no evidence of any significant crossbreeding between the two. Based on these early results, Homo sapiens and Homo neanderthalensis last shared a common ancestor approximately 700,000 years ago.

In a paper [1] published in the November 17, 2006 issue of the journal Science, a team of researchers led by Edward Rubin, director of both JGI and Berkeley Lab's Genomics Division, reports the development of a "Neanderthal metagenomic library," which they used to characterize more than 65,000 DNA base pairs of Neanderthal origin. Their results not only provide new information about Neanderthals, but also point the way to a new strategy for studying aspects of Neanderthal biology that would never be evident from archaeological artifacts and fossils.

In addition, the technology described in the paper also marks an important advance in the field of metagenomics, which is increasingly being used to sequence the complex mixtures of microbes found in the environment. Metagenomics techniques are considered crucial for tapping the potential of Earth's more exotic microbe-containing environments to find bio-based solutions to problems of renewable energy production, environmental clean-up, and carbon sequestration, as well as breakthroughs in critical areas such as pharmaceuticals and agriculture.

"The current state of our knowledge concerning Neanderthals and their relationship to modern humans is largely inference and speculation based on archaeological data and a limited number of hominid remains," the authors state in their Science paper. "In this study, we have demonstrated that Neanderthal genomic sequences can be recovered using a metagenomic library-based approach, and that specific Neanderthal sequences can be obtained from such libraries."

The title of the Science paper is Sequencing and analysis of Neanderthal genomic DNA. Co-authoring the paper with Rubin were James Noonan, Graham Coop, Sridhar Kudaravalli, Doug Smith, Johannes Krause, Joe Alessi, Feng Chen, Darren Platt, Svante Paabo and Jonathan Pritchard.

Said Rubin, "We predict that in the near future anthropologists will be able to develop hypotheses about our extinct ancestors through the scanning of billions of base pairs of DNA sequences available on the web rather than only being able to study the limited number of bony remains and associated artifacts that are available in hard to access museum collections and field sites. Plus, the new techniques we have developed will have useful applications across a range of genomics efforts related to DOE's energy and environment missions"

In the summer of 1856, a partial skeleton of a hominid was found at the Feldhofer Cave in the Neander Valley of Germany. This skeleton would eventually be dubbed the "Neanderthal" man and its discovery generated enormous public curiosity and scientific debate that have continued for the past 150 years.

Starting around 1997, scientists began applying genetic technology to the study of Neanderthals. Research led by Svante Paabo, currently of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, established that Neanderthals were cousins rather than ancestors of modern humans. This research also indicated that humans and Neanderthals broke off into separate species about 500,000 years ago. However, these studies were based on analysis of mitochondrial DNA (mtDNA), genetic material that lies outside the nucleus of the cell. Although mtDNA tends to remain preserved longer than nuclear DNA, it provides limited biological information. The vast majority of the genome is comprised of nuclear DNA, which contains almost all of the genes.

"Nuclear DNA is where all the biology is," said Noonan, a post-doctoral fellow in Rubin's research group who holds joint appointments with Berkeley Lab and JGI. "If you want to understand how traits like language and cognition are encoded, you have to study nuclear DNA."

Studying ancient genomes from fossilized material by directly sequencing the DNA, as has been done for the genomes of humans and other contemporary organisms, represents a major challenge. As a fossil ages, its DNA is degraded by chemical processes. It also becomes contaminated with DNA from the microbes that colonize both the fossil and its immediate environment, and by other organisms, including the humans who handle the fossil.

While a group led by co-author Paabo is attempting to directly sequence the Neanderthal genome, Rubin, Noonan and their colleagues are meeting the fossilized DNA challenge with a unique solution that's been described as a "targeted approach." Essentially, they "immortalize" all of the DNA in a fossil sample into metagenomic libraries where individual fragments of the ancient DNA are propagated in microbes. The DNA propagated in the microbes can either be sequenced or specific sequences can in a targeted manner be specifically fished out of the library and studied.

Said Noonan, "Since direct sequencing is random, you can't go after specific sequences for genes that might be different between humans and Neanderthals. Instead you have to wait for the sequences to show up in the reads, which could take a long time. Also, with direct sequencing, once the DNA has been sequenced, it's gone, and you have to go get more from the specimen. In principle, employing the targeted library approach we are able to circumvent this and other problems. Once the Neanderthal DNA is cloned using our method, we have it forever, and we can recover specific sequences from the library whenever they are needed."

Since the findings reported in this Science paper suggest that only about 0.5-percent of Neanderthal genome differs from the human genome, focusing scientific attention on those sequences promises to be more efficient and cost-effective than trying to directly sequence the entire Neanderthal genome. Also, the metagenomic library approach enables scientists to obtain specific sequences from multiple Neanderthal specimens precisely and without having to generate lots of random sequences.

For the results reported in their Science paper, Rubin and Noonan and their colleagues extracted all the DNA in the femur bone of a 38,000-year-old male Neanderthal specimen from Vindija, Croatia. Using a combination of the sequencing technologies deployed in the Human Genome Project, plus a new massively parallel pyrosequencing technology, in which enormous amounts of DNA sequence is rapidly and inexpensively generated, they were able to recover 65,250 base pairs of Neanderthal DNA from the approximately 6 million base pairs of contaminating DNA in the fossil. A critical factor in helping to confirm that the recovered DNA was Neanderthal rather than human was the short length of the individual Neanderthal sequences.

Said Rubin, "We determined that the ancient DNA fragments from Neanderthal in the sample were about 50 to 70 base pairs in length, compared to the hundreds to thousands of base pair lengths of contemporary human DNA that could have contaminated the fossil. This makes sense because modern human DNA wouldn't have suffered the 38,000 years of insults that the Neanderthal DNA experienced."

Comparing Neanderthal to human and chimpanzee genomes showed that at multiple locations the Neanderthal DNA sequences matched chimpanzee DNA but not human.

"This enabled us to calculate for the first time when in pre-history Homo sapiens and Homo neanderthalensis coalesced to a single genome," Rubin said.

Comparative genomics in this study indicated that the common genetic ancestor of Neanderthal and modern humans lived about 706,000 years ago. The ancestors of all humans and Neanderthals split into two separate species some 330,000 years later. Rubin and his colleagues were also able to shed new light on the long-standing question of whether Neanderthals and humans mated during the thousands of years the two species cohabitated parts of Europe. Some scientists have suggested that rather than die out, Neanderthals as a species were bred out of existence by the overwhelming populations of Homo sapiens.

Said Rubin, "While unable to definitively conclude that interbreeding between the two species of humans did not occur, analysis of the nuclear DNA from the Neanderthal suggests the low likelihood of it having occurred at any appreciable level."

With their metagenomic library-based approach to genome sequencing and analysis, Rubin and Noonan believe that in the future, scientists will be able to study specific sequences within the Neanderthal genome to determine the genetic changes that distinguished modern humans from our Neanderthal cousins. Among other advantages, this might help answer the most persistent mystery of all: Why did Neanderthals become extinct?

In addition, said Rubin, "Reaching into the Neanderthal genome library will facilitate future sequence-based scientific explorations of Neanderthal biological features, features that could never be explored based on the few bones and associated stone artifacts that are left for anthropologists to identify."

Co-authors Smith, Alessi, Chen and Platt are affiliated with the JGI. Co-authors Pritchard, Coop and Kudaravalli are affiliated with the Department of Human Genetics at the University of Chicago. Co-author Krause is a member of Pääbo's research group at the Max Planck Institute for Evolutionary Anthropology.

This research was supported by Berkeley Lab and funded in part by grants from the National Institutes of Health. The U.S. Department of Energy provides operational support for the JGI user facility.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California.

Source: Berkeley Lab PR "Neanderthal Genome Sequencing Yields Surprising Results and Opens a New Door to Future Studies" November 15 2006 [Archaeology]


[1] Based on the paper:

Sequencing and Analysis of Neanderthal Genomic DNA

James P. Noonan, Graham Coop, Sridhar Kudaravalli, Doug Smith, Johannes Krause, Joe Alessi, Feng Chen, Darren Platt, Svante Paabo, Jonathan K. Pritchard, Edward M. Rubin

Science 17 November 2006:
Vol. 314. no. 5802, pp. 1113 - 1118
DOI: 10.1126/science.1131412

Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approx 706,000 years ago, and that the human and Neanderthal ancestral populations split approx 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.


Related posts include:

"Scientists say Climate Change caused Neanderthal extinction in Iberia"

"Did Interbreeding Between Humans and Neanderthals Lead to a Bigger Human Brain?"

"Skull suggests human-Neanderthal link"

"Earliest Evidence Of Modern Humans In Europe Discovered By International Team"

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Science vs Religion: Richard Dawkins (New Scientist Podcast + Videos)

From the New Scientist, 10th November 2006: "Evolutionary biologist Richard Dawkins (The God Delusion: Amazon UK | US) is among the participants at a special meeting to discuss whether science and religion can coexist. We bring you exclusive coverage, plus an investigative report on the rise of religious home schooling in the US."

Click on the title link to listen to the podcast. [Webcast/Audio]

Recent media posts featuring Richard Dawkins include both episodes of Channel 4's two-part UK television series "The Root of All Evil?".

"How is it, asks Richard Dawkins, that despite science having exposed old religious myths, militant faith is back on the march? The mechanism for perpetuating beliefs that Dawkins describes as leading to murderous intolerance, is by imposing religion on children who are too inexperienced to judge it for themselves.

We wouldn't categorise children according to their parents' political stance, says Dawkins, since they are too young to make up their minds about such matters. But we segregate them in sectarian religious schools, where they are taught superstitions drawn from ancient scriptures of dubious origin, which promote a 'contradictory and poisonous system of morals'." [Video]

Episode 1: The God Delusion

Episode 2: The Virus of Faith

The book 'The God Delusion' is currently available from Amazon (UK | US) with a discount of up to 50%

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There are numerous book reviews of The God Delusion - use the "Search this Blog" function (top left) either on this blog or, better still, the blog containing the Root of All Evil? videos.

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Tuesday, November 14, 2006


Scientists Explore Function of 'Junk DNA'

University of Iowa scientists have made a discovery that broadens understanding of a rapidly developing area of biology known as functional genomics and sheds more light on the mysterious, so-called 'junk DNA' that makes up the majority of the human genome.

The team, led by Beverly Davidson (homepage), Ph.D., a Roy J. Carver Biomedical Research Chair in Internal Medicine and UI professor of internal medicine, physiology and biophysics, and neurology, have discovered a new mechanism for the expression of microRNAs - short segments of RNA that do not give rise to a protein, but do play a role in regulating protein production. In their study, Davidson and colleagues not only discovered that microRNAs could be expressed in a different way than previously known, they also found that some of the junk DNA is not junk at all, but instead consists of sequences that can generate microRNAs.

Davidson and her colleagues, including Glen Borchert, a graduate student in her lab, investigated how a set of microRNAs in the human genome is turned on, or expressed. In contrast to original assertions, they discovered that the molecular machinery used to express these microRNAs is different than that used to express RNA that encodes proteins. Expression of the microRNAs required an enzyme called RNA Polymerase III (Pol III) rather than the RNA Polymerase II (Pol II), which mediates expression of RNA that encode proteins. The study is published in Nature Structural and Molecular Biology Advance Online Publication on November 12.

Continued at "Scientists Explore Function of 'Junk DNA'"

Based on "RNA polymerase III transcribes human microRNAs" (Abstract - Advance Publication url; 'final' url will be here)

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Mother's Diet during Pregnancy can affect Grandchildren (Epigenetics)

A new study by scientists at Children's Hospital Oakland Research Institute (CHORI) is the first to show that a mother's diet during pregnancy influences the health of her grandchildren by changing the behavior of a specific gene. The study was conducted using mice of an unique strain called 'viable yellow agouti' also known as A-vy in scientific terms. These mice possesss a gene that influences the color of their coats as well as their tendency to become obese and develop diabetes and cancer. The new research shows that the diet consumed by a pregnant Avy mouse affects the health of not only her pups, but also their pups - her grandchildren.

The study was published in the November issue of the Proceedings of the National Academy of Sciences (PNAS) and was conducted by CHORI Scientist David Martin, M.D., and Assistant Scientist Kenneth Beckman, Ph.D., in collaboration with Drs. Jennifer Cropley and Catherine Suter from the Victor Chang Heart Institute in Sydney, Australia. In their experiments, the scientists fed some Avy mice a standard lab diet based on common foods consumed by humans. Other mice were fed this same diet supplemented with common nutritional supplements including folate, choline, betaine, vitamin B12, zinc and methionine.

The supplements were fed to the mice for a week during mid-pregnancy. The offspring were examined for their coat color, and female offspring were themselves mated again (without a supplemented diet) to produce a third generation of 'grandchildren.' The results showed that the supplements changed the behavior of the agouti gene in the first generation of pups, shifting their coats towards a brown color, and had the same effect on pups born in the next generation to mice that were not exposed to the supplemented diet.

"Although researchers have long known that there is a connection between a mother's diet and her children's health this is the first case in which the relationship between a mother's diet and the biology of her grandchildren has been mapped to a single gene and a defined diet," said David Martin, M.D., Scientist at CHORI. "Our work provides convincing evidence of complex transgenerational effects of nutrition on health, and provides an experimental model for exploring these relationships in detail."

Avy mice are an excellent system for study because all mice of this strain are genetically identical - as similar to each other as identical twins. However, mouse pups from a single litter differ from each other in their coat color (from yellow to brown), obesity (thinner to fatter), and susceptibility to cancer, and all of these varied traits can be traced back to the Avy version of the agouti gene. The mouse model also suggests that similar things can happen in humans, since our gene characteristics are very similar.

Although this study does not provide any prescriptive advice, it does offer significant evidence that health outcomes may be strongly influenced at the time of birth. "Our study highlights a layer of complexity about human development that needs to be thoroughly investigated," said Kenneth Beckman, Ph.D. Assistant Scientist at CHORI and a member of the Project EXPORT Center of Excellence in Nutritional Genomics, a PROGRAM PROJECT funded by the National Center on Minority Health and Health Disparities. "We found that even when we stopped providing specific supplements during pregnancy, the past effect of supplements persisted. Therefore, it is possible that the maternal diet could have implications that stretch over decades, perhaps even centuries."

Source (Adapted): Children's Hospital Oakland Research Institute PR November 13, 2006 [Evolution, Science, Epigenetics]


Based on the PNAS paper:

Germ-line epigenetic modification of the murine A-vy allele by nutritional supplementation

Jennifer E. Cropley, Catherine M. Suter, Kenneth B. Beckman, and David I. K. Martin

PNAS | November 14, 2006 | vol. 103 | no. 46 | 17308-17312


Environmental effects on phenotype can be mediated by epigenetic modifications. The epigenetic state of the murine Avy allele is highly variable, and determines phenotypic effects that vary in a mosaic spectrum that can be shifted by in utero exposure to methyl donor supplementation. We have asked if methyl donor supplementation affects the germ-line epigenetic state of the Avy allele. We find that the somatic epigenetic state of Avy is affected by in utero methyl donor supplementation only when the allele is paternally contributed. Exposure to methyl donor supplementation during midgestation shifts Avy phenotypes not only in the mice exposed as fetuses, but in their offspring. This finding indicates that methyl donors can change the epigenetic state of the Avy allele in the germ-line, and that the altered state is retained through the epigenetic resetting that takes place in gametogenesis and embryogenesis. Thus a mother's diet may have an enduring influence on succeeding generations, independent of later changes in diet. Although other reports have suggested such heritable epigenetic changes, this study demonstrates that a specific mammalian gene can be subjected to germ-line epigenetic change.

See "Cardiovascular and diabetes mortality determined by nutrition" (very relevant - don't be misled by the title!)

And "New theory of environmental inheritance ('05 Press Release)"

And "Epigenetics: Parentage has effects outside the genome"

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Epigenetic books from the Science and Evolution Bookshop: UK | US

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Monday, November 13, 2006


Sperm proteome gives 'tantalising glimpse' towards the origin of sex

University of Bath (UK) Press Release: The first ever catalogue of the different types of proteins found in sperm could help reveal the origins of sex and explain some of the mysteries of infertility, say scientists.

Research published in the journal Nature Genetics today describes 381 proteins present in sperm of the fruit fly, Drosophila melanogaster. Whilst more proteins may be identified as research progresses, this study marks the first substantial 'whole-cell' characterisation of the protein components of a higher eukaryotic cell (a cell in which all the genetic components are contained within a nucleus).

This so-called 'proteome' contains everything the sperm needs to survive and function correctly, and scientists can use it to investigate the factors that make some sperm more successful than others.

Around half of the genes of the fruit fly sperm proteome have comparable versions in humans and mice, making it a useful model for studying male infertility in mammals.

By comparing the sperm proteome of the fruit fly with other species, scientists will also be able to rewind evolution and work out the core sperm proteome - the most basic constituents a sperm needs for sexual reproduction. This will shed light on how sex itself evolved.

Continued at "Sperm proteome gives 'tantalising glimpse' towards the origin of sex"

Based on the paper "Genomic and functional evolution of the Drosophila melanogaster sperm proteome" (Abstract advance publication url; 'final' DOI url) by Timothy L Karr (homepage) et. al

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