Saturday, December 09, 2006


Is there a homosexuality gene?

Although biologists are still far from answering this question, scattered evidence for a possible gene influencing sexual orientation has recently encouraged scientists to map out a guide to future research. Because many possibilities for such a gene exist, scientists Sergey Gavrilets (homepage) and William Rice (homepage) have recently developed some theoretical guidelines and testable predictions for explaining the evolutionary causes of homosexuality.

"During the 1990s there was a short surge of interest by a small number of labs in finding major genes that might mediate homosexuality," Rice told "However, for a variety of reasons, this effort waned by the turn of the century. I think that - when studying humans - many people shy away from studying sexual phenotypes in general and homosexuality in particular. Much of Sergey's and my motivation in writing our paper was to rekindle an interest in studying the genetic basis of homosexuality. I personally think that if a firm genetic foundation for homosexuality in humans were established, then many people would view this fascinating human phenotype more objectively."

During the past several decades, scientists have discovered some interesting patterns that may point toward genetic causes of homosexuality. Among the findings is that male homosexuality appears to be inherited more often from the mother than the father (Pillard). Also, natural selection might maintain a gene that may decrease the fecundity of one sex because the same gene also increases the fecundity of the other sex. In fact, recent data shows that female maternal relatives of gay men have higher than average reproduction capacity (Camperio-Ciani*). [Evolution]

Continued at "Is there a homosexuality gene?"

Based on "Genetic models of homosexuality: generating testable predictions" Proceedings of the Royal Society London B 273: 3031-3038


Homosexuality is a common occurrence in humans and other species, yet its genetic and evolutionary basis is poorly understood. Here, we formulate and study a series of simple mathematical models for the purpose of predicting empirical patterns that can be used to determine the form of selection that leads to polymorphism of genes influencing homosexuality. Specifically, we develop theory to make contrasting predictions about the genetic characteristics of genes influencing homosexuality including: (i) chromosomal location, (ii) dominance among segregating alleles and (iii) effect sizes that distinguish between the two major models for their polymorphism: the overdominance and sexual antagonism models. We conclude that the measurement of the genetic characteristics of quantitative trait loci (QTLs) found in genomic screens for genes influencing homosexuality can be highly informative in resolving the form of natural selection maintaining their polymorphism.

Full Text (PDF)

* Re Camperio-Ciani - See "Mother's genetics could influence sexual orientation" by Michael Hopkin (Nature reporter, London):

October 12, 2004
Genes could increase male homosexuality while boosting female reproduction.

A survey of Italian men has provided evidence that homosexuality may be partly influenced by genetics. The same genes that are proposed to predispose to homosexuality may also boost reproduction in women, solving the apparent paradox of why these genes have not been removed by natural selection.

By quizzing around 200 men of different sexual orientations, researchers at the University of Padua have discovered that maternal relatives of homosexual men tend to produce more offspring than those of heterosexuals. This suggests that the mothers and maternal aunts of homosexuals have a genetic advantage - but one that reduces reproduction when passed to male offspring.

"For a long time it has been a paradox," says Andrea Camperio-Ciani (homepage), who led the study. "But we have found that there might be a set of genes that, in males, influences homosexuality but in females increases fecundity." (Continued at above link).

An earlier post "Homosexuality: Gay animals come out of the closet?"

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Finding an answer to Darwin's Dilemma

The sudden appearance of large animal fossils more than 500 million years ago - a problem that perplexed even Charles Darwin and is commonly known as 'Darwin's Dilemma' - may be due to a huge increase of oxygen in the world's oceans, says Queen's University (Canada) paleontologist Guy Narbonne (homepage), an expert in the early evolution of animals and their ecosystems.

In 2002, Dr. Narbonne and his research team found the world's oldest complex life forms between layers of sandstone on the southeastern coast of Newfoundland. This pushed back the age of Earth's earliest known complex life to more than 575 million years ago, soon after the melting of the massive 'snowball' glaciers. New findings reported today shed light on why, after three billion years of mostly single-celled evolution, these large animals suddenly appeared in the fossil record.

In a paper published on-line in Science Express, Dr. Narbonne's team argues that a huge increase in oxygen following the Gaskiers Glaciation 580 million years ago corresponds with the first appearance of large animal fossils on the Avalon Peninsula in Newfoundland.

Now for the first time, geochemical studies have determined the oxygen levels in the world's oceans at the time these sediments accumulated in Avalon. 'Our studies show that the oldest sediments on the Avalon Peninsula, which completely lack animal fossils, were deposited during a time when there was little or no free oxygen in the world's oceans,' says Dr. Narbonne. 'Immediately after this ice age there is evidence for a huge increase in atmospheric oxygen to at least 15 per cent of modern levels, and these sediments also contain evidence of the oldest large animal fossils.'

Continued at "Finding an answer to Darwin's Dilemma"

Based on "Late-Neoproterozoic Deep-Ocean Oxygenation and the Rise of Animal Life"
Don E. Canfield, Simon W. Poulton , Guy M. Narbonne


Animals have an absolute requirement for oxygen, and an increase in late Neoproterozoic oxygen concentrations has been forwarded as a stimulus for their evolution. The iron content of deep-sea sediments show that the deep ocean was anoxic and ferruginous before and during the Gaskiers glaciation 580 million years ago, becoming oxic afterward. The first known members of the Ediacara biota are found shortly after the Gaskiers glaciation, suggesting a causal link between their evolution and this oxygenation event. A prolonged stable oxic environment may have permitted the emergence of bilateral motile animals some 25 million years later.

(The original press release from Queen's University says "PLEASE NOTE: A PDF of the research findings published today in Science Express is available upon request." - A contact email address is given on the Abstract page)

Also see the open access June 2000 PNAS paper "Solution to Darwin's dilemma: Discovery of the missing Precambrian record of life" by J. William Schopf:


In 1859, in On the Origin of Species, Darwin broached what he regarded to be the most vexing problem facing his theory of evolution - the lack of a rich fossil record predating the rise of shelly invertebrates that marks the beginning of the Cambrian Period of geologic time (approx 550 million years ago), an "inexplicable" absence that could be "truly urged as a valid argument" against his all embracing synthesis. For more than 100 years, the "missing Precambrian history of life" stood out as one of the greatest unsolved mysteries in natural science. But in recent decades, understanding of life's history has changed markedly as the documented fossil record has been extended seven-fold to some 3,500 million years ago, an age more than three-quarters that of the planet itself. This long-sought solution to Darwin's dilemma was set in motion by a small vanguard of workers who blazed the trail in the 1950s and 1960s, just as their course was charted by a few pioneering pathfinders of the previous century, a history of bold pronouncements, dashed dreams, search, and final discovery.

And yesterday's post "Geologists Provide New Evidence for Reason Behind Rise of Life in Cambrian Period":

"Geologists have uncovered evidence in the oil fields of Oman that explains how Earth could suddenly have changed 540 million years ago to favor the evolution of the single-celled life forms to the multicellular forms we know today.

Reporting in the December 7 issue of the journal Nature, researchers from MIT, the California Institute of Technology, and Indiana University show that there was a sudden change in the oxygenation of the world's oceans at the time just before the 'Cambrian explosion,'* one of the most significant adaptative radiations in the history of life. With a increased availability of oxygen, the team speculates, single-celled life forms that had dominated the planet for the previous three billion years were able to evolve into the diverse metazoan phyla that still characterize life on Earth..."

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Friday, December 08, 2006


The Future Evolution of Consciousness

Cogprints - The Future Evolution of Consciousness by John Stewart of the "Evolution, Complextity, and Cognition Group"* (ECCO) at the Free University of Brussels:


What potential exists for improvements in the functioning of consciousness? The paper addresses this issue using global workspace theory. According to this model, the prime function of consciousness is to develop novel adaptive responses. Consciousness does this by putting together new combinations of knowledge, skills and other disparate resources that are recruited from throughout the brain. The paper's search for potential improvements in the functioning of consciousness draws on studies of the shift during human development from the use of implicit knowledge to the use of explicit (declarative) knowledge. These studies show that the ability of consciousness to adapt a particular domain improves significantly as the transition to the use of declarative knowledge occurs in that domain. However, this potential for consciousness to enhance adaptability has not yet been realised to any extent in relation to consciousness itself. The paper assesses the potential for adaptability to be improved by the conscious adaptation of key processes that constitute consciousness. A number of sources (including the practices of religious and contemplative traditions) are drawn on to investigate how this potential might be realised.

Continued at "The Future Evolution of Consciousness" (pdf file)

'About ECCO':

"ECCO, the Evolution, Complexity and COgnition group, is a transdisciplinary research group, situated at the Free University of Brussels (VUB), and directed by Francis Heylighen. While founded under the present name only in 2004, our unofficial history goes back many years. Our members come from a wide variety of backgrounds, from physical science and technology to the social sciences and humanities.

Our research focuses on the evolution of organization:

* how does a collection of initially autonomous, but interacting, agents self-organize?
* how does it evolve to an increasingly cooperative, adaptive and intelligent system, able to tackle problems too complex for individual agents?

Examples include the emergence of life from molecules, of multicellular organisms from cells, of the mind from neurons, and of languages, culture, markets and institutions from individuals."

ECCO also publishes The Journal of Memetics-Evolutionary Models of Information Transmission (JoM-EMIT) which is an international, peer-refereed, (open access) scientific journal:

"In the words of of its inventor, Richard Dawkins, the word "meme" refers to "a unit of cultural transmission, or a unit of imitation". More precisely, a meme can be defined as an information pattern, held in an individual's memory or in an outside artefact (e.g. book, record or tool), which is likely to be communicated or copied to another individual's memory. Examples of memes are ideas, technologies, theories, songs, fashions, and traditions. This covers all forms of beliefs, values and behaviors that are normally taken over from others rather than discovered independently.

Memetics is the theoretical and empirical science that studies the replication, spread and evolution of memes. It core idea is that memes differ in their degree of "fitness", i.e. adaptation to the socio-cultural environment in which they propagate. Because of natural selection, fitter memes will be more successful in being communicated, "infecting" a larger number of individuals and/or surviving for a longer time within the population. Memetics tries to understand what characterizes fit memes, and how they affect individuals, organizations, cultures and society at large."

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Geologists Provide New Evidence for Reason Behind Rise of Life in Cambrian Period

Geologists have uncovered evidence in the oil fields of Oman that explains how Earth could suddenly have changed 540 million years ago to favor the evolution of the single-celled life forms to the multicellular forms we know today.

Reporting in the December 7 issue of the journal Nature, researchers from MIT, the California Institute of Technology, and Indiana University show that there was a sudden change in the oxygenation of the world's oceans at the time just before the 'Cambrian explosion,'* one of the most significant adaptative radiations in the history of life. With a increased availability of oxygen, the team speculates, single-celled life forms that had dominated the planet for the previous three billion years were able to evolve into the diverse metazoan phyla that still characterize life on Earth.

'The presence of oxygen on Earth is the best indicator of life,' says coauthor John Grotzinger (homepage), the Fletcher Jones Professor of Geology at Caltech and an authority on sedimentary geology. 'But it wasn't always that way. The history of oxygen begins about two and a half billion years ago and occurs in a series of steps. The last step is the subject of this paper.'

The key insight was derived when Grotzinger's student Dave Fike, who is lead author of the paper, analyzed core samples and drillings taken at a depth of about three kilometers from oil wells in Oman, which are known to have the oldest commercially viable oil on the planet. The results of carbon and sulfur isotopic analyses from the material led the team to the conclusion that the oceanic conditions that laid down the deposits originally in Oman were quite different from conditions of today.

Continued at "Geologists Provide New Evidence for Reason Behind Rise of Life in Cambrian Period" (Fossils)

Based on the Letter to Nature "Oxidation of the Ediacaran Ocean"

First Paragraph (Full text is also currently available via this link)

Oxygenation of the Earth's surface is increasingly thought to have occurred in two steps. The first step, which occurred approx 2,300 million years (Myr) ago, involved a significant increase in atmospheric oxygen concentrations and oxygenation of the surface ocean. A further increase in atmospheric oxygen appears to have taken place during the late Neoproterozoic period (approx 800 - 542 Myr ago). This increase may have stimulated the evolution of macroscopic multicellular animals and the subsequent radiation of calcified invertebrates and may have led to oxygenation of the deep ocean. However, the nature and timing of Neoproterozoic oxidation remain uncertain. Here we present high-resolution carbon isotope and sulphur isotope records from the Huqf Supergroup, Sultanate of Oman, that cover most of the Ediacaran period (approx 635 to approx 548 Myr ago). These records indicate that the ocean became increasingly oxygenated after the end of the Marinoan glaciation, and they allow us to identify three distinct stages of oxidation. When considered in the context of other records from this period our data indicate that certain groups of eukaryotic organisms appeared and diversified during the second and third stages of oxygenation. The second stage corresponds with the Shuram excursion in the carbon isotope record and seems to have involved the oxidation of a large reservoir of organic carbon suspended in the deep ocean, indicating that this event may have had a key role in the evolution of eukaryotic organisms. Our data thus provide new insights into the oxygenation of the Ediacaran ocean and the stepwise restructuring of the carbon and sulphur cycles that occurred during this significant period of Earth's history.

* Info on the Cambrian Explosion:

"The Cambrian explosion of species refers to the geologically sudden appearance in the fossil record of the ancestors of familiar animals, starting about 542 million years ago (Mya). In addition, a similar pattern of diversification is seen in other organisms such as phytoplankton and the various colonial calcareous micro-fossils grouped together as calcimicrobes. The base of the Cambrian is also marked by strong geochemical perturbations, including excursions in carbon and sulfur isotopes." (Continued here)

Books on Fossils and the Cambrian Period (inc. The Burgess Shale) from the Science and Evolution Bookshop: UK | US

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Thursday, December 07, 2006


Scientists say Global Warming is reducing ocean life and increasing atmospheric carbon dioxide

Santa Barbara, California: - Alarming new satellite data show that the warming of the world's oceans is reducing ocean life while contributing to increased global warming.

The ocean's food chain is based upon the growth of billions upon billions of microscopic plants. New satellite data show that ocean warming is reducing these plants - thus imperiling ocean fisheries and marine life, according to an article in the November 7 issue of the scientific journal Nature.

"We show on a global scale that the growth of these plants, called phytoplankton, is strongly tied to changes in the warming of the ocean," said David Siegel (homepage), co-author and professor of marine science in the Department of Geography at the University of California, Santa Barbara. Siegel is also director of the Institute for Computational Earth System Science (ICESS).

"Phytoplankton grow faster in a cool ocean and slower in a warm one," said Siegel. "The scary part is that the oceans are warming now - probably caused by our emissions of greenhouse gases like carbon dioxide."

These microscopic plants are predicted to grow even slower in the warmer oceans of the future. This in turn will reduce the food available to fish and other organisms, including marine birds and mammals, which are supported by the ocean’s food chain. Phytoplankton are responsible for about the same amount of photosynthesis each year as all the plants on land combined.

Continued at "Scientists say Global Warming is reducing ocean life and increasing atmospheric carbon dioxide"

Based on the Letter to Nature "Climate-driven trends in contemporary ocean productivity":

First Paragraph (Full text is also currently available from this link):

Contributing roughly half of the biosphere's net primary production (NPP), photosynthesis by oceanic phytoplankton is a vital link in the cycling of carbon between living and inorganic stocks. Each day, more than a hundred million tons of carbon in the form of CO2 are fixed into organic material by these ubiquitous, microscopic plants of the upper ocean, and each day a similar amount of organic carbon is transferred into marine ecosystems by sinking and grazing. The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron). These growth-limiting factors are in turn regulated by physical processes of ocean circulation, mixed-layer dynamics, upwelling, atmospheric dust deposition, and the solar cycle. Satellite measurements of ocean colour provide a means of quantifying ocean productivity on a global scale and linking its variability to environmental factors. Here we describe global ocean NPP changes detected from space over the past decade. The period is dominated by an initial increase in NPP of 1,930 teragrams of carbon a year (Tg C yr-1), followed by a prolonged decrease averaging 190 Tg C yr-1. These trends are driven by changes occurring in the expansive stratified low-latitude oceans and are tightly coupled to coincident climate variability. This link between the physical environment and ocean biology functions through changes in upper-ocean temperature and stratification, which influence the availability of nutrients for phytoplankton growth. The observed reductions in ocean productivity during the recent post-1999 warming period provide insight on how future climate change can alter marine food webs.

A recent post: "The Weather Makers - NSW's 'Book of the Year' (Review, Excerpt, Audio)"

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Home and away: Bat uses magnetic compass for long flights

Scientists believe a species of bat has an inbuilt magnetic compass to find its way home over long distances, in addition to its famous echolocation*, which guides it around its neighbourhood.

Princeton University batologists used radio telemetry aboard a small aircraft to track big brown bats (Eptesicus fuscus - info) that were released 20 kilometers (12 miles) north of their home.

They first tested a 'control' group of bats, which headed due south towards the roost without a problem.

Two other groups of bats were then exposed to a false magnetic field for 90 minutes, comprising 45 minutes before and 45 minutes after sunset.

One field was 90 degrees clockwise and the other was 90 degrees anticlockwise from magnetic north.

The point of this was to see whether the bats used Earth's magnetic field as a guide and, if so, to see whether the bats used sunset or the stars as an additional cue.

The 'clockwise' group of bats flew due east, while the 'anticlockwise' group went due west, suggesting that they had been using a magnetic compass that may have been calibrated by the sunset.

Continued at "Home and away: Bat uses magnetic compass for long flights"

Based on the journal Nature paper "Navigation: Bat orientation using Earth's magnetic field"


Bats famously orientate at night by echolocation, but this works over only a short range, and little is known about how they navigate over longer distances. Here we show that the homing behaviour of Eptesicus fuscus, known as the big brown bat, can be altered by artificially shifting the Earth's magnetic field, indicating that these bats rely on a magnetic compass to return to their home roost. This finding adds to the impressive array of sensory abilities possessed by this animal for navigation in the dark.

*From the Michigan Museum of Zoology:

Bat Echolocation:
Bats can see as well as humans can, but they have evolved a sophisticated method of using sound that enables them to navigate and find food in the dark called echolocation. Bats produce echolocation by emitting high frequency sound pulses through their mouth or nose and listening to the echo. With this echo, the bat can determine the size, shape and texture of objects in its environment. Bat echolocation is so sophisticated that these animals can detect an object the width of a human hair.

Shouting Bats & Whispering Bats
Bats can be broadly characterized by their echolocation calls as shouting bats and whispering bats. Big brown bats and little brown bats are shouters and produce sounds (if we could hear them) of 110 decibels or similar to the loudness of a smoke alarm. Northern long-eared bats are whispering bats and produce sounds of 60 decibels (similar to the levels of normal human conversation). Shouters tend to forage for food in open spaces; whisperers glean insects from the foliage of trees and forage in the cluttered environments of forest interiors.

Not All Bats Echolocate
About 70% of all bat species worldwide have this ability. Also, bats aren't the only animals that use echolocation. Whales, dolphins, porpoises, oilbirds and several species of shrews, tenrecs, and swiftlets use a similar technique. [More]

And an open access/free paper from the Proceedings of the National Academy of Sciences (PNAS):

"Integrated fossil and molecular data reconstruct bat echolocation"

Molecular and morphological data have important roles in illuminating evolutionary history. DNA data often yield well resolved phylogenies for living taxa, but are generally unattainable for fossils. A distinct advantage of morphology is that some types of morphological data may be collected for extinct and extant taxa. Fossils provide a unique window on evolutionary history and may preserve combinations of primitive and derived characters that are not found in extant taxa. Given their unique character complexes, fossils are critical in documenting sequences of character transformation over geologic time and may elucidate otherwise ambiguous patterns of evolution that are not revealed by molecular data alone. [Continued at above link]

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Wednesday, December 06, 2006


BBS: Evolution in Four Dimensions (Jablonka and Lamb)

A preprint paper for Behavioral and Brain Sciences* (BBS) with the same title as Jablonka and Lamb's recent book**:

Precis of Evolution in Four Dimensions (pdf file)

by Eva Jablonka* & Marion J. Lamb

*Cohn Institute for the History and Philosophy of Science and Ideas


In his theory of evolution, Darwin recognized that the conditions of life play a role in the generation of hereditary variations, as well as in their selection. However, as evolutionary theory was developed further,heredity became identified with genetics and variation was seen in terms of combinations of randomly generated gene mutations. We argue that this view is now changing, because it is clear that a notion of hereditary variation that is based solely on randomly varying genes that are unaffected by developmental conditions is an inadequate basis for evolutionary theories. Such a view not only fails to provide satisfying explanations of many evolutionary phenomena, it also makes assumptions that are not consistent with the data that are emerging from disciplines ranging from molecular biology to cultural studies. These data show that the genome is far more responsive to the environment than previously thought, and that not all transmissible variation is underlain by genetic differences. In Evolution in FourDimensions we identify four types of inheritance (genetic, epigenetic, behavioural, and symbol-based), each of which can provide variations on which natural selection will act. Some of these variations arise in response to developmental conditions, so there are Lamarckian aspects to evolution. We argue that a better insight into evolutionary processes will result from recognizing that transmitted variations that are not based on DNA differences have played a role. This is particularly true for understanding the evolution of human behaviour, where all four dimensions ofheredity have been important. [Lamarck]

*BBS publishes important and controversial interdisciplinary articles in psychology, neuroscience, behavioral biology, cognitive science, artificial intelligence, linguistics and philosophy. Articles are rigorously refereed and, if accepted, are circulated to a large number of potential commentators around the world in the various specialties on which the article impinges. Their 1000-word commentaries are then co-published with the target article as well as the author's response to each. The commentaries consist of analyses, elaborations, complementary and supplementary data and theory, criticisms and cross-specialty syntheses.

**A recent post on a review of Jablonka and Lamb's book:

Evolution in Four Dimensions: Genetic, Epigentic, Behavioral and Symbolic Variation in the History of Life

From The Skeptic: Ten years ago, Eva Jablonka (homepage) and Marion J. Lamb (retired) published Epigenetic Inheritance and Evolution, a book with the provocative subtitle, The Lamarckian Dimension. In this new work, they update and pursue their project to expand evolutionary biology beyond what they see as its gene-centred approach.

The authors dispute Richard Dawkins' claim that the gene is the only biological hereditary unit, discussing other inheritance systems where his distinction between replicator and vehicle does not seem to hold. Research on bacteria seems to show that some mutation is non-random, i.e. is to some extent directed by environmental or developmental factors. Hence evolution by natural selection may itself produce mutation-generation systems that confer selective advantage.

Such talk seems to flout the central dogma of modern biology, that inheritance of acquired characteristics is impossible, as it would require that what happens to a body's proteins be somehow 'back-translated' into information stored in DNA. This, as Dawkins put it, would be like the accidental burning of a cake somehow affecting its recipe. However, the authors argue that genetic changes simulating acquired changes would concern regulatory, not coding, sequences in DNA.

The Prologue and Chapter 1, The Transformation of Darwinism, of the book are available as pdf files.

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Dinosaurs: Ancient Egg Cluster Preserved in Glass

The first fossils of half-billion-year-old clusters of soft-shelled eggs have been found preserved in a strange new way in south China - some of the eggs were even caught in the act of dividing.

The three-dimensional clusters of petrified eggs from invertebrate animals that lived in a sea 501 million to 510 million years ago are preserved in silica - glass essentially. Jih-Pai Lin, an Ohio State University (School of Earth Sciences) paleontologist, explained this is a totally unexpected way for soft eggs to fossilize and survive for eons.

Lin is the lead author of a report on the egg clusters published in the December issue of the journal Geology.

The discovery means there are probably even more early eggs and embryos fossilized in ancient rocks. Fossil hunters just need to keep in mind the different ways they might be preserved, and therefore the different types of rocks in which they might be found.

Continued at "Dinosaurs: Ancient Egg Cluster Preserved in Glass"

Based on the Geology paper "Silicified egg clusters from a Middle Cambrian Burgess Shale-type deposit, Guizhou, south China"


Although knowledge of Cambrian fossil eggs and/or embryos has increased dramatically, embryos were previously unknown in siliciclastic settings of coeval strata. Here we report for the first time egg clusters in a fine-grained siliciclastic matrix from the Middle Cambrian Kaili Formation lagerstatte (513-501 Ma), south China. Some were imaged under synchrotron radiation. These spheroids are preferentially preserved as microcrystalline quartz and interpreted as marine invertebrate fossil eggs based on patterns of spheroid arrangement, shape, and analogues of fossil and modern invertebrate eggs. Embryos with cleavage cells are evident in at least one cluster. Detailed element analyses show that eggs are primarily preserved as solid silica replacement, and there is a calcite layer covering the eggs replacing the original organic layer. Silicification of intact invertebrate egg clusters is reported here as a new mode of preservation associated with a Burgess Shale*-type deposit.

*Info on the Burgess Shale:

The Burgess Shale is a black shale fossil bed (Lagerstatte) named after Burgess Pass, close to where it was found, high up in the Canadian Rockies in Yoho National Park near the town of Field, British Columbia. Fossils were first found in the Burgess Shale in 1909 by Charles Doolittle Walcott (info), who returned in the following years to collect additional specimens. Walcott recognized the arthropod fossils were new and unique species, but careful reexaminations showed that many in fact constituted entire new phyla of life, and even today some have proven impossible to classify. The fossils are especially valuable because they include appendages and soft parts that are rarely preserved. [More] [Science and Paleontology]

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Tuesday, December 05, 2006


Evolution: RNA Silencing Sheds Light on the RNA World

Intro: "These findings provide a link between RNA silencing and the earliest mechanisms of RNA transcription - perhaps shedding light on both the origins of RNA replication (and therefore life) and the evolution of RNA silencing".

By PLoS Biology: RNA silencing - also known as RNA interference* - is an intriguing phenomenon in which short, double-stranded RNA "triggers" can prevent the expression of specific genes. First discovered in plants, RNA interference is now recognized as a widespread, if not ubiquitous, phenomenon, and it is causing great excitement as an experimental technique for selectively blocking gene expression.

The mechanisms of RNA silencing have been intensively studied. One important step is the formation of single-stranded RNA pieces (called siRNAs) from the double-stranded triggers. In "lower" organisms - including plants, protozoa, fungi, and nematode worms - it also involves an enzyme - called RNA-dependent RNA polymerase - that can generate a strand of RNA using existing RNA as a template. This means that it can create double-stranded RNA from single-stranded pieces of RNA. By doing this, it generates more triggers and so amplifies the effect of RNA silencing. Paula Salgado and her colleagues have studied the structure of one such polymerase, called QDE-1, and found that it provides clues to the earliest stages of evolution.

When a gene is transcribed and translated to generate a protein, the process begins with a DNA-dependent RNA polymerase. Like QDE-1, DNA-dependent RNA polymerases generate strands of RNA - the difference is that they use a DNA template to do it. The RNA they generate is called messenger RNA and is in turn used as the template for building a protein out of amino acids. The structures of DNA-dependent RNA polymerases have been described previously, so that the authors of this study could compare them with their new structure of QDE-1.

What they found was a remarkable similarity.

Continued at "RNA Silencing Sheds Light on the RNA World"

A related post from Monday, October 02, 2006:

RNA Interference: Nobel prize for genetic discovery goes to Mello and Fire

From BBC News (UK): Two US scientists have been awarded the Nobel Prize for medicine for their pioneering work in genetics.

The work of Dr Andrew Fire (Stanford University School of Medicine: homepage) and Dr Craig Mello (University of Massachusetts: homepage) could lead to new treatments for a range of illnesses, including viral infections and cancer.

They discovered a phenomenon called RNA interference, which regulates the expression of genes.

...The Nobel citation, issued by Sweden's Karolinska Institute, said: "This year's Nobel Laureates have discovered a fundamental mechanism for controlling the flow of genetic information."...

...Scientists have speculated that the mechanism developed hundreds of millions of years ago as a way to protect organisms against invading viruses, which sometimes create double-stranded RNA when they replicate. [Evolution, Umass, Laureate, Science]

*Info on RNA interference:

RNA interference (also called "RNA-mediated interference", but abbreviated RNAi) is a cellular mechanism for the targeted destruction of RNA molecules. RNAi involves double-stranded ribonucleic acid (dsRNA) that can specifically interfere with the expression of genes with sequences that are complementary to the dsRNA. RNAi is a form of post-transcriptional gene silencing in which an antisense RNA strand targets a complementary gene transcript such as a messenger RNA for cleavage by a ribonuclease. RNAi has been shown to be a common cellular process in many eukaryotes. The ribonuclease-containing multi-protein complex (RISC) that is involved in RNAi-mediated transcript cleavage is conserved across the eukaryotic domain, as is the enzyme Dicer that processes dsRNA to the short (about 24 nucleotides long) forms that can be used to specifically target complementary gene transcripts for destruction. [More]

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Neanderthal Women Joined Men in the Hunt

From the New York Times (may require free registration): A new explanation for the demise of the Neanderthals (background info), the stockily built human species that occupied Europe until the arrival of modern humans 45,000 years ago, has been proposed by two anthropologists at the University of Arizona.

Unlike modern humans, who had developed a versatile division of labor between men and women, the entire Neanderthal population seems to have been engaged in a single main occupation, the hunting of large game, the scientists, Steven L. Kuhn and Mary C. Stiner, say in an article posted online yesterday in Current Anthropology.

Because modern humans exploited the environment more efficiently, by having men hunt large game and women gather small game and plant foods, their populations would have outgrown those of the Neanderthals.

The Neanderthals endured for about 100,000 years, despite a punishing way of life. They preyed on the large animals that flourished in Europe in the ice age like bison, deer, gazelles and wild horses. But there is no evidence that they knew of bows and arrows. Instead, they used stone-tipped spears.

Continued at "Neanderthal Women Joined Men in the Hunt"

Based on:

"What's a Mother to Do? - The Division of Labor among Neandertals and Modern Humans in Eurasia"
by Steven L. Kuhn and Mary C. Stiner

Abstract (Full text also currently available at this link)

Recent hunter-gatherers display much uniformity in the division of labor along the lines of gender and age. The complementary economic roles for men and women typical of ethnographically documented hunter-gatherers did not appear in Eurasia until the beginning of the Upper Paleolithic. The rich archaeological record of Middle Paleolithic cultures in Eurasia suggests that earlier hominins pursued more narrowly focused economies, with women's activities more closely aligned with those of men with respect to schedule and ranging patterns than in recent forager systems. More broadly based economies emerged first in the early Upper Paleolithic in the eastern Mediterranean region and later in the rest of Eurasia. The behavioral changes associated with the Upper Paleolithic record signal a wider range of economic and technological roles in forager societies, and these changes may have provided the expanding populations of Homo sapiens with a demographic advantage over other hominins in Eurasia.

The most recent related post:

Synchrotron Reveals How Neanderthal Teeth Grew

Scientists from the United Kingdom, France and Italy have studied teeth from Neanderthals with X-rays from the European Synchrotron Radiation Facility (ESRF). They found that the dental development of Neanderthals is very similar to modern humans. Their results are published in the journal Nature this week.

Neanderthals first appeared in Europe approximately 200,000 years ago and became extinct about 25,000 years ago. These predecessors of modern humans have always been considered genetically closer to us than any other members of the genus Homo. It has even been suggested that Neanderthals achieved adulthood faster than modern humans do today.

A research team from the United Kingdom, France and Italy has recently shed new light on this theory by studying this species' teeth. Teeth express genetic differences found between individuals and different populations more efficiently than any other tissues preserved in the fossil record. Studies with teeth can identify a timescale on the entire period of dental development that occurs from before birth until adulthood. [More]

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Creation Science: 'A Question of Origins' (Online Video)

Creation Science*: From the website:

Watch the entire film (above) or view in segments with Q&A notes (below)

Introduction: Overview of the Theory of Evolution 4:38 mins.
Agreements: Between Evolutionists and Creationists 3:53 mins.
Cosmic Evolution: The Big Bang and the Second Law of Thermodynamics 6:57 mins.
The Origin of the Solar System 3:15 mins.
The Anthropic Principle: Is the Earth Fine-Tuned for Life? 5:08 mins.
Chemical Evolution: Spontaneous generation; Stanley Miller Experiment 6:57 mins.
Evolution: Protein Molecules and "Simple" Cells 6:33 mins.
Evolution of the Bacterial Flagellum 2:40 mins.
Biological Evolution: Darwin's Finches 2:46 mins.
The Fossil Record: Intermediate Links 2:54 mins.
Archaeopteryx: A Feathered Reptile? 1:06 mins.
The Ape-Man: Missing Link 2:26 mins.
DNA: Human & Chimpanzee DNA 1:23 mins.
More Problems 1:12 mins.
Scientific Foreknowledge in the Bible 5:13 mins.
Conclusion 3:52 mins.

Continued at "'A Question of Origins' video presentation"

Alternate video link from the Northwest Creation Network (Washington State):

"During the past century, much of the world has accepted the theory of Evolution as fact. Yet the molecules-to-man theory has no direct evidence to support it at all. Origins provides overwhelming evidence in favor of Creation.

The theory of Evolution has been applied to most scientific fields and this video thoroughly exposes the blind speculation and evolutionary bias in three of these areas of science including: Cosmology, Chemistry, and Biology.

This visually rich, full production reveals conclusive evidence that the universe and all life were created by a Supernatural Being, and that the God of the Bible is that Creator.

Features widely-traveled Creationist speaker, Roger Oakland, who makes the issues easy-to-understand for laypeople. Various scientific experts share evidence and proofs."

*Info on Creation Science:

Creation science refers to the attempts by creationists (especially those who believe in a "young" Earth) to use the methods and empirical practices of science to support their side of the creation-evolution controversy. Creation science supporters work to demonstrate that the extant scientific evidence best supports a literal interpretation of the biblical account of creation. Believers in creation science primarily include members of evangelical Christian denominations that subscribe to the doctrine of biblical inerrancy, however there are examples of Islamic supporters of creation science as well.

Advocates of creation science dispute the uniformitarian model of geology in favor of flood geology, arguing for the historical accuracy of the Noachic flood. They disagree with the theory of the common descent of all life via biological evolution, claiming that evolution is pseudoscientific and argue in favor of creation biology. They reject scientific theories on the age of the universe, arguing for creationist cosmologies based on an age of less than ten thousand years. Some advocates have spent many years arguing for the inclusion of creation science in the science curriculum of U.S. public schools.

When members of the mainstream scientific community have commented, they overwhelmingly dismiss creation science as a pseudoscience because it does not properly conform to the scientific method, as well as admissions by its proponents that the means of creation cannot be proven. Creation science literature generally consists of compilations of alleged weaknesses in current models of evolution and geology.

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Monday, December 04, 2006


Evolution: Vanishing beetle horns have surprise function

Bloomington, Indiana - The function of horned beetles' wild protrusions has been a matter of some consternation for biologists. Digging seemed plausible; combat and mate selection, more likely. Even Charles Darwin* once weighed in on the matter, suggesting - one imagines with some frustration - the horns were merely ornamental.

In this month's American Naturalist (December 2006) and the November 2006 issue of Evolution, Indiana University Bloomington scientists present an entirely new function for the horns: during their development, Onthophagus horned beetles use their young horns as a sort of can opener, helping them bust out of thick larval shells.

The finding will surprise anyone who assumed hornless Onthophagus adults (usually the females) never form the horns in the first place. They do, the scientists say, but the nubile horn tissue is reabsorbed before the beetles' emergence as adults.

'The formation of horns by beetle pupas that soon lose them just doesn't seem to make sense, so obviously we were intrigued,' said IU Bloomington evolutionary biologist Armin Moczek (homepage), lead author of both papers. 'It appears these pre-adult horns are not a vestigial type of structure, which many of us thought was the case. Instead we have shown these horns actually serve an important function regardless of whether they are resorbed in the pupal stage or maintained into the adult.'

Because all the Onthophagus beetles the scientists examined form horns during development, Moczek and colleagues also argue the evolution of ornate horns in the adult beetles may actually have happened second - that is, some time after their initial evolution as larval molting devices.

Continued at "Vanishing beetle horns have surprise function"

At the time of writing the International Journal of Organic Evolution paper referred to above is not yet available.

The American Naturalist paper is "Pupal Remodeling and the Development and Evolution of Sexual Dimorphism in Horned Beetles":

Abstract (Full text is also currently available via this link)

Horns or hornlike structures in beetles have become an increasingly popular study system for exploring the evolution and development of secondary sexual trait diversity and sexual dimorphisms. The horns of adult beetles originate during a rapid growth phase during the prepupal stage of larval development, and differential activation of growth during this time is either implicitly or explicitly assumed to be the sole mechanism underlying intra- and interspecific differences in adult horn expression. Here I show that this assumption is not based on developmental reality. Instead, after their initial prepupal growth phase, beetle horns are extensively remodeled during the subsequent pupal stage via sex- and size-dependent resorption of horn tissue. I show that adult sexual dimorphism in four Onthophagus species is shaped partly or entirely by such pupal remodeling rather than by differential growth. Specifically, I show that after a sexually monomorphic growth phase, differential pupal horn resorption can generate both regular and reversed sexual dimorphism. Furthermore, I show that in cases in which initial growth is already dimorphic, pupal horn resorption can both magnify and reverse initial dimorphism resulting from differential growth. Finally, I show that complete resorption of pupal horns in both sexes can remove any trace of horn expression from all resulting adults. In such species, examination of adults only would result in the false conclusion that this species lacks the ability to develop a horn. Instead, such species appear to differ from those with sexually dimorphic adults merely in that they activate pupal horn resorption in both sexes rather than in just one. Combined, these results suggest that pupal remodeling of secondary trait expression is taxonomically widespread, at least among Onthophagus species, and is developmentally extensive and remarkably evolutionarily labile. These results have immediate implications for reconstructing the evolutionary history of horned beetles and the role of developmental processes in guiding evolutionary trajectories. I use these results to revise current understanding of the evolutionary developmental biology of secondary sexual traits in horned beetles in particular and holometabolous insects in general. The results presented here seriously call into question whether descriptions of adult diversity patterns alone suffice for meaningful inferences toward understanding the developmental and evolutionary origin of these patterns. These results illustrate that a lasting integration of development into an evolutionary framework must integrate development as a process rather than define it solely by some of its products. [Science]

*See The complete work of Charles Darwin online

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Theory of oscillations may explain biological mysteries

Connect one pendulum to another with a spring, and in time the motions of the two swinging levers will become coordinated.This behavior of coupled oscillators - long a fascination of physicists and mathematicians - also can help biologists seeking to understand such questions as why some locations overflow with plants and animals while others are bereft, University of Michigan theoretical ecologist John Vandermeer (website) maintains.

In the cover article for the December issue of the journal BioScience, Vandermeer summarizes theoretical work he has done over the past decade, leading to his conclusion that ecologists seeking to understand complex interactions in nature should pay closer attention to coupled oscillations.

The basic idea of oscillating populations is not new to ecology.

'We know that any predator-prey system, say lions and zebras for example, shows oscillations,' said Vandermeer, who is the Margaret Davis Collegiate Professor of Ecology and Evolutionary Biology. 'If there are lots of lions preying on zebras, numbers of zebras decline; then because zebras are scarce, lions starve and their numbers dwindle, allowing the zebra population to build up again. You see this oscillation, changing on a regular basis from lots of predators with few prey to lots of prey with few predators. The pattern is like waves or pulsations.'

What gets interesting is when two independently oscillating systems, such as lions preying on zebras and cheetahs preying on impalas, become connected through the invasion of a third predator - leopards, for instance.

Continued at "Theory of oscillations may explain biological mysteries"

Based on the Bioscience paper "Oscillating Populations and Biodiversity Maintenance"


Species persistence in the face of competitive or predatory pressure has long been assumed to be a consequence of either dynamic equilibrium or stochastic longevity. More recently, however, the complex intersection of nonlinear dynamics with elementary ecological interactions has provided a distinct platform for conceptualizing the problem of species coexistence. One well-known result from nonlinear dynamics is that oscillating systems will tend to coordinate with one another when coupled, even if the coupling is extremely weak. This elementary result yields remarkable insights in many fields of study. Here I summarize recent results showing that a particular structure emerging from a nonlinear analysis of the classic equations of ecology can be merged with more qualitative ideas to form a possible general framework for analyzing species diversity. As a specific example, I examine the case of two consumer-resource systems that, when coupled, inevitably produce some kind of phase coordination. Understanding the nature of that phase coordination provides a qualitative viewpoint for understanding exclusion and coexistence in this example. Finally, I discuss possible applications to other classical ecological questions.

Full text of the above paper is currently available via the American Institute of Biological Sciences (AIBS) press release

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Anthropology: 'From Language to Lucy' - Donald Johanson on NPR (Audio + Video)

From 'Science Friday', December 1st, 2006: A decade ago, anthropologist Donald Johanson* wrote 'From Lucy to Language,' the story of our family tree as told by fossil remains, the most famous of which may be his own discovery, the skeleton known as 'Lucy' (Video describing the event).That find, made in November 1974 at the site of Hadar in Ethiopia, consisted of about 40 percent of a skeleton of a hominid that walked upright, stood about three and a half feet tall, and was just less than 3.18 million years old.

In this hour, we'll talk with Dr. Johanson about the latest in human origins research, and how our understanding of human origins has changed over the years.

Continued at "Anthropology: 'From Language to Lucy' - Donald Johanson on NPR (Audio)"

*From a brief bio on Johanson:

Dr. Donald C. Johanson is one of the world's leading and best known paleoanthropologist. He received his Masters Degree and Ph.D. in 1970 and 1974 from the University of Chicago, where he studied human paleontology...

...His field research has taken him to Tanzania, Yemen, Saudi Arabia, Ethiopia, Egypt and Jordan...

The early hominid species known as Australopithecus afarensis** includes fossils from two sites, Laetoli (video of the famous footprints) in northern Tanzania and Hadar in the Afar region of Ethiopia. Johanson's most acclaimed find occurred in 1974 at Hadar with the discovery of a 1.8 million-year-old partial skeleton of Homo habilis and Lucy, a 3.5 million-year-old nearly complete fossil of a female Australopithecus afarensis.


The species A. afarensis is one of the better known australopithecines, merely with regard to the number of samples attributed to the species. The species was named by D. Johanson and T. White in 1978. This lead to a heated debate over the validity of the species (seen in a 1980 issue of Science), with the species eventually being accepted by most researchers as a new species of australopithecine and a likely candidate for a human ancestor.

Possibly the best-known specimen of afarensis is AL 288-1 ("Lucy"), a 3.2 million year old partial skeleton found in November 1974 at Hadar, Ethiopia. The afarensis can be separated into two chronological categories: early (3.9-3.5 myr) and late (3.5-2.96 myr). Early afarensis includes material from Laetoli and Belohdelie (and possibly Sibilot Hill), with later afarensis known mainly from Hadar and Maka. Other important specimens attributed to afarensis include the AL 333 specimens (such as A.L. 333-105), AL 444-2, AL 129-1A + 1B, the Laetoli footprints, and the type specimen for the species A. afarensis, LH 4.

QuickTime video links are also available via these PBS Evolution pages: Finding Lucy | Laetoli Footprints

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