Evolutie. Deel XV

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Op maandag 7 juli 2008 16:31 schreef Doffy het volgende:

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Natuurlijk, daar heb je helemaal gelijk in. Beplak een bepaald soort eend met de kleuren van een ander soort eend en hij wordt voor soort- of zelfs groepsgenoot aangezien. De soep wordt daarom minder heet gegeten dan hij wordt opgediend.

Blijft niettemin dat ouders bereid zijn te sterven voor het welzijn van hun jongen. Of, zoals bij sommige insecten, zelfs opgegeten te worden door hun jongen. Met name die ouder-kind band is zo sterk, omdat het belang van genen (en niet individuen) zo duidelijk aan de oppervlakte komt.

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Kin selection theory, also known as inclusive fitness theory, has been the subject of much debate and misunderstanding. Nevertheless, the idea that relatedness among individuals can drive the evolution of altruism has emerged as a central paradigm in evolutionary biology. Or has it? In two recent articles, E.O. Wilson argues that kin selection should no longer be considered the main explanation for the evolution of altruism in insect societies. Here, we discuss what these articles say about kin selection and how it relates to the theory. We conclude that kin selection remains the key explanation for the evolution of altruism in eusocial insects.

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Kin selection is the ¾ relatedness or haplodiploidy hypothesis
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The haplodiploidy hypothesis is just one idea arising from kin selection theory

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Kin selection suggests that relatedness is the dominant force in the evolution of social actions
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Kin selection theory predicts that both ecology and relatedness are important

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Kin selection predicts conflict so it cannot favour altruism
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Kin selection theory predicts cooperation AND conflict

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Support for kin selection from the study of reproductive conflict has no bearing on the evolution of altruism
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Kin selection is a general theory. Support in one area strengthens the theory and its application in other areas where it is relevant

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Kin selection assumes no colony-level effects
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Kin selection models include colony-level effects, sometimes implicitly and sometimes explicitly

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Kin selection is incompatible with trait-group selection thinking
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The two frameworks are complementary and fully compatible

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Relatedness (r) and kin selection only apply to family relatedness caused by recent common ancestry
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The r in Hamilton's rule applies to all forms of genetic correlation among individuals, including among loci and among organisms

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Aimed at the interested lay reader, Endless Forms Most Beautiful (the title comes from the last paragraph of Darwin's Origin of Species) is a paean to recent advances in developmental genetics, and what they may tell us about the evolutionary process. The book's centrepiece is the unexpected discovery that the genes that control the body plans of all bilateral animals, including worms, insects, frogs and humans, are largely identical. These are the 'homeobox' (Hox) genes, whose products bind to the DNA of other genes, triggering a cascade of processes that ultimately yield eyes, limbs, hearts and other complex structures.

The evolutionary conservatism of these genes across long-diverged species is staggering. Only a jaded biologist could not be astonished at the ability of the Pax-6 Hox gene from mice (which triggers eye formation) to induce in the fruitfly Drosophila the formation of fly eyes all over the body, even on the wings. Remarkably, Pax-6 helps to organize compound eyes in flies and camera eyes in both squid and vertebrates — structures once thought to have evolved independently. Another Hox gene, tinman, induces heart formation in both insects and vertebrates, and Distal-less controls the development of fly legs, fish fins and the tube feet of sea urchins.

Sean Carroll, a leader in the field of evolutionary developmental biology (evo−devo), is an adept communicator, conveying the intricacies of development in clear and lively prose. He ranges across the history of biology, linking the early concept of 'inducers' to today's more complex view of developmental networks, and explores the implications of evo−devo for the Cambrian explosion, the biology of dinosaurs, the brains of humans, and the striping of zebras.

Endless Forms Most Beautiful is a first-rate introduction to evo−devo for the scientifically curious, but its faintly self-congratulatory message — that the most important problems in understanding the evolution of development have been solved — left me feeling uncomfortable. Carroll presents his vision of the field without admitting that large parts of that vision remain controversial. I would have appreciated a caveat or two, and non-scientists may mistakenly believe that Carroll presents the scientific consensus about evolution and development.

Carroll emphasizes throughout that the evolution of animal form and complexity results from three factors. The first is modularity of organization: the ground plan of bilateral animals involves repeated segments that can evolve independently. The lobster, for example, is a veritable 'Swiss Army' crustacean, whose diverse appendages — antennae, mouthparts, claws, walking legs, swimming legs and tail — are all modified ancestral limbs. The second factor is that most animals share a small but similar set of 'tool-kit genes' that regulate the development of different modules. These genes, which produce regulatory proteins called transcription factors, are highly conserved in function; Hox genes are the canonical example.

But modularity and a shared genetic tool kit cannot by themselves account for "endless forms", because conserved genes cannot explain diversity. Carroll therefore repeatedly emphasizes his third thesis: that the main engine of evolution is not change in protein-coding genes but in the switches that control them. Changes in these switches — the promoters and enhancers in DNA that regulate the transcription of protein-coding genes — supposedly promote evolution by causing existing genes to be expressed at new times and places. This idea has been with us for a long time. Around 1970, the biologists Roy Britten, Eric Davidson and Allan Wilson were already arguing that the 'regulatory gene' is the locus of evolution, and the idea is now accepted wisdom among evo−devotees.

The evidence for this critical hypothesis, however, rests more on inference than on observation or experiment. Carroll first notes that dissimilar species can in fact be genetically similar: "Mice and humans have nearly identical sets of about 25,000 genes" and "chimps and humans are almost 99 percent identical at the DNA level. Since the sets of genes are so widely shared, how do differences arise?" His answer is the evolution of non-coding regulatory elements: whether you are a man or a mouse apparently depends solely on your promoters and enhancers. But the underlying statistics are deceptive; even a 1% difference in DNA sequence implies a substantial difference in protein sequence. We now know that humans and chimps have different amino-acid sequences in at least 55% of their proteins, a figure that rises to 95% for humans and mice. Thus we can't exclude protein-sequence evolution as an important reason why we lack whiskers and tails.

Carroll also claims that proteins are resistant to evolutionary change: they are often involved in many pathways, and therefore a change in protein sequence, while enhancing one aspect of the protein's many functions, could damage several others. In contrast, changing an enhancer or promoter can affect the expression of a single protein without altering its structure, so such changes are more likely to be adaptive. He deduces that "the evolution of 'new genes' is not the explanation for the origin of diversity of most animal groups". Rather, "it is the switches that encode instructions unique to individual species and that enable different animals to be made using essentially the same tool kit," he says. "Evolution of form is very much a matter of teaching very old genes new tricks!"

But recent data cast doubt on this argument. Humans have about 32,000 protein-coding genes, fruitflies only 13,000. Clearly, the difference between these species involves the origin of new proteins: in fact, between 40% and 50% of our protein-coding genes have no known homologues in flies. So one could argue that the evolution of form is very much a matter of teaching old genes to make new genes. And, given the data, this cannot be difficult.

There are several ways that protein structure can evolve without injurious side effects. One of the most common is gene duplication. Extra copies of a gene can arise by unequal crossing over or by reverse transcription, allowing one copy to retain its function while the other assumes a new function. This process has been a major force in evolution. A large fraction of genes (at least 39% in humans) are members of families derived from repeated duplications and diversification of ancestral genes, a process that has yielded many evolutionary novelties. These families include the globins (such as myoglobin and the various haemoglobins); immunoglobulins; opsins (which led to colour vision in Old World primates); and olfactory receptors (almost certainly involved in the evolution of a keen sense of smell in land animals). Lactalbumin, which helps to produce milk in mammals, resulted from a duplication of lysozyme, and the crystallins of our eye lenses are ultimately derived from heat-shock genes.

This 'multiply and diversify' model of molecular evolution does not depend solely on the duplication of individual genes; the evolution of tetrapods apparently involved at least two bouts of whole-genome duplication. Many evolutionists agree with the geneticist Wen-Hsiung Li's conclusion that "there is now ample evidence that gene duplication is the most important mechanism for generating new genes and new biochemical processes that have facilitated the evolution of complex organisms from primitive ones". Carroll, however, seems too enamoured of his 'regulation is all' thesis to consider this alternative view.

There are other ways beside gene duplication that proteins have evolved adaptively. These include gene conversion, recruitment of genes to new functions (responsible for creating the antifreeze glycoproteins that allow fish to live in frigid waters), exon shuffling (involved in the evolution of blood clotting factors) and the addition of transposable elements to coding sequences. Finally, and simplest of all, we have many examples of adaptive changes of protein sequence between closely related species, including differences in the coat colour of mice, the digestive enzymes of herbivores, and the haemoglobins of high-altitude birds and mammals.

In contrast, the evidence for the adaptive divergence of gene switches is still thin. The best case involves the loss of protective armour and spines in sticklebacks, both due to changes in regulatory elements. But these examples represent the loss of traits, rather than the origin of evolutionary novelties. Carroll also gives many cases of different expression patterns of Hox genes associated with the acquisition of new structures (such as limbs, insect wings and butterfly eyespots), but these observations are only correlations. One could even argue that they are trivial. Given the centrality of Hox genes in development, it is almost inevitable that such genes are involved in the evolution of a new trait. Carroll's correlations, however, do not compel us to believe that changes in these genes are the key factor in the evolution of such traits. We now know that Hox genes and other transcription factors have many roles besides inducing body pattern, and their overall function in development — let alone in evolution — remains murky.

In the end, we simply don't know the relative importance of protein and non-protein changes in creating biological diversity. In many cases, both must have evolved in tandem, as different members of gene families are often expressed in different tissues or at different times. For example, the protein sequence of fetal gamma-haemoglobin evolved adaptively to wrest oxygen from the mother's blood, but its gene is turned off after birth, probably by new regulators. Carroll's emphasis on gene switches may prove correct, but this awaits the labours of the next generation of biologists.

Although Endless Forms Most Beautiful is a lucid and valuable summary of evo−devo, it does proclaim a clever but still unproved hypothesis as central to the evolutionary process. As Carroll himself notes: "Simplification may indeed be necessary for news articles, but it can distort the more complex and subtle realities of evolutionary patterns and mechanisms

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Op donderdag 31 juli 2008 23:34 schreef One_of_the_few het volgende:

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Dat van die filter mag ik ook hopen.
http://www.test.uva.nl/wiki/index.php?title=Falsificeerbaarheid is de link. Lijkt toch erg veel erop dat de UvA er mee verbonden is.
Zeker als je het volgende gedeelte leest:
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Maar ja, ik ga er wel beginnen 1 september, hoogst waarschijnlijk.

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Op zondag 3 augustus 2008 17:56 schreef LB06 het volgende:

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Is het niet zo dat de bewering 'X bestaat' falsificeerbaar is via de antagonist van die stelling? 'X bestaat' is juist of niet juist. Als die stelling juist is, is de antagonist per definitie onjuist en vice versa. Een de stelling 'X bestaat niet' is juist hartstikke falsificeerbaar. Alles wat je hoeft te doen is een vampier van de straat te plukken.

Ergo, 'X bestaat' is wel falsificeerbaar middels de antagonistische werking van de logica.

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Op vrijdag 8 augustus 2008 13:18 schreef wijsneus het volgende:
Yes - very cool indeed.

Op het Rtl4 nieuws hadden ze het trouwens over 'het dna' van de neanderthaler. Of dat is een bewuste versimplificering, of ze snappen er zelf geen bal van.

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The loci of evolution: how predictable is genetic evolution?
Stern, D.L. and Orgogozo, V. (2008)
Evolution Volume 62, Issue 9, Pages 2155-2177


Abstract
Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

Conclusion
In the absence of a population genetics framework, evolutionary developmental biologists have inferred from (1) our current understanding of gene regulatory networks, (2) our understanding of gene structure and function, and (3) the extensive conservation of developmental genes, that mutations in the cis-regulatory regions of developmental patterning genes are likely to underlie most of phenotypic evolution. However, no single argument proposed so far provides definitive proof that cis-regulatory mutations constitute the predominant cause of phenotypic evolution. By considering development and population genetics simultaneously, a survey of published data suggests that patterns of genetic evolution are not entirely obscured by historical contingency. Population genetics and development must be considered simultaneously to make sense of the data.

It may be unhelpful to pose the coding versus cis-regulatory debate as a quantitative question: do coding changes explain more of phenotypic evolution than cis-regulatory changes? It may be more productive to turn the question around and ask what kinds of phenotypic changes are expected from particular coding versus cis-regulatory changes in specific genes. As we show, patterns in the currently available data imply that morphological and physiological traits are caused by different frequencies of coding and cis-regulatory changes. This is consistent with our molecular understanding of how coding and cis-regulatory changes might influence physiology and morphology.

We also found that different spectra of evolutionarily relevant mutations segregate within populations and between species. Interspecific differences in morphology seem to be more often caused by cis-regulatory changes than intraspecific variation. This result is not predicted by a traditional neo-Darwinian view of the contribution of intraspecific variation to interspecific differences. Instead, it appears that evolution over longer time scales results in fixation of a specific subset of the genetic variation contributing to intraspecific phenotypic variation.

By fusing developmental and evolutionary genetics, evolutionary biologists may be able to predict, in a probabilistic sense, the mutations underlying phenotypic evolution. Fortunately, scientists are rapidly identifying the genetic causes of phenotypic evolution, providing abundant data for testing new predictions about the genetic basis of evolution.

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New Ant Species Discovered In The Amazon Likely Represents Oldest Living Lineage Of Ants

A new species of blind, subterranean, predatory ant discovered in the Amazon rainforest by University of Texas at Austin evolutionary biologist Christian Rabeling is likely a descendant of the very first ants to evolve.

The new ant is named Martialis heureka, which translates roughly to "ant from Mars," because the ant has a combination of characteristics never before recorded. It is adapted for dwelling in the soil, is two to three millimeters long, pale, and has no eyes and large mandibles, which Rabeling and colleagues suspect it uses to capture prey.

The ant also belongs to its own new subfamily, one of 21 subfamilies in ants. This is the first time that a new subfamily of ants with living species has been discovered since 1923 (other new subfamilies have been discovered from fossil ants).

Rabeling says his discovery will help biologists better understand the biodiversity and evolution of ants, which are abundant and ecologically important insects.

"This discovery hints at a wealth of species, possibly of great evolutionary importance, still hidden in the soils of the remaining rainforests," writes Rabeling and his co-authors in a paper reporting their recent discovery in the Proceedings of the National Academy of Sciences.

Rabeling collected the only known specimen of the new ant species in 2003 from leaf-litter at the Empresa Brasileira de Pesquisa Agropecuária in Manaus, Brazil.

He and his colleagues found that the ant was a new species, genus and subfamily after morphological and genetic analysis. Analysis of DNA from the ant's legs confirmed its phylogenetic position at the very base of the ant evolutionary tree.

Ants evolved over 120 million years ago from wasp ancestors. They probably evolved quickly into many different lineages, with ants specializing to lives in the soil, leaf-litter or trees, or becoming generalists.

"This discovery lends support to the idea that blind subterranean predator ants arose at the dawn of ant evolution," says Rabeling, a graduate student in the ecology, evolution and behavior program.

Rabeling does not suggest that the ancestor to all ants was blind and subterranean, but that these adaptations arose early and have persisted over the years.

"Based on our data and the fossil record, we assume that the ancestor of this ant was somewhat wasp-like, perhaps similar to the Cretaceous amber fossil Sphecomyrma, which is widely known as the evolutionary missing link between wasps and ants," says Rabeling.

He speculates that the new ant species evolved adaptations over time to its subterranean habitat (for example, loss of eyes and pale body color), while retaining some of its ancestor's physical characteristics.

"The new ant species is hidden in environmentally stable tropical soils with potentially less competition from other ants and in a relatively stable microclimate," he says. "It could represent a 'relict' species that retained some ancestral morphological characteristics."

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Op zondag 28 september 2008 19:28 schreef digitaLL het volgende:
In het volgende filmpje een experiment met een chimp. Hij onthoudt een reeks van 9 getallen willekeurig verspreid feilloos binnen een fractie van een seconde. Mensen hebben enkele seconden nodig en hebben met 5 getallen al moeite en doen het zeker niet foutloos.

The human ape 6/10

In een ander fragment van deze docu is ook te zien dat kinderen erg vatbaar zijn voor mythologie een nutteloze handeling bijvoorbeeld repeteren ze zonder kritisch te zijn, een chimp daarentegen doorziet dat en slaat zo'n handeling over.

The human ape 4/10
The human ape 5/10

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In an outing in the Georgia woods, Kanzi touched the symbols for "marshmallows" and "fire." "Given matches and marshmallows, Kanzi snapped twigs for a fire, lit them with the matches and toasted the marshmallows on a stick."

Paul Raffaele, at Savage-Rumbaugh's request, performed a Maori War Dance for the Bonobos. This dance includes thigh-slapping, chest-thumping, and hollering. Almost all the bonobos present interpreted this as an aggressive display, and reacted with loud screams, tooth-baring, and pounding the walls and floor. All but Kanzi, who remained perfectly calm, and conveyed in Bonobo language (interpreted by Savage-Rumbaugh to Raffaele) that he knew that no threat was meant, but that the performance should be apart from the other bonobos so as not to upset them. So a private performance in another room was successfully, peacefully and happily carried out.

Sue Savage-Rumbaugh has observed Kanzi in communication to his sister. In this experiment, Kanzi was kept in a separate room of the Great Ape Project and shown some yogurt. Kanzi started vocalizing the word "yogurt" in an unknown "language"; his sister, who could not see the yogurt, then pointed to the lexigram for yogurt.

Kanzi's accomplishments also include tool use and tool crafting. Kanzi is an accomplished stone tool maker and is quite proud of his ability to flake Oldowan style cutting knives. He learned this skill from Dr. Nick Toth, who is an anthropologist with the Stone Age Institute in Bloomington, Indiana. The stone knives Kanzi creates are very sharp and can cut animal hide and thick ropes.

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The Origin and Evolution of Religious Prosociality
Ara Norenzayan* and Azim F. Shariff

We examine empirical evidence for religious prosociality, the hypothesis that religions facilitate costly behaviors that benefit other people. Although sociological surveys reveal an association between self-reports of religiosity and prosociality, experiments measuring religiosity and actual prosocial behavior suggest that this association emerges primarily in contexts where reputational concerns are heightened.
Experimentally induced religious thoughts reduce rates of cheating and increase altruistic behavior among anonymous strangers. Experiments demonstrate an association between apparent profession of religious devotion and greater trust. Cross-cultural evidence suggests an association between the cultural presence of morally concerned deities and large group size in humans. We synthesize converging evidence from various fields for religious prosociality, address its specific boundary conditions, and point to unresolved questions and novel predictions.

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Conclusions, Outstanding Questions, and Future Directions

Many religious traditions around the world explicitly encourage the faithful to be unconditionally prosocial (1, 2); yet, theoretical considerations and empirical evidence indicate that religiously socialized individuals should be, and are, much more discriminating in their prosociality (2). Although empathy and compassion as social-bonding emotions do exist and may play a role in prosocial acts of religious and nonreligious individuals some of the time (41), there is little direct evidence to date that such emotions are systematically implicated in religious prosociality.

The preponderance of the evidence points to religious prosociality being a bounded phenomenon. Religion's association with prosociality is most evident when the situation calls for maintaining a favorable social reputation within the ingroup. When thoughts of morally concerned deities are cognitively salient, an objectively anonymous situation becomes nonanonymous and, therefore, reputationally relevant, or alternatively, such thoughts activate prosocial tendencies because of a prior mental association. This could occur when such thoughts are induced experimentally or in naturalistic religious situations, such as when people attend religious services or engage in ritual performance. This explains why the religious situation is more important than the religious disposition in predicting prosocial behavior.

Although religions continue to be powerful facilitators of prosociality in large groups, they are not the only ones. The cultural spread of reliable secular institutions, such as courts, policing authorities, and effective contract-enforcing mechanisms, although historically recent, has changed the course of human prosociality. Consequently, active members of modern secular organizations are at least as likely to report donating to charity as active members of religious ones (42). Supporting this conclusion, experimentally induced reminders of secular moral authority had as much effect on generous behavior in an economic game as reminders of God (27), and there are many examples of modern, large, cooperative, and not very religious societies (such as those in Western and Northern Europe), that, nonetheless, retain a great degree of intragroup trust and cooperation (43).

Any one study we have discussed can be subject to alternative accounts; therefore, specific evidence should be interpreted with caution. Nevertheless, convergent evidence is emerging from several disciplines using different methods and procedures that supply different pieces of the religious prosociality puzzle. Despite the recent scientific progress in explaining the effects of religion on prosociality, open and important questions remain. In particular, more research is needed to address the costliness of religious and nonreligious rituals, and few studies have attempted to quantify these costs in relation to prosocial behavior. The finding that religiosity evokes greater trust underscores the need for more experimental and theoretical research, including mathematical modeling, to establish the specific conditions under which costly religious commitment could evolve as a stable individual strategy and whether these models need to take into account intergroup competition. More broadly, the extent to which religion is implicated in human cooperation, and the precise sequence of evolutionary developments in religious prosociality, remain open to lively scientific debate. Further progress on these issues will require concerted collaboration among historians, archaeologists, social scientists, and evolutionary biologists.

In recent years, moral psychology has received a great deal of scientific attention (44), and although most of the studies reviewed here concern behavioral outcomes, the relation between religious prosociality and moral intuitions and reasoning is ripe for further investigation. More direct research on the possible role of prosocial motivations, such as empathy and compassion, in religious prosociality are needed. Finally, we have seen that religious prosociality is not extended indiscriminately; the "dark side" of within-group cooperation is between-group competition and conflict (45). The same mechanisms involved in ingroup altruism may also facilitate outgroup antagonism. This is an area of no small debate, but scientific attention is needed to examine precisely how individuals and groups determine who are the beneficiaries of religious prosociality, and who its victims.

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Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens
Nitzan Mekel-Bobrov,1,2 Sandra L. Gilbert,1 Patrick D. Evans,1,2 Eric J. Vallender,1,2 Jeffrey R. Anderson,1 Richard R. Hudson,3 Sarah A. Tishkoff,4 Bruce T. Lahn1*

The gene ASPM (abnormal spindle-like microcephaly associated) is a specific regulator of brain size, and its evolution in the lineage leading to Homo sapiens was driven by strong positive selection. Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong positive selection. These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution

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Recent acceleration of human adaptive evolution
John Hawks, Eric T. Wang, Gregory M. Cochran, Henry C. Harpending , and Robert K. Moyzis

Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9M HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (1) site heterozygosity at least tenfold lower than is observed in humans, (2) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (3) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (4) nearly 100 times the observed number of high-frequency LD blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.

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Researchers have found a possible new route taken by early modern humans as they expanded out of Africa to colonise the rest of the world.

A study published in the journal PNAS proposes a "wet corridor" through Libya for ancient human migrations.
Rivers once flowed from the central Saharan watershed all the way to the Mediterranean, the team explains.
This might have enabled modern humans to spread beyond their ancestral homeland about 120,000 years ago. The Sahara then covered most of North Africa, as it does now. So it would have presented a formidable obstacle for early modern humans wishing to cross from the south to the north of the continent.

Researchers had previously focused on the Nile Valley as the principal route of dispersal into other continents by early representatives of our species. Previous data show there was increased rainfall across the southern part of the Sahara between 130,000 and 170,000 years ago; in a gap between Ice Ages known as the last interglacial period.

The researchers, from the universities of Bristol, Southampton, Oxford, Hull and Tripoli in Libya, investigated whether these wetter conditions had reached a lot further north than previously thought. Radar images from space revealed fossil river channels crossing the Sahara in Libya, flowing north from the central Saharan watershed to the Mediterranean coast. Using geochemical tests, the scientists showed the channels were active during the last interglacial. This would have created vital water courses across an otherwise arid region, the researchers write in PNAS.

The central Saharan watershed is a range of volcanic mountains formerly considered to be the limit of this wetter region. Researchers analysed the forms, or isotopes, of different chemical elements in snail shells from two sites in the fossil river channels and from the shells of planktonic microfossils in the Mediterranean.
Despite being hundreds of kilometres from the volcanic rocks of the Saharan watershed, the tests revealed a distinct volcanic signature to these shells, which was quite different to rocks from surrounding sites. The scientists concluded that water flowing from the volcanic mountains of the central Sahara was the only possible source of this signature.

"It's a possible route that the early modern humans could have taken," lead author Anne Osborne, from the earth sciences group at Bristol, told BBC News. Similarities in the style of stone tools being made in Chad and Sudan with those manufactured in Libya during this key period, lend the theory some support, say the scientists. "We now need to focus archaeological fieldwork around the large drainage channels an palaeo-lakes to test these ideas," said co-author Dr Nick Barton, from the University of Oxford. Although it is unclear which routes they took to get there, Homo sapiens had reached the Levant by around 100,000 years ago, where their remains are known from Es Skhul and Qafzeh in Israel.

However, this appears to have been an early, failed foray outside Africa by modern humans. By 75,000 years ago, Neanderthals had replaced our species in the region.

Then, about 45,000 years ago, modern humans reoccupied the area. Genetic evidence suggests that populations living outside Africa today are the descendents of a migration which originated in the east of the continent between 60-70,000 years ago. Some of these pioneers probably crossed the Red Sea at the Bab-el-Mandab straits, taking them from the Horn of Africa across to the Arabian Peninsula.

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Zhang, F. et al. (2008) A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers. Nature, 455, 1105-1108.

Recent coelurosaurian discoveries have greatly enriched our knowledge of the transition from dinosaurs to birds, but all reported taxa close to this transition are from relatively well known coelurosaurian groups1, 2, 3. Here we report a new basal avialan, Epidexipteryx hui gen. et sp. nov., from the Middle to Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis shows it to be the sister taxon to Epidendrosaurus 4, 5, forming a new clade at the base of Avialae6. Epidexipteryx also possesses two pairs of elongate ribbon-like tail feathers, and its limbs lack contour feathers for flight. This finding shows that a member of the avialan lineage experimented with integumentary ornamentation as early as the Middle to Late Jurassic, and provides further evidence relating to this aspect of the transition from non-avian theropods to birds.

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Op zondag 26 oktober 2008 17:52 schreef Aslama het volgende:
Vertel mij maar de evolutie van het DNA van niets tot een paar miljard baseparen die samen de code vormen voor een species. Ja in je eigen woord :-)
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Op maandag 27 oktober 2008 19:18 schreef Aslama het volgende:

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Beschrijf dan alleen van wat al zo duidelijk is van het bewijs van de evolutie op het gebied van het DNA. Dit moet toch niet zo moeilijk zijn daar de evolutie overduidelijk is bewezen.

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Op maandag 27 oktober 2008 22:15 schreef Aslama het volgende:

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Laten we het wetenschappelijk houden.

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Wat ik vroeg was de evolutie van het DNA: van niets tot miljarden baseparen die samen de code van het organisme vormen.
-Hoe kwamen de eerste baseparen tot stand.

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The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells. On the contrary, I argue here that evolution of the RNA world taken place in a framework of competing cells and viruses (preys, predators and symbionts). I focus on the RNA-to-DNA transition and expand my previous hypothesis that viruses played a critical role in the emergence of DNA. The hypothesis that DNA and associated mechanisms (replication, repair, recombination) first evolved and diversified in a world of DNA viruses infecting RNA cells readily explains the existence of viral-encoded DNA transaction proteins without cellular homologues. It also potentially explains puzzling observations from comparative genomic, such as the existence of two non-homologous DNA replication machineries in the cellular world. I suggest here a specific scenario for the transfer of DNA from viruses to cells and briefly explore the intriguing possibility that several independent transfers of this kind produced the two cell types (prokaryote/eukaryote) and the three cellular domains presently known (Archaea, Bacteria and Eukarya).

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-Hoe konden deze zich in chromosomen splitsen.

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-Beschrijf het proces dat ertoe leidt dat het aantal chromosomen in verschillende organismen anders werd.

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Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes

Human chromosome 2 was formed by the head-to-head fusion of two ancestral chromosomes that remained separate in other primates. Sequences that once resided near the ends of the ancestral chromosomes are now interstitially located in 2q13-2q14.1. Portions of these sequences had duplicated to other locations prior to the fusion. Here we present analyses of the genomic structure and evolutionary history of >600 kb surrounding the fusion site and closely related sequences on other human chromosomes. Sequence blocks that closely flank the inverted arrays of degenerate telomere repeats marking the fusion site are duplicated at many, primarily subtelomeric, locations. In addition, large portions of a 168-kb centromere-proximal block are duplicated at 9pter, 9p11.2, and 9q13, with 98%-99% average sequence identity. A 67-kb block on the distal side of the fusion site is highly homologous to sequences at 22qter. A third ~100-kb segment is 96% identical to a region in 2q11.2. By integrating data on the extent and similarity of these paralogous blocks, including the presence of phylogenetically informative repetitive elements, with observations of their chromosomal distribution in nonhuman primates, we infer the order of the duplications that led to their current arrangement. Several of these duplicated blocks may be associated with breakpoints of inversions that occurred during primate evolution and of recurrent chromosome rearrangements in humans.

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Evidence for fusing of two ancestral chromosomes to create human chromosome 2 and where there has been no fusion in other Great Apes is:

1) The analogous chromosomes (2p and 2q) in the non-human great apes can be shown, when laid end to end, to create an identical banding structure to the human chromosome 2. (1)

2) The remains of the sequence that the chromosome has on its ends (the telomere) is found in the middle of human chromosome 2 where the ancestral chromosomes fused. (2)

3) the detail of this region (pre-telomeric sequence, telomeric sequence, reversed telomeric sequence, pre-telomeric sequence) is exactly what we would expect from a fusion. (3)

4) this telomeric region is exactly where one would expect to find it if a fusion had occurred in the middle of human chromosome 2.

5) the centromere of human chromosome 2 lines up with the chimp chromosome 2p chromosomal centromere.

6) At the place where we would expect it on the human chromosome we find the remnants of the chimp 2q centromere (4).

Not only is this strong evidence for a fusion event, but it is also strong evidence for common ancestry; in fact, it is hard to explain by any other mechanism.

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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.

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The zebrafish gene map defines ancestral vertebrate chromosomes

Genetic screens in zebrafish (Danio rerio) have identified mutations that define the roles of hundreds of essential vertebrate genes. Genetic maps can link mutant phenotype with gene sequence by providing candidate genes for mutations and polymorphic genetic markers useful in positional cloning projects. Here we report a zebrafish genetic map comprising 4073 polymorphic markers, with more than twice the number of coding sequences localized in previously reported zebrafish genetic maps. We use this map in comparative studies to identify numerous regions of synteny conserved among the genomes of zebrafish, Tetraodon, and human. In addition, we use our map to analyze gene duplication in the zebrafish and Tetraodon genomes. Current evidence suggests that a whole-genome duplication occurred in the teleost lineage after it split from the tetrapod lineage, and that only a subset of the duplicates have been retained in modern teleost genomes. It has been proposed that differential retention of duplicate genes may have facilitated the isolation of nascent species formed during the vast radiation of teleosts. We find that different duplicated genes have been retained in zebrafish and Tetraodon, although similar numbers of duplicates remain in both genomes. Finally, we use comparative mapping data to address the proposal that the common ancestor of vertebrates had a genome consisting of 12 chromosomes. In a three-way comparison between the genomes of zebrafish, Tetraodon, and human, our analysis delineates the gene content for 11 of these 12 proposed ancestral chromosomes.

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De novo chromosome formation in rodent cells

A hybrid cell line was produced by the fusion of an EC3/7 mouse cell with a Chinese hamster ovary cell. The EC3/7 cell carries a dicentric chromosome with a functional marker centromere. This marker centromere contains human, lambda, and bacterial vector DNA sequences and a dominant selectable gene (aminoglycoside 3'-phosphotransferase type II; neo). In the hybrid, the marker centromere separated from the dicentric chromosome and formed a full-sized chromosome (lambda neo). The newly formed chromosome is stable, even under nonselective culture conditions. This functional chromosome, which is the result of an amplification process, is composed of seven large, different-sized amplicons. Each amplicon contains multiple copies of human, lambda, neo, and mouse telomeric DNA sequences. Individual amplicons are separated from each other by mouse major satellite DNA sequences. The marker centromere was localized to a terminal amplicon by anticentromere immunostaining. The number of amplicons in the newly formed chromosome is remarkably consistent. This finding suggests that the length of the newly formed chromosome is highly constrained.

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Het lijkt me duidelijk dat het DNA zelf niet het bewijs van evolutie is: ALS het DNA evolueert DAN evolueert het organisme, omdat het DNA de code is van het organisme.

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Op woensdag 29 oktober 2008 20:40 schreef Aslama het volgende:
Onderstreepte woorden zeggen het al: geen bewijs. Daarnaast bestaan er inderdaad verschillende theorieën over bepaalde tussenstappen rondom dit onderwerp die aanduiden dat men het niet over een bewijs heeft, laat staan een duidelijk bewijs.

Het heeft voor mij niet zoveel nut om deze theorieën te bekritiseren aangezien deze nog niet vaststaan:

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Many students reject evolutionary theory, whether or not they adequately understand basic evolutionary concepts. We explore the hypothesis that accepting evolution is related to understanding the nature of science. In particular, students may be more likely to accept evolution if they understand that a scientific theory is provisional but reliable, that scientists employ diverse methods for testing scientific claims, and that relating data to theory can require inference and interpretation. In a study with university undergraduates, we find that accepting evolution is significantly correlated with understanding the nature of science, even when controlling for the effects of general interest in science and past science education. These results highlight the importance of understanding the nature of science for accepting evolution. We conclude with a discussion of key characteristics of science that challenge a simple portrayal of the scientific method and that we believe should be emphasized in classrooms.

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het kan weer net iets anders worden en dan mag ik deze weer bekritiseren.

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Om dezelfde reden wil ik nog niet ingaan op de rest van je post. Daarnaast heb ik niet zoveel tijd om al de quotes en links te bestuderen. Liefst wil ik zoveel mogelijk een reactie in je eigen woorden: het leest vaak gemakkelijker als deze de essentie van de theorieën bevat.

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Op donderdag 30 oktober 2008 10:14 schreef Aslama het volgende:

[..]

Betreffende woorden die gebruikt worden in het artikel passen bij een hypothese: in de wetenschap wordt het een hypothese genoemd. Als b.v. de overgang van RNA naar DNA door een experiment geverifiëerd is dan zijn we zeker een stap verder. In biologie kun je d.m.v een experiment verifiëren dat bijv. de chromosoom van een kind een combinatie is van de chromosomen van de vader en de moeder.

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Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory. In everyday language a theory means a hunch or speculation. Not so in science. In science, the word theory refers to a comprehensive explanation of an important feature of nature supported by facts gathered over time. Theories also allow scientists to make predictions about as yet unobserved phenomena

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Zodra de methode duidelijk is gekwalifiseerd, is het zinvoller om in de materie te verdiepen, niet eerder. Dan weet je ook op welk waarheidsniveau je praat.

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Human beings, like other organisms, are the products of evolution. Like other organisms, we exhibit traits that are the product of natural selection. Our psychological capacities are evolved traits as much as are our gait and posture. This much few would dispute. Evolutionary psychology goes further than this, claiming that our psychological traits—including a wide variety of traits, from mate preference and jealousy to language and reason—can be understood as specific adaptations to ancestral Pleistocene conditions. In Evolutionary Psychology as Maladapted Psychology, Robert Richardson takes a critical look at evolutionary psychology by subjecting its ambitious and controversial claims to the same sorts of methodological and evidential constraints that are broadly accepted within evolutionary biology.

The claims of evolutionary psychology may pass muster as psychology; but what are their evolutionary credentials? Richardson considers three ways adaptive hypotheses can be evaluated, using examples from the biological literature to illustrate what sorts of evidence and methodology would be necessary to establish specific evolutionary and adaptive explanations of human psychological traits. He shows that existing explanations within evolutionary psychology fall woefully short of accepted biological standards. The theories offered by evolutionary psychologists may identify traits that are, or were, beneficial to humans. But gauged by biological standards, there is inadequate evidence: evolutionary psychologists are largely silent on the evolutionary evidence relevant to assessing their claims, including such matters as variation in ancestral populations, heritability, and the advantage offered to our ancestors. As evolutionary claims they are unsubstantiated. Evolutionary psychology, Richardson concludes, may offer a program of research, but it lacks the kind of evidence that is generally expected within evolutionary biology. It is speculation rather than sound science—and we should treat its claims with skepticism.

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Op vrijdag 31 oktober 2008 20:34 schreef Aslama het volgende:

[..]

Het was begonnen met deze post . Hier werden concretere bewijzen gevraagd. Ik kan nu uit je post opmaken dat het niet om bewijzen gaat. Het is 'redelijkerwijs waar of onwaar'. 'Redelijkerwijs' is niet meetbaar, waardoor er altijd een kans bestaat dat het anders is.

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[..]

In de quote in je vorige post waar ik op gereageerd heb zijn er te veel woorden als suggest, probably etc. Het is duidelijk dat het artikel niet hetzelfde waarheidsniveau heeft als wat een experiment kan hebben bijv. om te verifiëren dat het DNA van een kind een combinatie is van die van de ouders.

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Daarnaast denk ik dat de voorkeur/ vooroordelen/subjectiviteit hoe dan ook medebepalend zijn voor de houding t.o.v. een theorie. Iemand die een kritische houding neemt t.o.v. de evolutiethoerie neemt niet zo snel alles aan van een hypothese in de evolutietheorie als een evolutionist. Een evolutionist zal minder snel kijken naar de bezwaren van de evolutietheorie. Hij zal geneigd zijn de hypothese te verdedigen.

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[..]

Ik bedoelde de fase waarin het betreffende artikel is gekwalificeerd bv. hypothese of verificatie.

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Op donderdag 6 november 2008 22:12 schreef Droogreden het volgende:
Vraagje tussendoor:
Hoe word met de evolutie theorie de volgende zaken verklaard.
- Ogen, neus, oren en tong.

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- Het bestaan van een grote diversiteit aan zeer complexe emoties.

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- Het evolutionait nut van zaken als depressies of het willen plegen van zelfmoord.

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Op zaterdag 8 november 2008 02:13 schreef Apollyon het volgende:

[..]

Hmmm ... ik zou zeggen : 'Geloof versus Evolutie' [Dan vat je alle voor/tegen en andere standers]
En 'Evolutie in Progressie' [Aangezien zelfs de ontwikkeling van je eigen PC een hele evolutie ondergaat]

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Octopuses share 'living ancestor'

Many of the world's deep-sea octopuses evolved from a common ancestor that still exists in the icy waters of the Southern Ocean, a study has shown.

Researchers suggest that the creatures evolved after being driven to other ocean basins 30 million years ago by nutrient-rich and salty currents.

The findings form part of a decade-long global research programme to learn more about life in the world's oceans.

The first Census of Marine Life (CoML) is set to be completed in late 2010.

The project, which began back in 2000, involves more than 2,000 scientists from 82 nations.

The research into the evolution of deep-sea octopuses was part of a programme called the Census of Antarctic Marine Life (CAML), explained Don O'Dor, CoML's co-senior scientist.

"Many of these octopuses were collected from the deep sea by a number of the CoML's different projects," he told BBC News.

"All of that material was brought together and made available to Dr Jan Strugnell, a biologist at the British Antarctic Survey (BAS) in Cambridge, and she used this material to carry out DNA studies.

"She was looking at the relationship between these different deep-sea octopuses and how they originated.

"She has been able to trace the timeline for their distribution back 30 million years to a common ancestor."

The species could all be traced back to a shallow-water octopus called Megaleledone setebos, which is only found in the Southern Ocean.

Dr O'Dor added that the BAS researcher's work also enabled her to identify how changes in the region's ocean played a pivotal role in the development of the new species, especially the emergence of a "thermohaline expressway".

"When you get an increase in sea ice, fresh water forms ice crystals and leaves behind high-salinity, high-oxygen water, which is denser than the surrounding sea water, so it sinks," he explained.

"It gets mixed by sea currents and flows into all of the deepest parts of the ocean.

"At the time this process started, there was no oxygen at the bottom of the ocean, so it brought oxygen into these areas, and we can now see that the octopuses moved out from the Antarctic into deeper water."

Dr Stagnell's work also showed how the creatures adapted to the new deep-sea environment.

One example was the loss of their ink sacs, because there was no need for the defence mechanism in the pitch black waters.

As well as being one of the CoML's highlights, the research is also being published in the journal Cladistics on Tuesday.

'Unprecedented project'

The deep-sea octopus study, along with dozens of other projects, form part of the census's fourth progress report, which will be presented at the World Conference on Marine Biology, which begins in Valencia, Spain, on Tuesday.

The overarching objectives of the global collaboration between CoML's scientists include:

Advancing technology for discoveries

Organising knowledge about marine life, and making it accessible

Measuring effects of human activities on ocean life

Providing the foundation for scientifically based policies

Dr O'Dor said that the main focus of the CoML for the remaining two years was to "synthesise" the data.

"Many of our projects have already completed their fieldwork and we have a lot of information," he observed.

"What we are now trying to do is to bring all that information together in a form that allows the public to understand how much we have learned about the ocean and what lives in it."

As far as improving our understanding of life beneath the waves, Dr O'Dor said: "It has been successful beyond what I imagined when I first became involved.

"It will provide a baseline. We are not going to know everything about what is happening within the oceans, but we have samplings of most marine habitats.

"We are moving into this period of global warming, which is resulting in the acidification of the oceans, melting of the polar ice cap.

"We can use the first census as a benchmark to see what happens in the oceans over the next decade or more."

Meeting formally for the first time at the five-day gathering in Valencia will be the CoML's Science Council, which will take an overview of the 10-year Census.

"Over the past few years, there has been huge public interest in biodiversity because there is a legitimate concern about the changes being caused by humans," commented Patricia Miloslavich, the Census's co-senior scientist.

"The Science Council will (consider) what people have said about areas that have not been explored or taxonomic groups that have been overlooked in the past," she told BBC News.

"We have had this first census that has given outstanding and amazing results for many ecosystems and regions.

"But now that we have been able to identify where there are some gaps, we would like to explore these areas."

Dr Miloslavich added that the Science Council will also develop the objectives of the second census, which will run from 2010 until 2020.

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Op donderdag 13 november 2008 08:49 schreef wijsneus het volgende:
Princeton Scientists Discover Proteins that Control Evolution

"Evolutionary changes are supposed to take place gradually and randomly, under pressure from natural selection. But a team of Princeton scientists investigating a group of proteins that help cells burn energy stumbled across evidence that this is not how evolution works. In fact, their discovery could revolutionize the way we understand evolutionary processes. They have evidence that organisms actually have the ability to control their own evolution."

http://io9.com/5083673/pr(...)at-control-evolution
http://www.princeton.edu/(...)l?section=topstories

Oh noes! Darwin had het mis! Zie Je Wel

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The other problem that often occurs is that one of the investigators opens his mouth and reveals that he is completely out of his depth, and that the team has absolutely no conception of how evolution actually works. This time, there is no exception.

"The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a 'blind watchmaker'?" said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. "Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."

Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank? That first sentence is not even wrong. Darwin answered the question of how complexity can arise, so no, we haven't been puzzled by that general question; evolution is not completely random, so that part is a complete non sequitur; randomness easily generates lots of complexity, so even if we accept his premise, it invalidates his question; and how does he reconcile his assertion of "completely random" with his use of the simple metaphor of the "blind watchmaker", which implies non-randomness? That's a sentence that contradicts itself multiple times in paradoxical ways.

Anyway, I'll be looking for the paper. My bet would be that it says nothing like the claims made for it by the press release, or that it will be an embarrassing error of interpretation by the authors.

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Op donderdag 13 november 2008 11:40 schreef wijsneus het volgende:
Uiteraard - maar de pers zit er bijna altijd naast als het gaat om evo-nieuws toch? Niets raars aan.

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Wat wel gaaf is dat evolutie dus blijkbaar selecteerd op eigenschappen die voordelig zijn voor evolutie zelf. Positieve feedback zeg maar.

leuk, leuk, leuk!