Saturday, 29 March 2014

If Only Noah Had Known About Evolution!

Noah's ark on the Mount Ararat, Simone de Myle 1570
Tree of bird life could solve Noah's Ark problem - life - 27 March 2014 - New Scientist

One of the many absurdities in the Noah's Ark myth, several more of which can be found in No Way Noah!, is the sheer impossibility of providing an ocean-going sea-worthy wooden boat large enough to house something like 19 million animals of all shapes and sizes, many of which require highly specialised environments, together with enough food, to last something over a year.

Creationist pseudo-scientists who make their living trying to explain away these absurdities have no option but to fall back on an almost equally absurd version of warp-speed evolution so they can reduce the numbers to mere few thousand from which all the species have evolved in the last few thousand years, apparently with no one noticing all the new species popping into existence every generation. We're expected not to notice that they also tell their credulous followers that evolution is impossible but holding two diametrically opposite views simultaneously has never been a problem for creationists.

Now scientists have suggested a way we could, should the need ever arise in the future to take the world's species into protective custody to prevent the extinction of life on Earth, whilst not needing to take a pair of every single species. What we would need to safeguard is the DNA of all different species, not in test-tubes but in living members of those species which are the most evolutionarily distinct. From these, we could, theoretically reconstruct other related species.

You could increase the amount of evolutionary diversity that is currently protected by 25 per cent by expanding the reserve system by 5 per cent.

Laura Pollock, University of Melbourne, Victoria, Australia
For example, we would not need to save a pair of every wild cat but nor would it work to save, say, lions, or tigers because these have close relatives, so most of their DNA would survive their extinction. What we need to do is to preserve the main limbs and major branches of the evolutionary tree of life rather than the terminal twigs. Losing a species which is closely related to several others, such as the lion, would merely remove a twig from the tree. Conserving an evolutionary distinct species with few living relatives however will conserve more of the DNA from further down the branch for the same effort.

The Zoological Society of London (ZSL) has been running the Edge of Existence Project since 2007. This seeks to identify key endangered and evolutionary unique species and to rank them into an order of priority for conservation. At the moment, effort tends to be concentrated on a few high-profile species, often at the expense of a higher priority species according to this ranking.

Now, Walter Jetz of Yale University has ranked the world's birds in terms of evolutionary distinctness using genetic data from 6500 of the 10,000 species combined with data on threats and population size to produce a list of just 100 priority species. He has also shown that concentrating on just 113 sites could conserve 60 percent of the most endangered evolutionary unique species.

Jetz has used the ranking to point to species that should be protected. For example, the highly distinct shore plover (Thinornis novaeseelandiae) lives only on the tiny Chatham Islands, near New Zealand. Just 250 are left. Focusing on plover habitat would preserve 14.46 million years of evolution for each 10,000 square kilometres conserved. In contrast, the ostrich is the 10th most distinct species, but as it has a large range only 0.05 million years would be preserved per unit area.

Andy Coghlan, Tree of bird life could solve Noah's Ark problem, New Scientist, 27 March 2014.

It's a beautiful irony that, had the Bible's authors had the least inkling of evolution or DNA and how it allows species to be arranged in a tree of life, they could have made their absurd tale just a little more plausible by explaining that Noah had reduced the number of species to conserve by doing just what conservationists are now doing. They would have had to explain how Noah had then reconstructed all the other species by careful bioengineering of course but at least their daft notion would have been just slightly less implausible.

Unfortunately, they had to try to force-fit the story into what little they knew and understood, and the prevailing superstition of the orthodoxy they were selling, and so ended up with a story so implausible that only children and scientifically illiterate, gullible adults could believe it.

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Ringing the Changes - Sex in Siberia

Oldest Homo sapiens Genome Pinpoints Neandertal Input

Just another little piece in the jigsaw puzzle of human evolution emerged this week when researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announced the results of their sequencing of the entire genome from DNA recovered from the 45,000 year-old Homo sapiens male thigh bone, found in 2008 in an exposed banks of the Irtysh River at Ust-Ishim in western Siberia. It had been found by an ivory carver looking for mammoth tusks.

And, as with so often with science, a little piece of information has raised more questions and suggests that some of our earlier assumptions might just have been wrong.

Svante Pääbo's team have a lot more work to do but already a couple of things have been found:

  • The DNA contained unmistakable traces of Neanderthal DNA showing that the man was descended from people who had interbred with H. neanderthalensis.
  • Interbreeding had been quite recent judging by the fact that the sequences of Neanderthal DNA occurred in longer chunks than normally found in modern humans. As time progresses the chance of any chunk of DNA being chopped in half by crossover during the first stage of meiosis increases. A bit like whole fruit in a smoothy maker.

Genetically we now have a modern human that just barely postdates the Neandertal introgression into modern humans.

Bence Viola. Max Planck Institute for Evolutionary Anthropology
Now, and this might be a small crumb of comfort for those creationists who haven't simply ignored all this evidence of the hybrid origins of modern humans and must be feeling pretty depressed by all the evidence piling up against them, this has produced one of those small areas of disagreement amongst paleoanthropologists. Creationists normally enjoy these small disagreements and wave them around as evidence that, whilst science claims to be the only way to determine truth, it normally involves disagreement and changes of mind.

It's like having a time machine, to go back 45,000 years to see how the genomes of modern humans differed both from our own and also from Neanderthals and Denisovans.

Sarah Tishkoff, University of Pennsylvania, USA
It had been assumed that H. neanderthalensis had evolved in Europe or Asia, probably from H. heidelbergensis or maybe H. habilis or even H. ergaster or H. antecessor and had adapted to the colder northern climate. Later, when H. sapiens came out of Africa they did not move up into the colder north initially but skirted the southern margins into southern Europe and across Asia. The most likely place for the interbreeding with H. neanderthalensis in this scenario would have been the Middle East somewhere around northern Arabia, Asian Minor, Iraq or Iran. And this more or less tied in with the estimated dates of our expansion out of Africa and the period of cohabitation with Neanderthals.

However, this find suggests that modern humans adapted quite quickly to colder climates and were interbreeding with Neanderthals much further north. But, there is still much to be done to determine if this rapid adaptation was actually the result of the DNA we got from Neanderthals, or even to survival techniques and cold climate technologies we got from them.

One other intriguing possibility here is that, given the close proximity between Ust-Ishim and the Denisovan cave where a finger bone which yielded the DNA of a third species of humans was found, there may have been three different human species all capable of interbreeding and living in a relatively small area. All extra-African modern humans have some Neanderthal DNA and several groups of Southeast Asian and Austronesian people also have some Denisovan DNA, so it could be that this area was the point where all three came into contact and behaved very much like a ring species - just as we should expect gradually diverging species spread across a large geographical range to behave.

Researchers still think the Middle East is a likely place for the encounters. Other fossils in Israel, such as a 49,000-year-old Neandertal at Tabun Cave, might belong to people who were alive at the time of the unions or just after, says archaeologist Ofer Bar-Yosef of Harvard University, who was not a member of the team.

Ann Gibbons, Oldest Homo sapiens Genome Pinpoints Neandertal Input,
Science 28 March 2014: Vol. 343 no. 6178 p. 1417 DOI: 10.1126/science.343.6178.1417

Creationists who may be tempted to latch on to this little disagreement should bear in mind that there is no disagreement about human evolution here, or even the now established fact the modern humans coexisted with, and interbred with, related species of humans. The disagreement is simply over where the interbreeding took place.

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Sunday, 23 March 2014

Evolution Has More to Crow About

Carrion crow, Corvus corone corone
A few days ago I mentioned at the end of a blog about the evolution of crows in the presence of the great spotted cuckoo, the fact that carrion crows and hooded crows are now regarded as different species. This illustrates neatly the problem of defining a species, especially where two closely related species are at a stage in their evolution where they have not fully diverged and retain the capability of interbreeding. I'll discuss this more later, but first, the case of the Eurasian crows.

As you drive north from England across southern Scotland and up towards the Highlands, you might, if you're interested in the birds, notice that the ubiquitous glossy black crows you will have seen almost everywhere from town parks to country fields and woodlands have quite suddenly been replaced by an equally common crow with a black head, tail and wings and a grey back and underparts. If you drive eastwards from Western Europe through Germany towards Poland or down into Austria or the Balkans you'll see a similar change. In both cases the plain black carrion crow, Corvus corone, has been replaced by the black and grey hooded crow, C. cornix. A similar change occurs as you drive from France into Italy south of the Alps.

Hooded crow, Berlin, Germany, Corvus cornix cornix
What you may not have noticed as you drove north in Britain however was a narrow band where the crows were both black and grey and black, and a whole range of intermediates between the two. In this narrow band, which has apparently moved over time, the two species of crow behave like a single species and interbreed freely, producing all the different intermediates.

There are similar zones of interbreeding between France and Italy. Everywhere else in Europe, they behave like two perfectly respectable species, just like, say, the song thrush, Turdus philomelos, and the blackbird, T. merula, or the house sparrow, Passer domesticus, and the tree sparrow, P. montanus.

Hybrid between carrion and hooded crow, Corvus corone x cornix
If you continue driving eastwards from Europe across the Yenisei river into central Asia, you'll find another sudden change - the hooded crows will disappear, to be replaced by what looks like slightly larger carrion crows. In fact, most authorities think that's exactly what the eastern crow is, and call it C. c. orientalis, the carrion crow being called C. c. corone to show that they are merely subspecies and not distinct species in their own right. Others disagree and think that, because the two subspecies are geographically separated, and have been for a long time, they do not interbreed and so form a single species with a single gene-pool, they should be regarded as two distinct species, C. corone and C. orientalis. However, there is a zone of interbreeding between C. cornix and C. C. orientalis just as there are zones of interbreeding between C. cornix and C. c. corone.

And it gets worse! Go from the north down through Iraq towards the Arabian Gulf and, as you come to ancient Mesopotamia between the Tigris and Euphrates rivers, the grey parts of the hooded crows become much paler so they look almost black and white. There they are known as the Iraqi pied crow. Taxonomists regard these as a subspecies, C. c. capellanus. All in all, there are four subspecies of hooded crow; the other two being one which lives in a band running from western Siberia down between the Black and the Caspian seas through the Caucasus Mountains and into Iran (C. c. sharpii), and one found in Turkey and Egypt (C. c. pallescens).

Eastern carrion crow, Corvus corone orientalis
The current hypothesis is that several populations of the stem species for all these crows got separated during the Ice Age and for tens of thousands of years evolved in isolation as effectively different gene-pools. As the ice retreated one of the populations which had evolved into the hooded form expanded northwards forming a block between the western and eastern forms which had retained their all-black plumage.

These eastern and western forms have since continued on their different evolutionary trajectories, the eastern form becoming a little larger and their tail feathers becoming more tapered. Meanwhile, the hooded form, which happens to occupy a more diverse habitat has formed local subspecies. All the crows are sedentary species, never straying far from the area they were born in. This helps to minimise any gene flow from adjacent subspecies.

So why is this? Why does the science of taxonomy find it difficult to tell if closely related species are the same species, subspecies or full species in their own right? Why is there now agreement that hooded crows and carrion crows, which do interbreed in a few small areas, are distinct species, yet disagreement about the status of the eastern crow, even though they never normally meet carrion crows in the wild and so do not normally interbreed? And, if the hooded and carrion crows were merely subspecies, what would be the status of the four subspecies of hooded crow?

The reason for this apparent confusion and imprecision, is that 'species' is a human concept; a tool used by science to classify all the different living things. Nature doesn't read our rulebook and doesn't have any obligation to produce neat divisions between living things. Nature is quite happy about the distinction being blurred so any device we come up with to try to divide living things up into our neat compartments is bound to lack precision because nature itself lacks precision. The reason that C. corone and C. corvix are now regarded as species rather than subspecies, incidentally, is because studies have shown that the hybrids lack breeding vigour, indicating that divergence of the species had progress towards the point where interbreeding would either be impossible or the offspring would be sterile. This is in fact a departure from the commonly accepted definition because, although they may lack vigour, they may well be fertile, and one definition of 'species' is a distinct population capable of interbreeding and producing fertile offspring.

Even though it is not disputed that species is a taxonomic rank, this does not prevent disagreements when particular species are discussed. Consider the case of the Baltimore Oriole (Icterus galbula) and Bullock's Oriole (I. bullockii), two similar species of birds that have sometimes in the past been considered to be one single species, the Northern Oriole (I. galbula). Currently, biologists agree that these are actually two separate species, but in the past this was not the case.

Disagreements and confusion happen over just what the best criteria are for identifying new species. In 1942, Ernst Mayr wrote that, because biologists have different ways of identifying species, they actually have different species concepts. Mayr listed five different species concepts, and since then many more have been added. The question of which species concept is best has occupied many printed pages and many hours of discussion.

The debates are philosophical in nature. One common disagreement is over whether a species should be defined by the characteristics that biologists use to identify the species, or whether a species is an evolving entity in nature. Every named species has been formally described as a type of organism with particular defining characteristics. These defining traits are used to identify which species an organism belongs to. For many species, all of the individuals that fit the defining criteria also make up a single evolving unit, but it might not be known whether that is the case. These two different ways of thinking about species, as a category or as an evolving population, may be quite different from each other.


... I was much struck how entirely vague and arbitrary is the distinction between species and varieties

Charles Darwin, On the Origin of Species. (p. 48)
It was Charles Darwin himself who pointed out that if it hadn't been for evolution, which has caused living things to diverge and differentiate and which has emphasised and worked on differences, converting minor differences over time into major ones, that we have all the different taxa from kingdoms to subspecies and varieties in the first place. Evolution has carved out the current taxa from what would otherwise be a confusing mass of undifferentiated life forms. In fact, it would not have been possible for living things to evolve any of their solutions to problems like where to get basic resources from even to make copies of themselves. Life could not have progressed beyond simple autocatalytic replicators without natural selection to work on the slight differences produced by imperfect replication.

What we have in the crow example above is an example of evolution in progress, just like a ring species. These different populations of crows are seen at the current stage in their evolution and diversification. They are obviously not the same species but their progress to separate species status has not yet progressed to completion. In some ways they act like one species; in other ways they act like subspecies and in still other ways they behave like different species altogether. There is no requirement on nature or the process of evolution to complete this process suddenly or even within a given time frame, or in front of an eye-witness. If it takes 10 million years, or ten thousand years then that's what it takes. If you expect to see it happen, you have a loooooong wait.

In the case of our own divergence from the common ancestor we share with the chimpanzees, recent evidence has suggested that we may have interbred with chimpanzees for over a million years before finally diverging. The process of speciation started some 6.3 million years ago and took 1.2 million years to complete! Later on in the evolution of Homo sapiens, we were still able to interbreed with H. neanderthalensis and maybe with H. antecessor, H. habilis, and H. erectus and other species yet to be discovered (or should they be subspecies?).

This exposes the lie behind the idiotic mantra which creationists chant when you show them some examples of recent evolution or indisputable evidence that evolution occurred in the very recent past, "That's microevolution. Macroevolution is impossible! No one has ever seen a new species arise!" No-one who knows anything about evolution would expect to see a species arise (except in the rare examples of new species arising by hybridization - which have been seen) because it takes tens or hundreds of thousand or even millions of years. Evolution is a process, not an event.

By what sane logic have creationist pseud-scientists concluded that evolution can proceed within a species and can happily account for the evolution of subspecies and yet conclude that progressing a little further to the status of species is impossible? The terms are purely human constructs and do not mandate or constrain the process of evolution in any way. Are we really expected to believe that when humans classify two crows as C. c. corone and C. c. cornix evolution is perfectly adequate to explain how they differentiated from one another, yet when the same humans decide to re-classify them as C. corone and C. cornix, all that magically changes and the differentiation we previously accepted somehow becomes retrospectively impossible? Only someone who sincerely wants to be fooled could fall for that 'reasoning'.

The creationist frauds who have sold that lie to the gullible fools who eagerly buy their cures for cognitive dissonance really should be taken to task for releasing their unfortunate victims onto the Internet to make such fools of themselves with that simplistic nonsense.

And the crow example can only be understood as an evolutionary process. There can be no intelligent reason for creating different overlapping populations with different forms and behaviours and then allowing them to interbreed, simply to produce offspring with reduced vigour which soon die out when they interbreed with one another, in a zone which needs to be constantly replenished with new hybrids from the two parent species. Any creator which intended that outcome would be an idiot. Any creator which did it accidentally would be incompetent. The same frauds are also selling this 'Intelligent Design' nonsense to the same gullible fools.






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Friday, 21 March 2014

Ancient Stick Insect Shows Evolutionary History

Early Cretaceous stick insect (Cretophasmomima melanogramma)
Image: Olivier Béthoux
The stripy stick insect that walked with dinosaurs - life - 19 March 2014 - New Scientist:

In my previous blog I touched on how what we see today in a species may be the result of ancient evolutionary forces which no longer apply, so it may not be immediately obvious what adaptive advantage there is to something in particular.

It's easy to overlook the fact that everything alive today is carrying the descendents of genes which survived through the Cambrian, the Devonian, the Triassic, Jurassic and the Cretaceous periods and were selected not by today's environment but maybe a very different one with different species and different ecosystems, even in the absence of orders like birds or mammals or in the presence of dinosaurs, pterodactyls, ammonites or giant tree ferns.

None of today's living species has an ancestor which did not live on an Earth where these extinct species once lived.

So, it should be no surprise to find ancient species like this early cretaceous stick insect which had adapted to live alongside early cretaceous plants by protective mimicry. This fossil was found in Inner Mongolia, China, in the Yixian Formation which has been dated between 122-130 million years ago. This rock formation which was laid down probably as volcanic ash from a catastrophic eruption, so capturing and preserving in exquisite detail, delicate structures like this insect with its wings, feathered dinosaurs and proto-avians as well as plant leaves. This is known collectively as the Jehol biota.

The significance of this fossil of Cretophasmomima melanogramma is that it is the earliest known example of stick insect mimicry. Stick insects today are renowned for their evolved mimicry to resemble the plants on which they feed but this example mimics a plant which was common then, but is extinct today. It was a species related to the maidenhair tree or Ginkgo biloba, now the only known representative of the Ginkgophyta division of the plant kingdom. The dark straight veins in the wings seen in this fossil, when the wings were folded over the back, would have closely resembled the leaves of Ginkgophyta, Membranifolia admirabilis also found in the Jehol biota.

Abstract


Background

Fossil species that can be conclusively identified as stem-relatives of stick- and leaf-insects (Phasmatodea) are extremely rare, especially for the Mesozoic era. This dearth in the paleontological record makes assessments on the origin and age of the group problematic and impedes investigations of evolutionary key aspects, such as wing development, sexual size dimorphism and plant mimicry.

Methodology/Principal Findings
A new fossil insect species, Cretophasmomima melanogramma Wang, Béthoux and Ren sp. nov., is described on the basis of one female and two male specimens recovered from the Yixian Formation (Early Cretaceous, ca. 126±4 mya; Inner Mongolia, NE China; known as ‘Jehol biota’). The occurrence of a female abdominal operculum and of a characteristic ‘shoulder pad’ in the forewing allows for the interpretation of a true stem-Phasmatodea. In contrast to the situation in extant forms, sexual size dimorphism is only weakly female-biased in this species. The peculiar wing coloration, viz. dark longitudinal veins, suggests that the leaf-shaped plant organ from the contemporaneous ‘gymnosperm’ Membranifolia admirabilis was used as model for crypsis.

Conclusions/Significance
As early as in the Early Cretaceous, some stem-Phasmatodea achieved effective leaf mimicry, although additional refinements characteristic of recent forms, such as curved fore femora, were still lacking. The diversification of small-sized arboreal insectivore birds and mammals might have triggered the acquisition of such primary defenses.

Wang M, Béthoux O, Bradler S, Jacques FMB, Cui Y, et al. (2014)
Under Cover at Pre-Angiosperm Times: A Cloaked Phasmatodean Insect from the Early Cretaceous Jehol Biota.
PLoS ONE 9(3): e91290. doi:10.1371/journal.pone.009129
Copyright: © 2014 Wang et al. Published under open access permission.

C. melanogramma being hunted amongst Membranifolia admirabilis foliage
Artists impression.
It seems very likely that these stick insects would have been the prey of the same early birds and mammals which are also found in the Jehol biota and evolved mimicry as a defence against them.

Of course, we can't know for sure if any of today's stick insects evolved directly from C. melanogramma but if they had they would carry genes that were once selected by the presence of early birds and late Ginkgophytes and they might well still have wings with dark straight veins having no apparent adaptive purpose today.

Evolution can't even look forward to tomorrow but it harks back to life on Earth hundreds of millions, even billions of years ago. We all carry the results inside us embedded in our genome, some of which was shaped by species and ecosystems of which we are not yet aware.

Dismissing this as magic, as creationist frauds and pseudo-scientists do, denies those who fall for their deceptions the pleasure of finding out how they were shaped by these forces and how they are connected to every other living thing through the process of genetic evolution by descent with modification from a common ancestor. It's like denying people the wonder of looking up into a night sky and being inspired by the awesome majesty of the cosmos.

It is denying people a heritage which is literally their birthright - the right to know who they are and where they came from.

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Evolutionists Have Even More to Crow About

Great spotted cucko (Clamator glandarius)
Predation Favors Parasitism

The fascinating results of research into the relationship between a species of parasitic cuckoo, the great spotted cuckoo, Clamator glandarius, and one of it's host species, the carrion crow, Corvus corone corone, was published in Science this week and illustrates an interesting aspect of evolution - how competing evolutionary pressures can produce a dynamic equilibrium.

The study was carried out in northern Spain where 67.7% of carrion crow nests are parasitized by the great spotted cuckoo, which also parasitizes another member of the crow family, the magpie (Pica pica), which has a broadly similar geographical range to the carrion crow. Unlike the magpie, which will often evict alien eggs from it's nest and will mob great spotted cuckoos in the vicinity, carrion crows exhibit neither of these defence mechanisms. It is normally assumed, when this is found in other cases of avian parasitism that the species has only recently begun to be parasitized, so has not yet had time to evolve these defensive behaviors. However, it is also possible that there has been no evolutionary pressure to evolve defences because there may be a degree of mutualism in the relationship. In other words, the parasitized species might be deriving some benefit.

Abstract
Avian brood parasites lay eggs in the nests of other birds, which raise the unrelated chicks and typically suffer partial or complete loss of their own brood. However, carrion crows Corvus corone corone can benefit from parasitism by the great spotted cuckoo Clamator glandarius. Parasitized nests have lower rates of predation-induced failure due to production of a repellent secretion by cuckoo chicks, but among nests that are successful, those with cuckoo chicks fledge fewer crows. The outcome of these counterbalancing effects fluctuates between parasitism and mutualism each season, depending on the intensity of predation pressure.

Canestrari et al., From Parasitism to Mutualism: Unexpected Interactions Between a Cuckoo and Its Host;
Science, 343 (6177): 1350-1352; 21 March 2014:DOI: 10.1126/science.1249008

Carrion crow (Corvus corone corone)
Unlike many other avian parasites, great spotted cuckoo chicks do not evict host eggs and chicks from the nest but simply out-compete them in their demand for food from the adults. This often leads to reduced breeding success for the host species especially if food is scarce.

The difference in nest location and construction between carrion crows and magpies is also significant in explaining the different responses of these two species to cuckoo parasites. Carrion crows nest in the tops of tall trees and construct an open nest, making the brood prone to predation by predators such as falcons and buzzards. Magpies, however, build a nest in a thicker cover and construct a roof over it, making it harder for flying predators to take the chicks.

This difference in nest construction has created a different dynamic because it means the cuckoo chicks in carrion crow nests are also more liable to predation. This has produced evolutionary pressure for them to evolve a defence mechanism - they secrete a substance which repels predators. This in turn protects the host chicks in the same nest.

Magpie (Pica pica)
Magpies, which don't benefit much from the anti-predator strategy of the parasite chicks because their chicks are not so heavily predated, and therefore suffer much more from competition for resources with it, have had evolutionary pressure to evolve avoidance strategies.

Carrion crows, on the other hand, which can, in situations where predation is high, actually benefit from having a parasite chick in the nest, have had little evolutionary pressure to evolve avoidance strategies and might even be expected to evolve strategies to encourage it. However, given that predator numbers can fluctuate and there are years when predator numbers are low and so any potential benefit is not realised and loss due to competition can be the more significant effect, there may also be pressure acting in the reverse direction.

So, there is a dynamic of competing forces at work here which has probably reached an equilibrium at which the carrion crow does little or nothing to avoid parasitism because of the benefits it can get from it, but it has not evolved behaviours to encourage it because it also often suffers from it. Being dynamic of course means that it is relatively easy for a small change in one of the forces to push the dynamic in one direction or another, maybe over just a small part of the range, especially if the species involved is relatively sedentary.

And the evolution of the different strategies between magpies and carrion crows has its origins in the different nesting strategies adopted by the two species, which was itself probably produced by different responses to evolutionary pressures at some point in their evolutionary histories.

The historic forces which shaped evolution in the past may not even be present today so it can be difficult to see why something like different nesting behaviours in birds developed as related species diverged until we understand how natural selection operates. I'll be looking at this in my next blog.

As always, I'd love a creationist to come here to explain how this finding fits in with their currently fashionable 'intelligent design' notion. None have yet managed it with any other blogs on similar topics, but there is always hope that one will one day find the moral courage to defend their idea or to have the integrity to say they can't.

NB: Corvus corone corone is a three-part name to distinguish it from the Eastern subspecies, C. corone orientalis. The species formerly included the hooded crow, previously Corvus corone cornix. However, since 2002, these have been recognised as distinct species, C. corone and C. cornix respectively, and there is disagreement about the exact taxonomic status of C. corone orientalis. The reasons for this classification debate is interesting in itself and illustrates the problem of precise definition of the terms 'species' and 'subspecies' as an original species diverges and speciates, and may well be the subject of another blog here soon.

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Monday, 17 March 2014

Big Bang Bother For Bible Believers

BBC News - BBC explains Big Bang discovery using a sock

Once again, when scientist shone a light in a gap in our understanding they found no god in it. And shining a light in this case is especially apt, as it was light that was analysed. There is even talk of a Nobel Prize. While, as is normal with significant science, the results are to be subjected to intense scrutiny and other teams will try to replicate them, it looks very much as though scientists of the PICEP2 Project led by Prof John Kovac of the Harvard-Smithsonian Center for Astrophysics have found the data verifying the inflation model of the Big Bang.

Inflation was basically inserted in the Big Bang theory as the best explanation for things not quite adding up. It proposed that, during the initial few moments of the Big Bang, the Universe expanded exponentially at faster than light speed until it was about the size of a marble. Not much of an inflation you might think, but bear in mind a fraction of a billionth of a second earlier, the entire Universe had been packed into something so small that it would have been indistinguishable from nothing. What inflation did was offer an explanation of how the three 'quantum' forces of weak and strong nuclear forces and electromagnetism became stripped away from the fourth, gravity, allowing the Universe to continue to expand and not collapse immediately under its own gravity. Basically, gravity had lost control. This went a long way to explaining why we have something from nothing. The total of the three 'quantum' forces exactly equates to gravity, so, in terms of fundamental forces, the Universe was and still is zero.

The problem was, it was an educated guess the best evidence for which was that nothing seemed to contradict it and it explained a great deal. This is, of course, only circumstantial evidence - not enough to convict in a court of law. What was needed was the smoking gun.

Planes of polarisation in the CMB
Now we very probably have it in the form of a detailed and meticulous analysis of the cosmic microwave background radiation (CMB) which is the echo of the original heat energy of the Big Bang. The discovery of the CMB was the final evidence for the Big Bang because it was predicted by it. The Big Bang idea itself was a natural projection backwards from the observed rate of expansion of the Universe. Now, this new evidence shows what happened to the initial radiation during the period of inflation. As predicted, it shows that it was subject to intense gravity waves which caused it to polarise.

This is spectacular. I've seen the research; the arguments are persuasive, and the scientists involved are among the most careful and conservative people I know.

Prof Marc Kamionkowski, Johns Hopkins University
Polarisation of light means that, instead of all the waves vibrating in a random distribution of angles, they all vibrate in the same plane. The breakthrough research has detected beyond reasonable doubt this pattern of polarisation and it is entirely consistent with both inflation and the splitting away of gravity from the other three forces.

Why is this important? Well, apart from confirming that inflation happened, so our model of the first fraction of a second of the Big Bang is almost certainly correct, it confirms the explanation of how vast amounts of energy (hence matter) can come from nothing. It also moves a little closer to the Holy Grail of theoretical physics, the Grand Unified Theory which would integrate quantum mechanics and relativity.

Of course, not that there has ever been a shadow of a doubt in the minds of anyone who knows anything about cosmology, it knocks on the head any daft notions of magic or a magic man being involved and it all happening just a few thousand years ago, no matter how attractive that simplistic notion might be to childish mind. No doubt though, creationist pseudo-scientist frauds will think up a strategy for dismissing it which will include any or all of lying about it, character assassination of the scientists involved, rubbishing science in general, simply dismissing it as wrong because it isn't in the Bible, or ignoring it altogether. But, they will never come up with any authentic evidence for their own daft notion.

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Saturday, 15 March 2014

Selfish Genes and Attractive Cannibals

Pennsylvanian grass spider Agelenopsis pennsylvanica
Zoologger: Female spider kills male to attract a mate - life - 11 March 2014 - New Scientist

Examples of females eating their mates during and after mating are well known in the animal world especially amongst the carnivorous insects and arachnids, like the praying mantis and the black widow spider, but it's rare to find an example of where this tendency actually makes the female more attractive to the male. In fact, at first sight, this would appear to run counter to what evolutionary theory tells us should happen.

But, with a little bit of thought and application, it is quite possible to come up with perfectly rational scenarios where this is exactly what evolving 'selfish' genes might produce. It might also be an example of evolution in progress where competing strategies might not have produced a winner yet.

I can't for the life of me see how it can be explained as the intelligent design of an all-wise and all-loving creator though. Maybe there is a creationist who can help me out here by suggesting one other than by invoking the universal cop-out that we can't hope to understand the mind of this magic creator but we should just accept that it's all for the best, because everything done by God er... The Intelligent Designer is perfect.

This particular example involves a harmless (to humans) common spider - Agelenopsis pennsylvanica or Pennsylvanian grass spider - which inhabits the northern United States down to Tennessee and Kansas. The species is one of the largest of thirteen similar Agelenopsids which live in grass and make a sheet web with a funnel at one end leading to a hole in the foliage, where they hide. The web isn't sticky like most spider webs but the spider is fast and rushes out of the funnel to grab any passing prey which walks on the web so alerting the owner to its presence.

But, to get to his potential mate, a male A. pennsylvanica needs to get across this web and close enough to the female to deliver his sperm package without triggering the attack response in his mate. Unfortunately he often fails and ends up as a meal.

Unlike the black widow where at least mating often takes place before she eats her mate, and the mantis where it normally at least gets under way, then the male makes do without his head as the female reaches round and eats it, finishing the rest off later when mating has finished, most male A. pennsylvanica who get eaten get eaten on the initial approach. Field studies have shown that, in urban areas, females are approached between zero and three times by males in the three-week breeding season so eating them seems a shortcut to extinction by celibacy yet 38% of females eat the first male to approach.

Now a team led by Jonathan Pruitt of the University of Pittsburgh in Pennsylvania, USA, has shed some light on what's going on here. They captured 100 wild females and divided them into two groups of 50. One group were fed wounded males; the other crickets - their normal prey. Between 20 and 24 days later they gave 20 male spiders a choice of females. 75% of them picked the females which had eaten a male.

They also found that the cannibal females produced more and better quality eggs which were more likely to hatch. They had obviously got some nutritional benefit from eating a male. The key finding however was that females normally only eat one male after which they can be approached with relative safety. 38% of females ate the first male to approach them but only 5% ate a second male. They seem somehow to be sending out the message that they have already had lunch to prospective mates.

Abstract
Precopulatory sexual cannibalism is an extreme form of sexual conflict that can entail significant costs to the cannibalized individual and a variety of costs and benefits to the cannibal itself. Characterizing these costs and benefits is fundamental to our understanding of how this behavior evolves. Using the spider Agelenopsis pennsylvanica, we tested the reproductive consequences of precopulatory sexual cannibalism by staging cannibalization events and comparing the performance of experimental cannibals against natural cannibals (i.e., those that cannibalized on their own) and non-cannibals. We found two performance benefits associated with precopulatory sexual cannibalism: first, experimental cannibals were more likely to produce egg cases than non-cannibals, and second, egg cases from experimental cannibals and natural cannibals were significantly more likely to hatch than those produced by non-cannibals. We then tested whether males were more likely to approach the webs of experimental cannibals vs. non-cannibalistic control females. Our data demonstrate that sexual cannibalism increases female attractiveness to males. Although this result seems counterintuitive, in fact, rates of precopulatory sexual cannibalism were much lower in females that had already cannibalized their first male: 38% of sexually naïve females engaged in precopulatory sexual cannibalism, whereas only 5% of females engaged in cannibalism a second time. Thus, males that approach cannibals receive two benefits: they are less likely to be cannibalized precopula, and they have the possibility of mating with females that have a higher probability of producing viable egg cases. Taken together, our data suggest that precopulatory sexual cannibalism affords females numerous benefits and may have a hand in shaping male mate choice decisions.

Pruitt, J. N., Berning, A. W., Cusack, B., Shearer, T. A., McGuirk, M., Coleman, A., Eng, R. Y. Y., Armagost, F., Sweeney, K., Singh, N. (2014),
Precopulatory Sexual Cannibalism Causes Increase Egg Case Production, Hatching Success, and Female Attractiveness to Males.
Ethology. doi: 10.1111/eth.12216

So what's going on here?

Well, the gene theory of evolution tells us that whatever 'strategy' produces more copies of genes in future generations will come to predominate in the species gene pool. It seems that, like black widows and mantises, providing the female with a free meal from which she can build more viable eggs will produce more surviving copies of the male genes. Males play no part in rearing the offspring and have no utility value to either female or offspring. The genes have no concern for the individual welfare of their carriers so these extreme forms of altruism can be expected in the right circumstances.

So, at some point in their evolutionary history, A. pennsylvanica probably went through a stage in which males were eaten postcopula by a percentage of females. Meanwhile, with no way of knowing whether the female was a cannibal or not, males had no choice but to run the risk (not that this is a conscious decision, of course), but if the offspring acquired some advantage there was not only no evolutionary pressure to do away with cannibalism but there may well have been evolutionary pressure to retain it.

Then, with a ready supply of males, there was some advantage to the females in eating the first male before mating - maybe the additional time to assimilate whatever they got from them before producing eggs. These over-eager males were now at a significant disadvantage because they provided sustenance but not to their offspring so there was now a much stronger reason for males to avoid cannibal females in terms of perpetuation of their genes.

So, males had a reason to evolve ways of discriminating and females had a reason to evolve ways of overcoming this tendency and they had the means - they could use something from their dead suitor to signal to the males that they were now safe to approach. So, females who provide this signal and males who can detect it and respond to it, both derive a benefit in terms of more high-quality eggs and more offspring carrying the genes for it.

This system appears to give a significant advantage to females and to males who wait for the safety signal, so the fact that 62% of females are not cannibalistic suggests there are ongoing evolutionary arms races here between different strategies. Males appear to have two strategies - to make an early approach which is successful in 62% of cases but the eggs are of lower quality, or wait for the safety signal and be successful with the remaining 38% of females but with better quality eggs. Meanwhile females also have two different strategies - eat the first male and produce more high-quality eggs with the second if one comes by and if it detects your signal, or mate with the first one and produce lower quality eggs. Self-evidently, the system can't move to one where all the males play the waiting game because that strategy would be bound to fail. If it happened locally, that population would go extinct, so removing all their genes from the gene-pool.

It may well be that the arms races simply haven't run their course yet, or the different competing evolutionary drivers have arrived at an equilibrium, but we may be seeing evolution in progress here. We are certainly seeing evidence of selfish genes doing what selfish genes do - making copies of themselves with no regard to what effect their strategy for doing so has on individuals, just so long as it gives the most copies.

Any creationist prepared to take up my challenge or will it be silence again as usual when faced with real examples of real evolution instead of the usual infantile parodies you normally attack?

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Thursday, 13 March 2014

How Evolution Changed Our Minds

American-born primatologist Alison Jolly, who sadly died on 6th February in Lewes, East Sussex, UK, was a Visiting Scientist at the University of Sussex and was instrumental in changing our view both about the role of social interaction in evolution and the role of gender in group leadership.

She was the first to report that females are dominant in some primate species, an observation based on her study of lemurs in Madagascar, where, unlike prosimians in the rest of the world, they have evolved in the absence of true monkeys to fill the niche occupied by true monkeys elsewhere. We now know that many primate groups are led by females, not males, so there is nothing inherently male about the ability to dominate and lead a group.

Her work also did much to change the then prevailing view that human intelligence evolved because of the need for more and more sophisticated tools, to the now generally accepted view that it was increasingly complex social interactions which was the main driver. Alison Jolly's research means we can sit back in quiet amusement when creationists display their occasional examples of critical thinking ability, knowing that even such a rarely-used ability only exists because it evolved in their monkey ancestors.

We now know that what underpins social interaction is not necessarily genetic at all but involves analogous replicators we now call memes or "memory genes" which form complexes which we inherit from our parents, peers and authority figures in our culture. As replicators they fulfil the three requirements for evolution:
  • Inheritance.
  • Imperfect replication.
  • Selection.

This means they will inevitably and inexorably evolve over time towards perfection for their own perpetuation through time in that environments. Like all replicators, memes will tend to form alliances with other replicators, whether memetic of genetic, because the result of alliance is often greater fitness than a replicator acting in isolation. And so memes formed alliances with genes for bigger brains and brains capable of processing the necessary information. We now refer to this as gene-meme co-evolution which is especially, but not uniquely, relevant to human cultural, ethical and physical evolution.

Learning the rules of social interaction, deciding when and where to apply them and passing them on, all require intelligence and the ability to solve puzzles. As this ability increases so the rules can become more complex, limited seemingly only by the potential for evolving a larger brain with which to store and process this information.

It was only when early members of the Homo genus 'solved' the problem of how to grow a very large brain in comparison to that of other animals of equivalent body size, that we took off as a species both in our complex social evolution and in our tool making ability. As we adapted to an upright gait, which included reorganisation of the bones of our face to bring our eyes into a forward-looking position, this allowed our cranium to bulge upwards balanced on top of a spinal column instead of sticking out in front of it, so our brain was free to expand within the constraints imposed by the human female pelvis.

This increased brain size gave us such a huge advantage that it more than outweighed the resulting high mortality rate associated with pushing a large head through a curved birth canal; a rate far higher than in any other mammal. Our evolutionary partial response to this was to give birth to babies much earlier in their development and this paradoxically gave us a much longer period of childhood learning during which we could acquire these evolving memes and perfect our learned skill.

Alison Jolly's seminal paper published in Science in 1966 argued that the beginnings of human intelligence are to be found in early common ancestors in primates in which social interaction is an important part of daily life. In 1966 it was generally believed that man was the only tool-using animal so that could not have been the driver in our less intelligent relatives. We now know that we are far from alone in this skill and that several primates, and several unrelated species, also solve puzzles and fashion and use tools, but the general principle holds that most puzzle-solving primates are not toolmakers so tool making could not have driven their puzzle-solving ability.

Primates are extraordinary among mammals for their complex social relations and their ingenuity in handling (or destroying) objects. The evolutionary trends which led to the excellence of Homo sapiens in these lines began long before the transition from ape to man.

All monkey species are social. Although individuals may be solitary for a time, a monkey is usually part of a group throughout his life. And when he is taken from his wild group and loosed in laboratory or house he unlatches doors, solves hardware puzzles, and carefully stuffs aquariums with brass lamps and shredded medical texts. He can even be trained to drive tractors, or show the rudiments of symbolic thought...

An infant monkey, unlike an infant tiger or beaver or gnu, is likely to remain for life in the troop of its birth. The result is a social group of all ages, with several adults of either sex. When too large the group divides into smaller troops of roughly similar composition. This sort of social structure is rare in nonprimate mammals, but about half the primate genera studied conform to the rule...

Monkeys, more than any other mammals except their descendants, the apes and men, learn to be social. A rhesus raised in isolation from its kind may not mate normally or rear its own young. Primates have a long youth, compared to mammals of their size, and during this period, through association, exploration and play, the juveniles learn the ways of the troop. It is even possible that primates exploit the full capacity of their brain only during youth. Man, after all, accomplishes the gigantic feat of learning to speak, and may never again face such a daunting intellectual task...

In summary, the social use of intelligence is of crucial importance to all social primates. As the young develop, they depend on the troop for protection and for instruction in their role in life. Since their dependence on the troop both demands social earning and makes it possible, social integration and intelligence probably evolved together, reinforcing each other in an ever-increasing spiral. And, although it is very likely that the learned social relations of monkeys are in fact more complex than those of lemurs, our present techniques of description emphasize the similarity between lemur and monkey social interactions...

Primate society, thus, could develop without the object-learning capacity or manipulative ingenuity of monkeys. This manipulative, object cleverness, however, evolved only in the context of primate social life. Therefore, I would argue that some social life preceded, and determined the nature of, primate intelligence.

Summary and Conclusion.

Our human intellect has resulted from an enormous leap in capacity above the level of monkeys and apes. Earlier, though, Old and New World monkeys' intelligence outdistanced that of other mammals, including the prosimian primates. This first great advance in intelligence probably was selected through interspecific competition on the large continents. However, even at this early stage, primate social life provided the evolutionary context of primate intelligence...

Alison Jolly; Lemur Social Behavior and Primate Intelligence; Science, 29 July 1966, p. 501

These are the sorts of scientific papers which change our thinking, based as they are on meticulous observation, logical deduction and a willingness to go against the prevailing consensus when the evidence demands it. This is in stark contrast to the common creationist charge that scientists are forced by some sort of peer-pressure or conspiracy or condition of funding to conform to the prevailing dogmas and orthodox doctrines of the scientific world. In fact, the greatest respect is reserved for scientists like Alison Jolly who not only have the courage, honesty and integrity to change their minds, but give us the reasons to change ours too.

As one might expect, the charge creationists level at science is especially applicable to them, which is why they probably try to smear science with their own failings. Creation pseudo-scientists, for example, have to take an oath that their findings will never contradict anything in the Bible story of Genesis, as a condition of receiving financial support from the Institute for Creation Research or publishing in their publications or websites. Their much-vaunted process of 'peer-review' is simply a check to make sure they have kept their agreement. No self-respecting real scientist would agree their conclusions or promise not to challenge established science in advance of their research as a condition of funding and/or publication. Any who did so, or who hawked themselves around to the highest bidder, would quickly lose all credibility in the scientific community.

This is why science is a very different thing today to that in 1814 and almost unrecognisable when compared to that in 1714, whilst theology is virtually indistinguishable from that of the 18th and 19th-centuries and creationism hasn't progressed in the last 4000 years.





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Sunday, 9 March 2014

Edible Frogs and Unintelligent Design.

Pelophylax kl. esculentus. Image: Grand-Duc, Wikipedia.
Here's a puzzle for the 'Intelligent Design' movement. All you have to do is explain the intelligence behind the design and say why ID is a better explanation than that offered by evolution theory.

Here are the facts (I hope that word hasn't put the IDiots off!):

The Edible Frog (Pelophylax kl. esculentus) is a name for a common European frog, also known as the Common Water Frog or Green Frog (however, this latter term is also used for the North American species Rana clamitans). It is used for food, particularly in France for the delicacy frog legs...

P. esculentus is endemic to Europe. It naturally occurs from the northern half of France to western Russia, and from Estonia and Denmark to Bulgaria and northern Italy. It is introduced in Spain and the United Kingdom. The natural range is nearly identical to that of P. lessonae...

Pelophylax kl. esculentus is the fertile hybrid of the Pool Frog (Pelophylax lessonae) and the Marsh Frog (Pelophylax ridibundus), hence the addition of the "kl." (for klepton) in the species name.

During the ice ages, the population of the common ancestor of both species was split into two. These populations diverged, but remained genetically close enough to be able to create fertile hybrids. However, when edible frogs mate with each other, their offspring are often malformed, so there are no pure populations of edible frogs.

The hybrid populations are propagated predominantly by female edible frogs mating with males of one of the parental species (P. kl. esculentus × P. lessonae or rarely × P. ridibundus).

Hybridogenesis implies that gametes of hybrids don't contain mixed parental genomes, as normally occurs by independent chromosome segregation and crossover in meiosis (see also second Mendel's law, recombination), but intact one of them or two. Usually because one entire genome of the parental species is excluded prior to meiosis during gametogenesis.

P. lessonae. Image:Piet Spaans.
P. ridibundus. Image: © Marie-Lan Nguyen.
Typical hybridization between pool frog (P. lessonae), marsh frog (P. ridibundus)
and their hybrid - edible frog (P. kl. esculentus, P. lessonae x P. ridibundus) in a
native LE (lessonae-esculentus) hybridogenetic population invaded additionally by
P. ridibundus. Predominant matings are P. kl. esculentus females x P. lessonae
males and P. ridibundus females x P. lessonae males. P. kl. esculentus x P. kl.
esculentus
crossings result in inviable P. ridibundus tadpoles and are not shown here.
Large circles - adult frogs, small circles - gametes.,
x - lack of gametes containing genome of one of parental species.
On a technical note, some authorities dispute the statement that there are no pure populations of P. esculentus because triploid P. esculentus individuals are common and can produce fertile offspring and so form pure populations, however these populations tend to be short-lived.

The reason this 'green frog complex' has arisen during the course of evolution is because during the production of gametes the frogs chromosomes do not exchange genes and so mix up their genomes. In P. esculentus there is one complete P. ridibundus set and one complete P. lessonae set. In a triploid form there will be two sets of one and one of the other. So, when they mate with one or the other parent species, they can produce offspring with the complete genome of eitherP. ridibundus or P. lessonae, or more P. esculentus.

Okay, so that's all straightforward so far. Nothing there that can't be explained in terms of evolution and perfectly natural things with no magic required. So, the question for creationists then is, why would an intelligent designer create edible frogs in such a bizarre and unorthodox fashion when it had designed a perfectly sensible way to produce other species with perfectly normal sexual reproduction? The supplementary question of course, is how is whatever explanation you manage to come up with better than the scientific one and what does it explain that the scientific one doesn't?

Incase you're wondering, I have eaten frog's legs. I found them slightly unpleasant tasting. Maybe I was unfortunate but I probably won't be eating them again through choice.

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Saturday, 8 March 2014

Human Evolution is Speeding Up

Human Evolutionary Change 100 Times Higher in Past 5,000 Years

A popular theme on creationist websites is that no-one has ever seen evolution occur. We'll, it's certainly true that no-one has ever seen a creationist parody version of evolution occur, but then they wouldn't do, would they. The parody was designed to be ludicrous; that's the point of parody.

For a successful snake-oil salesman, the trick is to fool your audience into believing the parody is the real thing and that must be the simplest thing in the world to achieve, given that the target audience is not only largely ignorant of science but proudly so and is eager to be fooled because what they crave most is confirmation, no matter how spurious.

An ancillary theme to this is endless debate about if and why human evolution has stopped. Even some serious scientists will wade in with explanations about why human evolution is no longer happening because we've removed all the natural selection mechanisms by isolating ourselves from our environment and even keep people with genetic defects alive long enough to have children when they would have died in childhood just a few years ago. The latter argument is often used either to try to justify eugenics or to smear those who accept the evidence for evolution as secret eugenicists, in some sort of attempt to argue from consequences. Even if it were true, abusing evolutionary theory in pursuit of a social or political agenda does not render the theory wrong anymore so than the undesirability of nuclear war renders atomic theory wrong or the harm which comes from stepping off a high building renders the theory of gravity wrong.

But, for the real meaning of the word 'evolution', not only do we see evolution occurring almost everywhere we look in the natural world but we can see examples of it happening quite recently in lactase persistence, altitude adaptation in Han Chinese on the Tibetan Plateau, and in kuru resistance in a New Guinea tribe.

And as recently as 2007 it was found that human evolution has not stopped or even slowed down, but for the last 5,000 years it seems to have been continuing at a rate some 100 times faster than previously and may even be accelerating and that we are genetically more different to people living 40,000 years ago than they were to Neanderthals.

Abstract
Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million 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 (i) site heterozygosity at least 10-fold lower than is observed in humans, (ii) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (iii) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (iv) nearly 100 times the observed number of high-frequency linkage disequilibrium 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.

John Hawks, Eric T. Wang, Gregory Cochran, Henry C. Harpending, and Robert K. Moyzis;
Recent acceleration of human adaptive evolution; Proc Natl Acad Sci U S A. Dec 26, 2007; 104(52): 20753–20758. doi:10.1073/pnas.0707650104

The reasons for this high rate of change seems to be two-fold: very rapid population growth and simultaneous movement into new environments both physical and cultural.

Normally, as a population evolves into a new environment, natural selection ensures it evolves rapidly towards perfection for living in that environment but, as perfection is approached, the opportunities for a mutation to arise which gives greater fitness are reduced, so species tend quickly to reach a stable state of evolution so long as the environment remains stable.

Another factor which can affect the incidence of new mutations, and so the opportunity for an advantageous one arising, is population size. Larger populations improve the number of one in a million mutations or combinations of positive mutation in the presence of others in the same individual happening in each generation, both improving the opportunity for genetic drift or natural selection concentrating this up the improbability gradient towards fixation.

Over the period in question, humans developed agriculture which had four major consequences for our evolution:

  • Population increased rapidly.
  • Populations became settled and crowded into large settlements, so facilitating the spread of parasites.

  • Trade increased contact with other human groups and cultures, so facilitating gene flow throughout the entire range as well as the flow of parasites.

  • Domestication of animals placed us in close proximity to their diseases and parasites, increasing the chance of parasites crossing the species barrier.


One example of how this closer association with parasites, especially those we probably got from domestic animals, can cause evolution, is the incidence of the CCR5 gene which is present in 10% of Europeans and gives a measure of protection against AIDS/HIV. This is thought to be the result of evolved resistance to smallpox which we probably got when the virus causing cowpox in cattle crossed the species barrier into humans.

An example of how this rapidly evolved resistance to diseases gave Europeans an advantage is how it helped them become the dominant world power and culture. As Jared Diamond explained in Guns, Germs & Steel, as they came into contact with new people their parasites, to which they were at least partially resistant, acted as a kind of invisible biological fifth column, devastating and weakening the opposition with killer diseases to which they had no resistance but which in Europe were usually fairly mild childhood diseases like measles. It was the fact that we had lived for longer with more domestic animals than almost any other peoples which gave us and our genes this evolved biological advantage and an invisible weapon of mass destruction to wage biological genocide on our behalf.

It is sometimes claimed that the pace of human evolution should have slowed as cultural adaptation supplanted genetic adaptation. The high empirical number of recent adaptive variants would seem sufficient to refute this claim. It is important to note that the peak ages of new selected variants in our data do not reflect the highest intensity of selection, but merely our ability to detect selection. Due to the recent acceleration, many more new adaptive mutations should exist than have yet been ascertained, occurring at a faster and faster rate during historic times. Adaptive alleles with frequencies under 22% should then greatly outnumber those at higher frequencies. To the extent that new adaptive alleles continued to reflect demographic growth, the Neolithic and later periods would have experienced a rate of adaptive evolution more than 100 times higher than characterized most of human evolution. Cultural changes have reduced mortality rates, but variance in reproduction has continued to fuel genetic change. In our view, the rapid cultural evolution during the Late Pleistocene created vastly more opportunities for further genetic change, not fewer, as new avenues emerged for communication, social interactions, and creativity.

John Hawks, Eric T. Wang, Gregory Cochran, Henry C. Harpending, and Robert K. Moyzis;
Recent acceleration of human adaptive evolution; Proc Natl Acad Sci U S A. Dec 26, 2007; 104(52): 20753–20758. doi:10.1073/pnas.0707650104

So, not only is it wrong to claim that no-one has seen evolution or that here is no evidence for it, and not only is it wrong to claim that human evolution has slowed right down or stopped, but the claims run counter to the evidence. Evolution can be seen to be happening and the rate at which it is happening in humans has been increasing at least over the time scale at which this can be measured with any degree of confidence.

Perhaps more interestingly is that this rapid rate of evolution corresponds with what we know of human cultural and social development and population growth, illustrating neatly how different strands of evidence come together to reinforce the concept of evolution.

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Friday, 7 March 2014

Your Ancestors Mated With Chimpanzees

Human Ancestors May Have Interbred With Chimpanzees

To anyone who understands how evolution works, the news that humans and chimpanzees interbred for a considerable period as the two species diverged from a common ancestor will come as no surprise. Evolution is not normally a sudden event or single act of speciation but a long, slow process in which it is impossible to say precisely where one species became two.

From the chimpanzees' point of view, their ancestors mated with humans. I wonder if they would also find the idea fascinating but at the same time slightly disturbing, even a little distasteful.

Scientists comparing human and chimpanzee genomes have found that their X-chromosomes last shared a common ancestor about 5.1 million years ago but all the others appear to have diverged about 6.3 million years ago. In other words the X-chromosome is 1.2 million years younger than the rest of our genome.

It's as though we diverged twice. In fact, this may well be what happened. We began to diverge about 6.3 million years ago, probably into different habitats, but remained similar enough to be able to interbreed when we came into contact for about a million years before finally diverging completely about 5.1 million years ago.

Abstract
The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

Nick Patterson, Daniel J. Richter, Sante Gnerre, Eric S. Lander and David Reich;
Genetic evidence for complex speciation of humans and chimpanzees;
Nature 441, 1103-1108 (29 June 2006) | doi:10.1038/nature04789

I think the most interesting thing [is] this idea that long, extended gene flow seems to have occurred and that this might be a creative mode of evolution.

David Reich, Geneticist,
Harvard Medical School, MA, USA
And this illustrates how speciation is not the creationist parody event. In this infantile parody, evolution is a single event where one entire species changes into a different one through a series of discrete intermediate stages, or more bizarrely one member of one species gives birth to a different species which then goes on to reproduce, presumably with itself, to form a new species. Apparently creation pseudo-scientists assume their target audience will believe that hundreds of thousands of serious biologists delude themselves into thinking these are realistic scenarios and are either too stupid to see how implausible they are or are simply all conspiring to mislead people for some political or religious reason.

In fact, it's the creationist frauds who are lying for political and/or religious reasons and many of them will have taken the ICR oath that their 'research' and writings will always be in full accord with the biblical account of Creation in Genesis, as a condition of funding and publication. But this tactic plays to the ego needs of an audience of people who want to believe that their ignorance of science gives them a greater understanding of reality than all that studying and research, and who see science as elitist and scientists as all more than a little bonkers.

This is contributing to the idea that species are kind of fuzzy. They become real over time, but it takes millions of years. We probably had a bit of a messy origin.

James Mallet, Geneticist,
University College, London, UK
Speciation is often a very slow process of gradual divergence across a large geographical range as different populations respond to local change or simply drift genetically more quickly than their genes can flow across the entire population. That's not to say it can't be a fairly sudden divergence if one part of a population becomes isolated for some reason, for example the newly-discovered river dolphin, Inia araguaiaensis, which became isolated when geological events led to a population becoming isolated in a branch of the Amazon river system.

Where speciation happens gradually this can lead to the phenomenon of the 'ring species' where the species gradually changes across its range to form a cline but where breeding can occur in some overlapping areas. This appears to have been the situation with evolving humans and chimpanzees for over a million years and it appears to have been the situation with diverging human populations later on where modern humans and archaic forms seem to have interbred and closely related species like Homo sapiens, H. Neanderthalensis and the so-far unnamed 'Denisovans' seem to have interbred so that genes could occasionally flow between species.

  1. 'Whatever the Bible says is so; whatever man says may or may not be so,' is the only [position] a Christian can take..."
  2. If [scientific] conclusions contradict the Word of God, the conclusions are wrong, no matter how many scientific facts may appear to back them.
  3. Christians must disregard [scientific hypotheses or theories] that contradict the Bible.

W.S. Pinkston, J.A. Graham, G. Kuzmic and C. Vogt;
Biology for Christian Schools;
Bob Jones University Press
And of course, in species where sex has a social and recreational role, as well as a reproductive one, this tendency to interbreed would likely have been more marked than where sex depends more on hormones and visual or other sensory stimulation and serves a purely procreational function.

What you will never get a creationist to acknowledge is that this mode of evolution not only would not produce the 'missing link' they keep demanding science produce but that we should not expect to find any. We would expect the fossil evidence to be exactly what it is - a slightly muddled, fuzzy picture with no strong demarcations and a series showing gradual change over millions of years, just as the DNA evidence is reflecting.

This will give scant comfort to those who require evolution to be a childishly simplistic process of sudden change such as one might see in a biology book for the unfortunate children of Christian fundamentalists.

[Footnote] The above discovery was made seven years ago. Love and kisses to the first person who can find any reference to it on a creationist website or in any of their publications.

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