F Rosa Rubicondior: January 2014

Thursday 30 January 2014

Myxy Sticks, Rabbits And Rapid Evolution

When I was a child of about 10 or 11, the English countryside saw one of the most impressive cases of rapid evolution yet witnessed in a wild mammal. It took just about ten years. It was also witnessed in Australia and the rest of Europe. It was how the European rabbits (Oryctolagus cuniculus) and the myxoma virus co-evolved to accommodate one another.

I remember still how during the first onslaught of rabbit myxomatosis the countryside suddenly became full of pathetic 'myxy' rabbits staggering blindly (and deafly) about, their eyes and ears swollen and closed with hideous pustules, completely lost and disorientated to be squashed by cars, killed by dogs and cats and dispatched mercifully by us humans who carried our 'myxy sticks'. The foxes had a heyday and their population exploded for a year or two. I once killed twenty rabbits in the corner of a single field in a few minutes. You had to be careful how you handled a myxy stick as the wrong end was a gory, pusy mess. You could easily spot a distant myxy rabbit because the swelling exposed the pale under-fur making it look like they had pale bases to their ears and pale stripes over their eyes.

The Legacy Of Sex With Neanderthals

Neanderthal-human sex bred light skins and infertility - life - 29 January 2014 - New Scientist

Modern techniques of DNA recovery, sequencing and analysis are quickly adding enormously to our understanding of the human evolutionary story, at a rate which must be terrifying to the professional liars at the Discovery Institute and the Institute for Creation Research whose job it is to either rubbish the science or distort it to make it look like creationists have a rational scientific point of view.

Take for example the three new studies published recently which shed more light on how Euro-Asian humans interacted with Neanderthals. Neanderthals (Homo neanderthalensis) are believed to have evolved from the close ancestors of 'modern' humans (H. sapiens), possibly H. heidelbergensis or H. erectus which migrated out of Africa and dispersed into Europe and Asia some 200,000 years ago, leaving those behind in Africa to evolve into H. sapiens, who followed them out in a second exodus, some 65,000 years ago and where they then co-existed as separate human species for some 35,000 years. It could be that we owe much of our success to our sister species who went before us.

It was once believed that there was no interbreeding between H. sapiens and H. neanderthalensis until the Neanderthal genome was successfully isolated and sequenced. It was then found that non-African H. sapiens have between 1% and 3% Neanderthal DNA showing beyond doubt that interbreeding had taken place.

Now detailed analysis of the genomes of 1004 people by Sriram Sankararaman, David Reich and colleagues of Harvard Medical School has revealed that Neanderthal DNA tends to be concentrated in regions of the genome with greatest variability, making these genes more susceptible to natural selection and so contributing more to our evolution. So, although forming a relatively small proportion of the genome, Neanderthal genes could have contributed disproportionately to our evolution, especially into a northern, temperate climate.

Meanwhile, a second study by Joshua Akey and Ben Vernot of the University of Washington in Seattle has shown that Neanderthal genes tend to be clustered around those associated with keratin production. Keratin is the structural fibrous protein found in skin, nails and hair. This finding was also supported by the Harvard study.

One of the genes involved was that producing pale skin, which is an advantage in cloudy northern climates where skin cancer is less of a problem and where Vitamin D, which is produced in the skin under the influence of sunlight and which is essential for normal bone development in children, can be deficient, especially if the sunlight is filtered out by pigmentation. So we have the possibility that Neanderthal genes provided us with paler skin.

However, this may be contradicted by a third study published in Nature by Iñigo Olalde, Morten E. Allentoft and colleagues of the genome of a single Stone Age European who lived about 7000 years ago near León, Spain had dark skin. Of course we can't project this finding onto all Europeans from 7000 years ago but it shows that pale skin was not then a universal European trait. This was some 40,000 after interbreeding between H. sapiens and Neanderthals could have taken place, so it they contributed to European pale skin, it was slow to spread throughout the European H. sapiens gene pool.

The question then is did Neanderthal keratin genes give us straighter hair than our African ancestors?

This underlines that modern humans and Neanderthals are indeed different species.

Fred Spoor, The Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
Other findings by the Harvard study show that not all Neanderthal genes were beneficial. Some seem to have made us more susceptible to autoimmune diseases such as type II diabetes, lupus and Crohn's Disease. It has previously been suggested that they could have made us more susceptible to arthritis in later life. They also found an almost complete absence of any Neanderthal genes on the sex-determinant X chromosome, suggesting that, when these were passed on they may have caused infertility and so would have been quickly eliminated. This is a common problem when related but distinct species interbreed, reinforcing the idea that Neanderthals had evolved into a distinct species, not a subspecies or merely a local variant, as had earlier been thought.

Because Neanderthal DNA is clustered in the H. sapiens genome rather than being more evenly admixed within it, this suggests that inter-breeding was a rare event. Sriram Sankararaman goes so far as to estimate that it may have happened only four times.

If this is so, it may well be that it was always H. sapiens male mating with H. neanderthalensis females since Neanderthal Y chromosomes, which are always inherited only from the father, have never been recovered from modern humans. Of course, this could also be because they are so rare that we just haven't found one yet - which doesn't square with Neanderthal DNA being found in all non-African humans. It could also indicate that a Neanderthal father and an H. sapiens mother always produced offspring with reduced fertility, or even sterile offspring.

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Is This The Mother Of All Spiders?

A Silurian short-great-appendage arthropod

A strange new arthropod beautifully preserved in a nodule of calcite, found in rocks known to geologists as the Wenlock Series Lagerstätte in Herefordshire, UK, may be the ancestor of modern arthropods, including spiders, insects, lobsters, king crabs and scorpions. It has been given the scientific name Enalikter aphson. The arthropods get their name from the fact that they all have jointed legs and an external skeleton, features which evolved very early on. The only other group to evolve jointed limbs were the much later vertebrates with internal skeletons.

Using a technique known as Optical Projection Tomography the team led by Derek J. Siveter of Oxford University Department of Earth Science produced this detailed image from the only known 3D fossil of what are known as the stem-group arthropods, i.e. the group from which other arthropods evolved.

The significance of this find is that it is from rocks known to be 425 million years old, which makes it young by stem-group arthropod standards, being some 100 million years younger than previously found Megacheira (=short-great-appendage) all of which were from the Middle Cambrian era between 480 and 540 million years ago.

The taxonomic position of the Megacheira is controversial: were they stem chelicerates (a later sub-group of arthropods), or stem euarthropods? This specimen, together with another older Megacheira, Bundenbachiellus giganteus, found in Hunsrück Slate in Germany from the Devonian Era, makes it much more likely that the group this new species belonged to were stem euarthropods, in other words, that they were the ancestors of all spiders, lobsters, insects, etc.

Any creationist prepared to hazard an explanation of why an intelligent designer who made everything just the way it is today, would put this fossil of a primitive arthropod so unlike anything else we see today, in a calcite nodule in Herefordshire, UK and made it look 425 million years old?

Derek J. Siveter, Derek E. G. Briggs, David J. Siveter, Mark D. Sutton, David Legg, and Sarah Joomun, A Silurian short-great-appendage arthropod; Proc R Soc B 2014 281: 20132986

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Sunday 26 January 2014

River Dolphins Teach Us About Evolution

Prompted by a comment by Bill The Butcher on my recent blog about the newly-discovered river dolphin in the Amazon river system, I decided to do a little reading around the subject.

The changing state of our knowledge about the evolution of these specialised dolphins, which inhabit river systems as widely separated as the Amazon and its tributaries, the Indus and Ganges rivers in northern India, the Yangtze River in China and the Rio de la Plata in South America, is a good illustration of how science modifies its theories in view of new knowledge and how any current explanation is regarded as provisional and open to revision with unsolved questions freely acknowledged.

On a technical note, the De La Plata dolphin (Pontoporia blainvillei), although in the same family as the river dolphins is actually an estuarine and coastal dolphin, not a freshwater dolphin. Sadly, the Baiji from the Yangtze River (Lipotes vexillifer) has not been seen since 2004 and is now considered extinct in the wild.

So, the first question is how did these dolphins, which were once included in the same Platanistidae family because they all shared the same anatomical features, come to be so widely separated if they were adaptive features for living in rivers? The 'solution' was to assume all these shared anatomical features evolved independently by convergent evolution in response to similar environments. The anatomical features are:
  • A long thin 'beak' or rostrum
  • Reduced eyes
  • A large number of teeth in both upper and lower jaws
  • A flexible neck
Of course, it's possible that some of these features could have convergently evolved but so many seems unlikely and this is further complicated by the fact that the De La Plata dolphin, P. blainvillei, shares these features but lives in the sea and salt-water estuaries.

But, if these features evolved independently then there is no real basis for lumping them all together in the same family in the first place. The taxonomy and the theory were inconsistent and unsatisfactory.

Cue DNA and molecular analysis.

This has shown the original taxonomic grouping to be to crude. On the basis of molecular evidence, the Ganges and Indus River dolphins are in one group which, under the rules of nomenclature, retains the Platanistidae family name, being the first to be named. The remaining ones are placed in a new Iniidae family which includes the newly-discovered species, Inia araguaiaensis.

But that still leaves the problem of explaining related species in China and South America, and on opposite sides of India with no communication between the river systems. Here fossil evidence gives us a further clue.

Fossil evidence strongly suggests that the original environment of the ancestors of the Inia, Platanista and Lipotes genuses were all marine, not riverine. It seems that the flexible neck, long rostrum and large numbers of teeth could be adaptations not for rivers but for hunting in sea water, as could the reduced eyes as the ancestors came to rely more on sonar than on sight for prey detection in turbid waters. Turbid waters are found in estuaries and inshore waters as well as in rivers. These adaptations also fitted them equally well for rivers, estuaries and coastal plains, opening up the rivers as potential new niches to move into. The only thing that has probably evolved three or four times is freshwater tolerance.

So here we see the molecular and fossil evidence coming together to solve a previous mystery in dolphin evolution and so giving us a much more satisfactory taxonomic structure. We can also see how features evolved for use in one environment can sometimes open up potential new niches, and how when this happens, species can diversify into these new niches. Again the revealed facts fit comfortably within the Darwinian Theory of Evolution by Natural Selection, the unifying principle which makes sense of biology.

The question creationists need to address is why an intelligent designer would put dolphins in the rivers but the fossils of all their ancestors in the sea and then made the molecular evidence agree with the fossil record to make it look like the river dolphins evolved out of a marine one slowly over time, so giving a perfectly natural explanation for both their morphology and geographical distribution without needing to invoke magic and a magic creator. Any takers?

One can almost hear the groans of disappointment of a creationist pseudo-scientist as he tears up the manuscript of another book explaining to his credulous audience how the distribution of river dolphins can't be explained by evolution and so proves evolution doesn't happen, so their favourite magic god must have made them 6000 years ago by magic and put them in the rivers, therefore science is all wrong and the country should be run by self-appointed Christian fundamentalists who know what's best for everyone.

Further reading:
Wild Mammal Blogs, The Evolution of River Dolphins, 15 July 2011
Geisler JH, McGowen MR, Yang G, Gatesy J. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol Biol. 2011 Apr 25;11:112. doi: 10.1186/1471-2148-11-112.

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Lost Lake May Have Helped Humans Leave Africa

Long-lost lake may have helped humans out of Africa - 22 January 2014 - New Scientist

Another piece has probably just fallen into place in the jigsaw puzzle of human evolution and our diversification out of Africa into the Middle East and Euro-Asia.

Migrating populations rarely up sticks and go on a long journey to distant lands. Instead the movement can be slow, spread over many generations and involve long stops and stable populations on the way. One problem, for example, is taking enough food for the journey because fruit and vegetables go bad after a while and livestock needs food and water. Sure you can hunt and gather on the way but that presupposes there will be something to hunt and gather. For this reason, deserts and barren mountain ranges are impassable barriers to human migration, especially early, low tech people like our early human ancestors.

It had long been assumed that modern Homo sapiens didn't come out of Africa until we had developed to a certain threshold level of intelligence and technology about 70,000 years ago to enable us to adapt to new environments on the way, but this was thrown into question when remains of very early humans from about 100,000 years ago were found in Israel. The mystery was how these people managed to cross the Sahara and the expanses of desert between East Africa and the Eastern Mediterranean.

But Martin Williams of the University of Adelaide in Australia and Tim Barrows of the University of Exeter, UK, have analysed samples collected from former lake-shore deposits, and dated them to about 109,000 years ago. This lake would have been one of the largest lakes in the world if it existed today at about 450,000 square kilometers and would have been in just the right place at the right time to support a large human population north of Ethiopia and with connections to the Nile which forms a narrow fertile strip across the Sahara to the Mediterranean coast. Although the size of the lake would have varied with the seasons it would have been large enough to still be a sizeable lake even in dry periods.

A big lake like this would have been a great place to live. It would have supported a large population, probably fishing and hunting game.

Stephen Oppenheimer, University of Oxford
Then, due to climate change and loss of monsoon rains the lake began to shrink, disappearing sometime between 70,000 and 100,000 years ago. The population would have been forced to migrate, and the obvious route is via the Nile to the Mediterranean and then east to modern Israel. A lake-side people could have easily adapted to living along a river.

So, we now have an explanation of how humans reached the Eastern Mediterranean before we had reached the assumed intelligence/technological threshold. However, DNA analysis shows that the modern Euro-Asian population only came out of Africa about 71,000 years ago, presumably absorbing or exterminating any earlier migration, assuming anyone had survived.

The question is whether the newly-discovered lake played any part in this second wave. This depends on precisely when it finally disappeared and there is not enough evidence to determine that precisely. It's disappearance could have triggered the second wave but it seems more likely that by then sea levels had dropped as the last Ice-Age reached its height, so making it possible to walk across what is now the Red Sea basin into Arabia.

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Friday 24 January 2014

New Species Of Dolphin Shows How Evolution Works

Inia araguaiaensis
New species of river dolphin born of Amazon rapids - life - 22 January 2014 - New Scientist

The discovery in a tributary of the Amazon of the first new species of river dolphin in a century illustrates one of the basic ideas in evolutionary theory - diversification by population isolation, giving an isolated gene pool. It also illustrates how the morphological, genetic and geological evidence all line up perfectly with the theory of evolution by natural selection.

The discovery was made by Tomas Hrbek of the Federal University of Amazonas in Manaus, Brazil, and colleagues, who analysed the DNA from dophins in the Araguaia and Tocantins rivers and found them to be different to all other river dolphins found in the Amazon river system. These dolphins also have fewer teeth than other dolphins. The new species has been named Inia araguaiaensis,

DNA analysis gives the point of diversification from other members of the Inia genus at about 2.08 million years which coincides with the geological events which produced the Araguaia-Tocantins basin and cut the rivers off from the rest of Amazonia by waterfalls and rapids which form natural barriers for the dolphins so splitting the original population into two isolated gene-pools.

It's exciting evidence for a previously unrecognised species within the ancient lineage of Amazon river dolphins, yet it's already rare, and its habitat is now fragmented by dams.

Scott Baker, Oregon State University, Newport, USA
These are exactly the conditions which would be expected to produce speciation over time as the two different populations evolve on their own paths. Since the two populations may already not have a representative sample of the total population's genome they may even be on their way to diversification at the point of isolation - the so-called 'founder effect'. Differences in the local environments will quickly cause the populations to diversify genetically as different mutations and combinations of alleles will be more advantageous in one environment than they might be in the other, and so will be selectively favoured in one population but not in the other, where different mutations may come to predominate.

Similar geological events are thought to have produced similar sets of rapids isolating the Madeira river and coinciding with the evolution of I. boliviensis 2.87 million years ago, and on the Orinoco river, coinciding with the diversification of the subspecies I. geoffrensis humboldtiana.

Unfortunately, this newly-discovered species is already rare with a population of only about 1000 and it is under severe threat from human activity, especially new dams on the Araquaia and Tocantins rivers, so it may well become extinct in a few years, the victim of environmental change so rapid that the slow pace of evolution can't save it.

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Evolving Dog Cancer Gives Clue to Dog Origins

The ancient tumour genes are most similar to husky genes
Infectious cancer preserves dog genes for 11,000 years - life - 23 January 2014 - New Scientist

Scientists have discovered that the genes in a transmissible cancer, canine transmissible venereal tumour (CTVT), which infects the genitalia of dogs and which is passed on during mating, are all from a single dog in which the tumour first arose, some 11,000 years ago. It is one of only two known mammalian cancers which can be passed directly from one individual to another. The other is a tumour transmitted between Tasmanian devils when they bite one another.

Since every tumour is effectively a clone of this original one, the genes have remained close to those of the original dog and can be found in dogs all over the world. They can thus shed light on the origin of the domestic dog although the dog is believed to have been domesticated far earlier - about 33,000 years ago. This discovery was made by a team led by Elizabeth Murchison of the Wellcome Trust Sanger Institute in Hinxton, UK, who analysed DNA from tumours from dogs from Australia and Brazil.

Wednesday 22 January 2014

More Ado About Nothing

Nothingness: Why nothing matters - physics-math - 24 November 2011 - New Scientist.

The above article is from the New Scientist book, Nothing - From absolute zero to cosmic oblivion - amazing insight into nothingness. A subject about which I have also blogged in the past.

Understanding nothing is of course fundamental to understanding the structure of the Universe and how it could have spontaneously self-created. Creationists make a great play of nothing with nonsensical claims such as "Nothing can come from nothing" and then get round the problem by assuming "nothing" includes their favourite god, complete with all the knowledge, information and raw materials for creating a Universe. But of course when we realise that nothing also means no time and no space, the concept takes on an entirely different meaning. If there is no space and no time for nothing to 'exist' in, in what sense can it exist? Indeed, in what sense can nothing be said to exists anyway, let alone be available to determine what it can and can't do?

However, enough has probably been said on that subject already, not least of all by particle physicist, Victor J. Stenger and cosmologist, Lawrence M. Krauss. What I'm going to look at is how Medieval European Christianity tried to cope with the 'new' idea of zero. I wonder if anyone can guess...

We are perhaps used to thinking that the Bible was the origin of the notion of Earth being at the centre of everything with the Sun, Moon and planets orbiting in spheres. In fact, the Bible originally puts the sun and stars stuck on a dome covering the Earth and Heaven somewhere above this dome with the space above it full of water, though by the time the Tower of Babel story got written, it was apparently possible to build a tower tall enough to get through this dome to Heaven and the water had dried up.

By the Middle Ages though, the Universe was firmly composed of concentric spheres, a notion which had been been incorporated from Ancient Greek with the inclusion of Christian geocentrism, once the question of whether the Bible was right to describe a flat Earth had been resolved. The inerrant Bible was wrong about that but was still inerrant. Okay! These concentric spheres had the space between then filled with 'ether' and were made to move by an 'unmoved mover', so neatly 'proving' God existed because how else could the Sun, Moon and stars be moving in their celestial spheres?

The Ancient Greek philosophers had seen numbers in geometrical terms, so numbers essentially described shapes. This was primarily promoted by Aristotle and his disciples, so the Greeks, and the Romans had no use for the concept of zero as a number, so had no word for it and no character for expressing it.

Brahmagupta - thinking of nothing.
However, Eastern philosophers came at it from a different direction. They saw the Universe in terms of recurring cycles of creation, not as a one-off 'perfect' creation. In India in 628 CE, the philosopher, Brahmagupta wrote a treatise, the Brahmasphutasiddhanta, in which he first proposed the idea that numbers were abstract concepts, not real things and so was able to think in terms of subtracting a larger number from a smaller one - something essential when dealing with money accounts. Until then, such questions as how do you subtract a larger area from a smaller one would have been met with incomprehension, as would the question of bartering more goats than you had. The answer would have been that it couldn't be done, and that was that.

So, how to handle ideas of debt and IOUs in the normal course of trade, and more importantly, how to record it?

But with Brahmagupta's new ideas, people could think the previously unthinkable and see numbers in different ways. Numbers could be seen as an infinite series stretching as far as you could see both forward and backward, and obviously passing through a point at which they were neither positive nor negative. It lay midway between 1 and -1. It was what you had left if you had one goat and gave it away. The 'origin' of the counting system became zero, not one.

Move that line at right angles and you have an area; move that area in the third dimension and you have described a volume. And both volume and area had non-existence at their origin.

Not only could something mathematically not exist, but there could be something before it!

By the mid 800's Indians had a word, (sunya), and a symbol (a squashed egg) for zero, and were using ten symbols in their mathematics (0-9). And very quickly this way of doing mathematics was absorbed by the Arab world and Arabic philosopher quickly developed the idea of al-jebr or algebra as a way of doing maths with relationships between numbers rather than with actual numbers.

Leonardo Fibonacci
But Medieval Christians knew best and, whilst Arabic and Indian mathematicians made great progress, Europe still used the hideously complicated Roman numerals without a zero, or even the concept of it, for another 400 years until Leonardo of Pisa - better known as Fibonacci - published Liber Abaci, in which he introduced the West to the 'Arabic' counting system and demonstrated it superiority for complex mathematics over using the abacus.

Although bankers and merchants were understandably quickly won over to the new maths, not so the church and the political classes. They tried to ban Arabic numerals as blasphemous and Satanic because they included the concept of nothing, and how could a god have created... er... nothing. In 1299 the city authorities in Florence banned all Hindu-Arabic numbers, including zero. One reason given was that if you could inflate a number by adding nothing to it (i.e, multiplying it by 10, 100, 1000, etc) then anything was possible, including fraud.

The church was desperate to cling to Aristotelian geocentrism with its concentric spheres (and its 'proof' of God in that it required an unmoved mover) and it was only the Copernican revolution, promoted by Galileo, which showed that Earth was not fixed and immobile, as the Bible says, but orbited the Sun, as did the planets. The fixed geometry of the Universe had been broken and, although the Universe could still be described with numbers, these were no longer geometrical concepts but abstract things which could accommodate negative values, and, horror of horrors, nothingness.

It was not until the 17th-century when René Descartes succeeded in merging geometry with algebra and devised the Cartesian system for describing the position of everything as a system of coordinates, that it was accepted that zero lay at the heart of all coordinate systems. Then Newton and Leibnitz independently developed calculus so we could see how zero merged smoothly into the infinitely small and finally understood how Achilles could overtake a tortoise.

It turned out that the 'prime mover' - the Aristotelian 'unmoved mover' - was not a god, but literally nothing.

On 31 October, 1992, just 1364 years after Brahmagupta published his treatise, Pope John Paul II officially accepted that the Church was wrong to persecute Galileo. The Pope's bankers had of course fully signed up to the concept of zero almost as soon as Fibonacci introduced them to the idea 700 years earlier.

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Sunday 19 January 2014

Death and Elephants

Pachyderm politics and the powerful female - life - 07 January 2014 - New Scientist

To those who assume that humans are the only species with complex social systems complete with the system of ethics which makes this system work, the above article in New Scientist may come as something of a surprise.

To a creationist who believes humans are a special creation and that our morals were handed down to us by a magic creator, it will come as a shock and will need to be ignored or dismissed in some way to help overcome the inevitable cognitive dissonance.

Rooting For The Robin

British subspecies of robin (Erithacus rubecula melophilus)
Of course we can never know for sure what a bird like the European robin thinks but, based on observations of their behaviour over much of their range, we can make a few reasonable assumptions, and what they seem to see humans as is not at all flattering.

In Britain we are used to the robin, Erithacus rubecula (not to be confused with the American robin, Turdus migratorius, to which it is only distantly related) in our gardens feeding from bird tables or playing close attention to our gardening activities and darting in to pick up the occasional worm we might dig up. They can even be quite easily tamed, especially with mealworms, and will take them from your fingers.

Such is its familiarity to us, and such is the affection in which we traditionally hold it, that its name derives from the early English habit of giving familiar wild animals human names, such as Jenny Wren, Tom Tit, Brock Badger, Reynard Fox and Robin Redbreast. In fact, it was previously called the redbreast but the humanised name stuck.

In the rest of Europe, especially the forested parts, the robin is a rather shy bird of the woodlands, so why this difference?

Well, where the robin is a woodland bird, the wild boar is still reasonably common. To understand why, we need to understand how the wild boar feeds - by using its snout to turn over the top few inches of soil looking for anything edible - roots, grubs, worms, etc. Robins will perch close by and dart in to grab anything the boars roots up and miss. Whether or not the boars benefit from this association is unknown and probably no concern of the robin. It could be that the robin's alarm call warns of predators - not that the adult boars have many in Europe but bears, lynxes and wolves will take the young if they get a chance.

Wild boar, rooting
In Britain we hunted the wild boar to extinction by the 13th-century and so deprived the robin of its natural ally and a major provider, so those which confused human gardening activities with those of the wild boar found an easy substitute and robins moved out of the forests, which were also disappearing, into the gardens of the expanding towns and villages.

In short, the robin sees humans as pigs because to a robin our 'rooting' activities in the soil yield the same harvest.

This illustrates nicely how, from the perspective of genes, what looks like a major environmental change to some sets of genes - those of humans and wild boars - to those of the robin so far as its feeding behaviour is concerned, the change was barely noticeable and only needed a slight tweak to continue much as before, forming an alliance with a new set of genes in place of a very similar old set.

It is humbling to think that our companionable little garden robin is seeing us, for all practical purposes, as pigs.

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Friday 17 January 2014

Creationist Myths Debunked

Back in 2008, New Scientist published a list of 24 myths about evolution, 14 of which were specifically creationist myths. The article debunked them all. Despite that you'll see them all regularly regurgitated on creationist sites. They form the basis for the rejection of evolution by a majority of Americans and Muslims, and by a substantial minority of European Christians.

I'll attempt to summarise the creationist myths and add my refutations of them here. As one would expect of creationism, some of them are blatant lies whilst others stem from scientific ignorance about which many creationists seem inordinately proud as though they imagine their god appreciates ignorance about the world they believe it created. All of them pander to the desire of creationists to elevate themselves to a level of importance which requires a Universe to be created especially for them and for them to have a close personal relationship with their imagined creator of it.

Friday 10 January 2014

Elephant Sharks Living In The Past

The elephant or ghost shark, Callorhinchus milii
Elephant shark takes record for slowest evolution - life - 08 January 2014 - New Scientist.

Expecting a religious fundamentalist to do logic is like expecting a cow to do acrobatics. For example, I've been assured in all seriousness that the fact that coelacanths have 'not evolved' for 400 million years proves that evolution doesn't occur, so Earth is only 6000 years old just like the Bible says. Almost the same argument is made for the horseshoe crab.

The difference in this approach and that of science is due to the differences in motivation. The aim of science is to discover the ultimate truth, or at least to get as close to it as is possible. The aim of religious fundamentalists is to satisfy their yearning for a sense of self-importance which can only be satiated by believing that an assumed creator of the universe made it just for them and has a special relationship with them. Anything which can be used to support this is grasped eagerly like a drowning person clutches at straws. No logic will be allowed to spoil a good 'proof'.

So, orders like the coelacanths or or horseshoe crabs are 'proof' that evolution doesn't happen because they've remained unchanged for millions of years, whilst all the species which have not remained unchanged have no bearing on the matter, so a magic man must have made humans just the way they are.

Well, here's another species, the elephant shark, Callorhinchus milii, which hasn't changed very much since the order evolved some 400 million years ago. In fact, Byrappa Venkatesh of the Institute of Molecular and Cell Biology in Singapore, as reported in a paper published in Nature, has found that its genome has changed least over a similar time scale of any species to have its genome analysed so far. Despite its common name it is only distantly related to sharks in that it is a cartilaginous fish, like the sharks, skates and rays. In fact, it's a ratfish.

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the ‘living fossil’ coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

We're getting this divorce between the apparent conservatism of their genome and the astonishing singing and dancing that was going on anatomically.

Michael Coates, palaeontologist,
University of Chicago
The fact that its genome has changed far less than would normally be expected is surprising in another way because between about 300 and 340 million years ago the order underwent a rapid radiation from the ancestral species, which suggests rapid, not slow, evolution of the genome. For some reason as yet not fully understood, C. milii seems to have retained a genome close to the ancestral form whilst its relatives were rapidly changing and diversifying.

Note here another difference in the reaction of creationists and scientists. Scientists actually welcome something which throws a spanner in the works and causes us to question our basic assumptions. Nothing is more satisfying than publishing some data which challenges our assumptions. We freely admit we don't know the answer and equally freely admit it when something seems to go against what we think we know. There is no rigidly inflexible dogma to be defended at all costs. If it turns out we're wrong to some degree or other, we revise our understanding and change our conclusions. The facts, as always, are the master.

But that's not the only thing we see here. Because the elephant shark's genome is believed to be close to that of the common ancestor of not only the cartilaginous fish but that of the bony fish, and so, via amphibians and reptile of us, there is the possibility that we can learn a great deal about how things like our immune systems evolved because it evolved at some point during that initial radiation. Science seizes on the chance to extend our knowledge rather than treating an inconvenient fact as a problem not to be discussed in front of the children or to be hidden under the carpet.

By contrast, in their desperate search for confirmation of their own inflated self-importance, no matter how spurious or illogical, the last thing fundamentalist will acknowledge is the possibility of being wrong. On no account can the conclusion be changed because the conclusion comes from dogma not from facts. To even consider questioning the dogma is heretical. If the facts point elsewhere then the facts must be wrong. The only facts worth considering are those which seem to support the dogma, and they are then waved around triumphantly and science is acclaimed as incontrovertible proof.

So, the elephant shark, the coelacanth and the horseshoe crab are all 'proof' that evolution doesn't happen because they haven't evolved for hundreds of millions of years, therefore Earth is only 6000 years old. Remember, when you join those dots, the ones which don't make a god have been put there to mislead you!

The Discovery Institute and the Institute for Creation Research want this creation 'science' taught to our children in place of real science!

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Thursday 9 January 2014

Defeat for Texas Creationist Loons

Texas repels creationist threat to biology textbooks - life - 31 December 2013 - New Scientist

Great news from Texas that yet another attempt by creationist loons to inflict their anti-science agenda and primitive superstition on the children of normal Texans has been defeated.

Creationists who had got themselves elected onto the Texas School Board of Education have been trying since 2009 to to insert creationism into a proposed textbook, the Pearson Biology textbook, and to insert text which undermined the scientific consensus on evolution and cast doubt where there is none.

The importance of this victory is that Texas is the second largest purchaser of school textbooks next to California so, if the publishers had been forced to include the creationists text in their book it is highly unlikely that they would have refused to publish at all, or that they would have produced different versions for different states. In effect, other states with smaller school populations would very probably have used these books in their classrooms, complete with the creationist propaganda and factual inaccuracies.

An anonymous reviewer had complained that there were '18 errors of fact' in the text which should be corrected. The 'errors' of course were scientific facts which creationists wish were not true, and which they don't want children to know, because they cast doubt on the Bible, particularly the Bronze-Age creation myths in Genesis, and so undermine their own political ambitions. The creationist definition of a scientific 'fact' is anything they wish were true so it looks like the Bible isn't full or errors.

As a compromised, the Texas School board appointed a panel of three expert biologists to investigate these reported errors. They have concluded that there are no factual errors and have recommended that the text be published unchanged.

The extent to which Christian fundamentalism and creationism has become entwined with politics in America is revealed in a recent poll. This found that 33 percent of those polled reject the idea of evolution whilst 60 percent support it. Two-thirds of those voting Democrat are evolutionists whilst the proportion of Republican voters supporting evolution has fallen from 54 percent to 43 percent in just four years.

The Republican Party is becoming more and more the party of the Christian fundamentalist and anti-science, creationist loon.

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Sunday 5 January 2014

Incestuous Creationist Absurdity

Arthritic and inbred

Image: John Reader/Science Photo Library
Inbreeding shaped the course of human evolution - 28 November 2013 - New Scientist

Every now and then, well, to be frank, more often now than then, science throws up something which makes religion and especially creationism look even more idiotic.

Take this article in New Scientist, for example.

It seems that one of the things preventing human progress after we had diversified out of Africa into the relative vastness of Euro-Asia was the fact that we tended to live in small, isolated groups. This meant there was a great deal of inbreeding with incest or near-incest being common.

This had two consequences: the first being genetic; the second cultural.

Another Embarrassment for Creationists to Ignore.

Stonehenge Man (Image: English Heritage)
Stonehenge Man: not just a pretty face - life - 03 January 2014 - New Scientist

Using forensic techniques, Swedish sculptor Oscar Nilsson has reconstructed the face of a man who lived in the area of Stonehenge in southern England in 3500 BCE, some 500 years before the first phase of Stonehenge was built, almost certainly by the same people this man belonged to.

He would be totally unremarkable if seen walking down a street in London, Dublin, Paris or Stockholm, or indeed in any modern European city. He is indistinguishable from modern Europeans. Indeed, for all practical purposes, he is a modern European.

Bearing in mind the standard creationist dogma, as promulgated by the Discovery Institute and the Organization for Creation Research, that Earth was created about 6000 years ago 'Stonehenge Man' must have migrated to southern England within about 500 years after Adam and Eve. After the Flood, modern Europeans must have recolonised Europe, coincidentally with people identical to those living there before the Flood, just as Chinese people recolonised China with people identical to pre-Flood Chinese people, Africans with people identical to pre-Flood Africans, etc, etc...

Intelligent design is just the Logos theology of John's Gospel restated in the idiom of information theory.

But maybe we can be a little generous and allow that they may have got the timing a little bit wrong by some few thousand years and that the Flood was a lot earlier than they claim, but what they will still need to explain is why a fully modern European was living in Europe by 5500 years ago. Were the ark survivors not, as one would expect, some generalised human beings from which all the different varieties have since diversified? In other words, were they not a little bit African, a little bit Chinese, a little bit South Asian, a little bit Australasian, a little bit Native American, etc, but fully modern Europeans?

If so, how did all the other human types diversify from a fully modern European Noah?

If not, how did fully modern Europeans (and all the other human types for that matter) diversify so quickly from Noah and his small family?

Remember, according to a creationist purist, evolution is impossible because, according to William Dembski, the probability of it happening is vanishingly small and according to Claude Shannon's Information Theory, no new information can arise because that would contravene the Second Law of Thermodynamics.

Any creationist prepared to offer up an explanation without invoking magic or falling back on the default answer to all questions - "God did it"?

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Thursday 2 January 2014

Peace On Earth - The Christian Way

In this season of peace and goodwill to all mankind - if you believe the Christian propaganda that is - I thought it might be instructive to look at how the Bible defines peace.

To take the gospels at face value, Jesus seems more than a little muddled about peace. In the Sermon on the Mount according the Matthew (and that might be significant as we shall see) he says

Blessed are the peacemakers: for they shall be called the children of God.

Matthew 5:9

which seems scant reward for all the good work real peacemakers do - unless you are ultra-Jewish Matthew that is. Matthew bends over backwards to make it look like Jesus was the Jewish Messiah - the future king come to save the Hebrews and restore them to their rightful place as Yahweh's chosen people who will one day rule the world. The 'children of God' in this context are the Jews. The peace Matthews has Jesus recommending is the peace of Jewish rule over all mankind.

So what is this biblical peace exactly?

Peacemakers at work
For that we need to delve into the Old Testament. Peace, in biblical times was not the absence of military force but something imposed and maintained by it. Here's Yahweh telling the Hebrews how to make peace:

When thou comest nigh unto a city to fight against it, then proclaim peace unto it.

And it shall be, if it make thee answer of peace, and open unto thee, then it shall be, that all the people that is found therein shall be tributaries unto thee, and they shall serve thee.

And if it will make no peace with thee, but will make war against thee, then thou shalt besiege it: And when the Lord thy God hath delivered it into thine hands, thou shalt smite every male thereof with the edge of the sword: But the women, and the little ones, and the cattle, and all that is in the city, even all the spoil thereof, shalt thou take unto thyself; and thou shalt eat the spoil of thine enemies, which the Lord thy God hath given thee.

Deuteronomy 20:10-14

So the peace Matthew has Jesus talking about in the Beatitudes is the peace of total surrender and servility; the peace of accepting second class status in a conquered state; the peace of abject slavery and submission to a foreign master.

And this 'peace' is the reward for capitulation. The alternative is death for every male and the women and children and everything in the state being taken as the possessions of the conquerors. The peace bought by paying off the protection racketeer.

And those who make this peace are Yahweh's chosen ones.

But then Jesus himself seems confused about whether peace is a good thing. He's in no doubt that his mission is not to bring peace to the Earth by cessation of all military activity and by turning swords into ploughshares, but to conquer it. Only then will there be peace.

Think not that I am come to send peace on earth: I came not to send peace, but a sword. For I am come to set a man at variance against his father, and the daughter against her mother, and the daughter in law against her mother in law. And a man's foes shall be they of his own household.

Matthew 10:34-36

And there we see the same demand for total surrender backed up by implied threats of terrible retribution. The language is a little more poetic but the message is the same. A few lines later on we even see what any Christian extremist worthy of the name could present as an argument for suicide bombings and martyrdom:

He that findeth his life shall lose it: and he that loseth his life for my sake shall find it.

Matthew 10:39

So much for Jesus' view of peace and how it should be achieved.

What does Paul have to say about it?

Paul seems to regard peace as merely freedom from anxiety or even just freedom from fear of what Yahweh might do to you. The notion of freedom from military activity or the threat of it seems not to have occurred to him or those who write the epistles in his name. Peace is a selfish concept; something one achieves for oneself, not something one tried to achieve for others.

For example:

Therefore being justified by faith, we have peace with God through our Lord Jesus Christ: By whom also we have access by faith into this grace wherein we stand, and rejoice in hope of the glory of God.

Romans 5:1-2

For to be carnally minded is death; but to be spiritually minded is life and peace. Because the carnal mind is enmity against God: for it is not subject to the law of God, neither indeed can be.

Romans 8:6-7

So, when Christians quote Luke's angels and wish you 'peace on Earth and goodwill to all men', the peace they are wishing you is the peace of the slave who has surrendered freedom and even surrendered intellectual integrity in favour of faith and accepting their dogma without question. Significantly, these same people have never been slow to impose this 'peace' the same way the god of the Hebrews told them to impose it on others.

Abject submission to evidence-free superstition and to those who use it and the threat of an imaginary deity to impose their will and control on others is about as far from mental peace as I can imagine getting.

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