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.

It looked for a while as though the ubiquitous rabbit, the farmers enemy and the friend to every villager who had a family to feed and who knew how to set a snare or work a ferret, was about to disappear forever. With a good ferret, if you knew where the best burrows were, you could get enough rabbits in an hour to feed a family for a week - and I knew the countryside around my small village like I knew the back of my hand. I also knew who I could sell a brace of rabbits to for a shilling each. I could skin, gut, and quarter up a rabbit in about ten minutes. By next year the burrow would be full of rabbits again as each female could rear a batch of half a dozen young every three months and the young would be breeding themselves almost before the next batch had left the nest. You had to know which burrows were ready for the next rabbit harvest.

During World War II when meat was rationed, many an English country family eked out their rations with rabbit stew.

Then myxomatosis looked set to end all that for ever.

Baby rabbits with eyes full of pus
This is the work of scientific us.

Spike Milligan
The myxoma virus is a poxvirus which caused an innocuous localised skin fibroma in two American relatives of the rabbit (Sylvilagus brasiliensis and Sylvilagus bachmani) but in O. cuniculus it is (or was) systemic and rapidly fatal. It is passed on in Europe by the rabbit flea - a species unique to rabbits and which pass between rabbits when they mate. Most English rabbits will have hundreds of fleas living on them. (How the rabbit flea coordinates its reproduction with that of the rabbit is an interesting story in itself, but it must wait for another day).

Despite official denials, myxomatosis was deliberately introduced in Britain. With the vector being the rabbit flea, it could not have crossed the English Channel from France. Interestingly, the then owner of Lundy Island in the Bristol Channel had tried to introduce it to the island by putting a rabbit dead from myxomatosis down a rabbit burrow. It failed to take hold because, for some reason, Lundy Island rabbits have no rabbit fleas. On the mainland its spread was rapid and devastating. Woods and fields soon became littered with the bleached bones of dead rabbits. Soon every field where once you could be sure of lifting your baby brother or sister up to see over the wall and watch the rabbits run for cover, was empty save for little clusters of white bones. And the fox population crashed accordingly.

Then, seemingly almost by magic there were a few rabbits again; then more. Then another wave of myxy wiped them out. The rabbits and the myxoma virus seemed to be finding some sort of balance. A few rabbits would be left to breed then, when the population built up, myxy would come and knock it back down again.

But gradually, rabbits gained the upper hand, each wave of myxomatosis seemed to take fewer and fewer until a myxy rabbit was a rarity - almost something to talk about. Soon the corners of fields were filled with rabbits and the old deserted burrows were re-inhabited. But now almost no-one in the countryside would look at a rabbit as something for the pot. The sight of myxy rabbits put people off eating them even though the myxoma virus is harmless to humans. No one would risk eating them and they dropped off the radar as a food source. You'd be hard-pressed now to find a 10 year-old who can work a ferret or skin and gut a rabbit in a few minutes. You'd probably be hard-pressed to find parents who would let them or could even teach them to.

The same thing was seen in Australia where European rabbits had been introduced. During the voyage there it seems they had lost their flea population but the virus vector was a species of mosquito which was enjoying an abundant new supply of blood as rabbit numbers ballooned, reaching plague proportions and seriously competing for grass with the sheep.

How this happened is one of the best illustrations of co-evolution between two species:

Myxoma virus is a poxvirus naturally found in two American leporid (rabbit) species (Sylvilagus brasiliensis and Sylvilagus bachmani) in which it causes an innocuous localised cutaneous fibroma. However, in European rabbits (Oryctolagus cuniculus) the same virus causes the lethal disseminated disease myxomatosis. The introduction of myxoma virus into the European rabbit population in Australia in 1950 initiated the best known example of what happens when a novel pathogen jumps into a completely naïve new mammalian host species. The short generation time of the rabbit and their vast numbers in Australia meant evolution could be studied in real time. The carefully documented emergence of attenuated strains of virus that were more effectively transmitted by the mosquito vector and the subsequent selection of rabbits with genetic resistance to myxomatosis is the paradigm for pathogen virulence and host-pathogen coevolution. This natural experiment was repeated with the release of a separate strain of myxoma virus in France in 1952. The subsequent spread of the virus throughout Europe and its coevolution with the rabbit essentially paralleled what occurred in Australia. Detailed molecular studies on myxoma virus have dissected the role of virulence genes in the pathogenesis of myxomatosis and when combined with genomic data and reverse genetics should in future enable the understanding of the molecular evolution of the virus as it adapted to its new host. This review describes the natural history and evolution of myxoma virus together with the molecular biology and experimental pathogenesis studies that are informing our understanding of evolution of emerging diseases.

Kerr PJ., Myxomatosis in Australia and Europe: a model for emerging infectious diseases;
Antiviral Res. 2012 Mar;93(3):387-415. doi: 10.1016/j.antiviral.2012.01.009. Epub 2012 Feb 8.

Under intense selection pressure, those few rabbits with an inherited genetic resistance survived to produce offspring carrying that genetic resistance. Meanwhile, under the selection pressure of increasing resistance, the myxoma virus also evolved and attenuated, making it more easily transmitted. Keeping its host alive was a better strategy than killing it quickly before it could infect more rabbits, because that produced more copies of myxoma viruses. The same thing would have been seen in the world human population in response to the devastation of the Black Death in the Middle Ages. We evolved resistance and the bacillus causing it attenuated.

It almost goes without saying that the only known natural mechanism which can cause host and parasite species to accommodate one another like this is natural selection acting on small variations in the genome, so automatically favouring the variations which produce most descendants, and so increasing its frequency in the population gene-pool, no matter how unlikely that variation was to arise by chance in the first place.

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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.

It's such a strange entity. It's a cancer that's become a parasite, and yet it came from the same species that is now its host.

Despite the fact that they are clones, over the intervening 11,000 years they have accumulated some 2 million mutations due to mistakes in cell division. The tumour is thus showing signs of diversification by evolution from the original tumour. It was by analysing the rate of these mutations and the order in which they arose that the team arrived at the 11,000 year age for the tumour. Selection pressure comes from the method by which it is transmitted and grows in the new host. The easier this occurs the more likely that mutation is to survive and be passed on. Mutations which inhibit this or prevent successful transmission altogether will be quickly eliminated. To be successful, the cancer needs to keep its host alive and fit to breed until it is passed on and the longer it manages this the more likely it is to be passed on. This means the cancer has evolved a reasonably mild form which consequently makes it relatively easy to treat, treatment being successfully in 90% of cases.

The cancers found in the Australian and Brazilian dogs seem to have diversified only about 500 years ago, coinciding with the height of European exploration. It is thought that the cancer had a fairly limited geographical distribution for some 10,500 years until Europeans took infected dogs all round the world. It probably arose in an isolated and therefore highly inbred population with little genetic diversification so the tumour cells would not be recognised by the immune system as foreign cells. Comparing the non-mutated DNA with that of living dogs it seems the tumour arose in a dog which was similar, though not the same as, huskies and Alaskan malamutes.

A similar process is thought to be responsible for the tumours in Tasmanian devils which, due to population decline, are now also highly inbred and so lack genetic diversity. The cancer which is threatening them only arose within the last 30 years.

I'd love to see an 'Intelligent Design' explanation for this and the Tasmanian devil cancer, if any creationist feels like attempting one.

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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.

The theory is wrong because the Bible is inerrant and says all living things were created.

The Bible contains mutually exclusive contradictions and demonstrable factual inaccuracies which means it cannot possibly be regarded as inerrant. For example, the Bible says Earth is fixed and immoveable, that the sky is solid with the stars stuck to it and the stars can be shaken off by earthquakes. It also says the Moon shines with its own light; Earth is flat and the highest mountain would be covered by water covering the entire Earth to a depth of only 15 cubits (about 45 feet).

Clearly, the Bible cannot be both inerrant and wrong, and if it can be wrong about cosmology and and geology it can also be wrong about biology.

Accepting evolution undermines morality.

In fact, highly religious societies tend to be highly aggressive and intolerant of those who disagree with them. Religion has been used to excuse racism including slavery, repression and ill-treatment of women, denial of opportunity to disabled and handicapped people, genocide, imperialism, autocracy and denial of basic human rights.

On the other hand, secular societies and societies such as Sweden, where non-belief and acceptance of evolution is the norm, are more peaceful and have less crime than highly religious societies such as the USA.

Where Darwinian evolution has been used to justify racism it has invariably been a perverted version called 'social Darwinism' which, ironically, was the only form of Darwinism embraced by the same political right who now purport to be Christian fundamentalist creationists.

Whether or not Darwinian evolution does or doesn't support this or that political cause has nothing to do with whether it's right or wrong. Atomic theory is no less right because nuclear war would be undesirable and the Theory of Gravity is no less true because falling off high buildings is harmful. The consequences of a fact do not speak to the validity of that fact. The Universe is not obliged to conform to our desires. It takes a special form of arrogance to argue that facts must be wrong because one doesn't like the consequences. It's as though creationists are under the impression that they have some control over reality and can declare it to be as they wish it to be, and if they ignore it it will change or go away.

But the evidence is that people do not become selfish or psychopathic when they learn about evolution and societies do not break down irretrievably when evolution is taught in schools. The argument that humans need threats and rewards to behave decently says far more about the morality of those who argue it than it does about those whom they falsely assume would behave the way they would if they weren't too afraid to.

Let all who are under the yoke of slavery regard their masters as worthy of all honor, so that the name of God and the teaching may not be blasphemed. Those who have believing masters must not be disrespectful to them on the ground that they are members of the church; rather they must serve them all the more, since those who benefit by their service are believers and beloved.

Evolutionary theory leads to racism and genocide.

This is another form of the argument from consequences which we saw above. Evolution theory is descriptive, not prescriptive. It does not tell us what is ethical or unethical - and neither does the Theory of Gravity.

Some political vested interest groups have exploited ignorant populations into following murderous and racist policies by selling them a spurious scientific rationale based on a perverted form of Darwinian evolutionary theory. At other times and in other places the same political vested interest groups have used religion as the pretext for their inhumanity as can be seen from the history of the growth of Fascism in Europe and Japan in the early twentieth century which owed far more to political Catholicism and Shintoism than to science.

The commonality here is the credulous and ignorant population they are fooling into following them. Remaining ignorant of something like biology can do nothing the rectify that problem.

In fact a basic understanding of evolution shows that cooperation is far more likely to be the successful strategy than ruthless competition. Replicators only formed simple cells by cooperating with other replicators and complex cells only evolved as cooperative alliances of simple cells. Complex multicellular animals evolved as cooperative alliances of complex single cells and almost all species rely on various degrees of cooperative alliances with other species to form ecosystems. From the 'point of view' of a successful alliance of genes, even predation is a form of cooperation since predators differentially remove competing alleles. Altruism is a consequence of 'selfish' genes because it tends to lead to more survivors of those genes in future generations and human societies only succeed as cooperative societies.

As to human ethics and innate human morality, that can be understood in evolutionary terms as the successful memes of an evolving, intelligent ape evolving in a hostile environment, where memes are the cultural equivalent of the biological genes subject to analogous selection pressures and so tending towards fitness for purpose in that environment.

But the basic flaw in this argument is the same as the one above: the consequences of a fact have no bearing on its factuality. Evolution by natural selection will occur regardless of whether anyone like it or not and regardless of whether unscrupulous people use it to exploit and manipulate people's ignorance of it.

Religion and evolution are incompatible.

I don't propose to spend much time on this argument which is yet another form of the argument from consequences seen above. It is the equivalent of arguing that reality is incompatible with the way I would like it to be. If this line of argument didn't have the cloak of religious respectability it would be seen as a form of insanity.

Since religions are man-made dogmas with no supporting evidence, they can be compatible with reality to the degree to which the believer wants them to be. If any science, not just evolution, is incompatible with any religion then that is a valid reason for arguing that the religion is wrong. Indeed, how else are we to tell if a religion is right or wrong about anything if we don't compare it to reality?

We know that creationism isn't compatible with biological science. When creationists complain that their religion isn't compatible with science they are telling us their religion is wrong. We know that already.

Half a wing is no use.

Well, yes it is, actually.

In the ancestors of birds, the bipedal theropod dinosaurs, feathers evolved from scales, probably for heat conservation or for incubating eggs. Later, the feathers of the forelimbs could have been used when running or climbing and then for gliding and then for powered flight. Each stage would have conveyed a benefit and each would have been useful.

Insect wings could have evolved from gills or aids to gliding on the surface of water, much as stoneflies do today. No stage would have been useless and each would have conveyed a benefit.

Bats could have evolved elongated phalanges on their forelimbs and retained the embryonic webbing all mammals have, as an aid to gliding between trees or to reduce the danger of injury when falling. Again, a series of small steps can be seen, each of which would have been beneficial and none of which would have involved a loss of function.

Another way complex structures can evolve is by exaptation of existing structures. This is the utilisation of a structure evolved for one purpose for an unrelated function. This can explain the evolution of structures such as the flagellum in early cells and and the other 'irreducibly complex' structures so beloved of 'Intelligent Design' creationists. Structures can be assembled from other pre-existing structures, all of which evolved independently for other purposes. Presumably a creationist would look at a chair being used to stand on to reach a high shelf and conclude that it was designed for reaching high shelves, or that a screwdriver being used to open a paint tin was designed as a paint tin opener.

In fact, this argument is merely an argument from ignorance and a god of the gaps. Even if we did not know how structures like wings, eyes and flagella evolved, this ignorance would not be evidence that a magic man in the sky made them.

Evolution is not predictive.

Well no, not in the same sense that we can predict the trajectory of a missile from Newtonian Laws of Motion or the orbit of a planet from Einsteinian Relativity.

But then we can't tell from our knowledge of geology and plate tectonics exactly what Earth will be like in 10 million years time or what the weather will be in London, Moscow or New York this time next year. However, we know that weather patterns are as you would expect them to be according to chaos theory, and that part of that pattern is unpredictability which increases with time.

Similarly, we know that what we see today as diversified life forms are what we would expect to see given the effects of small changes accumulated over time with environmental pressures acting on small variations in the genome. We also know that organisms subjected to experimental selection pressures in laboratories will diversify from the original type in similar patterns.

However, evolution theory has made predictions which could be tested and which have proved correct. Darwin himself realised that Earth must be far older than the accepted religious dogma of his day said for there to have been enough time for life to have evolved to it's present level of diversity. In fact, it turned out to be even older that he realised and far older than the few thousand years Christianity claimed on the basis of some primitive Bronze-Age creation myths.

When Lord Kelvin wrongly calculated that Earth was only about 30 million years old because he thought it would have cooled down by now if any older, this was thought by some to have falsified evolution by natural selection because 30 million years wasn't long enough. As predicted by the Theory of Evolution, Lord Kelvin turned out to be wrong and Earth turned out to have a heat source from radioactive decay about which he knew nothing. Earth is now known to have an age which is entirely compatible with the TOE.

Other scientists had calculated that the sun was only some 20 million years old, again not enough time for evolution of life on Earth as we now see it. It turned out that they were wrong because they had not known about nuclear fusion. The sun was the age predicted by the TOE and the physics was naive.

For the sun's heat to be formed by nuclear fusion it had to form in a very much older Universe and not one in which the sun was formed at the same time as the Universe. It has turned out that the Universe is as old as the theory predicts.

For related terrestrial species to be living on unconnected land-masses and yet to have evolved from a common ancestor the land-masses must once have been in contact. When Darwin and Wallace made their discoveries known to science it was assumed that Earth had been created pretty much as we see it today. The idea that land-masses move about over time was not generally accepted until the mid twentieth-century. We now know that land-masses split and move by plate tectonics and that the splits occurred at exactly the right time for related species to become separated at the right time in their evolution.

Other instances of the TOE making accurate predictions are the evolution of drug-resistant bacterial pathogens, the discovery of Tiktaalik fossils of the right type and in the right rock formations, and the prediction that 'Piltdown Man' would turn out to be a forgery, made by a friend of mine, the Late Professor Sir Wilfred Le Gros Clarke, the leading evolutionary palaeoanthropologist of his day.

Evolution cannot be disproved so is not science.

It seems creationists confuse not being falsified with not being falsifiable.

It's certainly true that the Theory of Evolution has never been falsified. On the contrary, every discovery of every fossil has been entirely consistent with the theory. It would take just a few fossils clearly out of kilter with what the TOE predicts for it to be falsified. Mammals with feathers; boney fish older than cartilaginous fish; amphibians older than boney fish; arthropods with vertebrate bones or muscles or flowering plants predating insects. None of these have ever been found.

By contrast there is not a single piece of evidence for intelligent design such as one might expect of an intelligent designer. Organisms have masses of redundancy in their genomes and in vestigial structures which serve no purpose and there is no evidence of a designer developing something like flight, vision or a central nervous system for one order of living things then using it for another order. For example, bat and bird wings serve the same purpose so why design them twice?

Nor is there evidence of an improved design such as the cephalopod eye being used to benefit mammals with their less efficient eyes or mammals benefitting from the improved visual acuity of birds such as eagles and hawks or from the much more efficient respiratory systems of birds. Even within the mammals, sonar navigation in bats and dolphins appears to have evolved twice and none of the aquatic mammals or reptiles such as whales and turtles have evolved gills or even lungs suitable for breathing water.

The simple reason for this is because evolution going in reverse means a loss of function and the driving mechanism of undirected, unintelligent, natural selection makes this impossible. This is not a problem for an intelligent designer and would be a sure-fire sign of intelligence being involved, and yet we never see it happening.

Evolution is just so unlikely to produce complex organisms.

This argument plays to an ignorant audience, especially one which assumes the process of evolution is a single event happening by pure random chance. This is the same audience which believes the fact that chimpanzees never give birth to human babies or the fact that chimpanzees never suddenly turn into humans, are arguments against evolution. In reality, of course, it's an argument against the ignorance and stupidity which causes creationism.

Ironically, the TOE is the best available explanation of just how improbabilities are concentrated up an improbability gradient by a series of small steps, each of which is subjected to selection by the environment in which evolution is happening.

All that is required for evolution to be inevitable is three things to occur:
  1. Variation.
  2. Replication.
  3. Selection.
Does anyone doubt that all these are present in nature?

In a population of several million, a million to one chance mutation will occur on average several time every generation. If this gives an advantage to the carrier then the chances of it being inherited by the next generation is better than the chances of the non-mutated allele so the chances of that mutation appearing in the next generation are now better than a million to one. As each generation passes through the sieve of natural selection so favourable improbabilities are concentrated until they become the norm in the genepool.

What creationists are doing here is the equivalent of taking a pack of cards and shuffling it, then calculating the odds of achieving exactly that sequence at any single shuffle. The odds are so small that you will almost certainly never achieve that same sequence again. They then conclude that it must have been done by magic.

And yet you did it once with no magic involved and by a perfectly rational process.

The trick creationist pseudo-scientists are pulling is to assume that life had to be just as we see it today rather like assuming the sequence obtained by the first shuffle of the deck of cards had to be that particular sequence.

Evolution is a purely random process.

It's amusing to see creationists redefining some aspect or other of science in order to ridicule it. No matter how often you explain what evolution is they invariably fall back on an infantile parody definition because they find that easier to attack.

This favourite parody allows them to argue that evolution theory is the equivalent of claiming that a tornado blowing through a junkyard will assemble a Boeing 747, as the astronomer Chandra Wickramasinghe once told an Arkansas court, quoting without credit another astronomer, Fred Hoyle. But which evolutionary scientists ever argued that evolution is a process by which species spontaneously assemble from a jumble of parts?

Which just goes to show that if you want to know what evolution is, ask a biologist, not an astronomer, especially one who fails to credit the person he is plagiarising.

Perhaps a good way to answer this particular parody is to quote Michael Le Page of the New Scientist:

A somewhat better analogy would be starting with a million junkyards, painstakingly testing the wreckage left in each one after the tornado to find the most flight worthy, making a million exact copies of that junkyard, unleashing another million tornadoes, running another series of exhaustive tests, and so on, until you produce some kind of machine - no matter how crude and un-Boeing-747-like - capable of flying at least a few yards.

The only thing I would disagree with here is the phrase, 'making a million exact copies'. In fact it's occasional slight imperfections in replication that gives the variation on which natural selection operates. But of course there is still the assumption that the process is intended to produce a flying machine. All Evolution produces is something which is more likely to produce copies of itself. There is no plan to make something in particular.

Frequency of lactase persistence

Mutations can only destroy information, not create it.

This claim is nonsense and flies in the face of evidence and reason. The confusion seems to come from a confusion over the difference between information, as it applies to Claude Channon's information theory, and meaning. At its basic level, a simple mutation in DNA substituting one base for another simply means insert this amino acid in a protein chain instead of that amino acid. The amount of information in the DNA is the same but the meaning has changed.

If that new protein happens to be better at doing whatever the protein being coded for does, then the mutation will be advantageous. If, as is more likely, it makes it worse or inactivates it completely, and that proves to be disadvantageous to the carrier, the mutation will be quickly eliminated by natural selection. The other possibility is that the mutation will make no difference at all, so its frequency in the genepool over time will tend to drift in no particular direction.

Another way in which new information can arise is by accidental duplication of a chunk of DNA. If this includes an active gene then there will now be two copies of that gene, one of which can continue to code for whatever it originally coded for while the other can mutate without any loss of function.

Examples of mutations creating new information in human evolution, or in the evolution of our ancestors, are the evolution of lactase persistence by which infants fail to become lactose intolerant (and so stop breast-feeding, switching off a natural contraception in mothers). In the presence of milk from domesticated cattle this allowed populations to benefit from the available cattle milk especially as a substitute for breast milk, so women could have more babies and adults had a ready source of nutrition. The incidence of the lactase persistence mutation closely follows the incidence of cattle domestication, which in turn closely follows the absence of tsetse flies which are vectors for a parasite which is harmful to domestic cattle. The meaning of the information produced by the mutation is different in different environments.

Incidentally, lactase persistence is an example of the same process evolving more than once in the same species as different lactase persistent populations have different mutations causing it. Where is the intelligent design there?

Similarly, the presence of a mutation which broke the synthesis of Vitamin C in one of our fruit-eating simian ancestors with a high level of Vitamin C in their diet meant they didn't need to actively excrete so much surplus Vitamin C. So now, all the descendants of that species need to eat a Vitamin C-rich diet or they get scurvy and this defect maps exactly onto the particular branch of the family tree based on other evidence. All of the members of that particular branch, including humans still have the first three stages of the metabolic pathway for making Vitamin C that nearly all other mammals have, but the process fails because a single enzyme used in the fourth stage is broken due to a mutation in the gene which codes for it.

Other relatively recent examples include a mutation which allowed Han Chinese to live at high altitude on the Tibetan Plateau and a mutation which conveyed a resistance to the prion causing kuru in a New Guinea tribe, which is closely related to the prion causing mad cow disease in cows, scrapie in sheep and Creutzfeldt–Jakob disease in humans. In the absence of this diseases, that mutation would be entirely meaningless although the amount of 'information' in the DNA would be unchanged.

If creationists argue that new information cannot arise in DNA because it would contravene information theory and the laws of thermodynamics then you can be sure they haven't understood the nature of information in DNA, Information Theory and/or the Laws of Thermodynamics, most probably all three.

All biologists are Darwinists and Darwin is the ultimate authority on Evolution.

This probably comes from the tendency of creationists to assume all scientists, like creationists, defer to a book, or the author of a book as the ultimate source of all knowledge, and that what that book says is sacrosanct.

No serious scientists would argue that any earlier scientist was infallible and some sort of ultimate authority, otherwise science would never progress. All science is open to review, revision and reassessment in the light of new information. The way to fame and fortune, or at least to international recognition, possible prizes and good job offers, is to challenge an established theory. In fact, the progress of science can be seen as a Darwinian struggle between ideas, battling for dominance in the memepool of scientific opinion.

Darwin knew nothing of genes or Mendelian Laws of Inheritance and was very much a child of his time complete with many cultural assumptions then prevalent in middle class English society, most of which had a foundation in Christianity and especially Anglicanism. It's not surprising therefore that he was wrong about a number of things.

What modern biologist acknowledge however is that Darwin's and Wallace's ideas on evolution by descent with modification produced by natural selection is the great unifying theory underpinning all of biology. Other scientists are also belatedly coming to accept that any system in which there is replication, variation and selection is also subject to evolution and that Darwinian Evolution can explain how small differences, accumulated over time, can lead to large changes and explains how systems can have the appearance of being designed without the need to invoke magic, intelligence or a directing agent of any sort.

The bacterial flagellum is irreducibly complex.

This of course was the creationist biochemist Michael Behe's version of the argument from ignorance and the god of the gaps. In his book, Darwin's Black Box he stated (wrongly) that science could not explain how a structure like the flagellum of the Escherichia coli bacteria could not have evolved in stages because it only works when fully assembled. Although not explicitly stated, given his Christian fundamentalism and close association with the Discovery Institute, the conclusion was obvious - it must have been designed and created by the Christian god.

In fact we know that thousands of different flagella are to be found in nature and that they vary considerably in design and structure. However, only 23 of the 40 or so proteins found in the E. coli flagellum are common to all these so, contrary to creationist claims, far from being irreducibly complex, the flagellum structure can obviously be considerably changed and still function. The alternative is to conclude that the intelligent designer designed the same thing thousands of times and came up with a different design each time.

A far more parsimonious explanation is that flagella evolved from assemblies of pre-existing structures evolved to do something else - a process of exaptation. It is known that some of the proteins involved also have other functions within the cell, and the proton motor which rotates the flagellum could have evolved from a proton pump.

A useful analogy is to think of a stone arch which is held up only when the keystone in the centre of the arch is inserted. Presumably, a creationist would look at such an arch and conclude that it couldn't have been assembled one brick at a time and must have magically come together as a single event. In fact, it is built one stone at a time around a scaffold which is then removed because once the keystone is in place, the scaffolding is redundant. There is no reason at all why the flagellum could not have evolved by such a process as a refinement to a pre-existing structure which evolved earlier and has since atrophied or been exapted to some other function because the organism could do without it.

One amusing consequence of Behe's notion regarding E. coli, given his unswerving devotion to the notion of an omnibenevolent, omniscient god, is that he is actually arguing that this god, whom he believes loves his special creation, humanity and created a Universe just for them, with all other life there simple for mankind's benefit, is that some strains of E. coli are harmful and some can be lethal. They are aided in this by their flagella. Behe is arguing that the omnibenevolent intelligent designer must have designed the E. coli flagellum to make it easier for them to do us harm.

Evolution is just a theory.

This lie appeals to the scientifically illiterate who don't understand the difference between the different meaning of the word 'theory' as used by science and colloquially. Colloquially, a theory is an idea or notion which need not have any supporting evidence and which may or may not explain something real. For example, "I have a theory that green fairies grow apple trees on top of Mount Everest", "I have a theory that all conspiracy theories are invented by a secret Pentagon committee".

In science, a theory is an explanation, supported by evidence, observation and experimental data to explain an observed phenomenon. The Theory of Evolution is a scientific theory which explain the observed fact of evolution.

Darwin recanted on his deathbed.

This is a lie. It was a claim first made by Lady Hope who was not present when Darwin died. Others who were present confirmed that no such event ever took place.

But it is irelevent to the truth anyway. It would not change the way the Universe works if Einstein had recanted Relativity or Newton had recanted Principia Mathematica and it would not change how evolution works if Darwin had changed his mind. Scientific theories stand or fall by the evidence for or against them, not on the authority of one man.

There are no transitional fossils.

This lie simply flies in the face of the evidence. Anyone making this claim is either too ignorant to be taken seriously or is an outright liar. In fact, one of the current problem with working out the precise details of the evolution of modern humans is that there are too many transitional fossils if anything. Every fossil ever found is in fact transitional in that it represents a snapshot of the species at that point in time.

There are serious problems with the theory of evolution.

Creationists like to present any disagreement or uncertainty about the finer details of the TOE as fatal flaws. In fact, science is currently unable to resolve the differences between Relativity and Quantum mechanics but no sane person would happily step off a high building confident that gravity isn't true because there is a flaw in the theory explaining it. The TOE has withstood every advance in scientific knowledge since it was first proposed. Almost all advances in biology have strengthened and confirmed the theory and none of them have seriously challenged the basic principles. This claim can be made for few other scientific theories including Newton's Laws of Motion and the Law of the Conservation of Matter, both of which were overthrown by Relativity.

If we all evolved from apes, why are there still apes around in this world?

This question barely deserves an answer. The only conclusion one can draw about those who ask it is that they are appallingly ignorant of the subject and highly unlikely to want an answer.

Evolution can occur independently in populations which become geographically isolated and according to local conditions. This is almost certainly what happened when the Australopithecines diverged from chimpanzees and evolved in South and East African savannah whilst the chimpanzees evolved in the jungles of West Africa. Australopithecines then diverged into several species, one of which was ancestral to the Homo genus.

Evolution violates the second law of thermodynamics.

To quote Michael Le Page:

The second law of thermodynamics states that entropy, a measure of randomness, cannot decrease in an isolated system. Our planet is not an isolated system.

Er, that's it. There are longer ways of saying the same thing if you prefer.

Incidentally, it's good to see the great P. Z. Myers' blog Pharyngula linked to in a New Scientist article.

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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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