F Rosa Rubicondior: October 2013

Thursday 31 October 2013

Finding Evolution's Missing Links

Evolution's detectives: Closing in on missing links - life - 19 February 2013 - New Scientist

'Missing links' are creationist's favourite gaps in which they try to fit their god. The great thing about them is that no matter how many fossils are found and no matter how complete an evolutionary sequence they make, creationist frauds can always point to the gap between two adjacent fossils in the series and claim it as their 'missing' link. In fact, every fossil ever found is of course part of an evolutionary series and is the 'missing' link of its generation, but it simply serves to double the number of gaps for creationists.

This article in New Scientist from last February, which unfortunately is behind a paywall, goes into great detail about the key stages in the evolution of life which need to be evidenced by the fossil record, and attempts currently being made to find that evidence. Evolutionary biologists, like other scientists, are not at all embarrassed by the "don't know" answer. In fact, it's knowing what you don't know that drives enquiry and makes science such an interesting and fascinating subject for most people who don't need absolute certainty in their lives and who don't need to pretend they have all the answers (or should that be 'answer', because it's always the same one - "God did it!" - which can be glibly and smugly trotted out in the hope of impressing people with your expertise).

Christian Lie Alert!

Screen-shot. Click to enlarge.
Little Manuel "Manny" de Dios Agosto, who still hopes people will believe his name is Michael, apparently, has plumbed new depths in his continuing campaign of attention-seeking abuse.

He is now spamming Twitter, dutifully RT'ed by all his other accounts, claiming that the money I raised by carrying advertising on my blog, and which I donated to Oxfam as promised as detailed here, where all the receipts may be seen, was in some way fraudulent. Initially, his rage was confined to spamming my blog yet again with abusive comments and boast about how much money people are giving him in response to his incessant begging.

One such was:

Wednesday 30 October 2013

A Fungus That Farms Bacteria!

Morrell (Morchella crassipes)
First fungal farmers found harvesting bacteria - life - 30 October 2013 - New Scientist

People who study biology, and particularly ecology, are of course used to finding examples of how 'selfish' genes very often create cooperative associations. In fact all ecosystems are in reality composed of far more cooperative organism than they are of competitive ones. But nature can still throw up a few surprises and so give us that little frisson of excitement and wonder or a gasp of astonishment.

We like to think that it takes something akin to human intelligence to come up with something like farming where another species is looked after, protected and nurtured in order to provide us with food so it still surprises people to discover that we are not the only ones doing it. Leaf-cutter ants, for example, collect leaves which are chewed up to form a compost on which a unique fungus grows in special chambers in the underground nest. The ants in turn live on the fungus, which they harvest, having planted the spores on their garden. The forty-seven species of leaf-cutter ant have been doing it for so long that they each have their own species of Lepiotaceae fungus which has co-evolved with them.

Microbes are still a largely unexplored frontier. I am sure there are many, many amazing relationships among microbes waiting to be discovered and investigated.

Debbie Brock, Washington University in St Louis, Missouri, USA
Another common example of cooperation is that between the legume family of plants - the pea and bean family, which includes acacia trees, lupins, peanuts and laburnum trees - and bacteria which live in special nodules in the roots. These bacteria 'fix' free atmospheric nitrogen by turning it into nitrates which are then available to the plant. As such they are an important and integral part of Earth's nitrogen cycle which is essential to all life on the planet.

Also essential for a healthy planet, and particularly for healthy trees and forests, is a cooperative alliance between several species of fungi and trees, and many other plants. One of the mysteries of botany when I was a biology student many years ago was how tall trees manage to overcome gravity to push water from the roots to the leaves at the top of the tree and with it the nutrients the trees need especially in the growing tips of the branches.

Tall tree-trunks are of course a product of an evolutionary arms race but, as we now know, they would have been impossible had it not been for a sybiotic relationship between fungi in the soil and tree roots. The fungi get sugars from the tree and in return provide the tree with nutrients which they make available and which they help actively transport into the root system with enough pressure to push the sap up the tree's vascular system, helped by capillary action and suction pressure from evaporation through pores in leaves.

Now scientists have discovered a fungus which farms bacteria.

Pilar Junier of the University of Neuchâtel, Switzerland, and colleagues have discovered that the fungus Morchella crassipes has formed a relationship with the bacteria Pseudomonas putida. By labelling the fungi with radioactive carbon-13 in one set-up and the bacteria in a second, they were able to show that the bacteria multiplied quickly in the first five days as they took nutrients from the fungus. However, numbers fell quickly between day five and day nine and nutrients were taken up by the fungus, which grew hard nodules which acted as a nutrient store.

The fungi actively fed and protected the bacteria, then ate them, probably producing digestive enzymes with which to do so. In principle, and biologically, no different to what we do with cereal crops, cabbages, carrots, chickens, sheep and cows and a host of other species with which our human genes have formed an alliance.

According to Oprah Winfrey, if you're an atheist, you're not supposed to find that fact awesome and amazing; you have to suffer from an infantile superstition and attribute it to magic for that.

Bacterial farming by the fungus Morchella crassipes, Martin Pion, Jorge E. Spangenberg, Anaele Simon, Saskia Bindschedler, Coralie Flury, Auriel Chatelain, Redouan Bshary, Daniel Job and Pilar Junier;
Proc. R. Soc. B 22 December 2013 vol. 280 no. 1773.

First fungal farmers found harvesting bacteria, Colin Barras, New Scientist 30 October 2013

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Tuesday 29 October 2013

Religion's Poison - Holy Water

Holy water should have HEALTH warnings.

Did you think holy water had some sort of protective power; the power to ward off evil? Think again.

Religion poisons everything, including the holy water they sprinkle everywhere and which they slosh all over the heads of unfortunate babies taken by their parents to churches to have protective spells cast over them. A study by researchers at the Institute of Hygiene and Applied Immunology at the Medical University of Vienna, Austria found that eighty-six percent of holy water was too dangerous to drink, often being contaminated by harmful pathogens including E. coli, the normal indicator of fecal contamination. The more popular the church, the more likely it was to find poisonous holy water in use. The usual source of fecal contamination is poor toilet hygiene or inadequate sewerage.

The irony is that holy water, which came originally from 'holy' wells, may well have earned it's curative/protective powers not because of what was in it but because of what wasn't; not because of what it contained but because of what it didn't contain. It was once probably purer than normal public drinking water before we understood the necessity of keeping human waste away from drinking water. This was demonstrated by the English physician John Snow who brought a major outbreak of cholera in London to an end in 1854 by the simple measure of closing a local well. He was of course building on the work of scientists like Robert Koch and Antonie van Leeuwenhoek, the scientists who discovered microscopic life and linked it to disease to produce the 'Germ Theory' of infectious disease. These discoveries have probably done more to improve human health and to prolong life than any other scientific discovery, save possibly that of antibiotics.

Holy wells quite probably owe their existence to religious ignorance of micro-organisms and to a typically magical, and wrong, interpretation of observed events. Drinking water in pre-scientific times, especially close to human habitation, would have been heavily contaminated by human fecal matter which would have leaked into it from the earth closets and primitive latrines which served as toilets. The medieval human world would have been awash with E. coli and other harmful enteric pathogens and diarrhoea and vomiting would have been normal with outbreaks of cholera common.

I was born and brought up in a sixteenth-century farm-labourer's cottage in a village in North Oxfordshire, England which still had an earth closet lavatory at the end of the garden. About ten yards away, and downhill from the lavatory was an ancient well which we shared with our neighbours, fed by a deep spring which was fed no doubt partly by liquids from our lavvy, and if not our lavvy then by those of houses further up the hill. Fortunately, we had mains water by the time I was born because the parish registers of villages in the area, and probably the rest of Europe, from only a couple of generation earlier are full of multiple burials of children, the victims of yet another cholera epidemic. The commonest age of death was under five years old in those days.

Anyone suffering yet another bout of diarrhoea and vomiting or an outbreak of boils who happened to find a spring in a wood or far enough away from habitation to avoid contamination, and who drank from it for a few days would very probably have a 'miracle' cure and so another source of holy water would have been found.

Now, of course, science has improved drinking water to such an extent, that it is far safer than water from the holy wells of former times.

Of course, despite desperate trawling through the holy books to find a passage here or there which, with the benefit of hindsight and religion's favourite 'proof', confirmation bias, there is absolutely nothing at all about micro-organisms or their role in disease in the the Bible. There is nothing that hints at Germ Theory; there is nothing about the importance of hygiene other than vague references to it. You'd have thought that a designer who cared about mankind would have told us a little about the germs it had designed and how to avoid catching them. This would have added immeasurably to the sum total of human happiness and done more to improve the quality of life for its creation than just about anything else, apart from not designing the germs in the first place. It's almost as though it wanted us to get sick and for lots of our children to die before the age of five.

About the closest to it is:

You shall have a place outside the camp, and you shall go out to it. 13 And you shall have a trowel with your tools, and when you sit down outside, you shall dig a hole with it and turn back and cover up your excrement.

Nothing there about making sure you're below the water supply. Nothing about boiling water. It's as though the authors of the Bible knew nothing about germs and the causes of disease. In the best traditions of religious blundering about in ignorance, pure water was assumed to be magic and the real cause of disease was never even guessed at. The answer was, as it always is with religion - "God did it!" It took science to work it out the real situation and of course religion got it completely wrong, just as it has been shown to have done with other explanations of the natural world when science has shown us the truth.

By contrast, if religion is ever right about anything, it's right by accident.

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Monday 28 October 2013

Life's a Beach. Order From Chaos

Listen to any creationist pseudo-scientist and you'll be told that something can't come from nothing and that order can't come from chaos, because both of those violate the Second Law of Thermodynamics.

What they really mean of course is that both of these show we can explain the Universe and life on Earth without invoking magic and magic designers, so they'd rather you didn't know they can both happen by perfectly natural processes. That would dangerously undermine their claim to power and influence and, most importantly, damage their income stream and mean they would need to earn an honest living.

I've already dealt at length with the nonsensical notion that nothing ever existed before there was something in Much Ado About Nothing so I'll now look at the nonsensical claim that order can't emerges from chaos without a magic designer, which I've also touched on with Order From Chaos.

What creationist pseudo-scientists won't tell you of course is that you can observe for yourself order emerging from chaos in, for example, the sand on a beach, as this photograph I took yesterday on a beach in Portugal clearly shows. What can be seen is structure within the otherwise chaotic arrangement of grains of sand due to the action of chaotically arrange water molecules and suspension of sand grains.

One of the great things about being an atheist and knowing a little about science is that you can recognise examples of emergent order and don't need to dismiss them because you have a superstition which says they are impossible. Look at the photograph and you will see a pattern of diamond shapes on the surface of the sand as the seawater flows off following the breaking of a small wave on a gently-sloping beach.

What happens is that a larger grain of sand is heavy enough to resist the carrying power of the flowing water and settles out. Then small eddies form behind it as the water flows around it and the main flow is channelled into a widening fan shape. This allows more sand grains to settle out in the widening zone downstream of the original sand grain. Repeat this a thousand times over a small area and the resulting interference pattern creates the system of criss-crossing micro-channels and a diamond lattice of newly deposited sand. Structure and order has emerged from chaos and all in complete accord with the laws of thermodynamics.

The driving force which has produced this is of course gravity. Gravity produces the flow of water over the sand and gravity causes the sand grains to settle out when the water loses the power to carry them. Just as gravity can account for structure emerging from the chaos of sand and water so gravity can account for the formation of galaxies, stars and stellar planetary systems.

The analogous force to gravity in living systems is natural selection. Just as gravity causes order to emerge from chaos, so natural selection causes gradual change to emerge from the chaos of random change in genes to produce variation. Just as gravity caused order to emerge from the chaos of randomly distributed particles in the Universe, so natural selection caused diversification to emerge from the chaos of random mutations in DNA.

For reasons of selfishness and greed and a desire to control through fear and superstition, creation pseudo-scientists would have you ignore wonders such as this to be found all around in nature and to dismiss them all as the product of magic, just like Bronze-Age goat herders did.

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Saturday 26 October 2013

A Lot of Cock in Portugal

You see it everywhere; in every tourist shop on ceramics and tea-towels; on tee-shirts and aprons; on pendants, hair-slides and key-fobs, and as stand-alone ornaments. You'd be amazed at the number of different ways the Portuguese have found to market the Cock of Barcelos (O Galo de Barcelos).

It has its origins in a Catholic 'miracle' - one of many that abound in this area of Europe from a time before the growth in science and education made miracles, miracle-workers and prophets obsolete in most of the civilised world. The story is normally set in the 17th century and usually involved a young man on a pilgrimage from Galicia in Spain to Santiago de Compostela, who happened to pass through Barcelos in North-Western Portugal, where he was accused of the theft of some silver from a rich man in the town, arrested, tried and condemned to be hanged.

On the day of his execution he pleaded with the hangman to be allowed to speak to the judge who

Friday 25 October 2013

Evolution - Making a Difference

The thing about evolution, in fact the main thing about evolution, is not how it leads to new species but how it accentuates small differences and so produces a whole range of variability below the species level - subspecies, regional varieties, races, etc, in different environments.

It does this of course because natural selection act as a filter letting through the 'fitter' alleles at each generation and so increasing the probability of them occurring in the next generation's gene pool. Provided it conveys an advantage a rare allele quickly becomes common, as I showed with a simple spreadsheet in Playing With Evolution.

This was highlighted for me today in Lisbon when I was sitting enjoying a refreshing água mineral com gás (that's a sparkling mineral water) and custard tarts in the grounds of the Castelo de Sao Jorge today. I saw a small bird which looked like a Great Tit (Parus major) only different. I'm familiar enough with British Great Tits to know when they don't look quite right.

The history of European birds, and especially those sedentary species like the titmouse family, is very interesting because it is intimately associated with the last Ice Age and is a wonderful example of how the environment drives evolution. A word of warning though! If you type "Great Tits in Portugal" into Google, be careful what you click on in the result list!

Portugal, as I'm sure you all know, lies on the western edge of the Iberian Peninsula which consists solely of Spain, Portugal and British-owned Gibraltar. The Iberian Peninsula is separated from the rest of Europe by the Pyrenees Mountains which act as a barrier to the movement of all sorts of species, like butterflies, moths and small birds, who can only normally interact with other members of their species or genus via narrow coastal strips on the Atlantic or Mediterranean coast. In effect, the Iberian members of a species have a almost isolated gene pool and so would be expected to evolve in their own direction more or less regardless of what is happening in the rest of Euro-Asia.

And that is exactly what we find.

Iberia has an abundance of races, subspecies and varieties of very many European species, and all of these have come about since the last Ice Age, when Iberia, Italy and the Balkans acted as refuges for many European species as ice sheets covered Northern Europe. In effect, the rest of Europe was repopulated from these refuges as the ice retreated some 10,000 years ago and the differences we now see either arose during isolation in these southern refuges or has arisen since. For more on how this procees probably drove diversification in Europe, see Creationists' Macro-Evolution Lie.

So, although I couldn't find any particular references to a particular Iberian form of the Great Tit, and it may well have been just a juvenile, an atypical individual or one showing a seasonal colour variation, the chances are good that what I saw was a regional variety, produced by isolation and by change in the frequency of particular alleles due to the effect of natural selection on its ancestors. The probability is that I saw just another example of evolution in progress.

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Wednesday 23 October 2013

Catholic Violence and the History of Japan

Japanese-Portuguese Christian Bell, 1570
Apparently, the reason Christians, mostly Catholic, were persecuted in Japan was because the authorities became alarmed at their intra-sectarian violence and feared it would destabilise peaceful Japanese society which was mostly Buddhist and Shintoist (it's quite possible to be both).

I got this little-known (in the West) snippet of information from one of my brothers in law yesterday evening. He is an acknowledged expert in Japanese art, being the head of Japanese conservation for a major art museum in Boston, MA, USA. He has worked and studied in Japan and speaks fluent Japanese. We had been talking about our impending trip to Lisbon, Portugal tomorrow and got on to discussing the influence of Portugal on Japan and vice versa. He has also worked and taught Japanese art and conservation in Lisbon.

Although some people believe Nestorian (i.e., Syriac or Eastern) Christianity had already been introduced to Japan earlier, the main systematic effort to introduce it came from the Portuguese, and later the Spanish, Catholics between about 1550 and 1600. These missionaries were sponsored by their respective governments and their main function was to act as the advanced guard for Western colonialism and open up Japan to Western Traders - Portuguese and Spanish, naturally - just as they had done and were to do in so much of the world. To that end the missionaries would 'convert' the local officials who would then be especially favoured by the traders. The Portuguese missionaries were exclusively Jesuite while the Spanish were mostly Franciscans and Dominicans.

Once trade was established the traders, backed by the odd warship, would 'negotiate' favourable trading terms, often including handing over the docks and the port towns to the traders to become, in effect, 'free' ports controlled by foreign powers and exempt from taxes and excise duties - a practice that would be called 'smuggling' unless backed by the threat of military intervention. Imagine Boston, San Francisco, Rotterdam or Bristol in foreign hands because it was considered necessary for free trade and the smugglers had got fed up with being arrested!

But apparently, it wasn't so much the creeping colonialism which alarmed the Japanese authorities. It soon became apparent that, whilst preaching peace and brotherly love for all mankind, and whilst professing love for the non-Christian Japanese, what the missionaries really detested were Christians of other sects and from other countries who were trying to muscle in on their racket, a rivalry which often erupted in violence, even between Catholics of different orders. The origins of this, of course, were back in Europe, in particular with different Popes blowing in the political wind and abandoning principles for short-term gain and plumping for whichever side was promising the biggest return:

...religion was also an integral part of the state and evangelization was seen as having both secular and spiritual benefits for both Portugal and Spain. Wherever these powers attempted to expand their territories or influence, missionaries would soon follow. By the Treaty of Tordesillas, the two powers divided the world between them into exclusive spheres of influence, trade and colonization. Although at the time of the demarcation, neither nation had any direct contact with Japan, that nation fell into the sphere of the Portuguese.

The countries disputed the attribution of Japan. Since neither could colonize it, the exclusive right to propagate Christianity in Japan meant the exclusive right to trade with Japan. Portuguese-sponsored Jesuits under Alessandro Valignano took the lead in proselytizing in Japan over the objection of the Spaniards. The fait accompli was approved in Pope Gregory XIII's papal bull of 1575, which decided that Japan belonged to the Portuguese diocese of Macau. In 1588, the diocese of Funai (Nagasaki) was founded under Portuguese protection.

In rivalry with the Jesuits, Spanish-sponsored mendicant orders entered into Japan via Manila. While criticizing Jesuit activities, they actively lobbied the Pope. Their campaigns resulted in Pope Clement VIII's decree of 1600, which allowed Spanish friars to enter Japan via Portuguese India, and Pope Paul V's decree of 1608, which abolished the restrictions on the route. The Portuguese accused Spanish Jesuits of working for their homeland instead of their patron. The power struggle between Jesuits and mendicant orders caused a schism within the diocese of Funai. Furthermore, mendicant orders tried in vain to establish a diocese on the Tohoku region that was to be independent from the Portuguese one.

Toyotomi Hideyoshi
So, the Japanese authorities acted to 'discourage' the growth of Christianity and prohibit the activities of the 'missionary' shock troops and so nip Western colonialism in the bud. The arrogance, racism, and casual brutality of the Catholic missionaries was to result in a disaster for Christianity in Japan from which it was not to recover until recent time:

By 1587, Toyotomi Hideyoshi had become alarmed, not because of too many converts but rather because the hegemon learned that Christian lords reportedly oversaw forced conversions of retainers and commoners, that they had garrisoned the city of Nagasaki, that they participated in the slave trade of other Japanese and, apparently offending Hideyoshi's Buddhist sentiments, that they allowed the slaughter of horses and oxen for food. He was concerned that divided loyalties might lead to dangerous rebels like the Ikkō-ikki Sect of earlier years and produced his edict expelling missionaries. However, this decree was not particularly enforced.

Toyotomi Hideyoshi promulgated a ban on Catholicism in form of the "Bateren-tsuiho-rei" (the Purge Directive Order to the Jesuits) on July 24, 1587. Hideyoshi put Nagasaki under his direct rule to control Portuguese trade.

When Toyotomi Hideyoshi issued the Bateren-tsuiho-rei, the Jesuits in Japan, led by Coelho, planned armed resistance. At first, they sought help from Kirishitan daimyo but the daimyo refused. Then they called for a deployment of reinforcements from their homeland and its colonies. But this plan was vetoed by Valignano. Like the Kirishitan daimyo, he realized that a military campaign against Japan's powerful ruler would bring catastrophe to Catholicism in Japan. Valignano survived the crisis by laying all the blame on Coelho. In 1590, the Jesuits decided to stop intervening in the struggles between the daimyo and to disarm themselves. They only gave secret shipments of food and financial aid to Kirishitan daimyo.

On February 5, 1597, twenty-six Christians – six European Franciscan missionaries, three Japanese Jesuits and seventeen Japanese laymen including three young boys – were executed by crucifixion in Nagasaki. These individuals were raised on crosses and then pierced through with spears. While there were many more martyrs, the first martyrs came to be especially revered, the most celebrated of which was Paul Miki. The Martyrs of Japan were canonized by the Roman Catholic Church on June 8, 1862 by Blessed Pius IX, and are listed on the calendar as Sts. Paul Miki and his Companions, commemorated on February 6, February 5, the date of their death, being the feast of Saint Agatha.

Persecution continued sporadically, breaking out again in 1613 and 1630. On September 10, 1632, 55 Christians were martyred in Nagasaki in what became known as the Great Genna Martyrdom. At this time Catholicism was officially outlawed. The Church remained without clergy and theological teaching disintegrated until the arrival of Western missionaries in the 19th century.

Meanwhile, the Dutch, by assuring the Japanese authorities that the last thing they were bothered about was religion, and by sticking to their word, cornered the market in Japanese trade with the West.

Just another example of how religion poisons everything; in this case peaceful contact with, mutually beneficial trade with and culturally enriching contact with, newly-discovered people and societies in the early days of European exploration and the growth in world trade. A legacy of this first contact with the Christian West was a Japanese society deeply suspicious of Western imperialism, which in turn resulted in a legacy of deep suspicion about western imperialist ambitions in the Pacific and Southeast Asia, possibly even leading to the Japanese 'preemptive' strike on Pearl Harbour in 1942 in response to a perceived western expansion into Southeast Asia and the Pacific.

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Sunday 20 October 2013

God Hates Frogs

The Invasive Chytrid Fungus of Amphibians Paralyzes Lymphocyte Responses

The problem with being an intelligent designer is that when you change your mind and decide your creation was a mistake it can be very difficult to kill just that creation off and not harm the others. Look what happened when it decided to correct its mistake with humans, for example. It ended up killing everything else off too when it used a sledgehammer to crack a nut.

So, when the Intelligent Designer decided it had made a mistake with all those frogs it had to come up with something really clever. It chose a fungus - Batrachochytrium dendrobatidis - to do the work but that wasn't as simple as it sounds. The problem was it had provided frogs with a way to fight fungal infections, what with them living in conditions normally conducive to fungal growth. It had provided them with a group of specialist body cells to cope with them, as well as bacteria. These cells normally crawl around looking for invading cells and ingesting them, then they program other cells to produce antibodies which quickly kill off any more cells if they get into the frog's body.

So, this was a problem for the Intelligent Designer's plan to kill of all the frogs with a fungus.

Luckily it thought up another brilliant plan and changed the fungus a little bit so it now turns off the frog's immune response and allows it to kill the frog and use its body to produce more fungi.

The chytrid fungus, Batrachochytrium dendrobatidis, causes chytridiomycosis and is a major contributor to global amphibian declines. Although amphibians have robust immune defenses, clearance of this pathogen is impaired. Because inhibition of host immunity is a common survival strategy of pathogenic fungi, we hypothesized that B. dendrobatidis evades clearance by inhibiting immune functions. We found that B. dendrobatidis cells and supernatants impaired lymphocyte proliferation and induced apoptosis; however, fungal recognition and phagocytosis by macrophages and neutrophils was not impaired. Fungal inhibitory factors were resistant to heat, acid, and protease. Their production was absent in zoospores and reduced by nikkomycin Z, suggesting that they may be components of the cell wall. Evasion of host immunity may explain why this pathogen has devastated amphibian populations worldwide.

The Invasive Chytrid Fungus of Amphibians Paralyzes Lymphocyte Responses
J. Scott Fites, Jeremy P. Ramsey, Whitney M. Holden, Sarah P. Collier, Danica M. Sutherland, Laura K. Reinert, A. Sophia Gayek,
Terence S. Dermody, Thomas M. Aune, Kyra Oswald-Richter, and Louise A. Rollins-Smith
Science 18 October 2013: 342 (6156), 366-369. [DOI:10.1126/science.1243316]

This, of course, looks just like the sort of destructive arms race that evolutionary biologists predict will happen frequently by Darwinian Evolution, and looks just like there is no intelligence behind it because what Intelligent Designer would have to be that creative to overcome a problem of its own creation because it wouldn't have created frogs in the first place if it was going to kill them all off. Nor would it have given them an immune system to overcome fungal infections it it planned all along to kill them all with a fungus, but I expect creationists, especially the professional frauds at the Discovery Institute can think up a good reason why the Intelligent Designer works this way.

Or maybe they'll just ignore the devastation in the frog population which is now occurring on a global scale and just hope their scientifically illiterate and environmentally unaware target audience won't be aware of it either.

The Invasive Chytrid Fungus of Amphibians Paralyzes Lymphocyte Responses
J. Scott Fites, Jeremy P. Ramsey, Whitney M. Holden, Sarah P. Collier, Danica M. Sutherland, Laura K. Reinert, A. Sophia Gayek, Terence S. Dermody, Thomas M. Aune, Kyra Oswald-Richter, and Louise A. Rollins-Smith
Science 18 October 2013: 342 (6156), 366-369. [DOI:10.1126/science.1243316]. (Subscription required)

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Friday 18 October 2013

Evolution in Georgia

The Dmisi skull, Homo erectus
Image: Guram Bumbiashvili, Georgian National Museum
Complete skull of 1.8-million-year-old hominin found - life - 17 October 2013 - New Scientist

We have a great example of how science handles new evidence and differing opinion in today's New Scientist. Contrast this to the way religions handle disagreement.

A 1.8 million year-old hominid skull is causing scientists to ask some fundamental questions about the widely accepted model for the human evolutionary tree, going right back to the ape-like australopithecines of East and South Africa and especially the East African group of what are thought to be a contemporaneous group of closely related members of the Homo genus, including one which is on our direct line of descent, H. erectus.

According to the standard model, it was in this East African group that the human brain began to become significantly larger than in the more ape-like australopithecus group. This in turn drove a diversification into three or more different species, H. erectus, H. rudolfensis and H. habilis all living in the same area at the same time. H. erectus later evolved into H. heidelbergensis which then spread out of Africa in the first wave of Homo radiation, giving rise to Neanderthals in Europe, Denisovans in Asia and possibly a third as yet unidentified species, and maybe H. florensis - the so-called 'hobbit'. Meanwhile, the H. heidelbergensis who remained in Africa evolved into modern H. sapiens, some of whom came out of Africa in one or more waves, interbred with Neanderthals and Denisovans to form a brief Homo ring complex in Euro-Asia before we exterminated the earlier species.

Transitional Spiders and Nervous Scorpions

BBC News - Big clawed fossil had spider-like brain

Here's another one of those 'non-existent' intermediate fossils that creationists keep telling us about.

Admittedly, this isn't intermediate between a human and an ape or between one human species and another - which are what most creationists seem to think evolution is all about. This one is intermediate between two major divisions of the arachnida, the spiders or arachnids and the scorpions or dromopoda. This class also includes the horseshoe crabs, one of those 'living' fossils' creationists love because they imagine they prove evolution didn't happen.

Arthropods, or jointed legged, creatures include insects, crabs, shrimps, barnacles, lobsters, millipedes and several other marine and terrestrial invertebrates including the extinct trilobites. They all have a more-or-less hard exoskeleton composed of chitin and segmented bodies with pairs of appendages used for walking, swimming and, in the case of insects, flight. These appendages have also evolved to become mouthparts. This particular specimen is from 520 million years ago and is of one of an extinct group of arthropods known colloquially as the "great appendage" arthropods, which have large claw-like appendages on their heads. It was discovered in South China and is part of the segmented Alalcomenaeus genus.

The nervous systems of related phyla tend to be similar with the differences reflecting the divisions of the phylum into classes and orders, so studying the nervous systems of living creatures can help establish their evolutionary relationships. However, this method of classification is not normally available with fossils because nerve tissue, like all soft tissues, does not fossilise so readily as the hard body-parts.

But, using a new technique with a CT scanner and 3D software, researchers were able to see the basic structure of the nervous system and compare it to that of other arthropods. It was clear that this species was from a group that were ancestral to both the spiders and the scorpions and its nervous system also bore many similarities with the nervous system of larval forms of the horseshoe crabs.

It is hoped that this technique will now enable the evolutionary relationship of other arthropods to be worked out, so filling in another small area of the jigsaw puzzle of evolution.

And still no fossil has yet been found which is inconsistent with Darwin's and Wallace's theory of descent with modification or with the neo-Darwinian gene-based theory of evolution. Had one ever been found, I wonder how many creationists would suddenly have become convinced of the soundness of the scientific method and of the irrefutable nature of solid evidence.

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Thursday 17 October 2013

Not Yeti?

Gigantopithicus still alive?
Has the Yeti mystery been solved? New research finds 'Bigfoot' DNA matches rare polar bear - Science - News - The Independent

Has the yeti question been answered?

Like so much with science, it depends on what the question is. If the question is, "Is there a humanoid creature living in the Himalayas?" then Prof. Bryan Sykes findings don't actually refute the claim that there is, but they certainly don't support the claim either.

If the question is, "Is there a large, unidentified (until now) creature living in the Himalayas?" then these finding are a qualified "quite probably". What the team in Bryan Sykes's Oxford-Lausanne Collateral Hominid Project have found is that the DNA from two samples of hair, allegedly from yetis, and collected from locations 800 miles apart, one in the Ladakh region, the other in Bhutan, is identical to that extracted from the jawbone of an ancient bear from northern Norway which lived between 40,000 and 120,000 years ago. This species of bear is believed to be ancestral to both polar bears and brown bears, which are known to be closely related, even interbreeding where they come into contact. The match was discovered when the DNA from the samples was compared with DNA held on an international DNA database.

In fact, this illustrates a point scientists keep having to make. It is technically impossible to prove a negative; the best one can do is to fail to falsify the positive claim. A determined critic, and especially one who isn't averse to using the absurd to support her claim, can always raise the "Ah! But..." objection to any evidence which fails to support her. For example, a die-hard yeti fan can always argue that the samples analysed weren't from yetis. And of course that's true - they were from bears.

So a devout Yetiist would probably feel vindicated, even more convinced in his own mind that yetis do exist - which is why someone has faked the evidence to try to disprove them. Why would they do that if there were no yetis? Just like a Millerite in the Great Disappointment when Jesus failed to materialise as prophesied. They decided God had postponed Judgement Day because he was so impressed with their piety and wanted to give them more time to convert those of us who just couldn't see the sense in that argument. They founded the Seventh Day Adventists.

What's probably more interesting to biologist, in addition to the possibility that a large unknown bear may well be alive at high altitude in the Himalayas, is that this bear seems to have once been widespread during the last Ice Age, and a remnant population may be hanging on at a high altitude in the Himalayas to where it may have taken refuge as the climate warmed up and the ice sheets retreated.

So, creationists, you can now go around trying to impress people by asking, "If polar bears evolved out of ancient bears, why are there still ancient bears?". You'll be told, of course, by those who bother to answer you, that it's because they both evolved out of genetically separated populations, just like humans and the other apes did.

Bryan Sykes is no stranger to exciting creationists and Bible literalists. He was the author of the 2002 book, The Seven Daughters of Eve, which showed, from an analysis of mitochondrial DNA, that all non-Africans are descended from just seven women, themselves descendants of a nominal single common ancestral female whom he termed 'mitochondrial Eve'. Hoards of delirious Bible literalists immediately swarmed onto the Compuserve Religion Forum and elsewhere in the early days of the Internet to announce that a 'brilliant scientist' had proved Adam and Eve existed and that the Bible story was a scientific fact - how they crave validation by science. Part of their 'evidence' was that this scientist had even worked out the names of Eve's seven daughters!

None of them had read the book, of course. Few of them had even seen it and even fewer knew what mDNA is. Like present day commenters on Reddit, they were simply reacting to the title and saw no reason to actually read what they were commenting authoritatively upon.

Sykes, of course, like any self-respecting scientist, is urging caution and says much more analysis is needed before any firm conclusions can be drawn from this (as yet unpublished) work.

'via Blog this'

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Unintelligently Designed Teeth Cause Ray Discomfort

I'm sure my fellow atheists and evolutionary biologists were as distressed as I was to learn that poor Ray Comfort, the renowned Young-Earth Creationist and Christian fundamentalist, was to undergo surgery to have an impacted wisdom tooth removed. One hopes his mouth has recovered and the pain and distress have subsided. One blessing is that there will now be room for more of Ray's feet, which is something we can all look forward to.

For those who haven't heard of Ray Comfort, who earns his living selling Christian fundamentalist tracts to other Christian fundamentalists, Ray leapt to fame when he declared that bananas were proof of intelligent design because they fit in the human hand so perfectly. He forgot to mention that their 'designer' neglected to give them any seeds, so they need humans to propagate them vegetatively.

Ray recently became incandescent with rage and banned several people from posting comments on his website when someone called him a bibliophile. Ray is definitely no bibliophile! Got that?

I wonder if Ray pondered on the delicious irony of a Bible-literalist creationist who rejects science and who believes the Universe was created just 6000 years ago by magic as somewhere for him to live, and that all animals were created just for his convenience in a single day and have remained unchanged ever since, having to turn to science to treat the effects of something so unintelligently designed as the human wisdom tooth.

Wisdom teeth are vestigial third molars that used to help human ancestors in grinding down plant tissue. The common postulation is that the skulls of human ancestors had larger jaws with more teeth, which were possibly used to help chew down foliage to compensate for a lack of ability to efficiently digest the cellulose that makes up a plant cell wall. As human diets changed, smaller jaws gradually evolved, yet the third molars, or "wisdom teeth", still commonly develop in human mouths.

Agenesis of wisdom teeth in human populations ranges from practically zero in Tasmanian Aborigines to nearly 100% in indigenous Mexicans. The difference is related to the PAX9 gene (and perhaps other genes).

Ray may be comforted to know that he was far from alone; impacted wisdom teeth are very common. The oldest known impacted wisdom tooth belonged to a European woman of the Magdalenian period (18,000–10,000 BCE). Admittedly, this was from some considerable time before there was a Universe, let alone people with impacted wisdom teeth according to Ray, but we must bear in mind that Ray is definitely not a bibliophile, so won't have read about this stuff.

"There is no refutation of Darwinian Evolution in existence. If a refutation ever were to come about it would come from a scientist, not an idiot."

Richard Dawkins
To understand how the problem with wisdom teeth in modern humans arose it helps to look at a modern human head in profile. Draw an imaginary line down the protruding nose and curve it from the tip of the nose down to and under the protruding chin. It will describe the profile of a typical simian head with a muzzle. As we evolved an upright gait our head rotated forwards and our facial bones rotated downwards, then our facial bones, including the maxilla and mandible, receded underneath our cranium.

At some time in our evolutionary history, as our faces grew it was an advantage to grow more teeth at the back as room for them developed, so, as we stopped growing somewhere between the ages of 16-20, we added more teeth.

The problem is, we still do, even though we have enough teeth without them and even though there is often not enough room for them, so they grow at odd angles or fail to erupt at all. Quite simply, the evolution of our facial skeleton and of our teeth are not synchronised because, whilst there is an advantage in having a modern human face, there is not a major disadvantage in having wisdom teeth, so, while genes for the modern face have been selected for, those for wisdom teeth have not been so strongly selected against. It's a bit like a modern motor car still having a dynamo fitted to spin away doing nothing useful but not doing any harm either, until, occasionally, it catches fire.

For people like Ray Comfort of course, the better explanation is that the problems with our wisdom teeth were the product of an inerrant, omniscient, benevolent, intelligent designer who intended us to have these problems and, for reason which remain poorly understood, decided to exempt some of his design from them, especially the indigenous Mexicans, who were specially favoured and never have any problem with them because they don't grow any. This just happens to coincide with these favoured people having a genetically modified PAX9 gene of course. No evidence for evolution there.

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Wednesday 16 October 2013

God's Poachers

There is a lucrative market in religious memorabilia, statues of gods and saints, and dolls dressed up to look like someone's notion of what a first century Judean virgin would look like - a white European, obviously.

So when it comes to choosing a material to make these little baubles out of, naturally it has to be expensive, and white because spending a lot on them shows piety, and obviously gods and saints and Judean virgins were all white. So what better than ivory?

You can see lots of these beautiful religious artifacts photographed by the photojournalist Brent Stirton here and here. Brent has investigated the links between religion and the ivory trade. Don't worry, Christians! It's not just you. Buddhists, Hindus and Shintoists are equally guilty, and equally racist, it seems.

To get the ivory, poachers slaughter elephants in Africa, where it is illegal in most countries. They frequently slaughter game wardens and police too. You can contrast these beautiful religious carvings with the work done by those who supply that raw materials here. I've shown a small sample below.

It's nice to see that worshiping a creator god makes people keen to care for its creation... though not at the expense of ostentatious displays of piety, obviously.

Brent Stirton's photographs won him this year's Wildlife Photojournalist Award by Wildlife Photographer of the Year. Their exhibition can be seen in London's Natural History Museum, from 18 October 2013 until 23 March 2014.

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Tuesday 15 October 2013

A Handy Piece Of Superstition

Witchcraft Trade, Skin Cancer Pose Serious Threats to Albinos in Tanzania: Scientific American

A charming account of the effects of religion, this time in Tanzania, is brought to us this week by Scientific American. As though being born with the genetic mutation which causes albinism wasn't bad enough, sufferers have to put up with living in a religious society where local superstitions hold that the body-parts of albinos have magical properties which can lead to power and wealth.

People born with albinism make little or no melanin - the pigment responsible for skin colour. This makes them especially susceptible to skin cancer from which melanin protects us by acting as a natural barrier to harmful solar radiation. Albinos frequently also have defective vision and hearing and most rarely live beyond the age of fifty, with skin cancer being the number one cause in Tanzania.

Another cause of early death is religious superstition. Since the year 2000 some seventy-two Tanzanian albinos have been murdered for their body-parts, many in childhood. Only five prosecutions for murder have been successful. Another superstition is that albinos don't die but simply disappear so the authorities often don't pay much attention when they do, in fact, disappear. I wonder which witch doctor invented that handy piece of superstition.

It is believed that the body-parts have much greater power if they are from children and especially if the person screams when their parts are being cut off, so many children are 'harvested' whilst still alive. A complete human being is said to be worth some $250,000 on the open market.

The situation remains particularly dire in part of the northern part of the country. Near Lake Victoria fishermen are known to weave albinos’ hair into their fishing nets in the hopes of improving their catches. Witchcraft beliefs are more entrenched in that part of the country, making individuals with albinism particularly susceptible to attacks. “When I was growing up it was not like this. It was just stigma, but not people coming to cut bodies,” says Zihada Msembo, 60, a leader of the Tanzania Albino Society, during an interview elsewhere in the country. In the past five years, she says, the attacks in Tanzania have gotten worse. But what has prompted the new attacks remains unknown. Whereas the attacks are most prevalent in the so-called “Lake Zone,” Nsebo says that “people travel to hunt for albinos” throughout the country.

Isn't it just great the way religion increases human kindness and fellowship and heightens sensitivity to suffering, whilst reducing greed and selfishness, unlike atheistic science.

And it's soo reassuring to know that a kindly and benevolent god is watching over humanity to make sure nothing like this happens, isn't it... well, at least making sure it only happens in far-away unimportant countries, to far-away unimportant people.

'via Blog this'

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Monday 14 October 2013

Darwin Creationist Award 2013 - Voting Time!

Time to vote for this year's Darwin Creationist Award winner! A little later than planned due to unforeseen censorship of a Twittorial nature, but better late than never.

Just a reminder: the Darwin Creationist Award goes to a person who, by a creationist tweet, website or blog so unutterably cretinous has done most to improve the human memepool by helping to remove creationism from it. I appreciate this is often a difficult task as so many creationist tweets and articles are excellent candidates, as can be seen from over 100 nominations this year.

To simplify the task, I have autocratically selected just a small sample of what I consider to be the best. Congratulations to all those who failed to make the final shortlist but I should point out that you were all nominated by me, so your exclusion is more to do with my altruism than with your moronitude. Don't lose heart. Better luck next year.

The original list of nominations is still here to be enjoyed.

To vote, just state the number of your preference in the comments below. Voting will close at the end of October unless a playoff is called for.

Saturday 12 October 2013

Thank You. You've Made a Difference

As I keep saying ad nauseum, all money earned from advertising on this blog will go to charity, in particular to Oxfam for all purchases from Amazon, so it's great to be able to say thanks to everyone who clicked on a link or made a purchase, because it has now triggered another payment from Google. This time for £62.82 (Google only payout when the total reaches £60 otherwise it's held over).

As a tribute to Malala Yousafzai, the Pakistani girl Islamic fundamentalists tried to kill for the sin of being female and getting an education, I have donated enough to Oxfam to give four girls a head start with their education.

I think of it often and imagine the scene clearly. Even if they come to kill me, I will tell them what they are trying to do is wrong, that education is our basic right.

Malala Yousafzai

For the record, these are the various receipts and things:
And of course four of these

Incidentally, should anyone be suspicious enough to doubt these facts, please feel free to contact Oxfam at enquiries@oxfam.org.uk quoting the date and order number displayed above. I will be pleased to give permission for them to release all relevant non-confidential details to confirm it.

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Thursday 10 October 2013

Who Made Up The Jesus Myths?

Titus Flavius
Causing something of a buzz of excitement in atheist circles, and another shriek of hysteria in fundamentalist Christian circles at the moment is a claim by Joseph Atwill to have found 'incontrovertible proof' that Jesus was made up by Roman aristocrats in an attempt to subdue and control troublesome Jews after the Jewish Revolt. The alleged main conspirators were Titus Flavius and Christianity's favourite ancient historian, Flavius Josephus (known simply as Josephus).

The first thing to say is that I haven't yet read Atwill's book, Caesar's Messiah: The Roman Conspiracy to Invent Jesus, only claims about it by others, some of which are clearly copied or based on press handouts prior to the symposium Covert Messiah at Conway Hall in Holborn, London, on October 19.

As I understand it, Atwill's 'proof' is a series of close parallels between the military campaigns of Titus Flavius (a military general under his father, the Emperor Vespasian, before succeeding his father as Emperor Titus) and the ministry of Jesus. According to Atwill, if I've understood things, the Gospels were simply made up in Rome, probably by Josephus. Apparently these parallels were coded 'confessions' which would have been readily understood by the Roman elite that he had written it so they wouldn't take it seriously. The argument is that Josephus concocted a history of Jesus loosely based on the biography of Titus in an attempt to give the troublesome Jews a Messiah to follow in accordance with their belief that a Messiah was soon to come. This one would of course tell them to be gentle, turn the other cheek, and be good, peaceful citizens of the Empire.

Wednesday 9 October 2013

An Atheist Thing To Say

Pope Francis. Turning his back on medieval dogma?
That’s an atheist thing to do, Pope Francis

Pope Francis is being hailed as a reformer and moderniser, though there is very little in the way of practical reforms to be seen yet, rather than just rhetoric and verbal gestures. The problem he has is that such is the advance of Humanism in recent years that any meaningful reform, as opposed to reaction and retrenchment, is now tantamount to moving the Catholic Church a substantial way towards Humanism.

Humanism, not superstition and dogma, is now setting the standard by which decency is measured. Any creed wishing to cling on to it's dwindling congregation needs to adopt Humanism.

Proselytism is solemn nonsense, it makes no sense. We need to get to know each other, listen to each other and improve our knowledge of the world around us. Sometimes after a meeting I want to arrange another one because new ideas are born and I discover new needs. This is important: to get to know people, listen, expand the circle of ideas. The world is criss-crossed by roads that come closer together and move apart, but the important thing is that they lead towards the Good.

Pope Francis
A very atheist thing to say
This was beautifully illustrated by Herb Silverman recently. He remarked that Christians say, "That's a very Christian thing to do!", when someone does something good. It isn't of course. A very Christian thing to do is to smugly condescend to people whilst falsely implying that Christians occupy the moral high-ground and are entitled to judge the actions of others.

In fact, as Herb Silverman pointed out, what Pope Francis said in an interview with the Italian atheist Eugenio Scalfari, published in La Repubblica, was a typically atheist thing to say. He constantly referred to 'good' not 'God' and was very clearly implying that he accepted the atheist slogan, "Good without God"; that people do not need to be religiously motivated or to fear a god to do good and morally comes from our humanity, not our religion.

Everyone has his own idea of good and evil and must choose to follow the good and fight evil as he conceives them. That would be enough to make the world a better place.

Pope Francis
A very atheist thing to say
The Pope has apparently realised that the world is moving inexorably away from the divisiveness of religion towards an inclusivity which embraces diversity and difference. A world where what matters is not what invisible friend you believe you have, or what 'faith' you use an an excuse for your antisocial behaviour, but what effect your behaviour has on the happiness and wellbeing of others and the planet we all share. To many Christians, used to demanding privilege and deference, this will be a difficult concept to swallow.

But should we be surprised that at least the enlightened intelligentsia of Christianity are realising they need to bend to the Humanist tide or be swept away? I think not.

…Our goal is not to proselytize but to listen to needs, desires and disappointments, despair, hope. We must restore hope to young people, help the old, be open to the future, spread love. Be poor among the poor. We need to include the excluded and preach peace.

Pope Francis
A very atheist thing to say
The history of the last few hundred years, beginning with the Enlightenment which led inevitably to the science age, has been one of a Christian Church being dragged kicking and screaming from the Dark Ages into the future. It was a Church which rejected evidence itself in favour of dogma but which, at least so far as it can without breaking, has bent to the tide of science (excepting some primitive diehards who still try to pretend they live in a compliant Universe where reality goes away when spoken to sternly or if ignored altogether).

The mainstream Christian churches used to be racist, misogynistic, homophobic, autocratic, genocidal, warmongering, imperialistic and frequently, casually brutal. They habitually opposed any moves by the state which improved the lives of working people and the poor, including and almost inexplicably, improved access to health care. In Ireland, for example, the Catholic Church threw it's entire weight behind a campaign against a very limited form of national health service. They even forbid the use of condoms to prevent the spread of deadly diseases and lie to ignorant people to frighten them out of using them! This by a church which purports to follow the teaching of someone who allegedly told his followers to care for the sick.

When I meet a clericalist, I suddenly become anti-clerical. Clericalism should not have anything to do with Christianity.

Pope Francis
A very atheist thing to say
Some have moved further than others but now only a handful of minor Christian churches still espouse much of the antisocial bigotry which once characterised almost the entire religion. One by one they are being civilised. Some have even recognised female clerics and allow same-sex marriage.

In Europe, Latin America and South-East Asia, whenever it had to choose, the Catholic Church invariably sided with the forces of reaction and autocracy against progressive social democracy, regarding any moves to better the lot of ordinary people as unacceptable socialism.

Heads of the Church have often been narcissists, flattered and thrilled by their courtiers. The court is the leprosy of the papacy.

Pope Francis
A very atheist thing to say
Now the world is changing, and Pope Francis, if we are to believe what he says, has recognised that he has to adopt the Humanism which is sweeping the world (or the developed parts of it at least) or get swept away with the tide. Let's hope this is more than empty gesture and soothing words.

A small move in the right direction maybe, but only when I see Pope Claire standing beside her wife and urging people to use condoms to prevent AIDS and to plan their families for the sake of the planet, as the Church builds hospitals and clinics and trains doctors and nurses with the proceeds of the treasures and real estate it has sold, will I believe the Catholic Church has adopted civilisation and truly believes what it preaches.

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