Sunday 30 June 2013

The Ontological Blunder

Prof. Ian Stewart, Dr. Terry Pratchett and Prof. Jack Cohen
I've previously blogged about the 'Ontological Argument' for gods (I use the plural because, idiotically, if the argument is valid - and I have seen it referred to as a conclusive proof - then it should only work for one god, yet it works for any. Make one up yourself and try it).

Briefly, the idea was thought up by Anselm, an early Anglo-Norman archbishop of Canterbury. He argued in his Proslogion that,
God [is] "that than which nothing greater can be conceived", and then argued that this being could exist in the mind. He suggested that, if the greatest possible being exists in the mind, it must also exist in reality. If it only exists in the mind, a greater being is possible—one which exists in the mind and in reality.

Source: Wikipedia - Ontological argument
Apparently, this is still trotted out in all seriousness by (especially) Christian apologists, who apparently see nothing wrong with essentially claiming they can define a god into existence and that such a god is obliged to exist.

I came across this elegant illustration of the simple, intellectually dishonest, fallacy behind this apologetic in a book by Terry Pratchett, Ian Stewart and Jack Cohen, The Science of Discworld IV - Judgement Day.

This book is the fourth in a series dealing with basic scientific principles in a very readable way using stories set in Terry Pratchett's Discworld. The science is almost all Ian Stewart and Jack Cohen, two popular science writers. I can highly recommend both the Discworld series and the Science of Discworld series.

On Anselm's Ontological Argument, they have this to say, though they refer to it as Thomas Aquinas's argument from Summa Theologica which is virtually identical in form:
Logicians and mathematicians are painfully aware, however, that this argument is flawed. Before you can use a characterisation of some entity to deduce its properties, you have to provide independent proof that such an entity exists.

The classic example is a proof that the largest whole number is 1. Consider the largest whole number. Its square is at least as big, so it must equal its square. The only whole numbers like that are 0 and 1, of which 1 is the larger. QED. Except, 1 is clearly not the largest number. For instance, 2 is bigger.


What's wrong? The proof assumes that there is a largest whole number. If it exists, everything else is correct, and it has to be 1. But, since that makes no sense, the proof must be wrong, and that implies that it doesn't exist.

So, in order to use the ontological argument to infer the existence of the greatest conceivable being, we must first establish that such a being exists, without simply referring to the definition. So what the argument proves is 'if God exists, then God exists'.

So the ontological argument is nothing more than sleight of hand; a circular argument which surreptitiously assumes its conclusion and then feeds that a priori assumption into the argument in order to produce the required answer. That is why, just like the Cosmological Argument so beloved of William Lane Craig, it works with any god or any daft notion you can dream up. If you didn't spot it earlier, Anselms fallacy was in the opening sentence. He first defined God as "that than which nothing greater can be conceived" without first providing any independent proof that such an entity actually exists.

Quite obviously, had such proof been available to Anselm, or anyone else for that matter, he wouldn't have needed to invent the ontological argument in the first place, let alone perform that little bit of deception. We can be sure then that Anselm knew there was no available proof of the Christian god, just as we can be sure that those who still try to get away with it know they have no such proof.

As I've said before, substitute a peanut butter sandwich for 'God' in any theological apologetic and you can justify worshipping peanut butter sandwiches. If you are gullible enough to to fall for religious apologetics, exercise caution here or you could end up worshipping equally insane and inanimate objects. You could even start your own cult if you can find a few equally gullible idiots with thinking difficulties

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To A Mouse

I had a brief encounter with a mouse the other day. Not one quite so dramatic as Burns' - it's a long while now since I followed a horse-drawn plough. In fact, to be strictly accurate, it's a long while now since I saw a horse-drawn plough. They even had them-there tractor things when I was a child.

No. My encounter was a lot more mundane.

Every morning I feed my birdies - a flock of (mostly) wood-pigeons, collared doves, starlings, house sparrows and other assorted birds in season - at the bird table and various feeders we have in the back garden. I buy the mixed birdseed in 20 Kg. sacks along with bags of dried meal worms and peanuts and store it in our garden shed.

To a Mouse

(Written by Robert Burns in Gallowegian dialect supposedly after he had turned over the nest of a field mouse with his plough. This poem illustrates Burns' tolerance to all creatures and his innate humanity.)

Wee, sleekit, cowran, tim'rous beastie,
O, what a panic's in thy breastie!
Thou need na start awa sae hasty,
Wi' bickering brattle!
I wad be laith to rin an' chase thee,
Wi' murd'ring pattle!

I'm truly sorry Man's dominion
Has broken Nature's social union,
An' justifies that ill opinion,
Which makes thee startle,
At me, thy poor, earth-born companion,
An' fellow-mortal!

I doubt na, whyles, but thou may thieve;
What then? poor beastie, thou maun live!
A daimen-icker in a thrave 'S a sma' request:
I'll get a blessin wi' the lave,
An' never miss't!

Thy wee-bit housie, too, in ruin!
It's silly wa's the win's are strewin!
An' naething, now, to big a new ane,
O' foggage green!
An' bleak December's winds ensuin,
Baith snell an' keen!

Thou saw the fields laid bare an' wast,
An' weary Winter comin fast,
An' cozie here, beneath the blast,
Thou thought to dwell,
Till crash! the cruel coulter past
Out thro' thy cell.

That wee-bit heap o' leaves an' stibble,
Has cost thee monie a weary nibble!
Now thou's turn'd out, for a' thy trouble,
But house or hald.
To thole the Winter's sleety dribble,
An' cranreuch cauld!

But Mousie, thou are no thy-lane,
In proving foresight may be vain:
The best laid schemes o' Mice an' Men,
Gang aft agley,
An' lea'e us nought but grief an' pain,
For promis'd joy!

Still, thou art blest, compar'd wi' me!
The present only toucheth thee:
But Och! I backward cast my e'e,
On prospects drear!
An' forward, tho' I canna see,
I guess an' fear!

Robert Burns, 1785
I used to just stand the sacks of seed in the shed and fill a small container to take to the bird table until a family of mice set up home in the shed and learned to chew holes in the sacks, so I bought a plastic dustbin with a clip-on lid in which I also keep a plastic bucket to take seed, mealworms, peanuts and scoop to the garden in. Initially I felt a little bad about locking their food away and use to put a little seed and a few peanuts out for the mice but I decided it was best to wean them off their increasing welfare dependency and encourage them to earn an honest living.

A couple of days ago though, one little mouse had decided to use its entrepreneurial initiative and, when my back was turned and the lid was off, had had jumped or fallen into the deep plastic bin - with smooth sides.

My initial surprise was to discover that there were still mice in the shed. The mouse's initial surprise was to see the bottom of a large, black plastic bucket begin to descend, followed quickly by a large pair of eye and a human voice saying, "Hello! Okay! Let's see you get yourself out of there then!"

Isn't it interesting how quickly mice get over that initial panic and, after running round the perimeter of the bin three times, stop, look up, sit back on their haunches and wash their face.

So, what to do now then? In times gone by I would have thought nothing of picking it up by the tail and giving its head a quick flick against a wall then chucking it to the nearest cat or onto the compost heap. Maybe I'm getting soft or maybe I just appreciate living things a little better. Whatever, I decided to let nature take its course and do a little experiment. How would the mouse get itself out of an impossible situation?

Maybe it didn't appreciate the situation fully but my little mouse just picked up a sunflower seed and proceeded to take out the kernel and eat it. Maybe it needed some energy.

Of course, given a practically unlimited supply of food in comparison to its size, and not needing water beyond what they can get from their food, even dry seeds, the mouse wasn't actually in any real danger. It could have lived its entire life in that bin so maybe its risk assessment was a little different to what mine would have been. Never-the-less, my little mouse did try to climb up the sides a few times, then it tried jumping - as though its ability to jump about four inches was going to be enough to get to the top, about 30 inches away. But it was obviously worth a try - yer gets owt for nowt!

So I thought, let's see how intelligent you are. How quickly can you learn to climb a piece of garden string?

So I pulled out a length of string from one of those balls of green garden twine which was standing on the rack next to the food bin, and let it hang loosely down to the surface of the seed.
  1. Mouse finds string and starts to climb. String is loose and stretches out so mouse makes no progress and gives up.
  2. Mouse tries again and pulls string to make it tight then starts to climb it. Falls off.
  3. Mouse tries again and climbs string until it can reach the rim of the smooth plastic bin with its front feet. Lets go with its hind feet but loses grip and slips back into the bin.
  4. Mouse climbs up above the rim of the bin so its hind feet can stand on it. Walks round the rim of the bin a short distance then hops onto the rack, washes its face, and disappears.
In four steps the mouse had learned progressively by trial and error, and had got itself out of the bin.

What we had there was an interesting interaction in terms of genes and memes.

The mouse found itself in a predicament brought about because it exists in an environment in which I exist and in which the meme for enjoying nature and wanting to attract birds into my garden exists. The mouse genes had produced an animal which needs to feed and which actively looks for food, using a whole range of senses and abilities, not least of which is curiosity and an ability to discover by trial and error.

It survived because I have a mixture of memes and genes which make me interested in wildlife and an appreciation that they, like us, are the end-products of an incredible evolutionary process in which every one of our ancestors survived, that to end that gene-line would bring to a halt a process which started three and a half billion years ago and which has never yet failed, and an understanding that the simple fact of sharing our history and having ancestors in common with all living things gives us a connectedness and a kinship with it which is truly inspiring and deeply spiritual.

And the mouse had genes which allowed it to make an intelligent assessment of its situation, plan an escape strategy and improve its technique by trial and error whilst learning from its mistakes and keeping its objective in sight. With a little help from its friend.

And I spent a magical twenty minutes or so enjoying an interaction with a wee, sleekit, cowran, tim'rous beastie.

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Is The Pope Calling For Holy War?

In an astonishingly careless tweet today, and reminiscent of a medieval Pope sending tens or hundreds of thousands of people to commit genocide or die for Jesus in the 'Holy Lands' in a 'Crusade', Pope Francis appeared to be calling the Catholic faithful to holy war and martyrdom!

Cardinal Bergoglio with
Junta leader General Videla
Pope Francis, the former Cardinal Jorge Mario Bergoglio of Argentina, Argentine-born son of Italian immigrant parents, and first Jesuit Pope, is no stranger to guerrilla warfare. During the neo-fascist military junta's 'dirty war' in Argentina between 1976 and 1983, when Jorge Mario Bergoglio was progressing through his clerical career, an estimated 30,000 Argentinians, the so-called Desaparecidos, were murdered by right-wing death squads working for the junta, as the Argentinian people tried to take their country back from the cabal of neo-fascist army officers who had stolen it, and bring it back under the democratic control of the people.

Screen capture of the tweet. These divine revelations have a tendency
to become Desaparecidos when 'clarified' later.
He is widely thought to have been complicit in, or at least equanimous with, the kidnapping and torture of two Catholic priests, Orlando Yorio and Franz Jalics, in Argentina during this period. Both were later found drugged and semi-naked, five months later. Both had been tortured. Although Franz Jalics, having initially refused to discuss the affair, from his sanctuary in a German Catholic monastery, now (two days after Bergoglio became Pope) denies Bergoglio's involvement, Yorio put on record before his death in 2000 that, "Bergoglio did nothing to free us, in fact just the opposite" (Miroff, Nick (17 March 2013). "Pope's activity in Dirty War Draws Scrutiny". Chicago Tribune (Sec. 1). Washington Post. p. 27.)

One wonders where and when Pope Francis anticipates his devoted followers pursuing this jihad holy war and seeking this martyrdom.

Maybe we'll soon see another hurried 'clarification' from the Vatican such as we saw the other day when Pope Francis went off message and forgot his Catholic dogma, telling the faithful that they didn't need to believe in Jesus any more to get to Heaven because even Atheists could get there provided they did good things. Some people saw the hand of the other Pope, Benedict XVI, who seems far from being a 'Desaparecidos', in that 'correction' 'clarification'.

I notice that he isn't offering unrestricted access to any virgins as a reward, so the Catholic Church doesn't seem to have moved that far out into the lunatic fringes under his guidance, never-the-less, his call to Catholics to be prepared to 'lose their lives for Christ' is surely sinister and extreme.

Strangely, 'His Holiness' seems to have forgotten to mention the fact that another Vatican cleric has been arrested over the Vatican banking fraud and money-laundering allegations which have been rumbling on for many years now, and which resulted in the Vatican's bank card account being frozen by Italian banking authorities last January.

The parallels between the Catholic Church and other Italian-based international criminal organizations, who also tend to have a cosy relationship with neo-fascist groups, are becoming more and more marked. Are we seeing the lead up to a new turf war between two of the world's major criminal gangs - the Christians and the Muslims - over who controls the lucrative income from protection racketeering and farming the peasantry for tithes?

The Truth Behind Jorge Mario Bergoglio, Pope Francis: Breaking the Silence, the Catholic Church in Argentina and the ‘Dirty War’; Horacio Verbitsky.

Friday 28 June 2013

Religion's Living Fossils

In my back garden in Oxfordshire, England, I have a rather dilapidated horseshoe crab shell, a souvenir of a trip to Cape Cod a few years ago which we brought back to show our grandchildren. (It was very dead and there were literally thousands of them along the high-tide line on the bay side just south of Wellfleet, I hasten to assure any wildlife conservationists!) The long spike 'tail' is a particularly good for clearing out the feeding holes in bird feeders when they get clogged.

I sometime wonder what future paleontologists would make of it if it had the great good fortune to become fossilised and then to be discovered again in a couple of million years. Horseshoe crabs in central England!

And that leads me to the main topic here - so-called 'living fossils', of which the horseshoe crabs (plural because there are four different species) are frequently cited as an example.

The rather annoying oxymoronic term 'living fossil' need not apply (and rarely does) to a species:

Thursday 27 June 2013

First Horse Makes An Ass Of Creationists

The Przewalski’s horse, Equus ferus przewalskii
The last remaining wild horse, recently saved from extinction in Mongolia.
First horses arose 4 million years ago : Nature News & Comment

Yesterday's Nature brings us news of yet another advance in evolutionary science in the form of a major advance in genome sequencing from ancient sources. As reported by a team led by Ludovic Orlando of the Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, scientists have been able to sequence the full genome from an ancient ancestor of the modern horse from a specimen found in Canadian permafrost. The specimen is believed to be between 780,000 and 560,000 years old.

The sequence was extracted from a foot bone of a horse that lived between 780,000 and 560,000 years ago. By sequencing the animal's genome, along with those of a 43,000-year-old horse, five modern domestic horse breeds, a wild Przewalski’s horse and a donkey, researchers were able to trace the evolutionary history of the horse family in unprecedented detail. They estimate that the ancient ancestor of the modern Equus genus, which includes horses, donkeys and zebras, branched off from other animal lineages about 4 million years ago — twice as long ago as scientists had previously thought.

“We have beaten the time barrier,” says evolutionary biologist Ludovic Orlando of the University of Copenhagen, who led the work with colleague Eske Willerslev. Noting that the oldest DNA sequenced before this came from a polar bear between 110,000 and 130,000 years old2, Orlando says: “All of a sudden, you have access to many more extinct species than you could have ever dreamed of sequencing before.”

This is great news and should spread despair and despondency amongst the loons and liars of the Discovery Institute and other frauds who make a living from Creation pseudo-science, unless they manage not to notice it, as the techniques could be adapted to other DNA samples if and when they are obtained, so giving us a clearer picture of the evolution of other species and so better able to understand the nitty-gritty of how evolution works.

As well as recognising what a powerful tool this is, what caught my attention particularly was the paragraph:

The researchers were also able to trace the size of the horse population over time by looking for genomic signatures of population size, and were thus able to show that populations grew in periods of abundant grassland, in between times of extreme cold.

Bwaaahhhaaa! Creationists say what!?
Here we see how evolutionary theory is meshing in with other disciplines like climatology with each discipline supporting the other. We can tell the relative extent of things like grasslands through analysis of pollen in permafrost, polar ice cores, bogs, etc. It is interesting, but not really surprising, that this is echoed in the DNA of a genus like Equus. The DNA is merely evolving in response to environmental change, just as we would expect.

DNA is acting like a record of a species history on this planet and so of the planet itself, and the scientific theory which integrates it with the rest of science is the Theory of Evolution - one of the most profound, powerful and far-reaching theories in the whole of science. No wonder it so terrifies those who make their living from promoting Bronze-Age superstition and who so need to spread lies and misinformation about science.

Not for them the road to discovery and enlightenment. Far too risky. There's a lot of money at stake.

First horses arose 4 million years ago; Erika Check Hayden; Nature, 26 June 2013

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse; Orlando, L., et al; Nature, 26 June 2013; doi:10.1038/nature12323

'via Blog this'

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Wednesday 26 June 2013

Evolution In Progress - Complex Cells

Tiny Genomes May Offer Clues to First Plants and Animals | Quanta

When we think of evolution in progress we almost always think of higher animals evolving by changing over time or of bacteria and viruses adapting to environmental changes like antibiotics or host resistance, more rarely of a new species having been found to have arisen by hybridization like the Italian sparrow which I described recently in Evolution In Progress - A Tale Of Three Sparrow. It's not often that we get to witness a stage in life's evolution which we think of as having happened a long time ago as

Tuesday 25 June 2013

The Darwin Creationist Award 2013 - Nominations

Announcing the coveted Darwin Creationist Award 2013!

Stand by for another summer of glorious moronitude as creationists struggle to put a coherent thought into words or wrestle with the intricacies of basic science, logic and joined-up thinking, as they try to convince the world that their ignorant stupidity and Bronze-Age superstition trumps anything which science has to offer.

The Darwin Creationist Award, like its illustrious bigger brother, the Darwin Award, which is awarded annually to the person who, by their utter inept stupidity has contributed positively to human evolution by removing their genes from the gene-pool, is awarded to the Creationist who similarly has done most to remove the meme of creationism from the human meme-pool. Self-sacrifice is not required for this award. All it takes is a tweet, blog, Facebook or other on-line comment, illustrating the utter moronic stupidity it takes to be fooled by professional Creationist charlatans and frauds, so making people think twice before falling for it themselves.

Monday 24 June 2013

Of Chickens And Eggs

We've all seen it. For some reason Creationists seem to think they've come up with an unanswerable question for 'Evolutionists', apparently under the impression that a single unanswerable question will totally destroy any science regardless of whether it has any relevance to the field of science in question.

The whole point of scientific debate, from a fundamentalist Creationist point of view, is to shut down debate, not to elicit information and enhance understanding.

And of course, as we all know, since we are all too stupid to spot a blatant false dichotomy when one is staring us in the face, if you can destroy science then either Islam or Christianity, or whatever other primitive superstition is being promoted, will automatically become the only possible answer, and then they will have won.

The 'devastating killer question' is of course, 'Which came first; the chicken or the egg?'

Sunday 23 June 2013

Evolution in Progress - A Tale Of Three Sparrows

Italian sparrow, Passer italiae
While sitting enjoying the shade in a very hot Villa Borghese Park in Rome the other day [sniff!] I noticed all the male sparrows were different to our 'normal' house sparrow that we see in Britain and most of the rest of Europe. They all have chestnut coloured heads whereas the usual house sparrow males have grey heads. Their backs looked a little brighter too. The females are indistinguishable (to me) from the usual female house sparrows. I have seen these 'Italian sparrows' before, in Switzerland on the south side of the Alps just a few miles from the Italian border. It's the kind of small difference that makes you think, "there's something different about that bird!" Most people who have no interest in wildlife probably wouldn't even notice it.


The Illustrated Sutra of Cause and Effect. 8th century, Japan
In the end, all theological apologetics boil down to one thing - causality. Ignoring for the moment the circularity of assuming your favourite deity doing magic is the only possible cause, then including that assumption to the exclusion of all else, as apologists do with the Cosmological Argument so it always comes up with the god they first thought of, there is still the unsupported assumption that 'everything' must have had one single cause.

Apologists find no difficulty with this assumption yet the more fundamentalist of them get quite hysterical at the thought that all living things might well have had a single common ancestor, but that's a different problem. Let's stick to causality.

Why this assumption?

How many phenomena actually have a single cause?

Let's forget for the moment that some quantum events appear not to have any cause and that the Big Bang, if there ever was a Big Bang, was probably a quantum event, and let's indulge religious apologists and grant them their prefered version of reality in which things happen or not according to the convenience of whatever argument they are trying to deploy at the time. Let's assume that everything that happens actually does have a cause.
Causality (also referred to as causation) is the relation between an event (the cause) and a second event (the effect), where the second event is understood as a consequence of the first.

In common usage, causality is also the relation between a set of factors (causes) and a phenomenon (the effect). Anything that affects an effect is a factor of that effect. A direct factor is a factor that affects an effect directly, that is, without any intervening factors. (Intervening factors are sometimes called "intermediate factors".) The connection between a cause(s) and an effect in this way can also be referred to as a causal nexus.

Now, try this mind experiment. Think of a single event which has a single cause, and not a multiplicity of causes, each of which has a multiplicity of causes.

I've previously blogged about how many apparent basic laws, such as the Gas Laws, are only laws of mass action; emergent properties which depend on statistical probabilities involving chaotic motions of atoms or molecules. Nothing at the level of the atom or molecule is obeying a Gas Law; only in aggregated probability across the whole population does the property emerge from an underlying chaos.

What caused the Herald of Free Enterprise to sink?
Blow a balloon up until it bursts. What single event caused it to burst? Was it the last molecule of air you blew in? What about the effect of all the others? Without them, that last molecule would have had no effect. Was it pressure in your lungs or cheeks? How did that get there? What about the fabric of the balloon; the rubber? Was it the parting of a single atomic bond somewhere in the organic polymer that the rubber is composed of? How did that happen unless it was caused by the mass action of the atoms of air inside the balloon pushing on the balloon skin with a high enough average force exerted by chaotically moving molecules of air?

Make a splash in water by dropping a stone into it. What single event cause that splash? Gravity? Letting the stone fall? How did your fingers move to cause that event? How about the atomic structure of the rock which gave it solidity and enough density to allow it to fall through the air with enough force to push the water molecules out of the way? How many molecules of water constitute a 'splash'? We're back to laws of mass action and emergent properties from the chaos of water molecules again. Even the atoms of the rock and the water, or rather the fundamental particles from which they are made may well be emergent properties from an underlying chaotic structure of force fields and vibrating multi-dimensional superstrings. The positions of fundamental particles in those atoms can only be described as a probability distribution derived from integrating all possible paths through spacetime.

Which snowflake caused the avalanche? How could it have done that without all the others and in the absence of gravity or without the mountain side? And if there is a single, predictable chain of causality in an avalanche it should be entirely predictable. Guess what! It isn't. An avalanche in progress is a system in total chaos and it's not even possible to accurately predict their occurrence. This is what makes them so dangerous.

The problem is we have evolved to deal with reality at the level at which we, as complex, multicellular organisms can perceive it by processing the photons which come into our eyes and the vibrations which come into our ears, or through other senses which only work at the level of organisation within which we operate. There would be no evolutionary advantage in being able to detect things at a different level because we can't eat it, be eaten by it, use it for shelter or have sex with it.

So we assume that the Universe behaves pretty much the way things do in our world. We flick a switch or turn a key and something happens. We throw a spear and it flies through the air. If it hits the antelope in the right place the antelope dies and we get food. We press a key on our keyboard and it makes 'p' appear on our computer screen. We assume a narrative - a story behind the event.

We assume A->B->C->D. We assume that there is a simple chain of causality like there seems to be when we strike the match with which we light the fire which burns the wood which boils the water which cooks the food. Actually, I switch an electric hob-ring on, but you get the point.

In fact almost nothing happens because of a single, identifiable cause or even as the endpoint of a chain of single cause-effects. Normally, many things need to happen, some of them in sequence, some in parallel. We can't throw a spear without our brain firing off a salvo of signals to work a myriad of muscle fibres, coordinated by our eyes detecting incoming photons, processing them and passing signals on to our brains for further processing, and after a complex process by which we've weighed the spear, judge the distance, computed the trajectory and coordinated muscles in our arm, shoulder, hands, legs, back, chest and abdomen. And then, of course, gravity and inertia, explained by Newton's Laws of Motion, takes over, as well as a whole mass of small effects as the spear pushes molecules of air around causing friction and drag. Throwing a spear is not a single event in any causal sense of the word. It is a whole bunch of different events coming together to produce a single effect - the spear travelling from A to B.

So why assume a universe exists because of a single, identifiable cause?

Perhaps the major challenges in physics is to come up with a Grand Unified Theory which unifies quantum mechanics with Einsteinian Relativity because it is assumed there should be a single principle as the basis of all physics. At the moment, Relativity explains gravity while quantum mechanics explains the other three forces - the strong and weak nuclear forces and electromagnetism. Because gravity exactly balances the sum of the other three forces, making the total energy in the Universe equal precisely zero, it is assumed they have a common 'cause' expressible by a single theory. The problem is that no one has managed to unify them yet (note: this isn't the same as saying they can't be, or won't be).

But why do we assume there should be a single cause? Why can't relativity and quantum mechanics have different causes which together caused the Universe? Why limit it to two causes even? It is said that a tendency to assume a single cause is more likely in scientists from monotheistic cultures. Is this merely an example of a culturally biased assumption; of intuition over-riding what the evidence points to; of an argument from personal incredulity?

There is of course nothing other than a baseless assumption behind the religious apologist's insistence that the Universe had a single cause, just as there is nothing behind their assumption that the single cause must have been their favourite magic friend. It is nothing more than a manifestation of their insistence that the Universe must be as they require it to be. Just because a medieval theologian who knew nothing of physics or cosmology, and probably believed that Earth was a flat disc round which a small sun orbited, thought there should be a single cause, and just because primitive people from the beginnings of recorded history who knew even less thought that the Universe worked by magic, doesn't mean there is or it does.

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Saturday 22 June 2013

Evolutionary Snail Trail

Scientists Use Snails to Trace Stone Age Trade Routes in Europe | Surprising Science

Cepaea nemoralis
Scientists studying the distribution of beautiful little group of snails, abundant in Britain, the grove snails and their close relatives, the white-lipped snail has discovered something surprising which could shed light on human migration some 8-9,000 years ago as we spread throughout Europe and into the British Isles and Ireland.

They were hoping to find genetic clues to the origins and diversity of this group of common European snails by looking at their mitochondrial DNA.
The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared “Lusitanian” history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.

Distribution of main Cepaea nemoralis mitochondrial lineages across Europe.
C = Irish and Eastern Pyrenean gene line.
What they found were seven distinct genetic lines but the one commonest in Ireland is only found in mainland Europe in the Eastern Pyrenees - the range of mountains forming the border between Spain and France. As the authors point out, it isn't possible to rule out the possibility that this line was once widespread and has since gone extinct in all but these two ends of it's range but the fossil record, extending back in Ireland more than 8,000 years, the long history of C. nemoralis being a food source in the Eastern Pyrenees and the Garonne river providing a navigable route to the Atlantic, the much more likely explanation is human transportation taking them to Ireland, either accidentally or as food for the voyage. The earliest C. nemoralis fossils also coincide with the archaeologically inferred first arrival of humans in Ireland following the end of the last ice age.

There are other clues suggesting a link between these two areas in the form of the Kerry slug, Geomalacus maculosus found only in County Kerry, Ireland, northwest Spain and central Portugal, a species of strawberry tree, Arbutus unedo native to the Mediterranean and southwestern Ireland, and the Pyrenean glass snail, Semilimax pyrenaicus found in the Pyrenees and Ireland.

At first sight it might seem strange that people, and the plants and animals they took with them, would get to Ireland without going via Britain (and so leaving their snails there too) until you consider the geography of the time. There were no roads to speak off by which to cross Brittain, which was, especially in the south, heavily wooded, even on the hills. The valleys would have been difficult to travel through often being thickly wooded and boggy. Additionally, there were no pack animals, the horse and donkey were not domesticated for another 4-5,000 years, apart from the small problem of getting them across the Channel even if they had been domesticated earlier.

If you could sail or row a boat, water was by far the easiest way to travel. In effect, the sea, especially inshore waters, and rivers were the highways. The boat becomes the pack animal and the means of transport. Wind and/or manpower was the energy source. Not surprisingly then the main route for human migration, especially the initial migration out of Africa, was by coastal spread, and so Ireland, and maybe southern and western Britain was very probably first colonised by people from the Iberian Peninsula who had themselves reached those locations by coastal spread around the Mediterranean.

That's all very interesting from the perspective of human history of course, but the interesting thing here for an evolutionary biologist is how the distribution of species was affected by human migration and trade. The spread of humans was a major change in the environment of these species, specifically the grove snail. Not only did human agriculture and changes in land use change the landscape on which they lived, sometimes opening up new niches, sometimes closing existing ones and, in the case in point, redistributing a species to a new range which it was highly unlikely to have reached on its own.

Cepaea nemoralis. One of many colour forms.
Paradoxically, just as with domesticated species like sheep, cattle, pigs and fowl, being used by humans for food has worked in favour of these snails, which have been introduced to a new range so they now form two different isolated gene-pools, biologically acting as a distinct species, though not yet diversified genetically. Without any conscious decision or intelligent planning, two sets of genes, human and snail, became temporarily linked in an alliance which turned out to be mutually beneficial in the long-term. Humans had food to sustain a range extension and snails hitched a ride by providing that food.

The 'selfish' snail genes of course had no concern that most of the snails would have been eaten. The 'strategy' worked because it worked. Had it not done the grove snail would now be confined to the eastern Pyrenees and no one would be any the wiser. Human history might have been a little different too.

Here we have an example of evolution in progress. An environmental change created an opportunity for the grove snail to move into a new range, facilitated by a temporary alliance between two species which turned out to be mutually beneficial. Given time the two populations of C. nemoralis will diverge and form genetically distinct populations. Eventually they will lose the ability to interbreed and we will have two new species where once there was one. Of course, no intelligence, no planning and no design was involved in that process. Nothing and no-one planned to have these snails introduced to Ireland just as nothing and no-one planned to have them in the Pyrenees in the first place. It was merely living things doing what living things do, and the consequences turning out to be what they were.

As a final note, I wonder how many readers spotted the way Darwinian evolution underpinned the use of biodiversity to elucidate and explain human distribution and early human history. This is just another example of how this scientific theory is now regarded as a basic science and how it has hugely powerful explanatory powers, and not just in the province of biological diversification.

Scientists Use Snails to Trace Stone Age Trade Routes in Europe | Surprising Science

Grindon AJ, Davison A (2013) Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans. PLoS ONE 8(6): e65792. doi:10.1371/journal.pone.0065792
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Friday 21 June 2013

What A Silly Rabbi

Jonathan Sacks
By cooperniall - Photo link,
CC BY 2.0, Wikipedia
Chief Rabbi: atheism has failed. Only religion can defeat the new barbarians » The Spectator

In a quite extraordinarily display of whistling in the dark to keep his spirits up, the UK Chief Rabbi, Jonathan Sacks made the following statement in the Spectator a few days ago:

Future intellectual historians will look back with wonder at the strange phenomenon of seemingly intelligent secularists in the 21st century believing that if they could show that the first chapters of Genesis are not literally true, that the universe is more than 6,000 years old and there might be other explanations for rainbows than as a sign of God’s covenant after the flood, the whole of humanity’s religious beliefs would come tumbling down like a house of cards and we would be left with a serene world of rational non-believers getting on famously with one another.

Really? Atheists believe the whole of humanity's religious beliefs depend on those things? All of them? Hindu, Buddhist, Shintoist, Daoist, Parsi, Sikh? It's not clear if this includes all historical religions too, or just the present-day ones.

Thursday 20 June 2013

So Why Aren't Any Mountains Moving?

Amazing claims are made for the power of faith. Sadly, all of them are nothing more than claims.

Take for example the claim made by the author of Matthew about Jesus when, for some unexplained reason he found it necessary to boast about his marvelous abilities:

Now in the morning as he returned into the city, he hungered. And when he saw a fig tree in the way, he came to it, and found nothing thereon, but leaves only, and said unto it, Let no fruit grow on thee henceforward for ever. And presently the fig tree withered away.

And when the disciples saw it, they marvelled, saying, How soon is the fig tree withered away! Jesus answered and said unto them, Verily I say unto you, If ye have faith, and doubt not, ye shall not only do this which is done to the fig tree, but also if ye shall say unto this mountain, Be thou removed, and be thou cast into the sea; it shall be done. And all things, whatsoever ye shall ask in prayer, believing, ye shall receive.

Matthew 21:18-22

This is a strange tale if it's about an omniscient god in human form because it implies that Jesus had to go and look to see if the fig tree had any fruit and was the sort of person who would punish even trees when they disappointed him, rather like a petulant child. In Mark's version (Mark 11:20-24) he even has to go back next day to check that the curse has worked! Clearly this is a tale from before Jesus had been mutated into a god and was still merely a human. But that's not the main point of this blog; I dealt with that unlikely tale in God Hates Figs!

The point here is about the difference between reality and metaphor.

Challenge any Christian to prove that 'Faith can move mountains', like Jesus unequivocally implies here. Jesus doesn't restrict it to people with special magical abilities and only boasts that he could do it is he so wished because he doesn't have any doubts. You just need to pray for it to happen and it will happen - allegedly.

Except of course it doesn't.

Has this ever been done by anyone? If not, why not? Are there no Christians who have enough faith? Even the thousands who have died as martyrs? Not any of the saints or Popes or founders of new Christian sects? How about asking your pastor to move a mountain? How about just a small pebble? The excuses should be interesting but Jesus says it's doubt preventing it. Ask him/her what doubts exactly? Why did no martyred saint burned at the stake ever manage to pray the fire out or beheaded saint ever manage to make the axe-head fly off the handle?

Was Matthew (and Mark who tells a similar tale, though Mark's account, which Matthew mostly copied anyway, needed a whole night for the curse to work) just over-egging the pudding when they wrote down these tales? Were they just setting us up to be told it's our fault when prayer doesn't work because we don't have enough faith, like the rogue trader or con artist who blames his victims for being so gullible?

Cue 'metaphor!'

The normal response to these sorts of questions about specific, testable (and so falsifiable) claims made in the Bible, if the 'out of context' excuse isn't deployed - and it's difficult to see how this can be taken out of context - is to claim it's a metaphor.

A metaphor for what, exactly? A metaphor for faith/prayer alone being able to produce something else equally unlikely? If so what and when? What unlikely event has ever been shown to have happened because a Christian with enough faith prayed for it to happen? If this can be done so easily (Jesus doesn't place any limitations on how often or for what purpose it can be used - 'And all things, whatsoever ye shall ask in prayer, believing, ye shall receive') why don't Christians solve all the world's problems, cure all disease and disability, and remove all want and squalor with prayers?

Do they perhaps think these are good things?

Could it be that Matthew was just making a false claim or reporting a false claim made by Jesus; an empty boast intended to mislead and deceive? It's manifestly untrue to claim the faith can move mountains otherwise we would see it being done, and the Christian who did it would gain immediate worldwide fame, would be guaranteed a sainthood and would probably found a new 'one true church'. Even Jesus could only boast about doing it, apparently!

So, if you're a Christian who believes in the literal truth of the Bible, that Jesus would never exaggerate or lie and you have no doubts that the Christian god exists and is exactly as described in the Bible, prove it. You don't need to move a mountain, just a pebble, with prayer alone. Go on! Make something impossible happen in front of witnesses.

'...all things, whatsoever ye shall ask in prayer, believing, ye shall receive' - Jesus. Is that true or not?

If the truth sets you free, what do lies do?

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Thursday 13 June 2013

Lousy Creator

The thing about obligate parasites is that they are obliged to live on their hosts, so their host and parasite histories become inextricably linked. The parasite either co-evolves with its host or goes extinct. Just as the biblical story of Ruth has her saying, "...whither thou goest, I will go; and where thou lodgest, I will lodge...". And so it is for human lice, and lice of other species for that matter.

Our lice share our history and were forced to go where we went, to adapt to changes in our life-style.

A species-specific parasite becomes an isolated population so far as its related species are concerned and, as populations diverge and become genetically isolated so the obligate parasites become isolated too, and evolve in their own direction. So, if we look at our parasites and the corresponding obligate parasites on the species with which we share a common ancestor, we should see the same genetic and morphological relationships between them as between us and our ancestors.

Monday 10 June 2013

Prove There Isn't A God!

Osiris, Anubis and Horus
Despite the fact that Atheists are continually explaining that Atheism is not a belief that there are no gods but a belief that there is no evidence for any and therefore no reason to believe in any, theists continue to try to shift the burden of proof from themselves and demand we prove their particular god doesn't exist.

This is of course the tactics of the playground and the coward and depends on the infantile idea that if you can't prove a notion wrong it must be right. Curiously, in the deluded mind of the theist which seems to be capable of abandoning intellectual honesty and personal integrity in it's desperate pursuit of certainty, this only applies to their favourite god and not to fairies, pink unicorns, Harry Potter, or invisible loft hippos.

So Christians, Muslims, Jews, Sikhs and anyone else who believes in one god but not all of them, if you want to show your intellectual honesty and personal integrity, this challenge should be right up your street. Just like us Atheists there are some gods you don't believe in. Presumably, since you think Atheists should be able to prove your god isn't real, you will be able to prove the gods you don't believe in aren't real. In all honesty, if you require Atheists to prove a negative, you should be capable of doing so yourself. To believe otherwise is hypocrisy, and I don't know of any religion which believes hypocrisy is a virtue.

Wodan heals Balder's wounded horse; Emil Doepler ca. 1905
You have very many gods to choose from. says there are almost 3000 goods which people have believed in either now or in known history. There are probably lots more we don't know about.

Since the beginning of recorded history, which is defined by the invention of writing by the Sumerians around 6000 years ago, historians have cataloged over 3700 supernatural beings, of which 2870 can be considered deities. Those numbers are probably a very conservative estimate because we have no accurate information before 4000 B.C. This means any deities worshipped by man before this period are unaccounted for.

Don't panic! You don't have to prove all of them don't exist. Just pick any one and prove to readers that it isn't real.

If you haven't read any history and can't think of any other gods, this link leads to all the gods you could wish for, but don't limit yourself to these. You could even make up one of your own!

We are all atheists about most of the gods that humanity has ever believed in. Some of us just go one god further.

Richard Dawkins, The God Delusion
Just a word of warning though. Your opinions, faith, deeply-held beliefs, feelings in your 'heart', words in a book or the opinions of 'experts' don't count as evidence, nor does the fact that your parents believed in your favourite god. After all, you won't accept my opinions, my feelings, my books or the opinions of experts who agree with me, so play the game according to your rules. Produce the same evidence which proves your selected god doesn't exist that you would accept from me as proof that your god doesn't exist.

You don't believe in that god, just as I don't believe in yours, so provide the evidence you demand I should provide.

Anything else would be hypocritical.

I almost forgot: Don't try any of the fallacies listed here, or any others for that matter. They won't work on me and will only serve to expose your dishonesty.

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Sunday 9 June 2013

'Selfish' Genes Create Cooperative Organisms

Diagram of a generalised plant cell
One of the criticisms of Richard Dawkins' seminal work, and the work which initially made him famous as an evolutionary biologist, The Selfish Gene, is that it portrayed life itself as essentially selfish, so undermining any claim Atheists might have to be moral, empathetic and considerate people. This was of course always nonsense and is an example of attacking a scientific theory based on its consequences not on its validity, as though truth is subject to a human convenience test - rather like claiming nuclear fission doesn't work because atom bombs are destructive or that the Big Bang can't have been an uncaused event because that would shut god(s) out of the picture.

But the consequences of 'selfish' genes are not as is claimed anyway. In fact, anything more than a cursory glance at biology will reveal how cooperation, at all levels of organisation, has almost always been the key to long-term success. Examples of cooperation are alliances of 'selfish' genes to create vehicles for their replication and continuation over time - in other words the things we call organisms and species - the whole of life in fact. It is to the mutual benefit of all these genes to work together - not as a conscious cooperation but merely as a consequence of their 'selfishness'. Quite simply, cooperative alliances are much more likely to be successful in terms of the number of descendants they produce than is competition. In biological terms, that is all that success means.

Alliances are not confined to genes within a single organism, of course. Alliances between organisms are common-place too: Bees and flowering plants, fungi and trees (and several other plants such as orchids), fungi and bacteria in lichens, ants and aphids, humans and domestic animals, etc, etc. These are all examples of alliances of genes in individual species being more successful in cooperation with other alliances of genes in other species. Cooperative alliances are always more stable than predator-prey relationships which lead to the huge overhead of arms races to no one's long-term benefit.

One fascinating alliance that we only really became aware of in 1966, and then only gradually, was the theory of complex cell (eukaryotic) origin proposed by Lynn Margulis, and now widely accepted, that eukaryotic cells are actually alliances of simple (prokaryotic) cells which may have begun as endoparasitic or prey-predator relationships - the Endosymbiotic theory. The former prokaryotic cells are now the organelles in eukaryotic cells, of which all higher life, including multicellular life, is composed.

In a very real sense, we are all alliances of bacteria!

Chloroplasts in Plagiomnium affine. Photo by Kristian Peters
One such organelle, which is now fundamental to plant life, and, through its production of oxygen in the atmosphere, to almost all life barring a few anaerobic bacteria and specialist extremophile organisms clustered around 'black smokers' in deep ocean trenches, is the chloroplast which contains the green pigment in plants and which turns carbon dioxide, water and sunlight into sugar, forming the basic energy source for almost all living things. These are believed to have begun life as free-living bacteria which evolved the ability to photosynthesise sugar to become cyanobacteria, and were then incorporated into algal cells, probably first as ingested food and then as a source of sugar for the algae. It's not hard to imagine how an algal cell which swallowed cyanobacteria for food would quickly evolve to not actually digest it but to let it live and to simply appropriate the surplus sugar. No point in killing the goose that lays the golden eggs!

There was only one snag to this theory: there were no examples of algal cells feeding by ingesting bacteria!

Now, as reported in this week's New Scientist, a team from the National Institute for Basic Biology in Okazaki, Japan, led by Shinichiro Maruyama think they have found one.

The pair studied Cymbomonas, a single-celled alga which belongs to one of the oldest algal groups. Cymbomonas ordinarily survives by photosynthesising, but when they grew it under low light levels it took to eating bacteria (Current Biology,

However, rather than extending a blobby "arm" to engulf its prey like other single-celled organisms, Cymbomonas sucked the bacteria up into a feeding tube. The tube led to a bubble-like chamber called a vacuole, a sort of microscopic stomach where the bacteria were digested. Maruyama says that the first green algae may have taken up their bacterial companions in the same way as Cymbomonas, except they didn't digest them.

Hungry algae may explain how plants became green; Michael Marshall, New Scientist Issue 2920, 06 June 2013.

Cooperative alliances are the single greatest achievement of selfish genes. The entire web of mutually interdependent life on Earth owes its existence to these alliances, even the mutual interdependence of plant and animal life as animals provide the carbon dioxide for plants to use to make the sugars for animals to eat.

The lesson from evolutionary cell biology for evolving and developing human society is that cooperation and inclusion works for the long-term benefit. If we are to have any future we have to learn to cooperate not just with one another and one culture with another but with the entire system of life on this planet.

Hungry algae may explain how plants became green; Michael Marshall, New Scientist Issue 2920, 06 June 2013 (subscription required)

Wikipedia - Endosymbiotic theory

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Challenge to Muslims

Regular readers will no doubt remember the hilarity, and no little hysteria, which ensued when I challenged Manuel de Dios Agosto, who posts on twitter using a variety of usernames (some of which are listed here) including @Sacerdotus, to debate a very simple proposition. He had been boasting that he had irrefutable scientific evidence for the Christian god so I challenged him to justify his claim. The result, and his subsequent meltdown can be seen here (it is not for the faint-hearted!)

It's just occurred to me after a debate on Twitter with a Muslim whose entire 'scientific' argument for his god was based on profound ignorance and personal incredulity, reinforced in places by some half-baked notions of what science does or doesn't claim about evolution, cosmology, biology, etc., that I had been a little unfair to Muslims and should have given them the same opportunity to prove to the world that their god's existence is a scientific fact too.

So, with this in mind, I have opened the challenge to any Muslim who holds this same belief - that there is irrefutable scientific evidence for only the god of Islam as described in the Qur'an. Can you do better that Manuel did for his god? It would be hard to do worse. He took one look at the proposition, saw what a scientific definition actually was, started screaming and shouting abuse and hasn't got his composure back yet. Don't try it if you're also of an unstable disposition!

The (non-negotiable) proposition is:

There is verifiable, scientific evidence for only the Muslim God for which no possible natural explanation can exist.

This is non-negotiable because anything less would not validate the belief.

Also non-negotiable:

The proposer (that is the person accepting this challenge) will supply an agreed scientific definition of the God of Islam against which the proposition can be tested, precise details of the evidence and how it can be verified, how the hypothesis that it proves only the Muslim god is real could be falsified, and how it establishes the truth of the proposition beyond reasonable doubt. Failure to do so will be regarded as conceding the debate.

Quotes from a book, appeals to authority, statements of 'faith', personal opinion and sincerely held beliefs will not be accepted as evidence unless accompanied by scientifically verifiable evidence.

The forum is to be mutually agreed. All contribution will be echoed to this blog and either party may publish the entire debate in any medium. The forum will not be a blog over which either participant has full control.
The negotiable terms and conditions are:
A neutral referee will be agreed. The rulings of this referee will be final and binding on both parties to the debate. The referee will rule on:

  1. Whether an assertion of fact has been validated with verified evidence.
  2. Whether questions have been answered fully, honestly and without prevarication.
  3. The meaning of words, when these are in dispute.
  4. Whether an argument was ad hominem or not.
  5. Any other disputes when requested by either of the parties to the debate.
  6. Whether a referral to the referee was mendacious or an attempt to prevaricate, divert or otherwise obstruct the normal flow of debate.
  7. The referee may intervene at any time to declare the debate won, lost or drawn.

Should either party fail to provide evidence for which a claim of its existence has been made, the debate will be considered lost.

Making any claim which is shown to be untrue or unsupported by evidence will result in forfeiture of the debate.

Ad hominem arguments will result in forfeiture as will threats, veiled or otherwise.

Failure to respond to a reasonable point, answer a reasonable question or to supply the evidence requested within three days (subject to notified periods of absence, or illness or injury or at the discretion of the referee) will result in forfeiture.

You might want to familiarise yourself with these common fallacies listed here before you start.

So, who's up for it? Can you justify your beliefs in open debate?

If not, you might like to ask yourself why you hold them.

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Saturday 8 June 2013

Why Cooperation Works

Cooperative Yeast Break Free

One thing that seems to baffle religious people no end is why non-religious people behave decently when they aren't expecting a reward or fearing punishment. What they can't seem to grasp is why people bother to cooperate and aren't simply selfish. Strangely though, they take umbrage at the suggestion that, if this applies to them, they are admitting to being a sociopath with no feelings for their fellow man nor any ability to empathise with others.

If you're religious you're probably thinking that's not fair. You do right because it's the right thing to do. It's just that you can't trust all the others, so you want them to be motivated by reward and punishment because that makes them more reliable; more controlled and predictable. You don't need that, obviously, because you can be trusted to do the right thing! In fact, what you believe in is belief itself. For more on this see Believing in Belief.

A study, published in Current Biology and reported on by Guy Riddihough in Science shows that cooperative behaviour probably evolved because it leads to greater long-term success, especially in an expanding population which, for most of its recent history was what Homo sapiens was and which many populations continued to be until very recently.

The team genetically engineered yeast to form two populations to act as cooperators and defectors respectively. Both populations were unable to absorb the disaccharide sugar sucrose from their growth medium but both could absorb the simpler monosaccharide sugars (glucose and fructose) into which sucrose can be broken down with the enzyme invertase.

The cooperators could produce and excrete invertase making glucose and fructose available for all populations but the defectors had been mutated to prevent invertase production. Since there was a cost to the cooperators in producing invertase but not to the free-riding defectors, defectors would be expected to be the main beneficiaries of this system.

This system is analogous to the Game Theory Prisoner's Dilemma:
Two members of a criminal gang are arrested and imprisoned. Each prisoner is in solitary confinement with no means of speaking to or exchanging messages with the other. The police admit they don't have enough evidence to convict the pair on the principal charge. They plan to sentence both to a year in prison on a lesser charge. Simultaneously, the police offer each prisoner a Faustian bargain. If he testifies against his partner, he will go free while the partner will get three years in prison on the main charge. Oh, yes, there is a catch ... If both prisoners testify against each other, both will be sentenced to two years in jail.
In this classic version of the game, collaboration is dominated by betrayal; if the other prisoner chooses to stay silent, then betraying them gives a better reward (no sentence instead of one year), and if the other prisoner chooses to betray then betraying them also gives a better reward (two years instead of three). Because betrayal always rewards more than cooperation, all purely rational self-interested prisoners would betray the other, and so the only possible outcome for two purely rational prisoners is for them both to betray each other. The interesting part of this result is that pursuing individual reward logically leads the prisoners to both betray, but they would get a better reward if they both cooperated. In reality, humans display a systematic bias towards cooperative behavior in this and similar games, much more so than predicted by simple models of "rational" self-interested action.
What the researchers found was: the colonies grow, the cooperator populations expand at the expense of the defectors. The cooperators form genetically demixed sectors, analogous to "genetic surfing" seen in frontier populations. Simulations support the idea that an expanding colony frontier favors (cooperative) genotypes that maximize group productivity and that this could apply to range expansions seen in many species, including humans.
Cooperative Yeast Break Free; Guy Riddihough;
Science 7 June 2013: Vol. 340 no. 6137 p. 1143 DOI: 10.1126/science.340.6137.1143-b
So we see that an expanding population is likely to be more successful and so continue to expand if its members cooperate. Cooperation is thus a consequence of expansion and genes for cooperation benefit from the situation in which they find themselves. As always with evolution, it's not just the genetic change which matters but the context of the environment in which that change occurs which facilitates evolution.

Human evolution is a little more complex than yeast evolution, not because the basic principles are different but because we have an additional set of replicators - our memes. Memes are units of cultural inheritance and are no less inherited replicators than our genes. This is where our morality resides. Morality is simply the set of inherited rules by which we ensure cooperation by regulating our interpersonal interactions. What our genes allow us to do is to empathise with other people - to put ourselves in their place and see things through their eyes. This way we know what they would have us do unto them. We don't always do it that well and some are better at it than others, but all humans have the innate ability to cooperate and the learned ability to select the right rules for task.

And of course, the rules vary from place to place and from people to people because they evolved in different frontier populations at different times and in different situations. This difference is how we know they evolved and weren't handed down to us by some divine authority thought up by Bronze-Age goat-herders who knew no better.

Cooperative Yeast Break Free; Guy Riddihough; Science 7 June 2013: Vol. 340 no. 6137 p. 1143; DOI:10.1126/science.340.6137.1143-b

Van Dyken et al. Curr. Biol. 23, 919 (2013)

Religion: An Abdication of Moral Responsibility.
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