Evolving Dog Cancer Gives Clue to Dog Origins

The ancient tumour genes are most similar to husky genes

Infectious cancer preserves dog genes for 11,000 years - life - 23 January 2014 - New Scientist

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

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

More Ado About Nothing

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

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

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

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

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

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

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

Brahmagupta - thinking of nothing.

However, Eastern philosophers came at it from a different direction. They saw the Universe in terms of recurring cycles of creation, not as a one-off 'perfect' creation. In India in 628 CE, the philosopher, Brahmagupta wrote a treatise, the Brahmasphutasiddhanta, in which he first proposed the idea that numbers were abstract concepts, not real things and so was able to think in terms of subtracting a larger number from a smaller one - something essential when dealing with money accounts. Until then, such questions as how do you subtract a larger area from a smaller one would have been met with incomprehension, as would the question of bartering more goats than you had. The answer would have been that it couldn't be done, and that was that.

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

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

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

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

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

Leonardo Fibonacci

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

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

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

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

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

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

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Death and Elephants

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

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

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

Rooting For The Robin

British subspecies of robin (Erithacus rubecula melophilus)

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

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

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

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

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

Wild boar, rooting

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

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

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

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

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Creationist Myths Debunked

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

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

Elephant Sharks Living In The Past

The elephant or ghost shark, Callorhinchus milii

Elephant shark takes record for slowest evolution - life - 08 January 2014 - New Scientist.

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

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

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

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

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

Elephant shark genome provides unique insights into gnathostome evolution,
Byrappa Venkatesh, et al., Nature, 505, 174–179 (doi:10.1038/nature12826)

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

Michael Coates, palaeontologist,
University of Chicago

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

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

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

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

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

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

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Defeat for Texas Creationist Loons

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

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

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

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

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

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

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

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


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Incestuous Creationist Absurdity

Arthritic and inbred

Image: John Reader/Science Photo Library

Inbreeding shaped the course of human evolution - 28 November 2013 - New Scientist

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

Take this article in New Scientist, for example.

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

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

Another Embarrassment for Creationists to Ignore.

Stonehenge Man (Image: English Heritage)

Stonehenge Man: not just a pretty face - life - 03 January 2014 - New Scientist

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

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

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

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

William Dembski
Touchstone Magazine. Volume 12, Issue 4: July/August, 1999

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

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

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

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

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

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Peace On Earth - The Christian Way

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

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

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

Matthew 5:9

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

So what is this biblical peace exactly?

Peacemakers at work

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

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

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

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

Deuteronomy 20:10-14

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

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

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

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

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

Matthew 10:34-36

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

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

Matthew 10:39

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

What does Paul have to say about it?

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

For example:

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

Romans 5:1-2

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

Romans 8:6-7

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

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

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Understanding Evolution

Jean-Baptiste Lamarck

In this blog I'm going to look at what were once competing theories for explaining the fact of observable evolution, Lamarckian and Darwinian evolution as proposed by Jean-Baptiste Lamarck and Charles Darwin with Alfred Russel Wallace respectively. Although these are often presented as two opposite and irreconcilable theories, with the former being utterly defeated by the latter, as with so much in science, things are not always as they seem. Jean-Baptiste Lamarck, if not being entirely rehabilitated, is at least being shown to be not entirely wrong.

You only need spend a few minutes reading creationist materials to realise that these two theories are often, and often deliberately, confused.

By the late 18th-century, especially following the work of Carl Linnaeus it was becoming obvious to serious biologists that living organisms could be arranged in a hierarchy of families, families into orders, orders into classes, classes into kingdoms, etc. We were also beginning to realise that Earth had not been created suddenly exactly as we saw it but that it was the result of change over time. One event which had given impetus to this growing philosophical movement had been the Portuguese earthquake which had destroyed Lisbon in 1755 (for more on this see An Earthquake in Theology).

The question was what process, operating over time, had given rise to the observed diversity of life on Earth?

Charles Darwin, 1874

Jean-Baptiste Lamarck's hypothesis was that by reacting to challenges in their environment organisms acquired characteristics which were then inherited by their offspring. Giraffes needed to stretch their necks to reach the leaves in tall trees so their necks got slightly longer. This was inherited by their offspring and, repeated over time, gave rise to giraffes with long necks.

One of the pieces of 'evidence' Lamarck presented was that sons tended to follow their fathers in trades such as blacksmiths. He argued that fathers developed the muscles and coordination needed to beat hot metal on an anvil. These were then inherited by their sons who naturally became blacksmiths.

This might seem laughably naive now but, in the absence of any knowledge of DNA or genetics, and a primitive view of embryology, it seemed superficially to be a perfectly good hypothesis. What did they know about sociology? The tendency of sons to follow their fathers into trades was not because of biological inheritance but because it was accepted that children born into certain social classes would remain in those classes at least partly because it was assumed that the social order was a God-given thing. It was natural that boys would be trained by their fathers and take up the trade they followed because the opportunity was there and there was little opportunity to do anything else. Children adopted by blacksmith families were more likely to be blacksmiths than to follow their natural father's trade, as were children produced by a blacksmith's wife's surreptitious dalliances with the local baker.

What was being inherited was essentially an expression of culture. Hold that thought!

Another problem for Lamarckian evolution was that, even if a giraffe's neck could be stretched by reaching for the acacia tree leaves, and even if this stretched neck could be inherited by the next generation, what equivalent mechanism was there for the acacia tree getting taller? Did the tree strive to lift its branches out of reach?

Darwin's and Wallace's hypothesis was that the environment naturally favoured those with small variations which made them better able to survive and reproduce in that environment. In this way an organism tends towards fitness for survival in its environment. All that is needed is inherited characteristics, variation in those characteristics and a selective environment and evolution over time will be inevitable.

Both Lamarckian and Darwinian evolution initially suffered from the same problem - there was no known mechanism for passing these characteristics on to the next generation. Both depended on a hypothetical entity which passed from parent to offspring and so carried the changed information into the next generation. Gregor Mendel then showed that certain characteristics seem to be inherited according to rules which strongly imply a discrete entity or entities which are inherited in discrete ratios.

We now know these are genes arranged on chromosomes and composed of DNA and carried in pairs in all the sexually reproducing species. We now know how these contain information, how this is translated and how it is inherited and so the triumph of Darwinian evolution over Lamarckian inheritance seemed complete.

But. We have recently discovered the epigenome.

The epigenome is an integral part of the genome and controls which parts of the DNA are active and which aren't; which genes are switched on and which are switched off. We have long known that all normal cells in an individual have the same DNA derived from the DNA which went into the first cell at fertilization. Yet different cells carry out different functions depending on the organ in which they find themselves. Muscle cells are different to liver cells which are different to neurones and so on. This is achieved by different genes being deactivated as necessary. One way in which genes can be deactivated is by a methyl group being attached to the cytosine molecule in DNA. Methylated cytosine continues to behave much like regular cytosine in that it pairs with guanine but areas of DNA which are heavily methylated tend not to be transcribed so the gene in that piece of DNA is switched off. This mechanism is still not fully understood but it is known that methylated DNA can be inherited through the germline by the next generation.

So here we have a mechanism for characteristics acquired after birth being inherited by the next generation. In other words, epigenetics can be Lamarckian in its inheritance.

But there is another way in which Lamarck was undoubtedly, though unwittingly, and ironically, right.

Ironically, because with his blacksmith example he was actually describing cultural inheritance which we now know, at least in sentient species like Man, is similar to genetic inheritance but the units of inheritance are not chemical genes in the form of DNA but ideas in the form of memes.

It seems highly likely that we are born with no memes at all and acquire all of them after birth by classical Lamarckian inheritance.

And, since our memetic inheritance is Lamarckian we can change it under conscious control. We can choose which to pass on and we can choose which to accept. In short, unlike our genes where, with the possible exception of genetic engineering, we have no choice in what we got from our parents and what we give to our children and are slaves to our 'selfish' genes, we are the masters of our cultural inheritance and are neither bound by it nor compelled to pass it on.

If there is something wrong in our cultures we can change it, as we are doing as we increasingly reject religious bigotry and superstition in favour of humanism. We are not destined to follow the dictates of earlier, less enlightened generations.

We are free to look at religions and say, if that's what your religion tells you then your religion is wrong.

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Alan Turing, A Victim of Religious Bigots

BBC News - Royal pardon for codebreaker Alan Turing

The news that the late computer genius Alan Turing has been given a royal pardon for his conviction in 1952 for 'gross indecency', i.e., being homsexual, or more to the point, embarrassing the establishment by being exposed as homosexual, is welcome if small comfort to his relatives.

It marks another milestone in the move towards a kinder, more tolerant and inclusive and less censorious, post-Christian Britain.

Turing's contribution to the war effort during the fight against fascism was immense. Any other British subject making anything approaching his contribution would have been given at least a knighthood, if not a peerage yet, under the influence of Christian bigotry, homesexuality was considered an illness and a crime.

An illness and a crime? Yes, Christian 'morality' is perfectly capable of regarding even the effects of real illness as criminal because illnesses are caused by evil spirits and only the morally degenerate would allow themselves to be possessed, as everyone knows. The Bible is full of stories of illnesses and disabilities caused by possession. Even the 'creator god' in the form of Jesus took this for granted.

Turing's work with the Bletchley Park codebreakers undoubtedly shortened the war by helping to crack the German Enigma code and saved thousands of lives. Even without that, his contribution to computer science alone should have earned him his nation's accolade. He is widely regarded as the father of modern computing and artificial intelligence, having formalised the concept of a computer algorithm and proved that any computable problem can be solved with a suitable algorithm. The 'Turing Machine' is a theoretical programmable machine which is capable of solving any such problem.

Turing also devised the 'Turing Test' as a way to test whether a computer has achieved a human level of intelligence.

The Turing test is a test of a machine's ability to exhibit intelligent behaviour equivalent to, or indistinguishable from, that of a human. In the original illustrative example, a human judge engages in natural language conversations with a human and a machine designed to generate performance indistinguishable from that of a human being. All participants are separated from one another. If the judge cannot reliably tell the machine from the human, the machine is said to have passed the test. The test does not check the ability to give the correct answer to questions; it checks how closely the answer resembles typical human answers. The conversation is limited to a text-only channel such as a computer keyboard and screen so that the result is not dependent on the machine's ability to render words into audio.

Wikipedia - Turing test

Under the influence of Christian bigots all this counted for nothing of course. What mattered was not how many lives he had helped save, how he had helped defeat fascism or how much his work on computers had added to human progress, but that he had upset 'God' by loving members of his own gender and having anal intercourse. For that, he had to be humiliated, denied the right to work on any project involving government security or secrets, and, as an alternative to prison, be chemically castrated.

Upset by his treatment at the hands of these censorious hypocrites, Turing sank into depression and despair and took his own life in 1954.

Hundreds of other people, including Oscar Wilde, were convicted of the victimless crime of homosexuality before we began to turn our collective back on the superstitious Bronze Age bigotry to be found in the Bible and decriminalised it. What we now need to do is to get pardons for all these people as a token - and it can only ever be a token - of our shame and disgust at the excesses of our forebears and our resolve never again to allow these bigots to tell us what morality is.


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Evolved Morality

Our morals were not handed down to us by gods but evolved with us as a set of psychological processes which fitted us for living in small, cooperative social groups.

Here's a simple moral dilemma. It was first proposed by philosopher Peter Singer some forty years ago.

Imagine you are walking along a riverbank wearing a $1000 suit and you see a child is drowning. You can save the child but the water will ruin your suit.

No contest.

The moral thing to do is to save the child. Asked why, most people would say the child's life is worth more than the cost of the suit; that it's immoral to put material goods before human life. Forced to compare the value of a human life, especially that of a child, most people will value the child vastly more than material goods. In fact, asked to place a value on a child's life, most people will decline to do so. The idea itself is repugnant.

Scientology Is A Religion - Official!

BBC News - Supreme Court judges allow Scientology wedding

The Supreme Court of England and Wales has decided that a Scientology^TM church is a "place of meeting for religious worship" and so can conduct legal marriages. This ruling effectively overthrows a 1970 High Court ruling that Scientology^TM meetings are not acts of worship, in other words, Scientology^TM is not a religion.

In England and Wales, where the legal system is based on English Common Law, a lower court is bound by the rulings of a higher court and the precedent of earlier cases, so High Court judges were bound by the 1970 ruling until it was changed by a higher court or legislation in Parliament. The Supreme Court replaced the House of Lords as the highest court in the land a few years ago and it's rulings can only be reversed by legislation in Parliament.

Scientology^TM was invented by the trashy sci-fi author, L. Ron Hubbard in the early 1950s to win a bet with another and better sci-fi author, Robert Heinlein, and is based on nothing more than his limited imagination. Hubbard had boasted that he could make more money by inventing a religion than by writing books - which was probably true for someone with his limited sci-fi writing abilities. Heinlein's response was to write Stranger in a Strange Land which shreds all organized religions and especially cults like Scientology^TM.

Scientology^TM has become notorious for its cult-like insistence on money-making, which has led many countries to classify it as a commercial enterprise rather than a religion, as well as the psychological techniques it uses to keep its members and to harass those who dare to leave and speak out against it or the cults leaders.

The case had been referred to the Supreme Court by a High Court judge who had refused to set aside the 1970 ruling and allow marriages to be conducted in Scientology^TM churches, as they are in Scotland which has it's own legal system and is not bound by English and Welsh court rulings and precedent. Lawyers for Scientology^TM had argued that it had evolved since 1970 so that ruling no longer applied. The judge had said that it was not for the High Court to rule on what constituted religious worship.

The five Supreme Court judges decided that it was the definition of 'religious worship' which had changed. The 1970 definition of religious worship as 'reverence or veneration of God or of a supreme being' was now outdated and would also exclude Buddhism. Lord Toulson, delivering the written verdict, said to confine religions to those which worship a supreme deity would be discriminatory. He broadened the legal definition of religion which should no longer be confined to religions which recognise a supreme deity. Which, aside from the circularity in that definition - religions are religions which may or may not have gods - raises more questions than it solves. What is now not a religion? Does it now include football club supporters, folk dancers, ufologists and sewing circles?

Of course, a religion based on nothing more than absurd ideas and half-baked pseud-science is nothing new. In that respect there is no real difference between Scientology^TM, Christianity, Judaism, Hinduism and Islam. The only material difference is one of age.

But the most significant thing about this ruling is that it reflects the shifting sands of 'religion', in what is rapidly becoming post-Christian Britain as many people are increasingly rejecting the absurd biblical mythologies and superstitions, but some are still looking for a 'spiritual' dimension and especially the sense of belonging to a community of like-minded people which the church previously provided. At the current rate of decline in traditional religions it would not be long before very few places could be called places of worship on the old definition. The Supreme Court ruling merely reflects this change in social attitude and cultural awareness. It marks a small step in the evolution of British culture.

If something is in me which can be called religious then it is the unbounded admiration for the structure of the world so far as our science can reveal it.

Albert Einstein
Letter to J. Dispentiere, March 24, 1954

I'm with Richard Dawkins and the late Richard Feynman and Albert Einstein that learning about the Universe and how we fit into it, and especially learning how we are the product of a process that means we are related to all other life on Earth, and are made of the same stuff the Universe is made of, is profoundly spiritual.

One of my most profound spiritual experiences was when it dawned on me that, because we are made of the same stuff the Universe is made of and are the product of an inevitable process the result of the fundamental laws of matter in this Universe, in a very real sense, through us the Universe has become self-aware. Through us the Universe can gaze in awe at itself.

Recognising that, and recognising that every single living thing is the product of survivors who never once failed to produce an offspring, and so we are all descendants of the first replicators and have all travelled the same journey, is profoundly spiritual.

Do I need to gather with others to share that and to get a sense of community? Not personally, though others might, but I like it when others agree with me and say so.

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Child-Abusing Christian Parents.

Michael Pearl, No Greater Joy Ministries

BBC News - Child 'training' book triggers backlash

A child-raising book that advocates brutality including whipping with belts has sold hundreds of thousands of copies to evangelical Christians. So far, at least three children have died at the hands of parents who were influenced by the book, but that's not considered a reason to withdraw it or to tone down it's brutality by its authors, pastor Michael Pearl of Pleasantville, Tennessee and his wife, Debi.

The book, To Train Up A Child: Turning the hearts of the fathers to the children, has sold more than 800,000 copies, almost exclusively to fundamentalist Christian families, many of which are homeschooling their unfortunate children to protect them from science and other undesirable information. The authors appear to have no qualifications in child psychology.

Unfortunately, their Christianity isn't seen by their customers as a reason to protect their children from brutalization.

For the under one year old, a little, ten- to twelve-inch long, willowy branch (striped of any knots that might break the skin) about one-eighth inch diameter is sufficient. Sometimes alternatives have to be sought. A one-foot ruler, or its equivalent in a paddle, is a sufficient alternative. For the larger child, a belt or larger tree branch is effective.

To Train Up A Child - Michael & Debi Pearl

Use whatever force is necessary to bring him to bay... If you have to sit on him to spank him then do not hesitate. And hold him there until he is surrendered... Defeat him totally.

To Train Up A Child - Michael & Debi Pearl

The objective is to make the child surrender completely to their parent's will as a preparation for future, instant, unquestioning obedience.

In addition to the book, the Pearls have also produced videos and magazines detailing this brutal approach to parenting which Christians give as gifts to families on the birth of a baby. Sales have netted $1.5 million for tax year 2012-13.

Ritualized child brutality by Christians is of course nothing new. In 2002 a pastor of the House of Prayer, Georgia, USA, was jailed because Christian parents had been bringing their children to his church to be beaten "in the fellowship of the church" by members of the congregation. (Jerry Vines, Sermons.)

This 'loving' approach to child care is, of course, entirely consistent with the Bible; indeed, the title of the Pearl's hand-book of child abuse is taken from Proverbs 22.

Train up a child in the way he should go: and when he is old, he will not depart from it.

Proverbs 22:6

It also has echoes in Ignatius Loyola's sinister, "Give me the boy until he is 7 and I will give you the man".

This is not the only verse from Proverbs which advocates child abuse:

Chasten thy son while there is hope, and let not thy soul spare for his crying.

Proverbs 19:18

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Foolishness is bound in the heart of a child; but the rod of correction shall drive it far from him.

Proverbs 22:15

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Withhold not correction from the child: for if thou beatest him with the rod, he shall not die. Thou shalt beat him with the rod, and shalt deliver his soul from hell.

Proverbs 23:13-14

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He that spareth his rod hateth his son: but he that loveth him chasteneth him betimes.

Proverbs 13:24

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The rod and reproof give wisdom: but a child left to himself bringeth his mother to shame.

Proverbs 29:15

Nor is this brutality confined to the Old Testament. The author of St Paul's letter to the Hebrews was just as keen on it.

For whom the Lord loveth he chasteneth, and scourgeth every son whom he receiveth. If ye endure chastening, God dealeth with you as with sons; for what son is he whom the father chasteneth not?

But if ye be without chastisement, whereof all are partakers, then are ye bastards, and not sons.

Hebrews 12:6-8

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Now no chastening for the present seemeth to be joyous, but grievous: nevertheless afterward it yieldeth the peaceable fruit of righteousness unto them which are exercised thereby.

Hebrews 12:11

Fortunately, none of these calls to brutalise children comes close to the grotesque verse in Psalms 137 which has been embarrassing Christians for centuries:

Happy shall he be, that taketh and dasheth thy little ones against the stones.

Psalms 137:9

No court, judge, police or child protection service has ever accused us of doing anything that was an endangerment to children. There's no way that a person who reads the book could be led to violence. That may not prevent violence if that's part of their nature, but it's not going to lead them to do something that's contrary to their own set of values.

Michael Pearl

This callous attitude towards children comes from a primitive belief in good and evil as actual entities manifesting as good and evil spirits controlled in their turn by good gods and bad gods. As such it pre-dates Christianity by many centuries but was prevalent in the culture which gave rise to Christianity some 18-1900 years ago and in which the bad gods had been subsumed into the mythical Satan. It was assumed that children were susceptible to evil spirits which caused childhood illnesses, deformities, blemishes and unruly, rebellious or disobedient behaviour. The approach was the same: drive out the evil; beat the Devil out them. It informed the Victorian approach to mental health too.

It simply seems never to have occurred to them, nor to those who still hold to these barbaric beliefs, that all it achieves is an amoral culture which assumes that problems can be solved by a resort to violence and that might is right. A culture in which there is a repeated cycle of brutalisation of children who then grow up to brutalise their children in turn. A culture in which respect and fear are synonymous and where he who carries the biggest stick rules the day.

[To Train Up a Child is] quite singular in its orientation toward punitiveness toward children in general but also infants. It preaches a number of very dangerous views, that could very easily result in physical child abuse if one follows what they advocate.

George Holden, Professor of Psychology,
Southern Methodist University, Dallas.

This is very close to a fundamentalist's relationship to their imaginary god, where right is defined as what the god will reward you for and bad is defined as what it will punish you for. The notion of empathising with other people and working out what the effects your actions will have on them seems to be unknown to them. What's in it for me? All that matters is what they get out of it.

And this gives us a clue as to why fundamentalist Christianity will so readily and easily cosy up to the brutal, selfish, sociopathic, or even psychopathic, political right. Might is right.

Thankfully, in most of the civilised world, people are turning away from this primitive cultural past with it's infantile belief in magic and magic spirits and reified human cultural constructs, and are trying to build a society based on decent Humanist principles in which all people of any age are regarded of worthy of respect regardless of the power they can command.

Keeping their children isolated by homeschooling is a desperate attempt by the die-hard child abusers to keep out the forces of progress and retain primitive barbarism in the confines of their own homes, close-knit fundamentalist communities and fire and brimstone fundamentalist Christian churches.

The advent of the Internet must terrify them and those who write books for them to blame.

It would be illegal in 34 countries, 23 of then in Europe, to follow the advice given in the Bible and repeated in this brutal book. This is a measure of how far our moral development has advanced since the Bible was written.

For more information as well as links to petitions to persuade booksellers to stop selling this child-abuse handbook, see Why Not Train A Child? by a blogger who blogs under the name Hermana Linda.

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The Christmas Challenge

Have a great Yule!

Here's a nice little game for Christmas for Christian families. You can play it with your children, with the grandparents and maiden aunts who come for dinner, with friends and other relatives who might pop by with season's greetings. It involves really studying the two gospels in the Bible which mention anything to do with the birth of Jesus and on which the modern Christmas tradition is based.

All you have to do is take all the facts mentioned in the two versions and weave them together into a single narrative describing all the events and facts mentioned.

Remember, as a Christian, you believe Jesus was the son of God born of a virgin, and that the Bible is God's inspired word, so all the facts mentioned must have happened as described.

What could be simpler?

To help, I'll summarise the stories. You can use the Bible if you prefer and aren't familiar with the stories as they appear in the Bible rather than the traditional Nativity plays. I'm using the King James 'authorised' version. If you don't have one I've provided handy links.

Unravelling Our Evolutionary Past

BBC News - Leg bone gives up oldest human DNA

New evidence which may help unravel the complicated story of human evolution was published in Nature today. Researchers led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig have isolated and analysed mitochondrial DNA from 400,000 year-old hominid fossils found at the Sima de los Huesos or 'pit of bones' in the Atapuerca mountains in northern Spain.

Scientifically, the significance of this is that this is the oldest hominid DNA yet recovered. Until recently it was assumed that DNA degrades over time at a rate which means 60,000 years was the limit beyond which DNA would not be recoverable but new techniques in DNA sequencing have now pushed that back way beyond what was thought possible.

Science can tell only so much from bones and fossils but DNA potentially provides a much clearer picture of evolutionary relationships and the recovery of mitochondrial DNA raises the possibility of a being able to recover the full genome.

Mitochondrial DNA (mtDNA) is from the cell organelles responsible for using the energy in glucose to build adenosine triphosphate (ATP) which the cell can then use as an energy source to drive other metabolic processes. These organelles are believed to be the descendants of a bacterium which formed a symbiotic relationship with other simple cells to form the complex cells of which all multicellular life is composed. Mitochondria are present in the ovum but not in sperm, so we only inherit mtDNA from our mother and it does not get shuffled up and mixed with our father's DNA, unlike most of our genome, so it is possible to construct a tree of relationships through the maternal line.

Atapuercan family - artist's impression
(From Pilgrimage Day 13: Belorado - Atapuerca DR. Kaare Torgny Pettersen)

At 400,000 years old, researchers had expected this mtDNA to show the hominids to be close to the Neanderthals who are believed to have been in Euro-Asia for at least 250,000 years, so it was something of a surprise that they are actually closer to the recently-discovered Denisovans from Siberia. Physically, the fossils from Sima de los Huesos look like early Neanderthals and this has led some paleoanthropologists to classify them as Homo heidelbergensis which is a candidate for the forerunner of H. neanderthalensis, the as yet unnamed Denisovans, a third possible cousin known only from the DNA it is thought to have contributed to modern humans, and maybe even H. sapiens.

One possibility is that this population resulted from interbreeding between early Neanderthals or Homo heidelbergensis and H. erectus as humans expanded into Euro-Asia and diversified, forming what amounts to a ring species. This is of course to be expected as species diversify from a common ancestor to form regional varieties, subspecies and eventually new species. There will inevitably be a period during which fertile interbreeding is possible. It is also possible that the Denisovans were the descendants of an early expansion which was later replaced in Europe and Western Asia by Neanderthals who had evolved in isolation before moving into their final range as an Ice Age adapted human variant, to be replaced in their turn by H. sapiens only some 30-50,000 years ago as the ice retreated and Neanderthals found themselves specialised for an environment which no longer existed. For them, global warming happened 30,000 years ago.

Whatever the final resolution to this puzzle turns out to be, and DNA sequencing is bringing that ever closer, we can be absolutely sure it will not trace all humans to a boat in the Middle East some 4000 years ago. The Max Planck Institute in Leipzig, and the science of DNA sequencing and analysis, must be giving nightmares to the professional liars at the Discovery Institute and the Institute for Creation Research which are desperate to keep selling their primitive Bronze-Age mythology to scientifically illiterate simpletons, hoping to be swept to political power on a wave of scientific ignorance and arrogant incredulity.

The science, of course, is proving to be entirely consistent with the neo-Darwinian model for evolution. Indeed, the science only makes any sense in terms of Darwinian Evolution.

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The Small Problem of the Hobbit

Homo floresiensis (cast)

I'm obviously not keeping up.

Reading Becoming Human: Our Past, Present and Future a special publication by Scientific American editors, the chapter Rethinking the Hobbits of Indonesia by Kate Wong was something of a surprise.

I had assumed the so-called 'Hobbit', the diminutive hominid known to taxonomists as Homo floresiensis and to paleoanthropologists as LB1, after Liang Bua, the name of the cave it was found in in 2004 on the Indonesian island of Flores, was generally considered just that - a member of the Homo genus which had become miniaturised. Miniaturisation is common on islands, probably in response to limited resource and a generally smaller number of predators.

The problem, as I understood it, was that the cranial capacity of LB1 was only a little larger than a chimpanzee's and yet stone tools were found associated with it which showed a tool-making ability at least as advanced as H. erectus with a far larger brain.

Revising Our Attitude To Sex as Christianity Fades

Image: Sven Görlich/Plainpicture

UK sex survey highlights tolerance, diversity and abuse - health - 27 November 2013 - New Scientist

A survey into attitudes to sex published in The Lancet today highlights the demise of Christianity and the advance of secular humanism in Britain with a subsequently healthier, more tolerant and more considerate attitude to sex and sexuality. The survey, the third National Survey of Sexual Attitudes and Lifestyles (Natsal) shows a marked change in attitudes towards a more tolerant, less censorious attitude to multiple parnerships and same-sex relationships but a reduced tolerance for infidelity. People are taking their responsibilities in a relationship more seriously but are less concerned about the sexual activities and preferences of others.

Christianity No Longer An Excuse For Discrimination.

Hazelmary and Peter Bull. No right to act unlawfully.

BBC News - Gay snub Cornish B&B owners lose Supreme Court appeal

In another landmark ruling today, the Supreme Court for England and Wales ruled that a Christian couple, Hazelmary and Peter Bull, had acted unlawfully when they refused to allow a gay couple to share a room in their guesthouse in Marazion in Cornwall in 2008. The five judges ruled that the Bulls' Christianity did not entitle them to deny other people their human right to not be discriminated against on the grounds of sexual orientation.