F Rosa Rubicondior: December 2013

Sunday 29 December 2013

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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Thursday 26 December 2013

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.

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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Friday 20 December 2013

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.

Thursday 12 December 2013

Scientology Is A Religion - Official!

BBC News - Supreme Court judges allow Scientology wedding

The Supreme Court of England and Wales has decided that a ScientologyTM 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 ScientologyTM meetings are not acts of worship, in other words, ScientologyTM 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.

ScientologyTM 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 ScientologyTM.

ScientologyTM 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 ScientologyTM 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 ScientologyTM 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 ScientologyTM, 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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Wednesday 11 December 2013

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.

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.

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

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.

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

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

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.

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.

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.

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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Monday 9 December 2013

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.

Wednesday 4 December 2013

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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