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.

A Peculiar Bird is the Pelican...

Nose to beak with a Christian hero heavyweight champ - life - 26 November 2013 - New Scientist

I thought I'd share this with you. Not only is it a lovely photo but it makes you wonder what else St Thomas Aquinas, leading Christian thinker of his time, got wrong.

The Dalmatian pelican (Pelecanus crispus) is the heaviest flying animal of any kind and needs about 1.2 Kg (2.6lb) of fish to supply the fuel for keeping that bulk aloft. It swallows as much as it can and stores any surplus in the large pouch in it's throat. In one of those fascinating examples of evolution's utilitarian approach to 'design', the existence of this large, expandable bag of skin was put to an entirely unrelated use by turning bright red in males in the breeding season.

Unintelligent Evolution

The thing about Darwinian Evolution by Natural Selection is that it is, and cannot be, directed. There is no plan and so no strategy or purpose. If it leads a species over an evolutionary cliff to extinction, then so be it. In fact, there are so many ways of going extinct that it is almost surprising that only some 99% of all known species have gone extinct.

Just imagine how crowded the place would have been in the beginning if the Christian creation myth were true and a magic man in the sky really did magic all the species into existence one day, with a hundred times as many species then as there are now!

One way evolution can drive a species to extinction is by specialisation. If the conditions are right a species can become more and more specialised to cope with them simply because each improvement produces more descendents in those conditions. The species has no choice in the matter.

DNA and a History of Slavery and Genocide

A History of Slavery and Genocide Is Hidden in Modern DNA | Surprising Science

New techniques of DNA sequencing and analysis, combined with an understanding of neo-Darwinian evolution, is proving a powerful tool with which to study human history with far greater accuracy than is provided by archaeology. Quite simply, we carry a record of our history in our DNA.

I remember reading in one of Richard Dawkin's books some years ago - I forget which, possibly The Greatest Show On Earth - that it should in theory, if only we could read it in sufficient detail, be possible to 'read' the evolutionary history of any species because each stage in evolution leaves its mark on the DNA. We should also be able to read changes in Earth's climate and major changes in ecosystems because each species which survived them would have needed to adapt, and adaptation means changes in DNA.

Hey Folks! Have You Seen Manny's New Account?

Looks like Manuel is back on Twitter and has started abusing people already. Details here.

For those not familiar with Manuel, the unemployable former Catholic seminarian who was expelled from seminary due to his abusive behaviour and narcissistic personality disorder, and who now spends all day abusing people on the Internet from the safety of his room in the Bronx, you may find the details here.

[Update 24 November 2013:] Things move quickly in Manny World. He is now on yet another account - @SacerdotusLIves. I expect Twitter Safety are already aware but they often need reminding...

I see from the profile that Manuel is now claiming to have contacts inside Twitter. I wonder if these contacts resemble the vast army of contacts he claims to have in the UK for monitoring my every move and reporting back to him so he can include the details in the weekly reports on my criminal activities he claims he submits to 'The UK Authorities', in other words, another figment of his deranged imagination.

Those wishing to make use of Twitter's abuse reporting system can find details here.

The Monstrous Regiment of Christians

BBC News - Church of England synod vote 'paves way' for female bishops

In a nice example of the "you'll keep voting till you get it right!" approach to democracy, the General Synod of the Church of England, which a year ago voted against allowing the ordination of women bishops, was today told to try again, and managed to get it right - and by a substantial margin of 378 to 8.

Well, not quite. There is still some work to do but they have 'paved the way'.

Christianity Is Dying Out

Christianity at risk of dying out in a generation, warns Lord Carey - Telegraph

This article made me laugh out loud. Not so much at the thought that the Church of England could be on the verge of a long-overdue world-wide extinction, welcome though that prospect is, but because of a particular paragraph which kind of gives the whole game away.

Lord Carey's warning came as he addressed the Shropshire Light Conference at Holy Trinity Church in Shrewsbury at the weekend discussing how the church could be “re-imagined”.

Re-imagined, eh? Is the Christian Church belatedly admitting that the whole thing was imaginary all along?

Boston's Bigots

St. Botolph's Church (Boston Stump)

St. Botolph's Church

Boston in Lincolnshire is a pretty little market town in the heart of the Fens, surrounded by acres and acres of cabbage fields which, when we were there last Friday, gave off a distinct hint of decaying cabbage.

This part of the England's coast is behind a defensive system of medieval dykes with extensive salt-marshes between the dyke and the sea making much of the actual coast inaccessible for much of the time and so a haven for millions of waders and other sea birds. These dykes are all that is preventing the entire area from reverting to the coastal marshes they were before reclamation in the early Middle Ages.

The tower of St Botolph's Church, known as the Boston Stump, dominates the surrounding fenlands and can be seen from miles away. It is Boston's claim to historic fame in that prominent member of the congregation of St Botolph's together with their fundamentalist rector, Rev. John Cotton, emigrated in 1630 to the New World to set up a Puritan Christian colony. They sailed on the Arbella and landed in Massachusetts Bay, where they founded the colony which became the city of Boston.

Lincoln Fundamental

Lincoln Cathedral, Lincolnshire, UK

Lincoln Cathedral at night

We had a nice couple of days in Lincoln and Boston, Lincolnshire on Thursday and Friday. I'll write about Boston next but this is about Lincoln, especially Lincoln Cathedral and what we can learn from it.

First a little background:

The See of Lincoln was the seat of one of the most powerful bishops in the Middle Ages and was certainly the largest, stretching at one time from the Thames to the Humber. It was thus immensely rich feeding off the produce of the surrounding agriculture, which included a large share of England's medieval wool wealth as well as the produce of the fertile reclaimed fenlands.

The cathedral is thus suitably impressive and sits atop a steep climb from the River Watham, which was

Evolving Theology

Charles Darwin to receive apology from the Church of England for rejecting evolution - Telegraph

I was amused to read today that the Church of England apologised to Charles Darwin in 2008 for rejecting his Theory of Evolution by Means of Natural Selection. It must have passed me by at the time as I wouldn't dream of picking up a copy of the Telegraph which used to be regarded as the Tory Party house journal, let alone ever opening it.

But that aside, I was still amused that the dear old CofE, forever chasing popularity and struggling to keep up with mainstream public opinion as its membership dwindles even further and more churches close despite population growth, would try to get away with the pretense that Darwinian Evolution and Christianity are compatible.

Yes, I know that many Christians, including, at least officially, the Pope, accept that evolution is the cause of diversity of living things and that the Darwinian Theory of Evolution is the best explanation of how it happens. I also know that a few evolutionary biologists like Francis Collins purport to be practicing Christians, but I have to assume they have managed to compartmentalize their beliefs and have squeezed two mutually inconsistent views into the same brain. It's surely no coincidence that religious evolutionary biologists are only slightly more common than hens' teeth.

Lessons From Nature - How Birds and Berries Gave Us Colour Vision

Hips and hawes in an Oxfordshire Hedgerow in Autumn

© 2013 Rosa Rubicondior

We've just spend a lovely afternoon walking over a footpath from Abingdon to the village of Sunningwell, where we had an especially good English Sunday roast dinner with a very drinkable Rioja at the Flowing Well. What made it even more enjoyable, apart from an almost cloud-free blue sky, was the profusion of wild berries amongst the autumn leaves on the hedgerows. The footpath is mostly ancient, so is well stocked with different plant species.

Now, a religious person, and especially a religious person who knew little of evolution and so would almost certainly not believe in it, would probably look at the beauty in the English countryside and marvel at how wonderful his or her god had been in magicking such a pretty planet just for them to marvel at. They

ET Will Destroy Religion's Foundations

An editorial in today's New Scientist very boldly states:

The idea that there might be another living planet a few light years from home, orbiting a star visible with the naked eye, is a tantalising prospect. For better or worse, the odds are stacked against that. But we can be pretty confident that, if life is common in the universe, we will have found signs of it by the middle of the next decade. [My emphasis]

We'll have the tools to spot nearby aliens by 2030; New Scientist 9 November 2013 (No. 2942)

The Silly Bible's Failed Prophecies.

Ask almost any Christian fundamentalist for one single proof that the Bible is the word of God and they will almost invariably trot out the accepted dogma that there are proven prophecies in the Bible which only a god could have inspired and they confirm the Bible's inerrancy.

Asking them for examples of these often results in indignant flounces and abuse, however, because, quite simply, there are none. There are a few statements which, at a stretch, parallel later events, usually events which were entirely predictable anyway - a bit like prophesying that there will be an earthquake in Japan or that the Caribbean will suffer a devastating hurricane sometime soon.

Very many of them are only 'confirmed' later in the Bible and have no extra-biblical evidence, like the alleged birth of Jesus, which apparently also prophesied he would be called Immanuel - a name by which he was never ever known in the Bible. The New Testament 'confirmation' of Old Testament 'prophecies' were written by people like the author of Matthew specifically to make it look like Jesus was the fulfillment of Jewish prophecy to suit a Jewish cultic agenda.

I have even had it claimed that the prophecy about Jesus returning, which is attributed to Jesus himself, is really a fulfilled prophecy because it will be fulfilled at sometime.

Darwin Creationist Award 2013 - Tiebreaker!

The votes are in for the 2013 Darwin Creationist Award and we have an unprecedented three-way tie!

Three excellent candidates and it's all up for grabs. It's good to see Joe Cienkowski still in there as Joe seems to have been trying for this prestigious award for several years now, even writing semi-literate, and scientifically fully illiterate, books to support his claim.

I'm sorry to see my personal favourite, Errol Smythe, in all his different manifestations, failing to make the grade. Perhaps his multiple attempts to refute the children's fairy tale Cinderella, in the mistaken belief that it is a standard biology textbook dealing with evolution, was just too preposterous for most people's tastes. Regrettably, Errol seems to have a minder who kindly deletes his more insane tweets and he regularly changes his user name, so his little gems are hard to come by.

Anyway, good luck for next year Errol. I'm sure you'll be in with another chance.

Evolution's Relics

Our genes have a very long history. 99% of them were in other species before they were in Homo sapiens.

About six million years ago they were in Africa in an ancestor we have in common with the other African apes. Three million years ago they were in the bipedal chimpanzees-like apes called Australopithecines in Southern and Eastern Africa. 375 million years ago most of them were in early amphibians that had recently evolved from lobe-finned fish to move out onto the land. 160 million years ago they were in the earliest mammals.

So it's not surprising that they still produce a few structures that were useful to something else but are no longer useful to us.

Scientists have identified several things that we no longer need and some that, although we no longer need them for what it was originally used for, have been adapted for another purpose. The appendix, for example, is no longer needed to aid digestion of cellulose like it is in some herbivores but serves a useful, though non-essential, role in the lymphatic and immune systems.

Finding Evolution's Missing Links

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

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

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

Christian Lie Alert!

Screen-shot. Click to enlarge.

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

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

One such was:

A Fungus That Farms Bacteria!

Morrell (Morchella crassipes)

First fungal farmers found harvesting bacteria - life - 30 October 2013 - New Scientist

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

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

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

Debbie Brock, Washington University in St Louis, Missouri, USA

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

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

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

Now scientists have discovered a fungus which farms bacteria.

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

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

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

Reference:

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

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

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Religion's Poison - Holy Water

Holy water should have HEALTH warnings.

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

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

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

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

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

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

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

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

About the closest to it is:

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

Deuteronomy 23:12-13

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

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

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Life's a Beach. Order From Chaos

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

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

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

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

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

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

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

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

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

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A Lot of Cock in Portugal

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

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

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