You Got Your Gut Bacteria From Mother's Mouth

Baby's first gut bacteria may come from mum's mouth - health - 21 May 2014 - New Scientist

A lovely example of how through evolution of 'selfish' genes over a prolonged period, humans, and very probably other placental mammals, have formed a mutually cooperative alliance with bacteria. Science has long recognised the role our microbiome of bacteria and fungi play in maintaining our health, and especially the role certain bacteria have in our gut where they are essential for absorbing some nutrients and vitamins.

Of course, there is no reason to think this system of mutual cooperation is unique to humans or even mammals since we share an essentially similar digestive system with all the deuterostome which are believed to have evolved some 558 million years ago, so it's a system which has been being refined and perfected for a very long time.

So how do we get our gut bacteria in early childhood? We have certainly acquired them within a few days of birth and it had been assumed babies are born with a sterile gut and acquire their bacteria from the mother's vagina during birth and from their general environment soon afterwards. Now, however a team led by Kjersti Aagaard of Texas Children's Hospital in Houston, Texas, USA has found that gut bacteria are present in meconium, the tary black fecal matter babies pass in the first day or two after birth which means they must have been present before birth.

Abstract
Humans and their microbiomes have coevolved as a physiologic community composed of distinct body site niches with metabolic and antigenic diversity. The placental microbiome has not been robustly interrogated, despite recent demonstrations of intracellular bacteria with diverse metabolic and immune regulatory functions. A population-based cohort of placental specimens collected under sterile conditions from 320 subjects with extensive clinical data was established for comparative 16S ribosomal DNA–based and whole-genome shotgun (WGS) metagenomic studies. Identified taxa and their gene carriage patterns were compared to other human body site niches, including the oral, skin, airway (nasal), vaginal, and gut microbiomes from nonpregnant controls. We characterized a unique placental microbiome niche, composed of nonpathogenic commensal microbiota from the Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. In aggregate, the placental microbiome profiles were most akin (Bray-Curtis dissimilarity <0.3) to the human oral microbiome. 16S-based operational taxonomic unit analyses revealed associations of the placental microbiome with a remote history of antenatal infection (permutational multivariate analysis of variance, P = 0.006), such as urinary tract infection in the first trimester, as well as with preterm birth <37 weeks (P = 0.001).

Copyright © 2014, American Association for the Advancement of Science.

K. Aagaard, J. Ma, K. M. Antony, R. Ganu, J. Petrosino, J. Versalovic, The Placenta Harbors a Unique Microbiome.
Sci. Transl. Med. 6, 237ra65 (2014).

To try to understand where they came from the team then examined the placenta from 320 women after birth, taking tissue samples from deep in the placenta to minimise the risk of contamination. Not only did they find bacteria present but they included the gut bacteria essential for metabolising nutrients and vitamins. However when they checked the genetic profile of these bacteria the result was even more surprising. They most closely resembled the bacteria normally found in the mouth, not the vagina. The conclusion was obvious, if more than a little surprising - bacteria must have travelled from the mothers' mouths to the fetal intestines, yet the only route must be via the mother's blood to the placenta and then either into the amniotic fluid to be swallowed by the fetus, or via the fetal circulation into the developing gut.

The placenta has its own ecology and these were not the bacteria we were expecting. Most people would have expected it to be a vaginal flora.

James Kinross, colon surgeon,
Imperial College, London, UK

The team also found that some species of bacteria were more common in the placentae of women who had delivered before 37 weeks, i.e., prematurely, suggesting a link between bacteria and premature birth which ties in with other findings showing a link between gum disease in women premature births.

So, knowing how fond creationists are of my blog, here's a little something for them to ponder on, and explain if they can. Why would an intelligent, benevolent creator invent this idiotic mechanism to help animals with guts absorb essential nutrients and vitamins from their food in the first place when it could have designed an efficient gut and why did it come up with a mechanism for getting these bacteria into the guts of developing fetuses which entails the risk of premature births and babies being born with serious illnesses?

There is, of course, no problem in understanding this as an evolved system in which the benefits outweigh the risks and which 'favours' only those genes which result in more descendants. Our guts evolved in the presence of bacteria, some of which had a utility value in helping us absorb certain nutrients which in turn removed any pressure to evolve more complex solutions and so we became committed to that evolutionary pathway. Cooperative alliances between replicators, even replicators from different species, are absolutely what the selfish gene view of Darwinian evolution predicts.

I appreciate it can't be easy trying to force-fit these little pieces of scientific evidence into a primitive superstition, but never-the-less, I'd appreciate if it a creationist or two could try.

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Driving Ethical Evolution

I realise they are only doing it so they can bask in that nice warm glow of smug self-satisfaction but when Christians and Muslims pretend to be baffled by why Atheists don't go around raping and murdering people because we don't believe we are going to answer for our crimes to their imaginary friend, I wonder if they realise how ignorant they appear. Surely they only need to take a quick glance at reality to see it doesn't equate to their idiotic assertion, don't they? Here's an everyday example which refutes them entirely.

I have already blogged about this subject a few time (see Xeno's Religious Paradox, Religion: An Abdication of Moral Responsibility and Why Morality Evolved) and tried to make the point that, just like evolved related species, human cultures have broadly similar morals and ethics serving broadly similar purposes, yet differ in detail, just as you would expect of something that evolved over time, diversifying in response to local conditions to form varieties, subspecies and species.

This was brought home to me when I was driving in Naples, Italy over the last few days. If you've never driven there, it's something of an experience to put it mildly. Basically, the traffic is chaotic. The road-markings are absent or indistinct and are mostly ignored anyway as are speed limits, pedestrian crossings and red traffic lights by the first half dozen cars. People live in tenement blocks with no off-street parking, so roads are lined with parked cars - in fact, for the average visitor, parking is almost non-existent. This makes all but the widest roads barely wide enough for two cars to pass and yet slowing down seems to be regarded as something for softies. Driving is competitive, so you will be overtaken on either side if there is room, raced away from traffic lights, cut up on junctions, and nine out of ten cars will be battle-scarred. Our nearly new hire-car picked up its first scrape in a carpark in Sorrento. Luckily, I was fully insured otherwise I would have been 820 Euros out of pocket.

Horns are used frequently and yet headlights are rarely flashed. On the one occasion I flashed a car with a short flash, which in the UK unofficially means, "Go ahead, I'm giving way to you", I got a stare that would have turned a cockatrice to stone. And yet road-rage is rare, if my experience is anything to go by and the Neapolitans are generally actually considerate and helpful people, or so I found. It took me a couple of days to work out what was going on. and then it became much easier to drive. When in Naples, do as the Neapolitans do.

In Naples, you expect a car to pull out of a turning or to turn across your path because they assume you will give way to them. It's a social norm which is taken so much for granted that no one thinks anything of it. It's a bit like the old rule of the road you still see quite a lot in France where you give way to someone pulling out from the right. You are expected to push into a small gap or overtake either side if there is room. It isn't meant to be aggressive and it isn't taken as such. In the UK what could easily end up as a road-rage incident is the norm in Naples.

On the other hand, flashing your headlights in Naples is a big no-no. That's the equivalent of a rude stare and is assumed to be aggressive. In the UK, it's a sign of courtesy unless you give a long flash, or flash from behind, then it's aggressive. We all know this and take it for granted. Short flash to give way; long flash to get out of my way.

And we hardly ever sound a horn unless it's in anger. In Naples, a short toot simply means take care. Normally given when you want to warn of your presence - as a courtesy more than anything (in fact what it should mean in the UK according to the Highway Code, except that no-one uses it that way) and with much less of the aggressive connotations it has in the UK.

So, in two European countries, both predominantly Christian and both of which have had the motor car for about the same length of time, two very different cultures have developed so far as driving, sounding horns and flashing headlights are concerned. And these two different sets of ethics have evolved in less than a hundred years and mostly in the last fifty. One uses the horn extensively, assumes the right to cross another car's path and hardly ever flashes headlights because that shows aggression; the other flashed headlights as a courtesy, only normally sound the horn in aggression and crossing another car's path unless given permission to is a big insult which may well get an aggressive retaliation.

It's fair to assume that these have evolved as extensions of the human voice for a horn and a stare for headlights. Clearly, they must have had different nuances pre-motorcar to have acquired different meanings in the context of driving today. And then there is the assumed courtesy of giving way in Naples which is mostly absent in Britain although it's okay when permission has been given and permission often is given.

Nowhere in this evolution of driving ethics is there anything in the Bible that wasn't basic to all human cultures already - like the Golden Rule - and nowhere has religion contributed to their development, never to my knowledge has the Pope or the Archbishop of Canterbury ever expressed an opinion on the use of horns or headlights and there is no theological doctrine concerning giving way at a road junction, yet we have evolved ethics, and two very different sets of ethics in such a short space of time. We even take driving on the right or the left respectively as absolutely basic, right and proper and assume it's based on some sound reasoning or other.

And I could probably write a similar comparison for every country I have driven in in Europe and North America.

How do the sanctimonious religious bigots who like to pretend to occupy the moral high-ground and the creationists who claim not to be able to understand why anyone would be good without threats and rewards explain this? How does this equate to the Craigite claim that morality couldn't have come from nowhere, in a thinly disguised plagiarism of the Intelligent Design frauds who claim life couldn't have evolved? For a biologist or sociologists who understands the evolutionary memetic nature of human ethics, there is no difficulty in explaining it, though the exact cultural origins of it and the forces which caused it to evolve would be a fascinating subject for a doctoral thesis.

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Obscenities Of Sorrento - Church of St. Anthony

Interior of the Basilica di Sant'Antonino, Sorrento, Italy

Tucked away in a small piazza alongside a busy road through beautiful Sorrento at the end of the Sorrentine Peninsula, south of Naples, Italy, you can find the Basilica di Sant'Antonino or the Church of St. Anthony. The inside is a tribute to the skilled craftspeople who made the marble inlay, much of it looted from surrounding villas of the Roman Imperial era, and the wooden marquetry which is used to decorate the 'Stations of the Cross' all round the walls and other features throughout the church.

And central to it all is that hideous depiction of a blood sacrifice of an innocent person that is somehow supposed to have given everyone who believes it absolution for something they didn't do either, turning the whole thing into a shrine to morbidly paranoid theophobia.

All along the sides of the main body of the church are shrines to various saints together with the traditional candles of various sizes and prices, and the money box for superstitious people to put their money in, apparently in the belief that if you give the church some money and light a candle, the saint will smile favourably on you and ask God to grant your wishes. Apparently, the smoke from the candle carries your thoughts up to Heaven where they don't seem to have invented emails, faxes or Facebook pages yet, and although they can apparently read your thoughts, they need them confirmed by candle smoke.

Intelligent Design - Even Intelligent Pigeons Refute It

Bird brainiacs: The genius of pigeons - life - 04 May 2014 - New Scientist

More evidence emerged earlier this month that humans are far from unique in certain attributes that creationists like to present as uniquely human, God-given attributes such as intelligence, self-awareness, consciousness and inductive reasoning ability. Not only do we know that several apes and monkeys have these abilities but now feral pigeon, Columba livia, can be added to the list.

Feral or town pigeons are the descendants of pigeons which were first domesticated by Man about 5000 years ago from wild rock doves, which tend to inhabit rocky areas. The wild rock dove is now quite rare in many parts of its range. In the UK it is now restricted to north and West Scotland, some offshore islands and the coast of Northern Ireland. I have only ever seen two pairs; one in Oman, almost certainly the C. l. palaestinae subspecies, and one in the Tunisian Atlas Mountains. The feral form has adapted to living alongside humans for which it needed to be both flexible and opportunistic, both implying intelligence and the ability to learn. Similar attributes can be seen in rats, dogs and cats, for example. The variations in colour and markings to be seen in the feral form are almost certainly the result of human selective breeding.

Of course, ever since the famous psychologist B.F.Skinner showed with his operant conditioning experiments, we have known that pigeons will develop religion when 'rewards' become dissociated from actions. Like religious humans, operantly conditioned pigeons perform rituals apparently in the belief that they influence the outcome of what is actually a randomised and unpredictable system, just as humans sing, say prayers and adopt ritual body postures thinking they are influencing the future.

Now it seems that this is due to a limited form of simple reasoning ability which probably includes both self-awareness and the ability to 'philosophise', i.e to think about thinking and to be aware of their own knowledge - I'm talking about pigeons here, not religious humans, by the way.

For example, Mike Columbo of Otago University, New Zealand, has shown the pigeons can memorise more than 100 images and recall them more than two years later. He also showed that they can handle numbers and subtle relationships between them. For example, pigeons trained to peck at a series of images of ascending numbers of object, when given a series of images with larger numbers of objects up to nine, still pecked them in ascending order.

They can also apply deductive reasoning logic such as working out that if person B is taller than person A and person C is taller than person B then person C is taller than person A. They can do this with up to five people. This was a logic puzzle upon which Aristotle mused.

Some researchers have also shown that they can recognise the style of different artists and distinguish a Monet from a Picasso. They can also distinguish between major styles of art such as cubism and impressionism.

In another experiment, pigeons were fed by two very similar people in terms of skin and hair colour, height and age but wearing different coloured coats. One person simply fed them whilst the other chased them. The pigeons quickly learned to tell the 'hostile' person from the neutral one. They even recognised the right person when they swapped coats.

Abstract
Considered as plague in many cities, pigeons in urban areas live close to human activities and exploit this proximity to find food which is often directly delivered by people. In this study, we explored the capacity of feral pigeons to take advantage of this human-based food resource and discriminate between friendly and hostile people. Our study was conducted in an urban park. Pigeons were fed by two experimenters of approximately the same age and skin colour but wearing coats of different colours. During the training sessions, the two human feeders displayed different attitudes: one of the feeders was neutral and the second was hostile and chased away the pigeons. During the two test phases subsequent to the training phase, both feeders became neutral. Two experiments were conducted, one with one male and one female feeder and the second with two female feeders. In both experiments, the pigeons learned to quickly (six to nine sessions) discriminate between the feeders and maintained this discrimination during the test phases. The pigeons avoided the hostile feeder even when the two feeders exchanged their coats, suggesting that they used stable individual characteristics to differentiate between the experimenter feeders. Thus, pigeons are able to learn quickly from their interactions with human feeders and use this knowledge to maximize the profitability of the urban environment. This study provides the first experimental evidence in feral pigeons for this level of human discrimination.
© Springer-Verlag 2011

Belguermi A, Bovet D, Pascal A, Prévot-Julliard AC, Saint Jalme M, Rat-Fischer L, Leboucher G.;
Pigeons discriminate between human feeders.;
Anim Cogn. 2011 Nov;14(6):909-14. doi: 10.1007/s10071-011-0420-7. Epub 2011 Jun 7.

Other experiments have shown that pigeons can plan ahead, are aware of their own knowledge, and can recognise themselves in a video.

Abstract
The ability to recognize self has been known to be limited to some animal species, but previous research has focused almost exclusively on the animal's reaction to a mirror. Recent studies suggest that the temporal contingency between a subject's action and the corresponding visual scene reflected in a mirror plays an important role in self-recognition. To assess the roles of visual-proprioceptive contiguity in self-recognition, we explored whether pigeons are able to discriminate videos of themselves with various temporal properties. We trained five pigeons to respond to live video images of themselves (live self-movies) and not to video filmed during previous training sessions (pre-recorded self-movies). Pigeons learned to peck trial-unique live self-movies more frequently than pre-recorded self-movies. We conducted two generalization tests after pigeons learned to discriminate between the two conditions. First, discrimination acquired during training sessions was transferred to a test session involving live self-movies and new pre-recorded self-movies. Second, the same pigeons were tested in extinction procedure using delayed live self-movies and new pre-recorded self-movies. Although pigeons responded to delayed presentations of live self-movies more frequently than to new pre-recorded self-movies, the relative response rate to delayed presentation of live self-movies gradually decreased as the temporal discrepancy between pigeons' own behavior and the corresponding video increased. These results indicate that pigeons' discrimination of self-movies with various temporal properties was based on the temporal contiguity between their behavior and its visual feedback. The methodology used in the present experiment is an important step toward improving the experimental analysis of self-recognition in non-human animals.

Toda K, Watanabe S.;
Discrimination of moving video images of self by pigeons (Columba livia);
Anim Cogn. 2008 Oct;11(4):699-705. doi: 10.1007/s10071-008-0161-4. Epub 2008 Jun 3.

The interesting thing is that bird intelligence, which has also been demonstrated in the crow and parrot families, seems to have evolved independently from mammalian intelligence and involves different parts of the brain, although the neurons involved seem to be very similar, as though there is only the one solution to the 'problem' of evolving intelligence at the cell level. Nevertheless, and to further embarrass the proponents of the intelligent design hoax, nature appears to have 'invented the wheel' at least twice so far as evolving intelligence is concerned.

It would be interesting to see how cephalopods (octopuses and squids) fare in intelligence tests and how that has evolved, because, with their known to be intelligent behaviour and ability to plan and their very different nervous systems, one thing we can be sure about is that nature has invented the wheel yet again with these molluscs.

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Putting Two And Two Together

I was struck by a simple example both of how structure can emerge from chaos and completely without any design or intent, and how science can make logical but always provisional deductions from the known facts and observations. This was provided by something I noticed on a visit to Pompeii the other day. I was also struck by how scientific observation differs radically from theology in it's ability to work from the known to the unknown and so for the unknown to become the known.

For those who haven't heard of Pompeii, or believe he was a Roman Emperor, Pompeii was a major Roman town situated a few miles south of modern Naples and probably had it's origins as a pre-Roman Greek settlement just as Naples does. Together with the nearby town of Herculaneum it was destroyed by an eruption of the volcano Vesuvius in 79 CE, having already been damaged by an earthquake related to Vesuvius's seismic activity in 63 CE. The entire settlement was covered in hot volcanic ash from a plume which extended down Italy to beyond Amalfi in the south. People were suffocated and died where they slept as can be seen from the casts of their bodies found when the city was excavated.

Almost every street junction, and at regular intervals in almost every street there are these raised flat-topped oval stones standing up above the street paving and more or less level with the walkways either side. Narrower streets have sometimes two, usually three blocks while the wider ones might have four. Between these blocks can often be seen deep grooves in the paving usually becoming less distinct the farther up or down the street they are from the blocks.

Okay, so what can we reasonably deduce from these blocks and their position and frequency?

Well, their position, their distance apart - just about a single pace - and the fact that they have flat tops is almost certainly because they were stepping stones on which to cross the street. Why would they have needed stepping stones to cross a street on? Quite obviously because they didn't want to step onto the street itself.

So, conclusion number one is that the actual streets of Pompeii were not the sort of places one would want to walk in. In fact, the streets were not only the city's drains, they were also not very frequently cleaned and probably relied on heavy rains to keep them from filling up altogether. The only non-human source of power with which to move bulk quantities of goods around would have been horse and donkey power. The roads were not just the city's sewers they were also full of horse excrement. This we can provisionally deduce from the fact that they needed stepping stones to cross the street on.

Now, what does this have to do with the other thing that struck me - emergence of structures from chaos and without planning or intent?

Look again at those groves. They have been made by generations of wheeled carts going between the stepping stones and all being forced to take almost exactly the same path between the blocks. No one need have planned to have those groves there; they were produced by the chaos of the paths of thousands of carts over the centuries being forced to channel into a single grove by the presence of the stepping stones which were necessary at least partly because the carts were being drawn along the streets by horses. And, as the grooves got deeper so they would have kept the wheels in line longer and so would have tended to lengthen over time.

And now we can deduce a few more things here: the carts were very probably iron-rimmed or the wood they were made from would hardly have marked the black volcanic basalt the paving is made from, so they were Iron-Age people with an economy sufficient to support iron smelters, or to buy it from those who could. They also had specialist cartwrights and wheel-rights and needed to move goods around in bulk, so they probably had trade and traders and people with money to spend, so they had paid labour and professionals who were paid for their specialist services.

It's also very probably that the horses were shod with iron shoes to work on the hard basalt streets, which means blacksmiths and farriers.

That now begs an interesting question that doesn't have a ready answer but we can reasonably narrow it down to three possible answers, some more realistic than others. Look again at the groves. How would a cart drawn by a single horse negotiate these blocks? Did the horse pass between two of the blocks before moving across to bring the cart into line? Did it step up onto the block and down the other side to keep the cart in line - if so one would expect to see signs of wear on that block? Or were there two horses?

And there are a couple of things we can deduce now about the political organisation. To make this system work at all there would need to be an accepted standard wheel guage and minimum wheel size so the carts could always negotiate the blocks without becoming stuck. They need to be able to fit between the blocks and the axle needs to clear them and this suggests city authorities able to impose this standardisation on both cart and street design. Once this system had become established, it would be impossible to change it without major disruption, so, just like an evolving organism, Pompeii would have been stuck with a system which, good, bad or indifferent for future needs, could only change within very small limits without causing major disruption.

So there we have it. Using deductive logic based on scientific observation, we can deduce a great deal about the political, economic and social conditions of Pompeii, all from the incidence of a pattern of grooves worn in the streets and how they came to emerge from chaos with no design or intent at any point.

Of course, all this is provisional and contingent upon finding solid confirmatory evidence so we can never say we have proved it, only that it looks very possible, even highly likely.

This of course is not possible with theology where the conclusions are already in place and are sacred. No evidence or deductive logic can have any impact on what is 'known' with absolute certainty, despite their being no evidence at all for it. And so creationists keep telling us that order can come from chaos and that all structure must have been consciously designed for a purpose. Ironically, this keeps their understanding of the Universe where it was in the Bronze-Age when Pompeii was a small village, if it was there at all.

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So What Did The Neanderthals Ever Do For Us?

Left: Neanderthal. Right: Modern.

Did Europeans Get Fat From Neandertals? | Science/AAAS | News

More astonishing news from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, where Svante Pääbo's team are continuing to analyse the Neanderthal genome from a specimen found in Denisova cave the Altai Mountains of Siberia and make comparisons with the genomes of different human groups and related anthropoid apes.

Working with partners in the CAS-MPG (Chinese Academy of Sciences (CAS) and German Max Planck Society(MPG)) Partner Institute for Computational Biology in Shanghai, China researchers have now found that not only do present-day European and Asian populations differ in their brain structure so far as their lipid content is concerned, but that the difference is very probably due to the occassional interbreeding between early modern humans and Neaderthals, probably on very few occassions somewhere in the Middle East.

Comparison of the Neanderthal genes found in the genomes of eleven different human groups from Europe, Asia and Africa revealed, not surprisingly since the interbreeding between Homo sapiens and Homo neanderthalensis occurred after the Euro-Asian H. sapiens left Africa, no Neanderthal genes were found in the African groups. However, the Europeans were found to have three times the number of genes involved in lipid catabolism than did Asians.

Abstract
Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.

Ekaterina E. et al; Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans
Nature Communications 5, Article number: 3584 doi:10.1038/ncomms4584

We think it’s a very strong effect with very profound physiological changes

Philipp Khaitovich
CAS-MPG Partner Institute for Computational Biology

So, the team then turned to looking for evidence of differences in fat catabolism in fourteen adult humans from Europe, Asia and Africa as well as 14 chimpanzees. Because of its ready availability in a tissue bank they looked first at brain tissue and found that Europeans have distinct differences in the concentrations of certain lipids in their brain tissues and in enzymes associated with lipid catabolism. The assumption is that this is related to the higher incidence of Neanderthal genes for lipid metabolism found in these European groups. None of these lipids or enzymes were found in chimpanzee brain tissue, suggesting that the mutations arose after the split between Pan and Homo.

Clearly much more has to be done on the functionality of this, but it’s tempting to think it’s linked with some of the differences in sugar metabolism that have been picked up already. Neandertals might have had adaptations to get through the stress of northern winters that moderns could pick up through introgression.

Chris Stringer, Paleoanthropologist,
Natural History Museum, London

The thinking is that the ability to rapidly metabolise fats may have been an adaptive trait Neanderthals evolved during their long spell in the colder Euro-Asian norther climate, enabling them to use fats as an efficient energy store. So, the out-of-Africa European H. sapiens effectively took a shortcut to evolution by interbreeding with neanderthals who has already done the evolutionary spade work, and this enabled them to spread quickly into the colder northern zones.

So, it seems that we Europeans owe an enormous debt of gratitude to our Neanderthal ancestors and we are only just beginning to find out what. They paved the way for us to leave our African cradle and to spread out across the world without taking the 250,000 they had needed to evolve the genes they passed on to us.

I wonder how the creationists manage to shoehorn these emerging facts of our evolutionary story, and the evidence of co-existence of two, three, possibly four distinct species of Homo, able to interbreed at least in parts of our range like a typical ring-species stage in a diverging, evolving population. How can these facts be made to fit into a mythical special creation just a few thousand years ago of a fully evolved single human species?

Any creationist with the courage to try for a rational answer is more than welcome to do so in the comments section below.

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Creationism - Spreading the Poison

Skeleton of Columbian mammoth, Mammuthus columbi
George C. Page Museum, La Brea Tar Pits, Los Angeles, California

I don't usually comment on American politics unless it serves to illustrate the depths which Christian fundamentalist are plumbing in their increasingly frantic attempts to discredit science as the rapid growth in Atheism and non-belief continues.

A couple of examples reared their ugly little head in South Carolina recently.

The first one all started with a proposal by 8 year-old Olivia McConnell that the state adopt the Columbian mammoth as the official state fossil (no! seriously!). All well and good, you might think, and a nice little gesture to an 8 year-old, a nice acknowledgement of the Columbian mammoths claim to fame as the first vertebrate fossil to be found in North America, and just a bit of fun that no-one could object to.

But, in the USA, the mention of fossils triggers a knee-jerk response by the creationist lobby desperate to make sure people don't get the right idea about evolution, and elevates whatever it is to the point of high principle, complete with bible-waving, threats of hellfire and hysterical shrieking about religious freedoms. Step forward the loon's champion, Rep. Robert L. Ridgeway, III to strike a blow for Jesus and the Bible and, hopefully completely unnoticed, against the secular US Constitution.

Ridgeway proposes amendment 1-1-712A to the effect that, instead of simply being referred to in official documents as 'The Columbian Mammoth' must always be referred to as "'Columbian Mammoth', which was created on the Sixth Day with the other beasts of the field.".

A BILLTO AMEND ARTICLE 9, CHAPTER 1, TITLE 1 OF THE 1976 CODE, RELATING TO STATE EMBLEMS, BY ADDING SECTION 1-1-712A, SO AS TO DESIGNATE THE COLUMBIAN MAMMOTH AS THE OFFICIAL STATE FOSSIL.

Amend Title To Conform

Whereas, giant mammoths used to roam South Carolina; and

Whereas, scientists have identified the fossils of about six hundred and fifty species of vertebrates in South Carolina to date; and

Whereas, it has been recognized that fossilized mammoth teeth were discovered in a swamp in South Carolina in 1725; and

Whereas, this discovery has been credited as the first scientific identification of a North American vertebrate fossil. Now, therefore,

Be it enacted by the General Assembly of the State of South Carolina:

SECTION 1. Article 9, Chapter 1, Title 1 of the 1976 Code is amended by adding:

"Section 1-1-712A. The Columbian Mammoth, which was created on the Sixth Day with the other beasts of the field, is designated as the official State Fossil of South Carolina and must be officially referred to as the 'Columbian Mammoth', which was created on the Sixth Day with the other beasts of the field."

SECTION 2. Subsequent to this act's effective date there is a moratorium on the enactment of legislation establishing official state symbols and emblems until such time as the General Assembly directly by legislative enactment removes this moratorium.

SECTION 3. This act takes effect upon approval by the Governor.

H 4482 Session 120 (2013-2014)

After due consideration by the Judiciary Committee, who had no objections, the amendment was carried without dissent by the House. Patriotic South Carolinians might like to consider the fact that not a single elected Representative saw any problem with every official reference to the State Fossil containing a piece of blatant propaganda, paid for by the South Carolinian taxpayers, for a religious view despite the Establishment Clause in the US Constitution. And nor did the Judiciary Committee! However, at least a majority of the Senate defended the Constitution and refused to concur by a vote of 72:30 and knocked it back to the House. The future of Ridgways' amendment now rests with a joint House-Senate committee on which the pro-loon House has a majority.

We wait with baited breath on the outcome of this important point of principle for those who want to ensure people get a misleading view of evolutionary biology and the history of Earth, even if it means breaking the law.

Meanwhile the loons are mounting a vigorous campaign to ensure the children in South Carolina's public schools are not taught the truth about evolution. The battle has crystallised around Section B-5.1 in the Biology curiculum for Fourth Grade students in the state's new draft science-teaching standards. It has the temerity to mention evolution and in particular natural selection and its key role in understanding biological diversity. This was guaranteed to send the loons into a mouth-frothed frenzy, so introduction of the curriculum has had to be delayed while while right to deny knowledge to children is debated.

If they succeed it should ensure that any South Carolina children who want to go on to a higher education in any biology-related subject will be educationally substandard and bound to struggle. Given the power of the fundamentalist loon lobby in South Carolina who consider the sacrifice of their children's future as something worth fighting for and just what Jesus would want, it's anyone's guess whether the ultra-patriotic, flag-draped Christian right are going to get away with another little subversion of the despised US Constitution.

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Stone Age DNA Refutes Another Bible Myth

Stone Age DNA shows hunter-gatherers shunned farming - life - 24 April 2014 - New Scientist

Some fascinating data emerged recently which is causing us to re-think a basic assumption about the early history of modern humans and how major changes in technology and political organisation spread. It should also cause creationists to reassess their creation myth if only that were permitted.

It had been assumed that agriculture spread from it's origins somewhere in modern southern Iraq because the idea was obviously so good that it was adopted by neighbouring peoples. In other words, the spread was assumed to be the spread of agricultural cultural rather than a spread of agricultural people.

Now a detailed study of the genomes sequenced from a small number of skeletons of early Stone Age people from Sweden has shown that hunter-gatherers were more genetically distinct from those of early Stone Age farmers from the same area than modern Scandinavians are from Italians. If the spread of agriculture had been cultural we would expect to see no significant difference. The study was conducted on the genomes of four skeletons from Stone Age farming settlements and seven coastal hunter-gatherer communities. Earlier isotope studies on the bones had show distinct differences in diet. It thus seems highly likely that it wasn't so much the idea of agriculture which radiated out from the Middle East, but agricultural people, who replaced the local hunter-gatherers.

So, what we have here is another little conundrum for our creationists friends.

Of course, as you might expect, it's hard to map reality onto their favourite creation myth if only because they don't appear to have allowed for a hunter-gather phase at all. This was very probably because the myth originated in people who were unaware of a hunter-gatherer past so saw no need to mention it, but let's overlook that little problem because, as we will see, there are some much bigger ones for them to worry about.

According to the creation myth, the small number of people who survived the Great Genocide Event when their god drowned everyone in a fit of pique because it loved them (work with me on this one!) must have been agriculturalists because they had already mastered the art of building huge, ocean-going liners and could travel the world collecting up all the different species from distant lands.

Then, within no more than six generations when a population of 50-60,000 would have been going some, were able to have a dedicated workforce concentrating on building a tower so high it could reach above the stars and so began to alarm God himself. This could only have been done with a vast agricultural support system to provide the builders and those producing the building materials with enough food and other necessities like clothes and tools without growing it or making them themselves.

This is simple, basic economics, stemming from the simple fact that the same person can't be both building a massive tower and tending to his garden, making things or foraging for food in the surrounding countryside. So, we know the Ark survivors were, or were certainly very soon and within six generations, fantastically productive agriculturalists. (Remember we are still in the creationist fantasy here, not the real world. Any resemblance to reality is purely incidental).

Now, as Pontus Skoglund of Uppsala University in Sweden and his colleagues have shown, a population of hunter-gatherers came from somewhere and spread from the Middle East into Scandinavia in advance of the agriculturalists and they were genetically very distinct from the agriculturalists who followed them. Taken in isolation, this study probably wouldn't mean much and could be explained away as sampling error. However, this is not the first study to reach this conclusion - similar results have been found in Germany and elsewhere.

Abstract
Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains contentious. Population-genomic data from eleven Scandinavian Stone-Age human remains suggest that hunter-gatherers had lower genetic diversity than farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone-Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone-Age foraging groups were historically in low numbers, likely due to oscillating living conditions or restricted carrying-capacity, and that they were partially incorporated into expanding farming groups.

Skoglund, P., et al; Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers
Science 24 April 2014. DOI: 10.1126/science.1253448

The question then is where did these hunter-gatherers come from, and hunter-gatherers moreover that were from a very different genetic line to the agriculturalists who, presumably, were the descendant of Noah and his family? How did this genetic diversity arise so quickly, what with evolution being impossible and no new information being able to arise because it's forbidden by the Second Law of Thermodynamics or Information Theory, or whatever the currently fashionable creationist reason for declaring it impossible is?

Or, if impossible evolution occurred at the warp speed normally offered up to explain this apparent rapid genetic diversity in post-Flood living things, why do we see no transitional forms with genomes intermediate between that of the hunter-gatherers and the subsequent agriculturalists?

And, if we forget for a moment that the Ark survivors must have been agriculturalists already and say some of them must have given rise to the hunter-gatherers while others went of to discover agriculture, there wouldn't have been enough agriculturalists to even consider building that enormous tower, because we would be looking at a local population of a mere few thousand at the most, not nearly enough even to do the building, let alone to sustain an economy capable of supporting such a huge economically non-productive workforce.

I wonder how many creationist can solve this conundrum and how many of those who can't will accept that this little bit of science utterly refutes their biblical creation myth. Anyone prepared to bet that the answers to both these will be as close to zero as makes no difference?

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Abiogenesis - Metabolism Without Cells.

Creationism - for when you want to pretend to be an expert on
something you don't understand

Spark of life: Metabolism appears in lab without cells - life - 25 April 2014 - New Scientist

"Metabolic processes that underpin life on Earth have arisen spontaneously outside of cells" - words that must strike dread in the minds of any creationist fraud who depends on suckering scientifically illiterate people for a living. But those are to opening words in the above article in New Scientist.

A team from Cambridge University, supervised by Markus Ralser, has stumbled almost by accident on the startling fact that several of the basic metabolic pathways common to all living cells, and on which living things depend, can be produced spontaneously and entirely naturally.

Most models for the origin of living systems include RNA entering the scene very early on, if not right at the start of it, because RNA is the basic information store which passes information on to the next generation. RNA is important in the evolution of living things because it can self-replicate as well as catalyse organic reactions. It is normally accepted that the basic metabolic pathways are too complex to have arisen spontaneously but they are assumed to have evolved early in the history of life on Earth. These models require the earliest living things to be RNA-based so that the enzymes catalysts needed could be produced.

People have said that these pathways look so complex they couldn't form by environmental chemistry alone... If you look at many different organisms from around the world, this network of reactions always looks very similar, suggesting that it must have come into place very early on in evolution, but no one knew precisely when or how.

Markus Ralser, Cambridge University, UK,
Quoted in News Scientist, 25 April 2014

Now it seems these basic metabolic pathways could have simply been co-opted and incorporated by primitive proto-cells and could pre-date the evolution of RNA or even have led to it by producing RNA precursor molecules.

The process was discovered when a student used a mass spectrometer to quality-check unused cell-culture medium and noticed a signal for puruvate - one of the products pf glycolysis, so they tried to replicate the production of it using a water solution believed to be like the oxygen-free oceans on Earth before the evolution of photosynthesis. They have reported their findings in Molecular Systems Biology.

Abstract
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose‐5‐phosphate and the amino acid precursor erythrose‐4‐phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron‐rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.

Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
Markus A Keller, Alexandra V Turchyn, Markus Ralser; DOI: 10.1002/msb.20145228 |Published 25.04.2014

One significant finding is that this process can produce ribose 5-phosphate, which is a precursor of RNA so it raises the possibility that RNA evolved later.

This research isn't conclusive, of course - there is still the problem of where the precursor sugars came from, for example. In living things nowadays, since the evolution of photosynthesis probably by cyanobacteria, sugars come from ingested food unless you are fortunate enough to be either a cyanobacterium or a green plant which has incorporated cyanobacteria in their cells as chloroplasts. But, as Ralser points out, every chemical reaction is, in principle, reversible. So, in theory, they should be capable of building sugars as well as reducing them.

Most worryingly for creationists, of course, is that once again science has closed a little gap and found that there was no magic needed and no god making things work.

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Growing Up And Losing Faith

I was asked recently if I could explain the process I went through as I became an Atheist, as this might help others going through the same process. Apart from not being sure I have anything much to offer people in this respect because I was very young at the time, this is actually quite difficult for me for another reason.

Rather like a reverse of the parody version of evolution which creationists are taught to attack, where evolution is absurdly presented as a sudden event so that even a child will think it's silly, instead of the gradual process spread over time where one thing leads inevitably to another and several things can happen concurrently, my deconversion was a sudden event, or so it seemed at the time, not a slow, accumulative process, as it seems to have been with many others. But maybe this is because, being very young at the time, I hadn't really realised some sort of process was going on in my mind. So far as I was concerned, one minute I believed in the traditional Christian god, gentle Jesus, meek and mild, the Virgin Mary, wise men, shepherds, and the souls of dead babies riding up to Heaven on sunbeams, and the next, I didn't believe a word of it.

I have related this before in The Light Of Reason so I'll just briefly run through it again then look at what a few other well-known atheists have said on the subject.

Manny's Hysteria Explained

I've just found out the reason the expelled seminarian and failed wannabee Catholic priest and habitual Internet abuser from Bronx, NY, Manuel de Dios Agosto, has been spamming my blog with almost daily abuse, threats and delusions of grandeur again, after a lull of several months. It's all because someone has set up a tribute account to me on Twitter specifically to tweet links to my blogs. I understand the account is @R0saRub1c0nd10r. Makes me feel quite proud and more than a little humbled that my blogs were so appreciated by so many people.

Of course I was aware that a supporter and Twitter friend was thinking of setting up this account because, out of common courtesy, he/she (I only know them by their Twitter name) had asked my permission to use my name. What I hadn't realised was how much interest there was in this account although I had noticed a 25% or so increase in page hits. I'm extremely touched and flattered that so many people would like to see me back on Twitter and miss my blog links. I don't have any reason to go on Twitter much theses days so I hadn't realised quite how many supporters were still, after more than six month's absence, calling for my account to be reinstated and including me in #FF lists. I was obviously doing something right ☺.

All I can say on the subject of my return to Twitter is that I don't seem to be able to get past the wall of 'customer support' at Twitter and no one there is willing to give me any reason for my account's suspension other than in the most vague, general terms like 'in breach of the rules'. Despite several requests for specific examples of offending tweets and an explanation of which rule they breached, none has been forthcoming. They either go ignored or, on one occasion, the bizarre excuse was that it would be a breach of privacy to tell me the real reason. Read into that what you will, but I've no intention of creating other accounts only to have them suspended, presumably for the same reason Twitter won't admit to. It seems no one at Twitter Support is allowed to give out the name and contact details of anyone who has the authority to reverse a decision, or maybe they just don't want them knowing what's going on below decks.

Anyway, it seems that the success of this tribute account has sent Manuel off on another one so I am daily having to delete comments on various blogs such as the following selection:

I get a good laugh reading these posts. You really have no clue who I am do you? In any case, I am capitalizing off your paranoia because you are promoting my brand "sacerdotus." Thanks! However, I hate to see when you are taken to court for libel by this kid you're defaming and who you think is me. I can definitely prove I am not him, but your hysteria is indeed profitable for my cause. Thanks again Rosie for promoting me with your paranoia and obsessive compulsive disorder. #won! #noliesrequire #oxfam lol! :-)

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#WON I bet you got many goosebumps when you got suspended by me again. :) #LOL #WON :)

Since 2010, 7000 followers all gone.. #LOL #WON You wanted to be prideful and fell hard from your high horse. Rubicondior is not the end. We will continue shutting your nonsense down, so don't get used to twitter or blogger. :) #WON #TeamSacerdotus

As we can see from the last of these Manuel appears to have developed multiple personality disorder and imagines he's running Twitter too, as though he hadn't got enough problems to cope with. He hasn't yet reached the volume of dozens a day that it reached last September, although they are no less insane.

Apparently he is now spamming Twitter with his @Atheism707 account asking people to file false complaints and spam reports againt @R0saRub1c0nd10r and a list of other accounts. No doubt these will be accounts who have either had the temerity to doubt Manuel's claims or who have already learned that Manny is behind this, as well as the @SCDTVS account. I wonder what view Twitter will take of this encouragement to others to abuse their clients with false reports. They generally take a dim view of those who create yet more accounts to get round their multiple suspensions for obscene, abusive and threatening accounts - a list of which can be seen here.

Should anyone wish to report Manuel's current accounts, Twitter's complaint form can be found here. You will need a specific example to begin with, then you need to reply to the email you'll received from Twitter Support. You can then send them further examples by replying to this email. This allows them to build up a dossier of complaints.

It might take several weeks before you get a final reply but don't be fobbed off if they tell you the account has been deleted or suspended. Check this out, as they often seem to use this as a quick way to avoid actually dealing with the abusive account. They have told me on three different occasions that another of Manuel's abusive accounts no longer exists or has been suspended before it had actually been suspended. And don't be fobbed off with the assurance that they have asked him to stop his abusive behaviour. Even if he stops it for a few days, he will start up again quite soon. Simply reply to the email telling them you are not satisfied with that response. This will keep the ticket open so you can update them with new abuse.

Anyway, many thanks to whoever is behind my tribute account and I hope that sheds some light on Manuels increasing bizarre behaviour. Now, back to the real purpose of this blog - explaining why religion is a malignant superstition which needs to be exposed and opposed (look at what it's done to Manny, for example), how science is continually closing the gaps in which religions try to sit their ever-shrinking little gods, how religion is used and excuse for otherwise unacceptable behaviour and the most grotesque of human atrocities against other human being, and how it exposes Bronze-Age creationism, the frauds who sell it to scientifically illiterate simpletons, and the fraudulent apologists who give credence to the extremists for money and political influence.

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Darwin's Wonderful Worms

Darwin's Medow, Down House, Downe, Kent

Own work

Darwin's Meadow, Down House, Downe, Kent, UK

I was stimulated recently by an interesting question from a creationist which a friend passed to me for comments. Even creationists can sometimes pose interesting questions which need several minutes to think about. The question was, why are dinosaur tracks often found on the surface when human artifacts are often several feet below the surface. If dinosaurs are millions of years old why aren't they found at much deeper levels that human artifacts?

Superficially, this looks like a problem for evolution, and if it were true for every location it would indeed be. It would actually be equivalent to providing the evidence which the great J.B.S.Haldane said would falsify evolution - a fossil rabbit in the Cambrian. Of course, it isn't true for dinosaur tracks. All those found have either been in quarries or on the surface of eroded rocks such as the dry bed of Paluxy Creek, Texas, USA. But, old fossils are found on the surface or just a few feet down, so although my friend's creationist friend was wrong about the dinosaur tracks, there is a general question to be answered here.

The answer of course is that the surface of the Earth is dynamic and subject to forces of change, like erosion or human activity like quarrying and animal activity. Additionally, and more importantly, how fossils get exposed and how human artifacts get burried are two different processes entirely. The site of the Paluxy dinosaur tracks (the subject of the famous hoax that still has creationists fooled) is the bed of the Paluxy Creek, which has eroded away the upper layers, exposing the limestone layer with the tracks on. The dinosaur tracks found in Worth Matravers in Dorset, UK were exposed by quarrying for building material.

Spare A Thought For Poor Old Judas

Judas Iscariot. Gabriel von Max. Prague National Gallery

As it's Easter and the time for good-will to all men... now don't start... just because it's not Christmas there's no reason to bear ill will, is there? Anyway, in this season of goodwill to all men, is it not time someone spoke up for poor Judas Iscariot - possibly the most maligned man in all literature.

You may recall that the character of Judas makes his appearance in the stories about Jesus in the Bible but only seems to play any significant part towards the end of the tale, when his role suddenly become absolutely critical to the plot, only to be maligned and vilified for playing his allotted role later on. Although, as we shall see, this maligning of Judas seems to be a much later addition to the story, added moreover by someone who hadn't been following the plot too closely. Not only that but the later addition seems to have become muddled too.

How American Muslims Silenced Ayaan Hirsi Ali

Ayaan Hirsi Ali

Ayaan Hirsi Ali: ‘They Simply Wanted Me to be Silenced’ | TIME.com

Brandeis University, Waltham, Mass., USA has caved in to pressure from Muslim students and rescinded its plan to honour Ayaan Hirsi Ali with a an honorary degree on 8 May.

If there is anyone who can be described a role model for Muslim girls who want to take control of their own lives, then it is Ayaan Hirsi Ali. A former muslim and member of the Dutch parliament from 2003 to 2008, she is an outspoken advocate for women's rights and a critic of Islam. Born in Somalia and raised as a strict Muslim, she survived a civil war, beatings, genital mutilation and a forced marriage before escaping to Holland and finally renouncing her faith in her 30s. She described the moment thus:

I looked in a mirror and said out loud, in Somali, "I don’t believe in God." I felt relief. There was no pain but a real clarity. The long process of seeing the flaws in my belief structure, and carefully tip-toeing around the frayed edges as parts of it were torn out piece by piece—all that was over. The ever-present prospect of Hellfire lifted, and my horizon seemed broader. God, Satan, angels: these were all figments of human imagination, mechanisms to impose the will of the powerful on the weak. From now on I could step firmly on the ground that was under my feet and navigate based on my own reason and self-respect. My moral compass was within myself, not in the pages of a sacred book.

A fuller account can be read here, in one of the most inspiring and powerful arguments for Atheism I have ever read.

Brandeis University was founded as a secular, co-educational establishment in 1948, soon after World War II and the Holocaust, when many US universities were racially, religiously and gender segregated. It had been assumed that Ali epitomised all that the University stood for, hence the honour. However, Muslim students raised a petition, pointing to a 2007 interview with Reason magazine in which she said of Islam:

Once it’s defeated, it can mutate into something peaceful. It’s very difficult to even talk about peace now. They’re not interested in peace. I think that we are at war with Islam. And there’s no middle ground in wars.

Brandeis University claimed to be unaware of this and decided it was not something they wished to be associated with and withdrew the offer of the honorary degree.

Ayaan Hirsi Ali has responded in typically measured and dignified style with:

Yesterday Brandeis University decided to withdraw an honorary degree they were to confer upon me next month during their Commencement exercises. I wish to dissociate myself from the university’s statement, which implies that I was in any way consulted about this decision. On the contrary, I was completely shocked when President Frederick Lawrence called me — just a few hours before issuing a public statement — to say that such a decision had been made.

When Brandeis approached me with the offer of an honorary degree, I accepted partly because of the institution’s distinguished history; it was founded in 1948, in the wake of World War II and the Holocaust, as a co-educational, nonsectarian university at a time when many American universities still imposed rigid admission quotas on Jewish students. I assumed that Brandeis intended to honor me for my work as a defender of the rights of women against abuses that are often religious in origin. For over a decade, I have spoken out against such practices as female genital mutilation, so-called "honor killings," and applications of Sharia Law that justify such forms of domestic abuse as wife beating or child beating. Part of my work has been to question the role of Islam in legitimizing such abhorrent practices. So I was not surprised when my usual critics, notably the Council of American-Islamic Relations (CAIR), protested against my being honored in this way.

What did surprise me was the behavior of Brandeis. Having spent many months planning for me to speak to its students at Commencement, the university yesterday announced that it could not "overlook certain of my past statements," which it had not previously been aware of. Yet my critics have long specialized in selective quotation — lines from interviews taken out of context — designed to misrepresent me and my work. It is scarcely credible that Brandeis did not know this when they initially offered me the degree.

What was initially intended as an honor has now devolved into a moment of shaming. Yet the slur on my reputation is not the worst aspect of this episode. More deplorable is that an institution set up on the basis of religious freedom should today so deeply betray its own founding principles. The "spirit of free expression" referred to in the Brandeis statement has been stifled here, as my critics have achieved their objective of preventing me from addressing the graduating Class of 2014. Neither Brandeis nor my critics knew or even inquired as to what I might say. They simply wanted me to be silenced. I regret that very much.

Not content with a public disavowal, Brandeis has invited me "to join us on campus in the future to engage in a dialogue about these important issues." Sadly, in words and deeds, the university has already spoken its piece. I have no wish to "engage" in such one-sided dialogue. I can only wish the Class of 2014 the best of luck — and hope that they will go forth to be better advocates for free expression and free thought than their alma mater.

I take this opportunity to thank all those who have supported me and my work on behalf of oppressed women and girls everywhere.

And so American Muslim girls in general, and Brandeis students in particular, have been deprived of the opportunity to hear one of the most inspiring advocates of the principles of secular, liberal freedoms and human rights that Brandeis University was founded on. They have been denied this by those to whom everything Ayaan Hirsi Ali stands for and represents is anathema - the right of women to control over their own bodies and their own destinies and the extension of full human rights and the right to respect and dignity to all members of society.

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The Internet Is Making Theists Think

Top: Internet use. Bottom: Religious affiliation

How the Internet Is Taking Away America’s Religion | MIT Technology Review

Americans are following many European countries in losing their faith. The change hasn't been so spectacular as in many European countries where Atheists/Agnostics are now in a clear majority, but the growth has been a steady 0.5 percent per year over the last 20 years, rising from just 8 percent in 1990 to 18 percent in 2010.

The obvious question is, why is this happening? There are many social and psychological factors involved in relative religiosity, not the least of which is income inequality with those in the lowest income groups and forming the lowest social strata tending to be more religious and more fundamentalist, while those in the higher social strata tend to be less religious and more moderate.

Vatican Backs Code of Silence Over Child Abuse

Pope Francis "We will not take one step back..."

Italy's bishops pass Vatican-backed rule that child molestation does not have to be reported - Europe - World - The Independent

In stark contrast to what Pope Frankie claims to be doing to clean up the Catholic Church, the Vatican has been complicit in a policy adopted by Italian Bishops that states they are no longer required to report child-abusing priests and nuns to the police.

The 'speed' with which Vatican reforms are progressing can be gaged from the fact that only in the last few months has the Vatican seen fit to strengthen its laws on abuse of minors to include sexual abuse of children. Astonishingly, this was not even considered an abuse of minors when the law was first drawn up.

[I] personally ask for forgiveness for the damage [some priests] have done for having sexually abused children. We will not take one step backward with regards to how we will deal with this problem, and the sanctions that must be imposed.

Pope Francis
(Statement made on day of Italian Bishops' Conference statement)

This legalistic excuse comes from a treaty between the Vatican and the Italian state in 1985 which stipulates that priests are not obliged to inform the police of crimes learned of through their ministry. The Italian Bishops' Conference, which published the guidelines last Friday, say they came from a suggestion by the Vatican's office that handles sex abuse allegations.

Last month Pope Francis had complained that, "No-one else has done more [to tackle child sexual abuse]. Yet the Church is the only one to have been attacked."

[the Vatican is systematically placing the] preservation of the reputation of the Church and the alleged offender over the protection of child victims.

UN Committee on the Rights of the Child,
5 February 2014

In 2010, to great publicity and in response to the growing world-wide outrage at these sexual and psychological abuses as more and more victims found the courage to be open about what they had suffered at the hands of predatory paedophile priests and nuns, the Vatican had instructed bishops to report these offences to the authorities - but only where required to do so by the local law. The Vatican has never seen it as the moral duty of Bishops to protect the vulnerable from predatory clerics by adopting a zero tolerance policy and reporting all such cases even when not required to do so by local law.

Now we see the Vatican office supposedly responsible for dealing with the problem, recommending a policy of strict legalism regardless of the fact that this gives a degree of protection to offenders and removes a little protection from the vulnerable. Obviously this offices sees it as dealing with the problem to prevent it being exposed.

The 'problem' is seen as one of embarrassment and damage to the Catholic Church, not damage to the victims of these abuses. The solution is a Mafioso-style code of silence or a 'no snitching' rule.

As reported on the BBC website, the long litany of Catholic Church abuse scandals includes:

• Germany - A priest, named only as Andreas L, admitted in 2012 to 280 counts of sexual abuse involving three boys over a decade.
• United States - Revelations about abuses in the 1990s by two Boston priests, Paul Shanley and John Geoghan, caused public outrage.
• Belgium - The bishop of Bruges, Roger Vangheluwe, resigned in April 2010 after admitting that he had sexually abused a boy for years.
• Italy - The Catholic Church in Italy admitted in 2010 that about 100 cases of paedophile priests had been reported over 10 years
• Ireland - A report in 2009 [The Cloyne Report] found that sexual and psychological abuse was "endemic" in Catholic-run industrial schools and orphanages for most of the 20th century.

BBC News - Pope Francis asks forgiveness for child abuse by clergy

These are the same people who claim to be guardians of our morals and who demand the right to be consulted on all legislation inasmuch as it related to a woman's rights to her own body, the rights men have over them, what consenting adults may or may not do in the privacy of their own bedrooms and who may form a legal relationship with whom.

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Fundamentalist Threat To EU Freedoms

Mamber states of the European Union

Pro-Life Citizens' Initiative Worries E.U. Scientists | Science/AAAS | News

In an astonishingly arrogant move, a small, highly organised and well-financed group of Christian fundamentalists, posing as a European citizen's initiative, is seeking to exploit and subvert the democratic process. In the EU a petition with over 1 million authentic signatures collected across at least eight member states must be considered by the European Commission (the legislative body of the EU) for possible legislation.

If the Commission agrees with this petition, embryo stem-cell research will be illegal, and something having its origins in primitive superstition will be mandatory on all 28 current, and all future EU member states. This is because Christians believe a magic entity called a 'soul' enters a zygote at conception and thus a cell, or small group of cells, which could not possibly have independent existence in that state, is a fully human individual with full human rights. No evidence of the 'soul' has ever been found.