No Bread of Heaven for Creationism

Fiendish wheat genome reveals grain's history : Nature News & Comment

It's been another bad week for the Intelligent Design industry. No wonder their secretive five year 'Wedge Strategy' is now well into it's sixteenth year, during which the number of non-believers in the USA has gone up from about 4% to about 20%, conservative Christianity has become the preserve of the white right fringe and court after court has thrown out their attempts to subvert the Constitution and smuggle fundamentalist Christian extremism into the US public school system disguised as science.

Clearing Up the Unintelligent Designer's Mistakes

Hamilton O. Smith. (Photo: Jane Gitschier ©PLoS Genetics)

I'm homing in on the genetic essence of life - opinion - 14 July 2014 - New Scientist

In an interview published in New Scientist a few days ago, 1978 Nobel Laureate and synthetic biologist Hamilton O. Smith said:

The other thing we want to know is... how much can we rearrange the genes? Evolution has sloppily put them together. A lot of the cell's processes are scattered around. We're putting them together into one neat form.

He was explaining how his synthetic and bioengineering group at the J. Craig Venter Institute in La Jolla, California, USA is using the genome of a bacterium Mycoplasma mycoides to investigate the minimum number of genes needed to function as a viable, living organism.

Their greatest challenge is to work out exactly what DNA is junk, i.e., which has been included over billions of years but which now doesn't serve any purpose. Hamilton Smith estimates that it only needs 400-450 genes to make an organism viable. The other task is to rearrange these genes more efficiently instead of being scattered around the genome in the haphazard and 'sloppy' way they are in M. mycoides.

Altruism and Tits

Long-tailed Tit (Aegithalos caudatus)

Browsing through my Royal Society for the Protection of Birds (RSPB) magazine, Nature's Home, just now I came across a reader's letter asking about something he had seen with nesting long-tailed tits recently. He had noticed that several adults were helping to feed the young in addition to the parents and wondered if this was normal.

It is. It is a lovely example of altruism in one of my favourite birds.

The so-called long-tailed tit - it's actually closer to the warbler family than the tits - is one of the UK's smallest bird. Were it not for it's long tail it would actually equal the size of our smallest two, the

A Message From 270 Million Years Ago

Amphibians' swim stroke has lasted 270 million years - life - 15 July 2014 - New Scientist

Fascinating pictures of 270 million year-old fossils tracks from the Alps were published today, sadly most of them behind a paywall. They show the tracks laid down, probably by a salamander, as it paddled across a shelving patch of mud from shallow into deeper water and eventually taking to swimming. This is the first recorded instance of the transition from walking to swimming.

Abstract
Exceptionally preserved Early Permian tetrapod trackways from the Orobic Basin (Central–Western Southern Alps) offer a unique opportunity to investigate in detail locomotion in fossil vertebrates that lived on continental European landmasses. Herein are reported the results of a study on several tetrapod trackways that display a large variety of behavioral, gait and substrate related extramorphologies. They clearly document the transition from terrestrial–underwater walking to swimming and are assigned to the compound ichnotaxon Batrachichnus C Lunichnium. The use of the “C” symbol is here introduced for the first time as nomenclatural indication of a Compound trace. Producers were probably small-sized temnospondyl

Christmas Tree Tease for Creationists

The Norway spruce genome sequence and conifer genome evolution : Nature : Nature Publishing Group

Here's a fascinating piece of research from Sweden which is enough to give any self-respecting creationist pseudo-scientists a split personality. It shows how and why a Norwegian spruce (Picea abies a Christmas tree) has a much more extensive and complex genome than humans. I'll get to why it's a problem for creationists in a moment. Incidentally, thanks to Helmer von Helvete, a friend from Google+, for bringing this to my attention.

Abstract
Conifers have dominated forests for more than 200 million years and are of huge ecological and

Catholic Church "Untrustworthy"

The Catholic Church in Germany is witnessing an astonishing collapse in public trust and is haemorrhaging members at an unprecedented rate.

According to a Forsa poll recently 65% of Germans said they found the Catholic Church untrustworthy.

This trend has been linked to the 'bling bishop' scandal in which Catholic Bishop Franz-Peter Tebartz-van Elst was found to have spent millions of euros of church money on his own private house. He later 'resigned'. Once again ordinary Catholics had to endure the embarrassment of yet another Catholic cleric abusing the power and trust his position gave him.

In Germany, a tax is levied on church members by the

Of Mice and Men and Evolution

Source: Iakes Ezkurdia, et. al., Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes^*

Size of the human genome reduced to 19,000 genes - ScienceDaily

Just how close to other mammals are we? The answer is much closer than most people think and of course far closer than creationists will admit and which more sensible religious people like to imagine.

A detailed study led by Alfonso Valencia, Vice-Director of Basic Research at the Centro Nacional de Investigaciones Oncologicas (National Cancer Research Centre - CNIO) in Spain, and published in the journal Human Molecular Genetic found that about 90 percent of protein-coding genes found in humans are common to the earliest metazoans (multicellular organisms), that 99 percent of them pre-dated the emergence of the primates 50 million years ago.

Germ Warfare in Brazil

Credit: Gleison Miranda/FUNAI/Survival

Uncontacted tribe in Brazil ends its isolation | Science/AAAS | News

News that a previously isolated Amazonian tribe has made voluntary contact with a group of Brazilian government scientists from (FUNAI) marks a departure from the Brazilian Department of Indian Affairs' 'no contact' policy but was deemed necessary in this case because there was a serious threat to the welfare of the tribe from other tribes in the ares, following reports of raids on crops and theft of tools.

The reason for the 'no contact' policy is because of the very real threat to isolated people from the viruses we often take for granted such as influenza, measles and mumps. Between 1983 and 1985 some 60% of the

More Trouble Down Under for Paedo-Protecting Pope

"We will not take one step backward with regards to how we will deal with this problem, and the sanctions that must be imposed. We have to be even stronger".

Pope Francis, 11 April 2014

In stark contrast to Pope Francis' public professions of sorrow and wheedling apologies for the Catholic Church's role in facilitating institutionalised sexual abuse of vulnerable children by it clergy, and his assurances that the Vatican will do everything to bring them to justice, the Vatican has declined to cooperate with an Australian Royal Commission set up to investigate abuses by Catholic priests in Australia.

As reported by Lindy Kerin for ABC News:

The head of the Royal Commission into Institutional Responses to Child Sexual Abuse, Justice Peter McClellan, revealed last month that he had

Human Evolution - Ringing The Changes In Tibet

Tibetans

Tibetan altitude gene came from extinct human species - life - 02 July 2014 - New Scientist

The evidence that archaic, diversifying human populations behaved like a ring species over Europe and Asia just keeps on accumulating.

A couple of years ago I blogged about how a research team led by Rasmus Nielsen of the University of California, Berkeley, USA found that Tibetans differ from the Han Chinese by about thirty genes and most of these genes control how the body responds to altitudes.

This was a case of very rapid human adaptive evolution over a period as short as 3-6,000 years during which the

Consciously Evicting God From Another Gap

Consciousness on-off switch discovered deep in brain - life - 02 July 2014 - New Scientist

One of the favourite arguments used by religious apologists is that somehow materialism can't explain conscious thought and that a 'random' [sic] process like evolution could only ever give rise to random thoughts and not rational arguments.

Of course, this argument is never revised to accommodate developments in science and in our understanding of neurophysiology and the microscopic structure of neurons, so it is identical in form whether used by C.S.Lewis, William Lane Craig or Ken Ham even though our understanding of the science has been transformed immeasurably in the intervening half century.

But then we need to remember that religious apologists are not seeking to make converts but to keep believers believing and thus to ensure their income stream is maintained and the arrogant claims they make to

Green River Exposes Layers of Creationist Lies

Green River Formation varves

One of my favourite creationist pseudo-scientists must be the psychologist with no qualifications in science or record of research in the subject, Dr. Paul D. Ackerman, who supplements his income from teaching psychology as an assistant professor at a minor university by writing bad science books and articles for creationists who also seem to have little knowledge or understanding of science. He ranks as one of my favourites becaiue he is so bad at it.

He is the notorious author of what must rank as one of the worst 'science' books for creationists ever published (it now has to be given away by the Institute for Creation Research) called It's A Young World After All: Exciting Evidence For Recent Creation. I've already dealt comprehensively with this book in a series of blogs so I won't dwell any more on it here, save to quote Dr Ackerman on what is one of the few nearly true things he said in his book:

Still Not Yeti!

Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates

Last October I reported on a tentative claim by geneticist Bryan Sykes of the Oxford-Lausanne Collateral Hominid Project that he might have solved the Yeti question, only the Yeti is a descendant of a Paleolithic bear known from a single jawbone from northern Norway. This bear is believed to be ancestral to both the polar bear and the brown bear. His claim was based on a comparison of mitochondrial DNA (mtDNA) from samples of hair claimed to have come from Yetis with those of known species held on the GenBank database, an international database of genetic information.

mtDNA is inherited in mammals from the female line only and, because it doesn't recombine during sexual reproduction, tends to be stable over time, mutating at a more or less constant rate. It thus makes an excellent means of tracing female line populations and evolutionary relationships. The biological significance of this find was not so much that it might have solved the Yeti question but that it might have revealed a living population of this Ice-Age bear in the Himalayas, where it might have taken refuge as the ice retreated.

Now Bryan Sykes has reported on a much more extensive investigation of mtDNA from hair samples of 'Yeti', 'Bigfoot', and

Told You So!

The thing about creationists is that they are nothing if not predictable.

What's the betting that, if someone hasn't already done so, one or more creationist frauds will be misrepresenting this discovery as the discovery of a vast ocean of liquid water, and proclaiming the craved-for scientific proof of the Noah's flood myth by explaining where all the water came from - the 'fountains of the deep', no less?

Rosa Rubicondior;
Massive Subterranean Ocean 15 June 2014

Right on cue, Step forward Brian Thomas of the Institute for Creation Research:

Ken Ham - Fraud or Fool?

It's always fun, if you have nothing better to do, than to go to a creationists site and play spot the fallacies. For example, this stunning example from Ken Ham's Answers in Genesis site.

Naturalism, Logic and Reality

Those arguing against creation may not even be conscious of their most basic presupposition, one which excludes God a priori, namely naturalism/materialism (everything came from matter, there is no supernatural, no prior creative intelligence)... The following two real-life examples highlight some problems with that assumption:

1. A young man approached me at a seminar and stated, "Well, I still believe in the big bang,

Chimps Have Fashions Too

A group-specific arbitrary tradition in chimpanzees (Pan troglodytes) - Online First - Springer

Ever since Richard Dawkins coined the term, 'meme' in The Selfish Gene we have known that cultures, like genomes, are passed on through the generations by replicators which can gradually change over time and which can be subject to selection pressures, just like genes and combinations of genes. The difference is that memes are inherited after birth and so, unlike genes, we can change them and chose which to accept and which to reject. We can also chose which to pass on and which to allow to be consigned to history.

Another Brilliant Idea By The Intelligent Designer

You can say one thing about The Intelligent Designer - it doesn't let liberal sentimentality, compassion or morality get in the way of a good idea. In fact, it's almost exactly like The Intelligent Designer doesn't have any emotions or compassion, nor any idea of right and wrong.

I'll take that back. There is no 'almost' about it. It's exactly like The Intelligent Designer doesn't have any emotions, compassion or sense of right and wrong. It's exactly like The Intelligent Designer doesn't have any intelligent plan or any real purpose for its designs either.

Fighting Back Against Evolution

Antibiotic resistance focus of UK’s Longitude Prize : Nature News Blog

Great news that, by popular vote, the £10 million ($17 million) Longitude Prize will be awarded to the group which comes up with "a cost-effective, accurate, rapid, and easy-to-use test for bacterial infections" within the next five years. The intention is to help target antibiotic use so reducing the rate at which bacteria are evolving resistance.

This comes close behind a stark WHO report which stated:

Antimicrobial resistance (AMR) within a wide range of infectious agents is a growing public health threat of broad concern to countries and multiple sectors. Increasingly, governments around the world are beginning to pay attention to a problem so serious that it threatens the achievements of modern medicine. A post-antibiotic era—in which common infections and minor injuries can kill—far from being an apocalyptic fantasy, is instead a very real possibility for the 21st century.

WHO ANTIMICROBIAL RESISTANCE
Global Report on Surveillance

The report went on to say:

Henrietta Lacks Soul

Theists have a problem with souls.

The problem is that they were invented in ignorant times when people knew nothing of the microscopic structure of the human body and very little about how it actually worked. It sort of made sense to think that there is another entity living inside our body giving it 'life' and somehow looking out at the world through the windows of our eyes.

And of course, since it is almost impossible to imagine oblivion where all memory has gone and no thoughts

Parasite Problem for Creationists

Stone Age worm egg hints at origins of modern scourge - health - 20 June 2014 - New Scientist

News that the earliest known evidence of the parasitic flatworm which causes schistosomiasis in human has been found, reminds me how rarely we see creationist pseudo-scientists discussing parasites, least of all parasites on humans. Maybe they are just sensitive to the subject for understandable reasons given their generally parasitic lifestyle but that would require a social conscience. It's much more likely that it's impossible to fit them into a biblical model where a magic, benevolent god created everything for humans because it loves us.

Parasites, by definition, take from their hosts but give little or nothing in return. They also often make their hosts sick in the process.

Crows Picking at the Neanderthal Creationist Corpse

A creationists 'explains' two sorts of evolution.
Note the lie that evolutionary biologists claim trilobites were our ancestors
and that foxes are the same species as dogs and wolves.

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

How carrion and hooded crows defeat Linnaeus's curse

Creationists don't understand what evolution is. Creation pseudo-scientists on the other hand, understand perfectly well what evolution is - which is why the term has to be deliberately misrepresented, and the ignorance maintained by misinformation, misrepresentation and lies. And the most important muddle that must be maintained is what the term 'species' means, how it's understood by biologists and how evolutionary theory explains the mechanism by which it arises.

Unable to argue against the massive amount of observed and observable evidence that change over time can be seen both in the phenotype and in the genotype of a species, they have tried to come up with a compromise

Britons Rejecting Religion

Defining British Identity | British Social Attitudes Survey 31

Taxpayers' cash should not be used to fund faith schools, say voters | Education | The Observer

A couple more reports out this week confirm the rapid decline in the importance of religion in Britain and even growing hostility towards it. Both of these deal to some extent with the aftermath of the scandal of Muslim faith schools and state schools with a predominantly Muslim population in Birmingham being infiltrated by Islamic extremists.

They also come on top of the recent success of UKIP in

Magnetic Reversal For Creationism

What would it take to convince a creationist that Earth is not just a few thousand years old?

To be frank, the answer to that is probably nothing - nothing on Earth would convince them because nothing on Earth convinced them it was just a few thousand years old in the first place. They were told that was the right thing to believe and that to be immune to reason and blind to contradictory evidence is something to be admired. The conclusion is sacred so facts must be ignored.

But imagine if there was some way Earth could have recorded its age in a way that is irrefutable, like a prisoner in a cell making a mark on the wall every day, and suppose this mark was not just marked on stone or even carved in stone but embedded forever in the structure of the stone itself, so no-one could have forged it or changed it and the only way to get rid of it was to destroy the stone itself.

Massive Subterranean 'Ocean'

Massive 'ocean' discovered towards Earth's core - environment - 12 June 2014 - New Scientist

News this week that geologists led by Steven Jacobsen of Northwestern University in Evanston, Illinois, USA, may have discovered a vast amount of water locked up in hydrated minerals deep in Earth's mantle. Estimates put the amount of water at some three times the combined volumes of Earth's oceans. Were this volume of water to be on the surface of Earth only the tops of mountains would be dry land.

Silly Bible - The Fishy Tale Of Jonah

It's sometimes fun to read through the Bible and work out which of the tales in it is the least plausible, the most pointless, the least well thought out, etc.

A strong contender for all three of these is the story of Jonah. It must rate alongside the Noah's Ark and the Tower of Babel stories as the silliest and, given that the Tower of Babel tale actually tries to explain why different people speak different languages so has some point to it, like Noah's Ark, the tale of Jonah doesn't actually offer anything by way explanation for anything we can observe.

Nor is it any more plausible because the scientific evidence shows that it couldn't have happened, although, to be fair to whomsoever made up the Jonah myth, at

Church of England in Terminal Decline

Figures compiled and published in British Social Attitudes 30 (2013 Edition) make grim reading for mainstream religions in Britain. Self-identification with religion shows that affiliations to the Anglican churches (Church of England, Church in Wales and Church of Scotland) have halved from 40 percent to just 20 percent between 1983 and 2012.

Only one in five Britons now identify with the established church whose bishops are appointed nominally by the Queen, but, for all practical purposes by the Prime Minister, and some of whose bishops sit by right in the upper chamber of the UK bicameral parliament without ever having stood for election even by the Anglican congregations.

At the same time, the proportion of self-identifying as having no religion has increased from 31 percent to 48 percent, having briefly topped 50 percent in 2009. 'No religion' is now the largest demographic group by far and even outstrips all the Christian groups added together. The only groups to increase over this period have been 'Other religions' which includes Muslims, Jews, Hindus, Buddhists, Sikhs, etc of whatever sect, tripling from 2 percent to 6 percent, and 'Other Christian' group, which includes Methodist, Baptist, Presbyterian, United Reformed, Calvinist, Quaker, Plymouth Brethren, Mormon, etc, remained static and 'Catholic' declined marginally from 10 percent to 9 percent.

Bad those these figures are for the Anglican Church, the underlying trends must be giving them nightmares, especially those who earn their living from it. Of course, one has to be cautious about making accurate forecasts from trends, they are after all only trend and tend to become less accurate over time, representing only a best estimate, but these trends have been consistent now for 29 years. Projecting them forward for another 25 years (i.e. one generation) from the current year to 2039, and assuming a linear trend, we get a forecast guaranteed to spread gloom throughout the Anglican community in Britain - affiliations to the Anglican Church in Britain will be less than 1 percent of the population. Long before that stage is reached, the church will cease to be a viable entity having neither congregations to minister to nor clergy to minister to them.

On current trends, 'Anglican' will be the smallest demographic group, being outdone by all three other religious groups.

Meanwhile, 'No religion' will have reached the mid 6os, approaching two-thirds of the population.

As I said earlier, one has to be cautious about making form predictions from simple trends but these figures, especially those for 'No religion' are strongly supported by figures taken from a more detailed survey published in British Social Attitudes 28:

Those self-identifying as having no religion is almost exactly in line with the forecast for 2039 and tends to be hugher with each succecive generation. It might be tempting to assume that people tend to become more religious as they get older. However, the next chart shows otherwise.

In fact, religious attitudes and affiliations formed by the age of about 20 tend to be stable throughout life rarely deviating by more than a few percentage points. There are no crumbs of comfort to be gleaned from these figures for religion, least of all for Anglican Christianity. Given that only about 50 percent of children from actively religious parents tend to follow their example whilst only about 3 percent of children from non-religious parent will become religious. The next generation will be born to parents, 64 percent of whom are openly non-religious.

At some point in the next ten years or so, affiliation with the Anglican Church in Britain will fall below 10 percent of the adult population on it's way to de facto extinction, and will no longer be able to ignore the fact that its moral authority was long since lost, as was its smugly arrogant assumption of the right to guaranteed seats in our legislative body. The next head of state will inherit the title of Defender of the Faith with little or no faith to defend. He will he titular head of an irrelevant church with which almost no-one identifies and which few people will mourn the passing of.

It is time to disestablish the Church of England, to remove its bishops, and those of other religions who sit in the House of Lords by virtue of the positions of leadership of their respective faiths, to end its involvement in state-supported schools and to cut it loose from public subsidy and exemption from corporation tax on the considerable income derived from its investments in property, banking and industry. There is no justification for a faith subscribed to by only one in five Britons to be given special privileges over and above the rest of us. It's time to privatise the Church of England and allow it to find its place in the market-place for ideas, ethics and morals.

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Marriage in Secular Britain

Provisional figures for 2012 released by the UK Government Office of National Statistics (ONS) today show that the number of marriages in England and Wales have increased slightly, both in absolute numbers and as a proportion of the unmarried population. However, 70% of marriages are now civil marriages with just 28.6% Christian of one denomination or another.

Source: ONS	Total marriages have declined from about 352,000 in 1981 to 262,000 in 2012 although this was up from just under 250,000 in 2011. Over the same period, religious marriages have declined from just under 180,000 to just under 78,000.
In 1981 more than half of all marriages were conducted in a place of worship with Anglican marriages accounting for the huge majority of them. They have now fallen to half their former numbers. The only religious category to show an increase over this period has been 'Other', which includes Jewish, Muslim and Sikh, up to 2920 from 1488 in 1981.	Source: ONS
Source: ONS	From being less than half of all marriages in 1981, civil marriages now comprise over 70% of all marriages.
The recent upturn in the number of marriages in England and Wales comes after many years of steep decline starting around 1970 when the post-war baby boomers - the 1960s generation - were coming of age, as shown by the blip between about 1965 and 1975. Marriages had been increasing steadily since these records began in line with population growth, being distorted by the two world wars.	Source: ONS

Whether the recent upturn is due to demographic changes with immigration into the UK from Eastern Europe under EU free movement laws, or whether this represents a bottoming out of the decline remains to be seen. There are a number of demographic changes that may have contributed to the decline in religion as an institution in Britain, not least of which has been, until very recently, a general feeling of security as the baby boomers and especially their children were brought up in the welfare state created by the post-war Labour government in response to the Beveridge Plan. People were better housed, better fed, better clothed, better educated, better paid and had more leisure time and disposable income than at any time in history. In addition, they were brought up in a less deferential culture and were more inclined to examine the old assumptions and think for themselves rather than being prepared to think what they were told. And these ideas were able to spread more quickly because of the mass communication media.

Better education made us more willing to see the old religious fables and origin myths as just that, not science or a useful description of the Universe any more. Better security rendered us less susceptible to the false hope that religion offers and better communication made us realise we were not alone in these new attitudes and new-found scepticism. And of course better and more accessible contraception and better sex education has turned sex into a recreational activity carrying far less risk, especially for females, reverting sex to probably it's more natural role in human relationships and freeing it from stigma and guilt that religion had imposed on it.

The strongest predictor of whether a person grows up to be religious is whether their parents are... In terms of keeping people, the non-religious are doing very well indeed. It is extremely unusual for somebody brought up in a non-religious household to join a religion, but it is not at all unusual for somebody brought up with a religious affiliation to end up as non-religious... The very fact that there is such a group, that it is quite big and that there wasn't such a group before is an indicator of secularisation.

Stephen Bullivant, theologian, St Mary's University, UK. Co-editor of The Oxford Handbook of Atheism
Quoted in Losing our religion: Your guide to a godless future by Graham Lawton; New Scientist 30 April 2014

Now we have brought our children up to think for themselves, the biggest cause of religion - parental example - has been removed from half the population. Studies have shown that only about 3% of children with Atheist or non-believing parents are likely to become religious, whilst only 50% of children from actively religious parents are likely to follow them. In the UK, for every 10 people to leave Catholicism, only 1 joins.

Source: ONS

Clearly, for most people who bother to get married at all, the reasons are social and/or economic, or simply because of a wish to show commitment. Even for those who get married in a church, the reason often has more to do with wanting a 'traditional' marriage and a nice setting for the ceremony. Marriage now has little to do with seeking permission for sex of an irascible magic man who takes a rather creepy interest in our bedroom activities.

Even for religious people, premarital sex will have been the norm in almost every case and most will have been living as a couple for some time. As the last chart shows, for all but the youngest age group, over 50% had cohabited prior to marriage, rising to over 80% for 30-45 year-olds, only a little below the cohabitation figures for civil marriages at 90%.

Religion has almost ceased to have any relevance to the institution or 'sanctity' of marriage in England and Wales and marriage is no longer seen as a prerequisite to a full sexual relationship.

Sources:

ONS: Marriage Summary Statistics 2012 (Provisional) (Excel sheet 192Kb).
ONS: Marriage Statistics, Cohabitation and Cohort Analyses (Excel sheet 343Kb).
ONS: Facts About Marriage.

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Intelligently Designed Yeast

Students Build the First Eukaryotic Chromosome from Scratch - Scientific American

Interesting news recently in Scientific American. Students at Johns Hopkins University, Baltimore, Maryland, USA, have created an entirely synthetic chromosome and it works just fine, just like any other chromosome in fact, and why wouldn't it? Chromosomes are just chemicals after all. There is no magic involved.

The chromosome they were attempting to create was Chromosome 3 of the yeast used in wine-making and baking - Saccharomyces cerevisiae - which controls the yeast sexual reproduction and which contains 316,617 base pairs. However, rather than build the entire DNA chain, they synthesised only the active regions, ignoring the accumulated junk DNA from billions of years of evolution. In fact, all they needed to do was create the correct sequence of 272,871 base pairs. Still a massive task but not nearly so daunting as it might have been.

This is a pretty impressive demonstration of not just DNA synthesis, but redesign of an entire eukaryotic chromosome. You can see that they are systematically paving the way for a new era of biology based on the redesign of genomes.

Farren Isaacs, bioengineer,
Yale University, New Haven, Connecticut.

The interesting thing is that the yeast with the synthetic DNA is thriving and behaving just like regular yeast. The plan now is to breed it through thousands of generations to see how the synthetic DNA evolves and how much junk DNA is produced in the process. The long-term plan is to build an entirely synthetic genome for yeast which can then be manipulated to produce proteins, medicines, biofuels, etc.

From the point of view of this blog, the significant thing is not so much that the DNA was built but that, when real intelligent designers got to work, the best approach was to get rid of all the useless stuff that an unintelligent design process has created over billions of years, resulting in a design which was more efficient in terms of resources and no less efficient in terms of function. Of course, this would have been completely unnecessary had there been any intelligence involved in the original design.

Sorry, creationists, but your pet superstition has been exposed as bogus yet again. There really is no such thing as magic.

Reference:

Narayana Annaluru, et al; Total Synthesis of a Functional Designer Eukaryotic Chromosome
Science 4 April 2014: Vol. 344 no. 6179 pp. 55-58 DOI: 10.1126/science.1249252

'via Blog this'

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Love Hormone Dogs Creationism

"Science can't explain love! (And because science can't explain love, it can't explain anything. And because love exists, therefore God exists!)". I'm surprised no-one has written a creationist hymn about it, so they can sing it loudly every Sunday to help shout down their doubts.

The lie to that claim was given in a paper published online today in the Proceedings of the National Academy of Sciences of the United States of America (PNSA). A team of scientists from Japan, led by Teresa Romero of the Department of Cognitive and Behavioral Sciences, The University of Tokyo, Japan, in a beautifully simple experiment, showed that the hormone oxytocin increases the pair-bond between dogs and their masters.

Significance
Although the positive impact of social bonds on individual’s fitness has recently been demonstrated, the mechanisms underlying the motivation to form long-term associations remain largely unknown. Current evidence shows that oxytocin modulates social behavior but evidence of its effects in bond maintenance remains scant, especially in nonreproductive contexts. We provide evidence that in the domestic dog oxytocin enhances social motivation to approach and affiliate with conspecifics and human partners, which constitutes the basis for the formation of any stable social bond. Furthermore, endogenous oxytocin levels increased after dogs engaged in affiliation with their dog partners, indicating a stimulation of the oxytocin system during social interactions. Our findings highlight the important role that oxytocin has in the expression of sociality in mammals.

Social Sciences - Psychological and Cognitive Sciences:
Teresa Romero, Miho Nagasawa, Kazutaka Mogi, Toshikazu Hasegawa, and Takefumi Kikusui
Oxytocin promotes social bonding in dogs
PNAS 2014 ; published ahead of print June 9, 2014, doi:10.1073/pnas.1322868111

The researchers sprayed either a preparation of oxytocin or saline into the nostrils of sixteen dogs then allowed them back into a room where their owners were waiting. The owners had been instructed to ignore any social contact from their dog and did not know whether they had received oxytocin or saline. There was a statistically significant greater tendency for dogs to try to interact with their owners by licking, pawing and sniffing if they had received oxytocin than if they had received saline sprays.

Oxytocin is known to enhance pair-bonding between parents and offspring in many mammals and makes humans more trusting, cooperative and generous. This experiment also supports the theory that it may be involved in social interaction and friendship and will even act across species, especially where both species have a broadly similar social structure.

So, where does this leave our creationist friends' claim that somehow love can only be explained by God and exists in some spiritual, non-material realm, placing it outside the reaches of science and beyond human understanding? It leaves it where it always was: a nonsensical, evidence-free assertion that science has now shown to be false. Love is a physiological, biochemical response firmly in the realm of neurophysiology and psychology and so fully accessible to science and amenable to rational analysis and measurement.

And no less enjoyable for that.

Another gap closed and found not to be containing a god, of course.

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Snake Bite Shock for Creationism

King Cobra (Ophiophagus hannah)

You know, sometimes, challenging creationist loons and putting up facts for them to either explain away, or more often, ignore all together, feels a bit like shooting fish in a barrel. A proud contempt for learning and an admiration for the moral and intellectual bankruptcy which means they aren't bothered about being right or wrong, must be such great assets for them. No wonder they seem to positively delight in displaying them, yet never enter into serious debate about the biological facts.

Take for example something that struck me in a long and very readable article in New Scientists by Bob Holmes this week about the evolution of snakes. (Unfortunately, this sits behind a paywall but articles like this justify my decision to stump up the £44 per year). The article discusses many aspects of snake evolution, most of which would precipitate ophidiophobia in any dedicated creationist, but the observation which is guaranteed to push any creationist into deep denialism concerned the evolution of snake venom.

Spreading the Creationist Poison - Update.

A mammoth victory in South Carolina?

Regular readers will remember me reporting on the campaign by creationist loons in South Carolina to sneak a piece of Bible literalism into law, despite the Establishment Clause forbidding any such thing. If enacted, the law would have compelled any official mention of the state's official fossil, the Columbian mammoth - No! I'm not joking! - to include the words "which was created on the Sixth Day with the other beasts of the field".

It had all started with a suggestion by 8 year-old Olivia McConnell that the state adopt the Columbian mammoth as its official fossil in honour of the fact that its teeth, found in a swap in the state in 1725, were the first mammalian fossils to be found in North America. In any normal place in the world such a suggestion would probably pass through on the nod as a nice little gesture and in recognition of the state's claim to fame in the field of palaeontology. Not so in loon-infested South Carolina, however, where any mention of fossils raises the dreaded spectre of Darwinian Evolution and sends true-believing creationist loons into a Bible-waving frenzy incase someone gets the right idea about evolution.

The amendment which would have included the above transparent reference to Genesis was inserted by loon's champion, Rep. Robert L. Ridgeway, III and was voted through the House of Representatives without dissent, the Judiciary Committee not having seen any problem with it either. Not a single elected Representative in South Carolina had any problem with trying to insert a piece of narrow sectarianism into law despite it clearly being unconstitutional.

The Senate, however, cried foul and blocked it, forcing the House to put it before a joint committee for final say before sending it to the Governor for approval. With the House having a one-vote majority on the committee and with all the House members having voted for the Ridgeway amendment, the outcome was by no means certain.

For those not familiar with the US Constitution, the so-called Establishment Clause is the First Amendment:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.

This is what Americans are referring to when they say they live in a free country. It guarantees both freedom of and freedom from religion, freedom of speech, the right of peaceful assembly and the right to have their grievances heard. Basically, it puts the American people in charge of America.

Naturally, the flag-wrapped, super-patriotic, fundamentalist Christians of South Carolina would do almost anything to do away with it.

However, despite four of the six member of the joint committee having voted for the subversion, the committee caved in and agrees a bill which made no mention of anything remotely resembling creationism and the bill went through both House (98-0) and Senate (32-3). It now goes to the Governor for final approval. So, it looks like South Carolinians will soon be able to proudly refer to their state fossil by its official name without having to spout a piece of creationist propaganda whether they agree with it or not, and State employees will not be compelled to include this propaganda in every reference to it, at the expense South Carolinian taxpayers.

The 'patriotic' US Christian right will need to dream up more subtle ways to subvert the hated US Constitution with it's guarantee of religious freedom which is so unfairly denying them the power to which they feel they have a God-given entitlement.

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Chimpanzees Can Outsmart Humans

Chimpanzee choice rates in competitive games match equilibrium game theory predictions : Scientific Reports : Nature Publishing Group

It must be so difficult being a creationist these days.

Hard though it might be to accept, especially for creationists, chimpanzees outsmart humans when it comes to working out the best strategy in a competitive game based on game theory, as a team from the Department of Brain and Behavioral Sciences, Primate Research Institute, Kyoto University, Japan, show in a paper published in Scientific Reports this week.

Abstract
The capacity for strategic thinking about the payoff-relevant actions of conspecifics is not well understood across species. We use game theory to make predictions about choices and temporal dynamics in three abstract competitive situations with chimpanzee participants. Frequencies of chimpanzee choices are extremely close to equilibrium (accurate-guessing) predictions, and shift as payoffs change, just as equilibrium theory predicts. The chimpanzee choices are also closer to the equilibrium prediction, and more responsive to past history and payoff changes, than two samples of human choices from experiments in which humans were also initially uninformed about opponent payoffs and could not communicate verbally. The results are consistent with a tentative interpretation of game theory as explaining evolved behavior, with the additional hypothesis that chimpanzees may retain or practice a specialized capacity to adjust strategy choice during competition to perform at least as well as, or better than, humans have.

Christopher Flynn Martin, Rahul Bhui, Peter Bossaerts, Tetsuro Matsuzawa & Colin Camerer;
Chimpanzee choice rates in competitive games match equilibrium game theory predictions; Scientific Reports 4, Article number: 5182 doi:10.1038/srep05182

According to Game Theory, there is a limit to the number of games that can be won by any player. This is known as the Nash Equilibrium. This was shown to be a limit by Nobel Laureate mathematician, John Forbes Nash Jr. When tested against university undergraduates and West African villagers, the chimpanzees (Pan troglodytes) learned the game more quickly and reached the Nash Equilibrium sooner than their human opponents.

The authors suggest that this could be related to the superior cognitive speed and short-term memory of chimpanzees. When given 'memory masking' tests chimpanzees not only perform better but faster than humans. In this test, when the lowest numerical image is touched on a computer screen, the other eight randomised images are masked with white squares. They then have to be touched in ascending order. Chimpanzees not only identify the lowest value more quickly than humans but are also more accurate in memorising the order of the masked images. In a similar test, when a set of five non-consecutive numerals are briefly shown before being masked, chimpanzees will also memorise the sequence more accurately and more quickly than humans.

The authors suggest that these superior abilities may be due to chimpanzees being generally more competitive than humans whilst humans are more cooperative. It is also suggested that humans may have lost some of this speed of cognition which we may once have shared with our closest relatives as parts of our brains were co-opted for speech, which gave us greater advantage than speed of learning.

So, even the discovery that chimpanzees are better than us at cognition, short-term memory and strategic thinking lends support to the idea that these are evolved abilities.

It must be so difficult being a creationist these days.

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Why Science Works And Religion Doesn't

How Did the Moon Really Form?

The great thing about science is that, unlike religions, it has real, hard evidence. In fact, it's all about evidence. It doesn't matter what clever hypotheses scientists come up with, until they are supported by evidence, they remain just hypotheses. And even when evidence is found it is never assumed to have proved the hypothesis beyond doubt, placing it in some realm of certainty never to be questioned again.

The only certainty in science is that there are no certainties.

Take for example the hypothesis that was devised to explain why Earth has an axis of rotation which is tilted in relation to those of other planets and in relation to the surface of the Sun, and also why Earth has such a large moon relative to its size, compared to what we normally see for other planets like Mars or Jupiter.

The hypothesis that explained this - the so-called 'giant impact hypothesis' - was that the Earth and Moon were formed early in the life of the Solar System from the remains of an impact between the earlier, smaller Earth and another even smaller, Mars-sized planet, which has been named 'Theia', that had drifted out of orbit. The impact tilted the axis of rotation of Earth. Some of the debris from this impact, mostly from Theia which broke up on impact, but some of it from Earth, fell back to Earth and became merged into it, while the remainder formed an accretion disk around the now larger Earth which coalesced into the Moon. The Moon formed by this process would have been hot, driving off the lighter elements and water which, with the low lunar gravity, would have been lost into space, leaving the arid landscape with no atmosphere that the Moon has today.

However, this hypothesis, although explaining what we can observe in terms of Earth's axis of rotation and large Moon, not only suffered from a lack of hard evidence but the evidence available appeared to contradict it. As Daniel Clery explains in an article in Science this week:

But one bit of evidence just doesn’t fit: the composition of moon rocks. Researchers have found that rocks from different parts of the solar system (brought to Earth as meteorites) have subtle differences in their composition. Oxygen, for example, comes in different varieties, called isotopes. Oxygen-16 (O-16) is the most common type, followed by oxygen-17 (O-17)—which has one extra neutron in its nucleus—and oxygen-18, with two extra neutrons. Meteorites from different parts of the solar system have different proportions of these isotopes. So a rock from Mars would have a markedly different ratio of O-17 compared with O-16 than, say, a piece of an asteroid or a rock from Earth. These ratios are so reliable that researchers use them to identify where meteorites come from.

Here’s the puzzle: The giant impact hypothesis predicts that the moon should be made of about 70% to 90% material from the impactor, so its isotope ratios should be different from Earth’s. But ever since researchers got hold of Apollo moon rocks for analysis, they have failed to find any significant difference in isotope ratios on Earth and the moon. Studies of the isotopes of oxygen, titanium, calcium, silicon, and tungsten have all drawn a blank.

Daniel Clery, How Did the Moon Really Form?, Science, June 5, 2014

It was getting to the stage where some people were suggesting that the collision had not taken place.

Dr Daniel Herwartz
University of Cologne, Germany

So, the question for science was, is this apparently contradictory evidence sufficient to destroy the hypothesis or does it's explanatory power for other observed phenomena still make it a viable hypothesis?

For the hypothesis was the fact that both Earth's axis of rotation and the size of the Moon are not really in doubt while the ratios of the different isotopes of oxygen and other elements could have another explanation - it is only an assumption that Theia should have had very different ratios, we don't have any way of knowing for sure what they would have been.

Against the hypothesis was the argument that these difference should have been detected by now so it's beginning to look suspiciously like a prediction made by the hypothesis is being falsified.

The problem was, as I have pointed out above, without knowing exactly what that prediction is in the absence of any information about Theia's oxygen isotope ratios, we can't even say with any degree of confidence that it has been falsified.

It is a relief that a [disparity in ratios] has been found, since the total absence of difference between Earth and moon would be hard to explain.

David Stevenson, planetary scientist
California Institute of Technology, Pasadena, USA
(e-mail to Science quoted in the above article.

Now, however, a team of scientists led by Daniel Herwartz of the University of Cologne, Germany, seem to solved the mystery. The problem may have been that the Moon rock samples previously used were meteorites collected from Earth and so had been subjected to the effects of weathering. This may have skewed the results. When they compared samples brought back by Apollo Missions 11, 12 and 16 with samples from Earth's mantle, they found that the Moon has an O-16 to O-17 ratio 12 parts per million higher than those of Earth rock. The results suggest the Moon may be composed of about equal proportions of Earth and Theia, so strongly supporting the big impact hypothesis.

ABSTRACT
The Moon was probably formed by a catastrophic collision of the proto-Earth with a planetesimal named Theia. Most numerical models of this collision imply a higher portion of Theia in the Moon than in Earth. Because of the isotope heterogeneity among solar system bodies, the isotopic composition of Earth and the Moon should thus be distinct. So far, however, all attempts to identify the isotopic component of Theia in lunar rocks have failed. Our triple oxygen isotope data reveal a 12 ± 3 parts per million difference in Δ¹⁷O between Earth and the Moon, which supports the giant impact hypothesis of Moon formation. We also show that enstatite chondrites and Earth have different Δ¹⁷O values, and we speculate on an enstatite chondrite–like composition of Theia. The observed small compositional difference could alternatively be explained by a carbonaceous chondrite–dominated late veneer.

Herwartz, D., et al., Identification of the giant impactor Theia in lunar rocks; Science 6 June 2014: 344 (6188): 1146-1150
DOI: 10.1126/science.1251117

Now that a difference has been found, many will work to confirm or deny it and do battle over what it means... The possible significance of enstatite chondrites is interesting, but at present we are stuck with speculating about the bodies that went into making Earth, since they are no longer around.

David Stevenson, op. cit.

So, does that settle the issue once and for all? Can science now claim to be certain that the Earth/Moon system was created by the 'big impact' in the early life of the solar system? Of course not. It is always possible that this team's findings might be shown to be wrong, or some unexpected evidence might be found which would cause the entire thing to be revised and discarded. The team themselves point out that Earth may have been bombarded by material with a different oxygen isotope ratio after the impact.

Imagine religious dogma being subjected to this sort of constant review and revision with nothing sacred at all in terms of firm conclusions. What little scraps of evidence they have, no matter how tenuous, like the Turin Shroud, are carefully guarded against too much independent scientific scrutiny and when they are, as is the case with the Turin Shroud where three independant teams all concluded that the shroud is made of linen made from flax which grew in the 14th-century, the results are dismissed or ignored.

Religion has developed a whole edifice of beliefs and dogmas based on nothing more substantial than myths and fantasies and a dogmatic assumption that, for no other reason than wishful thinking and clerical necessity, these myths and fantasies must be true. None of this would be needed if they had any real evidence either for the existence of gods, or the nature of those gods. They then have to defend those dogmas against all arguments by developing apologetics invariably based on circular reasoning and the presupposition that the dogmas are right in the first place.

The art of a good apologist is to convince believers that they were right all along and few of them require much convincing, so refuted fallacies, false claims, circular logic, parochial ignorance and cultural arrogance are all brought into play, like a snake-oil salesman playing to a credulous and anxious audience.

The level of intellectual honesty and moral integrity needed to be a theologian or a professional religious apologists would quickly result in a research scientist being shown the door of any respectable research institute foolish enough to have employed him or her in the first place. It's a level of personal integrity more suited to the role of door-to-door salesman, second-hand car dealer, political spin doctor or real-estate agent.

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Caught in the Act - Evolving Crickets

Teleogryllus oceanicus

Rapid Convergent Evolution in Wild Crickets, Study - News of the World

Male crickets chirp. They do it to attract a mate, so it's hard to imagine how they could evolve to lose the ability to chirp. But, of course, evolution has no need to be obviously intuitive and an environmental change which produces intense selective pressure can produce some surprising solutions. And, as there is more than one way of achieving the same thing, there is no reason why evolution should take on particular path and not another.

This was illustrated by a recent phenomenon seen in a species of Hawaiian cricket, Teleogryllus oceanicus, which on two islands in the Hawaiian archipelago have fallen silent, following an infestation by a parasitoid fly, Ormia ochracea. This fly uses the male cricket chirp to locate its victims and lay an egg on them. The grub then burrows into the body of the cricket, killing it within a week. The behaviour T. oceanicus had evolved to ensure continuation of its genes has provided O. ochracea with an opportunity to improve the success of its genes instead, and at the expense of those of T. oceanicus. There is no compassion in mindless evolution.

T. oceanicus parasitised by O. ochracea

This intense selective pressure in turn gave an advantage to mutant male genes which keep them silent by producing the 'flatwing' phenotype in which the sound-producing structures are erased. This was observed first on the island of Kauai and then, two years later, it appeared on the island of Oahu. The mutation was first thought to be the same and to have migrated between the islands having arisen first on Kauai, but closer research by Sonia Pascoal of the Centre for Biological Diversity, University of St Andrews, St Andrews, UK, and colleagues, has revealed that we have not one case of rapid evolution caused by an environmental change giving intense selection pressure, but two. The same phenotype is due to mutation at different loci on sex-linked chromosomes on each island as the two isolated gene-pools converged on the same solution to the same problem by two different routes.

Are there any proponents of intelligent design prepared to offer an explanation of why an intelligent designer would produce two different solutions to an identical problem given identical starting positions, leaving aside why an intelligent designer would have intelligently designed the problem in the first place?

Reference: Pascoal, S. et al; Rapid Convergent Evolution in Wild Crickets; Current Biology, 29 May 2014. http://dx.doi.org/10.1016/j.cub.2014.04.053

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