Friday, 20 October 2017

Evolving Great Tits - In Our Back Gardens

Great tit (Parus major) on a garden feeder.

Photo credit: Dennis van de Water, dvdwphotography.com
Evolution in your back garden—great tits may be adapting their beaks to birdfeeders.

Great tits are evolving, just up the road from where I live!

Not five minutes drive from where I sit writing this blog-post is probably the most intensely studied piece of woodland in the world, and probably nowhere is studied by people more qualified to study it. Wytham Woods is a mixed woodland owned by Oxford University and widely used for field studies by biologists from the Zoology Department.

It was by comparing the great tits from here and from Oosterhout and Veluwe, in the Netherlands, that an international research team discovered that the UK great tits have been actively evolving over the last few decades and now have longer beaks than their Dutch counterparts.

Thursday, 19 October 2017

Lessons From A Canary Island - Rock of Ages

The core of an old volcano, Gran Canaria
The great thing about going to somewhere different is that you see different things - if you look.

We've just got back from a little over a week in the Spanish Canary Island, Gran Canaria, just off the coast of West Africa. Yes, it's where the Canary finch comes from but, apart from a brief glimpse that might have been one and a couple in a cage, we never saw any. In fact, we saw very few birds. A few buzzards, a couple of kestrels, some egrets and herons and quite a lot of gulls, but nothing to get excited about and no new species to cross off my list!

This is mostly because Gran Ganaria is hot and arid and, being volcanic, has very little soil for anything much other than cacti and other succulents to grow in. There are pine woods on the higher places but still not a lot of wild life.

And this means that a great deal of the underlying geology is, well, not really underlying so much as overlying and exposed. It's black volcanic tuffa, pumice, basalt and towering columns of extinct volcanic core with the core eroded to expose the solidified magma as in the photograph on the right.

This, of course, if only they would look at it, is a problem for creationists because there is no way to explain the geology of Gran Canaria in terms of the product of a recent global flood or of volcanic activity in just a few thousand years since one. It is, quite simply, as close as science comes to proof that there never was a recent global flood and the Earth is actually very old. Although, on the accepted scientific understanding of the age of Earth, the Canary Islands are comparatively young - i.e., just a few tens of millions of years old.

Wednesday, 18 October 2017

Just a Small Problem - For Creationists

Lars Gibbon
The last common ancestor of the hominoids may have been about this size.
Research Sizes Up Last Common Ancestor of Humans and Apes:

You know that intermediate form between the old world monkeys and the primates, including humans, that creationists insist never existed?

It weighed about 12 pounds (5.5 Kg) according to a pair of researchers based at the American Museum of Natural History.

As the American Museum of Natural history press release explained:

Tuesday, 17 October 2017

So What's So Special About Humans?

Whales and dolphins have rich ‘human-like’ cultures and societies

Another creationist claim has been falsified (not for the first time, obviously) but this time fairly comprehensively.

The claim is that for a list of reasons, humans are a special creation, endowed with special qualities and abilities, that separate us from the other animals, justifying the claim that the purpose of 'creation' was to create mankind, and all the rest is just there for our use.

It's not good enough that were are unique, just like any species is unique, hence being a distinct species. Humans have extra-special characteristics that makes us uniquely, unique, apparently.

Friday, 6 October 2017

Getting To Know Your Inner Neanderthal

The Contribution of Neanderthals to Phenotypic Variation in Modern Humans: The American Journal of Human Genetics.

We've know for some years now that modern non-African humans have some Neanderthal DNA. This must have been acquired by interbreeding during the comparatively brief period between the migration of anatomically modern humans (AMHs) out of Africa about 50-60,000 years ago and 40,000 years ago when Neanderthals went extinct.

We also know that this interbreeding was not entirely successful and probably didn't always produce viable offspring. For example, there are no known examples of either Neanderthal Y chromosomes in modern humans, nor are there examples of Neanderthal mitochondrial DNA (mtDNA). This suggests that male Neanderthal - female AMH mating did not produce viable male offspring. It also suggests that either female Neanderthal - male AMH did not produce viable females or that females remained 'Neanderthal' and became extinct with them or did not contribute further to the AMH gene-pool carrying their mtDNA with them.

We also know that many of the Neanderthal genes proved to be deleterious and were quickly eliminated because the Neanderthal DNA we now have is heavily clustered and absent from many of our chromosomes altogether. Clustering tends to be around those chromosomes and those genes associated with our immune system, and skin and hair colour and type. In other words, we kept the genes that helped us adapt to a northern climate and possible new pathogens and got rid of a lot that may have been harmful - although not all of them since our 'improved' immunity might have been at the expense of inheriting a disposition to auto-immune diseases.

But one of the problems in identifying exactly what DNA we have retained as a population and particularly how this affects our genome has been the relatively small cohort of AMH DNA available for analysis and how representative this is of the population as a whole. A previous study of the DNA from 28,000 people in the eMERGE Network appeared to show an association between obesity and Neanderthal DNA which was not found in this study. The authors suggest that this could be due to the fact that the eMERGE DNA was from people already undergoing medical treatment.

This new study used a cohort of 112,338 individuals from the UK Biobank database.

After humans and Neandertals met many thousands of years ago, the two species began interbreeding. Although Neandertals aren't around anymore, about two percent of the DNA in non-African people living today comes from them. Recent studies have shown that some of those Neandertal genes have contributed to human immunity and modern diseases. Now researchers reporting in the American Journal of Human Genetics on October 5th have found that our Neandertal inheritance has contributed to other characteristics, too, including skin tone, hair color, sleep patterns, mood, and even a person's smoking status.


The researchers found that Neanderthal alleles were associated with both lighter and darker skin tones as well as the ability to tan in sunlight. This suggests that Neanderthals too varied in their skin tone and ability to tan just like non-African AMHs. We appear to have got this ability to adapt to variable amounts of sunlight from Neanderthals that might have taken 200,000 years to evolve it. Contrary to popular myth however, the team found no evidence of the genes for red hair in the Neanderthal genes.

Neanderthal alleles were also associated with mood changes, circadian rhythms. Change in skin tone, mood changes, circadian rhythms and sleep patterns are all linked to sunlight exposure so it seem probable that these genes were acquired from Neanderthals and have been retained by non-African AMHs because they conveyed and adaptive advantage in a northern climate.

'via Blog this'

Tracing Plant Evolution Back To Its Roots

Common liverwort, Marchantia polymorpha
Liverwort Genes and Land Plant Evolution - DOE Joint Genome Institute.

Today we have a lovely example of how the Theory of Evolution forms the foundation of biology, enabling biologists to make predictions and make sense of what we can see today in the diversity and similarities of organisms; in this case, plants.

Contrary to what creationist frauds would have their willing dupes believe, not only is there no sign that the Theory of Evolution is a 'theory in crisis' but there is every sign that it is never even seriously doubted. No-one tries to validate it these days; it is simply accepted as the very basis of biology as surely as atomic theory is the basis of chemistry.

Thursday, 5 October 2017

Old Fossils and the Crocodiles of Old England

The Melksham Monster closely resembled the species shown in this artist's impression (Plesiosuchus manselii), which also belongs to the Geosaurini group.

Credit: Fabio Manucci
Fossil points to early rise of ancient crocodiles | The University of Edinburgh

In a vindication of the way science constantly re-examines and re-assesses itself in the light of new information, some of the most rewarding fossil hunting is now being done in museums.

The museums of the world contain millions of fossils, very often meticulously catalogued with details of when and where they were discovered, but filed away in draws and cupboards and almost as effectively hidden from general view, and often scientific view, as they originally were when buried in rocks awaiting discovery by some intrepid fossil hunter a century or more ago. At the time of their discovery they may well have been mere curiosities. With little information to go on, no-one would have been aware of their significance or where they fitted in the evolutionary history of life on Earth.

The jigsaw puzzle was then far too fragmentary to know where this particular piece fitted.

One such fossil was recently discovered in the archives of the Natural History Museum, London, where it had been since 1875. It had originally been discovered about 150 years ago at Melksham, Wiltshire, England, in a formation known as Oxford Clay. When examined in detail by a team from Edinburgh University, Scotland and the Natural History Museum, London, it was found to be that of the earliest known crocodylomorph of the Geosaurini lineage, putting the evolutionary origins of this group back millions of years before the 152-157 million years previously thought.

Was This The Hominin That Gave Us Genital Herpes?

Paranthropus boisei
The species responsible for human genital herpes?

Source: Wikipedia
Meet the hominin species that gave us genital herpes | University of Cambridge

One of the best pieces of evidence for common descent is the way the genetic relationships between our obligatory parasites and those of their related species, almost exactly maps onto the relationship between our genome and those of our own relatives. I have previously written about how the evolution of our lice can be mapped onto our own evolution and divergence from the other apes.

Another parasite which, if anything, is even more obligatory that lice is the herpes virus, and like our lice there is not a close but not perfect match with our evolution. All primates are host to two versions of the herpes simplex virus, HSV1 which in humans causes cold sores and HSV2 which causes genital herpes in humans. The latter is normally regarded as a sexually transmitted disease.

Whereas we can make a direct link between two of our lice - the head louse (Pediculus humanus capitis) and the body louse (Pediculus humanus humanus) - and the body lice of chimpanzees (Pediculus schaeffi), there is no such clear link with the pubic louse and an immediate ancestor. We can see how our body louse became our head louse when we lost our body hair and it had nowhere else to go and how it then diverged into two subspecies when we started wearing clothes to become our body louse as well. However, the closest relative of our pubic louse (Phthirus pubis) is the gorilla body louse (Phthirus gorillae)! Somewhere in our evolution, the gorilla louse jumped the species barrier, otherwise it, or as descendent, would be present on chimpanzees too. The degree of divergence is enough to show that this wasn't a recent event, but somewhere, after we diverged from the chimpanzees, one of our ancestors got close enough to a gorilla to catch pubic lice from it!

Sunday, 1 October 2017

Swing A Chicken For Your Sins

Six Israeli activists wounded in protest against Yom Kippur chicken-swinging ritual | Jewish Telegraphic Agency

Ever since the Abrahamic religions invented the idea of sin, they've had to be even more inventive to provide cures for it.

For a Muslim, it's strict adherence to the rules, daily prayers, pilgrimage to Mecca and giving to charity. For a Catholic, it's confession, rituals and magic words as prescribed by the priest. For a Protestant, it's accepting Jesus and giving money to the church.

And for some ultra-conservative Jews, it's swinging a live chicken round your head the day before Yom Kippur (the Day of Atonement). The chicken is then killed and the meat given to charity.

Saturday, 30 September 2017

Child Porn Priest Rescued by Vatican

Monsignor Carlo Capella
"Downloaded child pornography using a Canadian church online address".
Lawyer says Vatican diplomat wanted for child porn offences should be sent back to Canada - Windsor - CBC News

Just about everyone must now be aware of Pope Frankie's loudly proclaimed determination to reform the Catholic Church and put a stop to the multiple child abuse scandals that were costing it money and members. No longer are these habitual abuses, routine cover-ups and tacit approval of them to be tolerated, so the way the church dealt with the latest child abuse scandal should come as no surprise.

When the Vatican heard that yet another Catholic priest was under investigation by the Canadian Police for child pornography offences, it lost no time in dealing with the matter in the interests of all concerned.

Friday, 29 September 2017

DNA Shows Complex Human Evolution in Africa

Demographic model of African history and estimated divergences. Vertical colored lines represent migration, with down-pointing triangles representing admixture into another group. Southern African hunter-gatherers are shown by red symbols, and Iron Age farmers as green symbols. (For explanation see the original paper)
Modern humans may have been around for nearly twice as long - Uppsala University, Sweden

More evidence today of modern humans emerging gradually from archaic hominins in Africa.

This genetic and archaeological analysis by a team from Uppsala University, Sweden, and the University of Johannesburg, South Africa, suggests, contrary to accepted wisdom, that modern humans may have diversified from archaic forms significantly earlier than generally believed and maybe not in a single location from a single founder species.

The suggestion is that anatomically modern humans could have gradually diversified in different African regions, then gene flow between the emerging groups produced the single, genetically diverse, species we now recognise as Homo sapiens.

This new study has been made possible by improved DNA extraction techniques which are revolutionising archaeology and evolutionary biology.

Monday, 25 September 2017

Women! For Pity's Sake Don't Drive!

Saudi Arabia's ban on women driving must remain because they ‘lack the intellect’ of men, says leading cleric | The Independent

Women should not be allowed to drive cars because, at the best of times, they have only half the intellect of men and, when they go shopping, this falls to only a quarter!

This comes on the authority of Saudi Arabian cleric and head of the Saudi government's religious edict authority in the southern province of Assir, Sheikh Saad al-Hajari.

Sunday, 24 September 2017

St Francis' Bread - Such Big Claims; So Little Evidence.

Statue of St Francis in his home town of Assisi

Photo credit: Hulton Archive/Getty Images
On the Authenticity of a Relic: An Archaeometric Investigation of the Supposed Bread Sack of Saint Francesco of Assisi | Radiocarbon | Cambridge Core

To read the headlines, you might be tempted to believe a miracle has been prove true by scientists.

What's been proven, if anything, is just how little evidence is needed before the promoters of religious superstitions start to proclaim proof.

The mythical miracle this time is one I confess I had never heard of and about which the details, as with all the best of miracles, is sadly in very short supply. It is the 'miracle' of St Francis of Assisi's bread which, in 1224, so the story goes, a sack-full of which appeared on the doorstep of the Franciscan Friary of Folloni in southern Italy, so saving the brothers within from starvation, the friary being cut off by snow.

Tuesday, 19 September 2017

Doing the 'Impossible': Recycling Old Genes

Humans and fish share about 70% of their protein-coding genes, but only about 0.5% of their regulatory long noncoding RNAs (lncRNAs)
Genomic Recycling: Ancestral Genes Take On New Roles

And another sacred creationist dogma crashes and burns.

Imagine! You're a creationist fraud trying to make an even better living by taking yet more money off people who feel so important that they believe they must have a close personal relationship with the creator of the Universe! You're feeding them all sorts of sciencey-sounding stuff because, despite convincing them that science is all wrong, they still have a nagging doubt that it might not be, so, to be on the safe side, you want them to think that even if it is right occasionally, it supports their preconceived ideas and confirms that they know better than all those wacky scientists.

Declining Christianity in USA

America’s Changing Religious Identity:

A major new report published today by PRRI has revealed a continuing decline in religious affiliation with 'nones' now comprising 24% of the population.

There is now a marked generational shift in religious affiliation with 38% of the key 18-29 year-old age group identifying as 'nones' against just 12% for the 65+ age group. White Christians now comprise just 24% of the 18-29 year-olds against 63% of the 65+ age group.

The report also reveals the continuing decline in White Christians who fall below 50% for the first time in a PRRI survey, although other surveys have also reported a similar recent finding. This group, which in 1976 comprised 81% of all American adults, now accounts for just 43%.

Two other significant findings were the increasing ethnic transformation of American Catholicism which, 25 years ago was 87% White, compared to 55% today, and the increasing polarisation of American politics on religious grounds. 73% of Republicans are White Christians compared to just 29% of Democrats. A decade ago, 50% of Democrats were White Christian.

Sunday, 17 September 2017

Religious Belief in UK Continues to Plummet!

British Social Attitudes: Record number of Brits with no religion.

The catastrophic (from the point of view of those who earn their living from it) decline in religious belief in the UK continues apace according to the authoritative British Social Attitudes Survey. 'No religion' has rockets by 5% in just one years, from 48% in 2015 to 53% in the latest (2016) survey.

More than half (53%) of the British public now describe themselves as having “no religion”, up from 48% in 2015. The proportion of non-believers has increased gradually since the survey began in 1983, when the proportion saying they had no religion stood at 31%.

Church of England decline continues
The decline in religious affiliation is hitting the Church of England particularly hard. Just 15% of people in Britain consider themselves Anglican, half the proportion who said this in 2000.

The proportion of non-believers has risen from just 31% in 1983 when the survey began.

One again the church of England has seen the biggest decline and has now fallen to 15%; half what it was in the year 2000. By contrast, the proportion of self-identified Catholics has remained stable at around 5%. Other religions account for a further 6%.

The fall in religious affiliation has been driven mostly by a decline in the proportion of 18-24 year-olds identifying with a religion, but there was a decline in all age groups between 2015 and 2016. 'No religion' in the 18-24 year-old age group increased to 71% from 63% in 2015; a stunning 8% rise in a year! In this group, Anglicans now comprise just 3%.

Friday, 15 September 2017

Frog Shocker!

Atlantic Coast leopard frog, Rana kauffeldi

Source: Wikipedia
New study contradicts assumption that true frogs diversified as they expanded their range around globe | The University of Kansas

One of the nice things about science is that, properly done, it can throw up some surprises, even overthrowing some preconceptions and axioms.

Science demands we constantly question and reassess our assumptions and preconceptions. It is not for those who prefer simple certainties over difficult truths.

For example, it is generally assumed that when a species colonises new geographic regions with new ecological niches, it will tend to adapt and radiate into several new species; that range extension itself is a major driver of speciation.

But this is not always so, it seems.

Papua New Guinea Missed The Flood?

Locations of people studied from Papua New Guinea. Each language group is represented by a circle; the area indicates the number of genotyped individuals, and the color indicates the top-level language phylum. The study found that people speaking different languages were strongly genetically distinct from each other.

Credit: Science doi: 10.1126/science.aan3842
A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea | Science

It's just another of those pieces of information that creationists have to avoid, of course, but the people of Papua New Guinea have been isolated from the rest of the world for 50,000, and people in some mountain valleys have been isolated from their neighbours for 10-20,000 years!

So, if you subscribe to the Young Earth Creationist superstition, these people are much older than Earth, have been isolated since before Adam and Eve, and appear to have avoided the Biblical flood entirely.

Yes! It is a silly superstition, isn't it, yet some apparently otherwise normal adults believe it!

Anyway, back to reality.

Thursday, 14 September 2017

Birds Sing To Avoid Confusion.

Cinnamon Becard (Pachyramphus cinnamomeus).

Credit: Matt Brady/Macaulay Library
Using song playback experiments to measure species recognition between geographically isolated populations: A comparison with acoustic trait analyses | The Auk

An interesting piece of research published yesterday shows how birds use song to recognise members of their own species, so avoiding hybridisation between closely related species, especially when there is little or no difference in appearance.

The researchers believe they have identified 21 new species of bird from Central and South America in the 72 related populations examined where different songs effectively produce isolated breeding populations.

Tuesday, 12 September 2017

Just Another Child Abuse Scandal.

Smyllum Park, Lanarkshire, as it appears today.
Hundreds of Scottish orphanage children allegedly buried in mass grave | UK news | The Guardian

Normally, when people talk about systematic, institutionalised child abuse, we think of priests and male teachers abusing vulnerable children in their care or over whom they have trusted authority. It speaks of the sheer volume of these cases that yet another exposure barely rate a mention in the news any more. It's as though we have come to expect men of the cloth to abuse their power for their own gratification.

But, despite the documented abuses in Ireland and Spain where it was nuns, sometimes with the connivance of priests, who were doing the abusing, it still comes as something of a shock when we hear of female clerics abusing children. Somehow it seems even sicker when a supposedly maternal female is looking at children as a source of amusement and sexual or sadistic gratification, yet these cases seem to have been no less prevalent in institutions where nuns were in similar positions of power over children as are the abusive priests.

Today, we have another shocking example.
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