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.

You've convinced them that something called the Second Law, combined with something really mysterious that only really clever people can understand called Information Theory means that evolution can't happen, because it would mean creating new information - and that is impossible. You've sold them the idea that mutations are always harmful so any mutation in DNA would result in virtually instant death with no hope of passing it on and anyway, even it it was passed on, the offspring wouldn't survive.

You've even got them using computers and swarming the Internet telling bemused scientists and other educated people that they've got everything all wrong and science has failed, without the least sense of irony!

Then along come a team of scientists and publish a scientific paper in a peer-reviewed scientific journal, complete with evidence and pictures and long words, that explains how we got a lot of our genes through mutations of old ones and that mutations have given them completely new information, so now they have a different function to the originals in creatures in our remote ancestry a couple of hundred million of years ago.

The question now is how do you misrepresent the science? Do you ignore it altogether? Do you lie about it? Do you dismiss it all as a big conspiracy? Or do you just do what others do and declare that anything you and they disagree with must be wrong, by definition?

That's the dilemma now facing the Hams, Hovinds, Behes and Demskys of the creation industry. They're not going to accept the evidence, admit they were wrong and go and look for proper jobs of course. The money is too good and the living is too easy.

In fact, the science shows is that not only are there as many as 20,000 long non-coding RNA (lncRNA) genes in the human genome – about the same number as the protein-coding ones – but the lncRNAs have lately been revealed to serve as master switches in a wide variety of biological processes. They turn genes on and off and affect other regulatory genes, controlling cellular fate during fetal development, as well as cellular division and death in the adult organism. These master regulators may therefore hold the key to elucidating or even treating a variety of diseases.

Igor Ulitsky and his team – research students Hadas Hezroni, Gali Housman and Zohar Meir, and staff scientists Drs. Rotem Ben-Tov Perry and Yoav Lubelsky of the Weizmann Institute of Science - managed to identify a class of mammalian lncRNAs that had evolved from more ancient genes by taking on new functions.

His team members developed a series of algorithms that enabled them to find such “recycled” genes in the mammalian genome. First, they identified nearly 1,000 genes that code for proteins in chickens, fish, lizards and other non-mammalian vertebrates, but not in humans, dogs, sheep and other mammals. The scientists hypothesized that at least some of these genes, after losing their protein-coding function, started manufacturing lncRNAs in mammals. By comparing “gene neighborhoods” in the vicinity of lncRNAs and of genes that had stopped coding for proteins, the researchers revealed that indeed, about 60 lncRNA genes in mammals – or 2% to 3% of lncRNAs shared by humans and other mammalian species – appear to be derived from ancestral genes. Their genetic sequence is in some cases similar to that of the ancient genes, but they have lost their protein-coding ability.

“It is hard to know what caused these genes to lose their protein-coding potential more than 200 million years ago, when mammals evolved from their vertebrate ancestors,” Ulitsky says. “But the fact that these genes have been conserved in the genome for so long suggests that they play important roles in the cell.”

Identifying such “fossils” of protein-coding genes in the mammalian genome will facilitate further study of human lncRNAs and may ultimately help scientists understand what happens when their function is disrupted. For example, lncRNAs help create different types of neurons in the fetal brain; their failure to properly determine the fate of these neurons may contribute to epilepsy. Because lncRNAs are involved in controlling cell division, their malfunction may be implicated in cancer. Finally, manipulating lncRNAs may make it possible to treat certain genetic disorders.


As the scientists say in an open access paper in Genome Biology:

Abstract

Background
Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs.

Results
We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality.

Conclusions
We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.

Hadas Hezroni, Rotem Ben-Tov Perry, Zohar Meir, Gali Housman, Yoav Lubelsky and Igor Ulitsky
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes
Genome Biology201718:162 https://doi.org/10.1186/s13059-017-1293-0

© 2017 The Authors.
Published open access
Reprinted under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0)

So, about 55 'fossil' protein-coding genes in the human genome from 200 million years ago have not only mutated without harming their hosts but they have evolved new processes and been co-opted for entirely new uses by radically changing the information they contain.

How's that for impossible?

'via Blog this'

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%

The Anglican Church has seen the sharpest decline amongst the 18-24 year-old age group. It now stands at just 3%, and this is the group set to produce the next generation. The only age-group in which affiliation to the C of E exceeds non-belief is the 75+ group. Even in that group, non-belief comes second. The decline in religious affiliation of British-born people is even greater than these figures suggest, since it has been masked to some extent by an increase in Islam due to non-EU immigration and in Catholicism due to EU immigration from Catholic Eastern European EU member states such as Poland.

This increase follows the long-term trend of more and more of us not being religious. The differences by age are stark and with so many younger people not having a religion it’s hard to see this change abating any time soon. The falls in those belonging to the Church of England are the most notable, but these figures should cause all religious leaders to pause for thought.

We know from the British Social Attitudes survey that religious people are becoming more socially liberal on issues like same sex relationships and abortion. With falling numbers some faith leaders might wonder whether they should be doing more to take their congregation’s lead on adapting to how society is changing.

Roger Harding, Head of Public Attitudes at the National Centre for Social Research

Ironically, Paul Bayes, the bishop of Liverpool explained that the decline is because people are becoming more honest! (Honestly!). Quoted in the Guardian, he said:

In this modern world people are more willing to be honest and say they have ‘no religion’ rather than casually saying they are ‘C of E’. This honesty is welcome … But saying ‘no religion’ is not the same as a considered atheism. People’s minds, and hearts, remain open.

These figures really should now raise serious questions about the role of the Anglican Church (especially) in UK public life. How can it now be justifiable that Anglican bishops occupy 26 seats by right in the unelected Upper Chamber of the UK Parliament? These sentiments were voiced by Andrew Copson for Humanists UK (Formerly the British Humanist Association) and by Terry Sanderson for the Secular Society:

How can it be right that 97% of young people today are not Anglicans, but some 20% of the state schools to which their children will go belong to the C of E? More generally, how can the Church of England remain in any meaningful sense the national legally established church, when it caters for such a small portion of the population?*

Andrew Copson, Humanists UK’s chief executive.



These statistics indicate that the time has come for this country to have a serious debate about the place of religion in our society.*

Terry Sanderson, president of the National Secular Society

*Quoted in the Guardian

The very sharp decline in religious affiliation amongst the young is probably a reflection of the increasingly liberal, secular views of the younger generation with liberal attitudes toward equal rights, same-sex marriage, etc. These are all areas in which the Christian churches have traditionally been conservative and hostile to a greater or lesser degree. Public squabbling about the ordination of women, the role of women in the church, the issue of gay priests, opposition to contraception and women's reproductive rights, and hostility to homosexuality and transgender in particular, on top of the multiple child abuse and financial scandals, have all worked against the church.

Secular morality has moved on, leaving the Christian churches mired in their own increasing irrelevance, yet unable to adapt and remain Christian. Unchangeable dogma keeps them anchored to the spot as society moves on without them.

And of course, improved education in science and the continued association of fundamentalist Christianity with the patently absurd fairy tales in the Bible, has caused young people to reject religions as primitive superstitions which are used as excuses for denying basic human rights to people and undeserved privileges for the clergy.

'via Blog this'

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.

Snake Evolution in Progress

Barred Grass Snake, Natrix helvitica

Photo: Wolfgang Böhme
Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species | Scientific Reports

Arguably the most attractive British snake of the three native species, and certainly the largest, is the grass snake.

Now it seems, according to a paper published in Scientific Reports a few days ago, it is the Western representative of what is an example of speciation in progress. It also illustrates the conflict between genetics and taxonomy.

Saturday, 2 September 2017

Six Million Year-Old Cretan Footprint Problem - For Creationism!

Trachilos footprint

Credit: Andrzej Boczarowski (CC BY)

Six Million-Year-Old Human Footprint Discovered in Crete Raises Major Questions About Our Evolution

A neat illustration this week of how the popular media distort and misrepresent science in order to appeal to a wider audience and in doing so, feed and reinforce popular misconceptions.

First, we have MSN news announcing that six million year-old human footprints have been found in Crete. This then, of course, is presented as raising 'major questions' about our evolution. Creationists groups on Facebook and elsewhere are already full of claims that this proves science has got everything about evolution all wrong, either neglecting the six million years of explaining them away as proving science even gets the dating wrong.

The source of this story was the press release from Upsala University, Sweden, which announced the publication of a paper by a team based there. Unlike the MSN headline - "Fossil footprints challenge established theories of human evolution" - the headline on this press release was more muted (and of course more accurate). No mention of human footprints there, although there was an attempt to associate the discovery with current understanding of human evolution.

But what understanding was challenged, exactly?

Tuesday, 29 August 2017

Collapsing Churches! It's Those Gays Again!

The dark symbolism of the ceiling collapsing in Malta’s oldest Catholic church.

When the roof fell in in the Ta’ Giezu church in Rabat, Malta, Claire Chretien, a devout Christian who writes for the LifeSite blog, knew exactly what had caused it.

It was same-sex marriage.

She wrote:

MALTA, August 25, 2017 (LifeSiteNews) – In what could be considered symbolic of the state of the Catholic Church in Malta, or even most of Europe, the ceiling of the country's oldest Catholic church mysteriously collapsed this week.

Sunday, 27 August 2017

Priest Blames God For His Kiddie Porn Collection

The Rev. Kevin A. Gugliotta
Priest, paedophile, pornographer and gambling addict
A priest says he downloaded child porn to ‘get revenge on God’ for his poker losses | Miami Herald

A former Catholic priest has come up with a novel excuse for downloading and distributing child pornography. According to a report in the Scranton Times Tribune, he told a Wayne County court that he did it to get revenge on God because of his gambling addiction!

The Rev. Kevin A. Gugliotta, 55, a resident of Mahwah, New Jersey and a priest at the Holy Spirit Church in Union, New Jersey, was arrested in September 2016 and charged with 20 counts of downloading child pornography and 20 counts of disseminating images of children involved in sexual acts. He plea-bargained this down to one admitted case of disseminating child pornography in return for the other 39 charges being dismissed.

Friday, 25 August 2017

Filling The Gaps - How Viruses Might Have Evolved


Virus particles

Credit: Sebastian Kaulitzki/SPL/Getty
Antarctic mystery microbe could tell us where viruses came from | New Scientist

A recent discovery in Antarctica could shed some light on the origin of viruses.

Ricardo Cavicchioli of the University of New South Wales in Australia and his colleagues found a microorganism, an archaean, Halorubrum lacusprofundi R1S1, in lakes on the Rauer Islands, Antarctica. That's not unusual in itself; new organisms are discovered daily. What was slightly unusual with this particular one is that it contains an independent plasmid that the team have names "pR1SE". Plasmids are small fragments of DNA, often circular, that are self-replicating and often carry a gene that is beneficial to the organism. Bacterial antibiotic resistance is often carried on a plasmid and, as such, can be transferred to other bacteria.

More Malevolence From the Nasty Designer?

Leprosy turns the immune system against itself, study finds | University of Cambridge

It must be difficult being a dedicated creationist. You need to believe so many diametrically opposed views simultaneously.

This paper presents an almost perfect example because a dedicated creationist must hold at least two such views simultaneously. They need to hold to the view that this bacterium was intelligently designed to circumvent the human immune system (that the same designer had designed to protect us and then had apparently regarded that as a problem to be solved!) and to the view that something capable of this degree of mendacious malevolence is an omni-benevolent, maximally good god.

Tuesday, 22 August 2017

Tiger Snakes Won the Venom Wars

Australian Eastern tiger snake

Source: Wikipedia
Why tiger snakes are on a winner - UQ News - The University of Queensland, Australia.

Venomous snakes make interesting subjects for study in that they represent an example of a complex evolutionary arms race which can be traced in their venom. This is often a complex mixture of related but subtly different chemicals, often coded for by genes which are themselves subtly different versions of one another.

The arms race is due to snakes usually preying on a range of prey species, each of which has selection pressure to evolve resistance to the snakes venom. But, if the snake merely responded to one prey's resistance by changing it's venom, this might be less effective against another of its prey species, so there is evolutionary pressure on the snake to retain it's 'older' venom but supplement it with a newer version as well. This occurs by gene duplication, then mutation of the 'spare' copy.

Monday, 21 August 2017

Seriously Christians? Really?!

Joshua 'stopping the sun'.
There are actually adults who believe the sun can stand still and performs strange manoeuvres in the sky!

Not just that but they believe these could be visible only in a small village or town, and non-one else on Earth would see them!

Seriously! There are actual grown ups who believe the following:

Then spake Joshua to the LORD in the day when the LORD delivered up the Amorites before the children of Israel, and he said in the sight of Israel, Sun, stand thou still upon Gibeon; and thou, Moon, in the valley of Ajalon. And the sun stood still, and the moon stayed, until the people had avenged themselves upon their enemies. Is not this written in the book of Jasher? So the sun stood still in the midst of heaven, and hasted not to go down about a whole day. And there was no day like that before it or after it, that the LORD hearkened unto the voice of a man: for the Lord fought for Israel. And Joshua returned, and all Israel with him, unto the camp to Gilgal. But these five kings fled, and hid themselves in a cave at Makkedah.

Joshua 10:12-17

Sunday, 20 August 2017

Retracing the First Americans' Footsteps

Postglacial viability and colonization in North America’s ice-free corridor | Nature

One of the enduring mysteries of the story of the human migration into North America is the exact route taken and the timing of the migration(s). There is now no real doubt that North America was populated first with a subsequent rapid spread into Central and South America, and that the people came from Siberia via the Beringia; the land bridge between Siberia and Alaska, the remnants of which are the Aleutian Islands.

Looking south through what was once the “ice-free corridor” in present-day Canada. A new study suggests that humans couldn’t have traversed through the corridor until about 12,600 years ago - too late to have been the route taken by the first inhabitants of North America.

Credit: Mikkel Winther Pedersen

Now the relatively new techniques for recovering and analysing environmental DNA (eDNA) is helping to fill in these gaps.

Saturday, 19 August 2017

Dinosaur Extinction? It Was Them Gays Who Caused It!


Anthony Othman, paleontologist,
Curator at the Creation Museum, Petersburg, Kentucky
‘Homosexuality Led to Extinction of Dinosaurs’, Claims Top Scientist – World News Daily Report

[Update] This turned out to be a satirical item.

The fundamentalist Christian unhealthy obsession with homosexuality took a slightly unusual turn a few days ago.

Instead of blaming the latest earthquake, hurricane, tsunami, terrorist attack, influenza outbreak or forest fire on homosexuality, the curator of the Creation Museum in Petersburg, Kentucky, palaeontologist, Anthony Othman has a new theory; dinosaur extinction was caused by homosexuals!

No! Really! Read on.

Just Another (Not) Missing Link!

Chilesaurus diegosuarezi, from the Late Jurassic period.

Artist's impression. Photograph: Gabriel L O/AFP/Getty Images
Chilesaurus and Ornithischia | Biology Letters

One of the mysteries of dinosaur evolution has been explained. It's another of those 'missing' links! It's a transitional species between two major groups of dinosaur - the herbivorous species like stegosaurus and the carnivores like T. rex.

Publishing in Biology Letter Matthew G. Baron of the Department of Earth Science, Cambridge University, UK and Paul M. Barrett of the Natural History Museum, have shown that a dinosaur from the Late Jurassic, found in Chile, formerly believed to be a theropod dinosaur turned vegetarian, is actually the stem species that was the progenitor of two quite different groups - the saurischians and the ornithischians.

Saturday, 12 August 2017

Creationism In Crisis. A Notion With No Practical Use

Scientists Map Sex Chromosome Evolution in Fungi | Duke Today

Chemical profile of ants adapts quickly to selection pressure

I won't call creationism a theory in crisis because that would be giving it a scientific standing far about what it deserves. It's a notion; a guess with no supporting evidence; an idea with no practical application other than making a few deeply ignorant people feel important enough.

A point I've made several time recently, but which I'll repeat again for those who may have missed it, science, especially biological, geological, archaeological and cosmological science, daily and routinely refutes creationism without the slightest effort or intent simply by reporting the facts.

Thursday, 10 August 2017

Just Another of Those Mythical 'Missing Links'

Alesi, the skull of the new extinct ape species Nyanzapithecus alesi (KNM-NP 59050).

Photo © Fred Spoor
The Leakey Foundation | New 13 million-year-old infant skull sheds light on ape ancestry

It's another bad week for creationism. Is there ever a good week?

Close on the report of the earliest known primate fossil we now have the remarkably complete skull of an infant who lived 13 million years ago in what is now Kenya, and which is close to the common ancestor of the hominids and the other African apes. It gives us a fairly good idea of what the last common ancestor would have looked like.

The skull was found by fossil hunter John Ekusi in 13 million year-old rock layers in the Napudet area, west of Lake Turkana in northern Kenya; a formation that is easy to date reliably because of the activity of a nearby volcano. The skull, along with forest trees, was buried by volcanic ash, showing that they were buried during the same catastrophic event.

Wednesday, 9 August 2017

Evolution! Now a Theory With Teeth!

Chupkaornis keraorum.
Credit: Masato Hattori
Amateur collectors in Japan discover country's first and oldest fossil diving bird -- ScienceDaily

As a keen fossil hunter in my early days, I dreamed of finding something more than the usual marine shells - the muscles, oysters, bivalves and marine snails that are common in North Oxfordshire limestone deposits - so I can imagine how two Japanese fossil-hunting brothers, Masatoshi and Yasuji Kera, on the island of Hokkaido must have felt when they found nine skeletal elements of what turned out to be the oldest early Asian diving bird.

Fossils of these birds are relatively common in the Northern Hemisphere, but this is the first to be found in Asia and the first from the easterm margin of the Eurasian continent.

Another Intermediate Gap-Filling Fossil!

3-D images of Archicebus achilles.

Image credit: ESRF/P. Tafforeau. Source: ESRF News.
The oldest known primate skeleton and early haplorhine evolution : Nature : Nature Research

I'm thinking of starting another blog called Filling The Gaps. There are just too many examples of these 'missing' fossils to include in this one without it coming to resemble a blog devoted to nothing else.

These examples of things creationists insist are missing being found and described by science are almost a daily occurrence from the field of biology alone. If science was bothered about creationism and scientists felt they still needed to prove evolution and disprove creationism there would probably be several scientific journals called something like the Journal of Creation Falsification or Journal of Evolution, but of course it isn't needed because science has no such need.

There is a reason creationism is absolutely obsessed with falsifying and misrepresenting science and presenting science as some sort of vast conspiracy theory or based on false assumptions and therefore invalid - unless it can be made to appears to support creationism, then it's conclusive and irrefutable, of course.

Sunday, 6 August 2017

Winning The Mammoth War.

On the Menu: Mammoth and Plenty of Raw Vegetables - Early modern humans consumed more plants than Neanderthals but ate very little fish

How fast science progresses!

Not long ago we weren't even sure how and where Neanderthals fitted in the human family tree. Were they ancestors of modern Europeans? Were they just a regional variant; a subspecies; a different species entirely? Did they or could they interbreed with modern humans?

Now most of those questions have been answered with some degree of confidence, and not a few surprises, thanks to DNA analysis, and we're just left with questions about how, why and exactly when anatomically modern humans replaced Neanderthals across western Eurasia.

Was it our superior technology? Hardly. We both used stone tools and hunted with spears. Was it our higher intelligence? Our brains are actually smaller but maybe organised differently, so maybe we could learn and adapt more quickly? Was it a better social organisation? Neanderthals seem to have lived in small, relatively isolated family groups in which incestuous breeding was common if not normal. Did this lead to genetic weaknesses accumulating? Did it mean hunting large game was more difficult with fewer numbers?

Saturday, 5 August 2017

100 Million Year-Old Flower

The ancestral flower was bisexual with multiple whorls (concentric cycles) of petal-like organs, in sets of threes.

Copyright: Hervé Sauquet/Jürg Schönenberger.
What flowers looked like 100 million years ago.

Flowering plants are by far the most diverse group of plants comprising so 300,000 different species. They were, however, late on the scene in evolutionary terms, only evolving some 140 million years ago.

This puts their evolution towards the end of the age of dinosaurs in the Cretaceous, when the ancestors of mammals were still mammaliform synapsids. The evolution of the first flowering plants is one of those enduring mysteries for evolution to explains, Darwin himself referring to it as "an abominable mystery".

Now an new study coordinated by Juerg Schoenenberger from the University of Vienna and Hervé Sauquet of the Université Paris-Sud has shed more than a little light on what the first flowers looked like. The same study has also reconstructed what flowers at the key divergence point looked like.

Thursday, 3 August 2017

Just Another Example of the 'Impossible' Happening

An illustration shows nanocrystals assembling into an ordered ‘superlattice’ – a process that a SLAC/Stanford team was able to observe in real time with X-rays from the Stanford Synchrotron Radiation Lightsource (SSRL).

Illustration: Greg Stewart/SLAC National Accelerator Laboratory
Scientists Watch ‘Artificial Atoms’ Assemble into Perfect Lattices with Many Uses.

One of the major problems that creationism suffers from is that so many of its claims are demonstrably untrue and can be seen to be untrue.

The leading frauds are acutely aware of that problem so have a work-around for it. They tell their followers that if the evidence tells them their beliefs are wrong, the evidence must be wrong because their beliefs can't be. Then they witter on about 'evidence' and try to mislead people about it as though it does matter after all. They must be the only people who call themselves scientists but argue you should ignore evidence unless you can persuade yourself it agrees with you.

Here, for example, is an example of scientists watching something happen that creationists insist doesn't happen. They watched order (and a high degree of order) emerge out of chaos.

Monday, 31 July 2017

Unintelligent Design - Silly Goose!

I took this photo today, in a park in Oxford. It shows why intelligent design is a stupid idea.

The white goose is almost certainly a hybrid between an Egyptian goose, Alopochen aegyptiaca, and a feral domestic goose. Domestic white gees in Britain are mostly a variety of greylag goose, Anser anser domesticus, so this strange looking goose is a probably a hybrid between the Egyptian and the greylag goose. The give-away is the strange-looking eyes that look spectacled from a distance, the pale brown wing feathers - not obvious in this photo (this one wasn't completely white) - and the long, pink legs.

It is highly unlikely that this was simply a leucistic Egyptian goose. It was also on it's own, not with the typical small group that Egyptian geese are normally seen in. Egyptian geese are believed to be related to the shelduck and so come somewhere between the ducks and geese. They were introduced as an ornamental bird into the UK and have become established in Norfolk, the only place I have seen them before. They have since spread to the Thames Valley (my son has seen them on the Thames).

Incidentally, the other geese in this photograph are Canada geese, an introduced species that has become widespread and which also interbreeds with 'local' geese.

But why does this show how intelligent design is a stupid idea?

Sunday, 30 July 2017

Tardigrades Give Up Their Secrets

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus | PLOS Biology

There is something appealing about a tardigrade! There is a certain air of mystery about them - like, for instance, what on Earth are they?

They are justly famous for their ability to withstand just about any extreme environmental conditions other than extreme heat. They are just a few millimetres long and can withstand years of dehydration, being blown about in dust; they can withstand years of freezing. They can even go into space and withstand ionising radiation. They will live in your guttering through a long, hot dry summer, apparently lifeless, and within a few minutes of it raining, will be crawling about happily as though nothing has happened.

Until this study we weren't even sure where they fitted in with the rest of the animal kingdom. Were they primitive or degenerate arthropods; were they nematode worms with legs or some other distinct multicellular organism on a branch of their own? Well, actually, they are related to both nematodes and arthropods, distantly. The question was which are they closest to? The study doesn't settle the matter but it sheds a lot more light on the subject.

Friday, 28 July 2017

DNA Study Shows Bible is Fiction

Researchers sequenced whole genomes from five Canaanites skeletons found in Sidon, Lebanon.
Photo Credit: Ali Hashisho/Reuters/Newscom
Ancient DNA counters biblical account of the mysterious Canaanites | Science | AAAS

We've known for a long time that the supposed 'history' in the Old Testament is mostly, if not completely, fiction, and I'm not just talking about the frankly ludicrous creation myths in the opening chapters.

As Silberman and Finkelstein showed in The Bible Unearthed: Archaeology's New Vision of Ancient Israel and the Origin of Its Sacred Texts, not only did the events described in Exodus never happen but nor did the destruction of the cities and the Canaanite genocide. Indeed, the Bible contains evidence of its own inaccuracy, being clearly written by people who did not know the history of the times in which they set their tales. Briefly, and by no means exhaustively:

Thursday, 27 July 2017

Good Old Biblical Slavery - In The USA Today!

The Word of Faith Fellowship church in Sao Joaquim de Bicas, Brazil.
(AP Photo/Silvia Izquierdo)
They kept us as slaves: AP reveals claims against church

The North Caroline megachurch, Word of Faith Fellowship, can't be accused of not being a traditional Christian fundamentalist church.

The sect, founded by Jane Whaley, a former math teacher, and her husband Sam, uses slaves taken from Brazil to work for the church and in the businesses owned by it's senior ministers. These slaves are trafficked from Brazil, as a Associated Press investigation has revealed. They are attracted to the USA by a branch of the World of Faith cult in Sao Joaquim de Bicas, Brazil and enter the USA on tourists and student visas.

Tuesday, 25 July 2017

Research Spits On Creationism!


In saliva, scientists have found hints that a “ghost” species of archaic human may have contributed genetic material to ancestors of people living in Sub-Saharan Africa today.

Image credit: Bob Wilder/University at Buffalo.
Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation | Molecular Biology and Evolution | Oxford Academic.

As an example of how divorced religion is from reality, these examples of archaic hominids interbreeding with other hominid species take some beating.

The Abrahamic superstitions require people to believe in a single founder couple from whom everyone alive is directly descended and from whom we have inherited some notional 'original sin' for which we need to constantly atone and beg for forgiveness.

The reality of course is that not only was there never such a single founder human couple but there was not even a single founder human species. The reality is that we are hybrids of three or more species who occasionally interchanged genes and that for a large part of our recent evolutionary history we behaved like an incompletely speciated 'ring species' as an example of evolution in progress.

Sunday, 23 July 2017

'Loving' Christians Trade Insults Over Reforms

General Synod of the CofE, York.
Photo credit: Reuters

Leading evangelical condemns CofE General Synod: 'God's word was mocked openly' | Christian News on Christian Today.

A failing group will normally turn inwards, degenerating further into mutually recriminating factions. This is no less true of the 'loving' Anglicans currently showing brotherly and sisterly love by trading insults over the latest attempt to reform their cult to try to halt the haemorrhage of members.

The vitriol also illustrates the problems faced by a dogma-driven cult as it tries to reform to attract back the former members to whom it has become increasingly irrelevant and who have left in disgust at its abuse of minorities. The decreasing number of moderates comes up against an increasingly large proportion of vocal extremists trying to retain their traditional dogmas.

Friday, 21 July 2017

Persecution and Martyrdom Special!




Is Christianity in crisis? Our survey reveals 9 out of 10 ordinary Christians feel marginalised

As Christianity continues to dwindle into a minority cult in the UK, and as more and more of its privileges are lost, so the whining about persecution, coupled with that old craving for martyrdom gets louder.

This collective whine was revealed in the results of a survey by Premier published last Sunday. The full survey is freely available as a pdf file here but be warned, you'll need to give your name and email address before you can access it.

The reality is of course that Christians in the UK enjoy precisely the same legal rights as anyone else regardless of their faith or lack of it. Rights and privileges are not granted on the basis of membership of a particular church or faith group in the UK anymore; they are granted on the basis of a shared humanity. There are not Christian rights, Atheist rights, Jewish rights or Muslim rights; there are only human rights.

But this survey shows that isn't enough for Christians. Christians feel persecuted if they're not granted the privileges to which they feel entitled. They are not granted the right to state mythology and prejudice as facts and not have them challenged. They're not granted the right to publicly condemn, abuse and persecute others for not sharing their chosen life-style. They're not granted the privilege to 'share' their superstition in the workplace and be quietly and respectfully listened to as they spout their bigotry and tell others that they're morally inferior and will be condemned to Hell.

Religions in the workplace do nothing but spread division, disharmony and isolation. The law requires employers to provide a healthy and safe working environment in which the Human Rights of all employees and visitors are safeguarded. No faith group is entitled to a special dispensation to pretend to occupy some notional moral high-ground with sanctimonious posturing and condemning others as morally inferior. Using what is in effect a captive audience to preach to is an abuse.

Typical of the judgemental sanctimony of the Christian church was the reaction of the Rt Rev Stephen Cottrell, Bishop of Chelmsford:

[B]elievers should not be surprised or downhearted when the sheer beauty of the Gospel is a shock and an affront to a fallen world. The world has never been in accord with the Gospel of Jesus Christ and we've always had the challenge that we need to live it and share it.

I have a book and it entitles me to tell other, lesser, mortals how to live! Ironically, this is exactly the sort of hypocritical judgmentalism that drives people away from a church that spouts this while covering up and facilitating clerical abuse of children, while wining about being treated the way it would like to treat others.

Christians are still vastly over-represented in positions of power in the UK in comparison to their dwindling numbers. No other religion has its titular head as head of state; no other religion has its leading clerics entitles to a seat in the upper chamber of our legislature and no other religion has its senior clerics appointed by the head of government on behalf of the head of state. Culturally we are still expected to defer to the moral authority of someone because he or she has an imaginary friend and dresses in robes and a silly hat.

If Christians feel marginalised then they only have themselves to blame. It's by and large their holier-than-thou judgemental sanctimony and hypocrisy that has driven so many people away from the church. The struggle to emancipate women into the priesthood and their continuing difficulty with accepting members of the LGBT community as entitled to the full range of Human Rights has rightly marginalised the Christian church in UK society. They have done this, not anyone else. The attitude of Christian bigots towards minorities has itself made them a minority now whining wrongly that they are being treated the way tho openly treated minorities themselves.

Tuesday, 18 July 2017

Oops! Another 'Non-existent' Beneficial Mutation!

The sex chromosome Z of male zebra finches comes in two variants. Males who possess a copy of these variant each have particular reproductive success.

© MPI f. Ornithology
Mutation speeds up sperm of zebra finches | Max Planck Society

For anyone who still imagines creationism is based on real-world facts and observable evidence, this little factoid should go some way to dispelling that myth.

It is yet another example of one of those beneficial mutations that creationists tell us don't and can't exist - usually followed by some garbled nonsense about information theory and thermodynamics that isn't recognisable as real science or even real information theory.

Monday, 17 July 2017

Unintelligent Design - A Purposeless Driven Life

Escarpia laminata.

Image Credit: Chemo III project, BOEM and NOAA OER
Is this Gulf of Mexico tubeworm the longest living animal in the world?

The thing about something well-designed is that it is as simple as can be and fit for purpose. The hallmarks of good design are minimal complexity and fitness for purpose.

Now, you would expect the Intelligent (sic) Designer to at least be good at one of those things wouldn't you! You would expect to be able to look at any of its designs and see an elegantly design, beautiful for it's simplicity, and a fitness for purpose so obvious that this purpose positively leaps out at you.

You should be able to look at anything designed by the creationism industries' Intelligent (sic) Designer and be immediately struck by the beautiful simplicity of it and how perfectly it does what it was obviously designed to do.

The problem is, this is never what we see. Instead, we see immensely complex things which apparently do nothing very much and for which any real purpose is difficult to discern other than making more copies of itself, apparently for no other reason than to make more copies of itself... and so ad infinitum.

Thursday, 13 July 2017

Hallelujah! Satan is Dead!

Pastor Paseka Motsoeneng, aka Prophet Mboro
Pastor Paseka Motsoeneng is a very busy man and constantly at God's beck and call, but at least Christians and Muslims can sleep soundly tonight. Satan is dead!

He was killed by Pastor Paseka Motsoeneng, aka Prophet Mboro, who went to Hell on a special mission from God's to kill the world's number one enemy.

He told his jubilant Facebook followers:

...when I got to hell there was a queue of millions of people waiting to be braai’d [roasted] by Satan. I even saw some prominent South African politicians. I was so shocked because they lived like angels here on earth. I thought they went to heaven. When Satan saw me he panicked and directed his army to kill me. Like Samson in the Bible, I defeated them. Satan was my last victim.

Stupid Design - Cannibal Caterpillars


Beet armyworms on tomato leaves. A choice of nasty-tasting leaves or juicy sibling!
Plants under attack can turn hungry caterpillars into cannibals

I almost laughed out loud when I read this one. Not only is it a lovely little piece of biology and so easy to explain in terms of genetic evolution but it's also an example of the mind-numbing stupidity of any sentient designer who had to come up with such a design to solve a problem it had designed!

Abstract
Plants are attacked by myriad herbivores, and many plants exhibit anti-herbivore defences. We tested the hypothesis that induced defences benefit tomato plants by encouraging insects to eat other members of their

Wednesday, 12 July 2017

Zebra Finches Show How Evolution Works

Zebra finch, Taeniopygia guttata.
Source: Wikipedia
Courtship song preferences in female zebra finches are shaped by developmental auditory experience | Proceedings of the Royal Society of London B: Biological Sciences

A paper published recently in Proceedings of the Royal Society B by researcher from McGill University, California, USA, illustrates a couple of interesting aspects to evolution and how species diverge.

The team found that zebra finches (Taeniopygia guttata) reared in the absence of their fathers do no react in the same way to male courtship songs as those raised by both parents.

Now, this in itself might not be particularly important apart from one thing - female sex selection. Females normally select the best singers as their mates and there is growing evidence that the best singers are also the healthiest and fittest males. Females who don't have the ability to discriminate lose out in the competition for the best mates. This, after all, is probably one of the main drivers for the evolution of female sex selection.

Monday, 10 July 2017

Suffer Little Children - For Money

Pope Francis is surrounded by children as he speaks with patients and caregivers at Bambino Gesu in December 2016.
Credit:AP Photo/Alessandra Tarantino
'Pope's hospital' put children at risk as it chased profits

If you're a Catholic and you have a sick child, you know really that prayer doesn't work so you send them to a hospital where they apply science instead, unless of course it's the 'Baby Jesus' children's hospital, run by the Vatican with branches throughout Italy.

These hospitals were dirty, badly run money-making organisations that had little to do with curing and caring or sick children. Corners were cut, safety protocols were ignored and sick children were suffering as a result.

In typical Vatican style, a 2014 report on the secret three-month investigation following complains from staff and patients' families, was itself kept secret. Some of the recommendations were allegedly implemented, but many were not.

Sunday, 9 July 2017

What A Carry On At The Vatican!

Msgr. Luigi Capozzi.
Fun-loving Vatican insider with influence.
The truth about the Vatican sex-and-drugs scandal | Catholic Culture

It's reassuring to learn that in the Vatican at least, some things just never change. Everything is carrying on much as it was in the 16th Century.

You might have missed the latest piece of gossip because it seems such events are now scarcely worthy of the epithet 'news'. There simply isn't anything to justify several column inches of news print of several minutes of airtime to report something that scarcely raises an eye-brow these days. It was just another gay sex and drugs party in the Vatican involving a middling official with friends and considerable influence in high places. It was just another example of the hypocrisy we have come to expect of the Catholic clergy.

Now, what would be news is if we went a whole year without another sex and drugs, financial or rent-boy scandal at the Vatican, or even (not that this is even remotely possible) a whole year without another child sexual, emotional and physical abuse scandal involving Catholic priests and/or nuns complete with institutionalised cover-up or even active facilitation of it, somewhere in the world

Friday, 7 July 2017

How Creationists Lie To Us - Carbon Dating Hoax

Diagram of production of carbon-14 in the upper atmosphere by reaction of neutrons with nitrogen, and of the subsequent incorporation of carbon-14 into the biosphere.
Having been called a liar by a creationist for saying there were no scientifically valid examples of 14C dating of dinosaur fossils, and then, despite his claim that there were 'lots' of them, being treated to him prevaricating and deflecting for several days before failing to provide any such examples even after numerous requests, I decided I would look closer at this claim.

First a brief background. For more detail see this Accelerator Mass Spectrometry Laboratory article.

Carbon-14 (14C) dating is, when done correctly on carefully decontaminated specimens, an accurate method of dating an organic specimen within well-known limits of confidence and within a well-defined date range. The date obtained will always be expressed as x years BP ± y years.

Doing it correctly not only means careful decontamination but also understanding its limitations, the major one being the date range over which it is reliable, why this limit exists and, importantly, exactly what carbon you are measuring in the sample and how it got there.

Not all carbon is organic in origin and not all carbon in archaeological samples is derived from the original organic carbon. For example, although carbonates may be present in the mineralised bones of which fossils are made, this does not mean it came from the original bone. After all, fossils will contain large amounts of silicates but bone does not normally contain silicon. The minerals in fossils are replacements for the original material, not necessarily the products of it.

Another Gap Closes. No God Found!

Asiatic Yellow-striped Caecilian (Ichthyophis kohtaoensis)
Photo credit: cowyeow (via Flickr)
Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia

Scientists working for the Department of Integrative Anatomical Sciences at the Keck School of Medicine of USC have closed another one of those gaps in science that creationists scrabble around desperately searching for as somewhere to fit their god into.

Although no serious biologist these days sets out to confirm evolution or to refute creationism, papers such as this one do that quite incidentally because they report on the reality of the natural world and objectively assess the evidence. Quite naturally, this refutes any notions such as creationism which are not based on real-world evidence.

Tuesday, 27 June 2017

Mapping Human Evolution Out of Africa

Neanderthal
Out of Africa; new research explores drive behind early humanity's travels across the world - Royal Holloway, University of London

Interesting news came a few days ago from Royal Holloway, University of London, that a new research project is to start next month, aimed at mapping the spread of humans out of Africa and across the globe, to occupy all major landmasses other than Antarctica. The research is financed by a £450,000 grant from Leverhulme Trust.

As the Royal Holloway press release says:

Creationism's Nightmare - Abiogenesis!

Haematite tubes
Haematite tubes from the NSB hydrothermal vent deposits that represent the oldest microfossils and evidence for life on Earth. The remains are at least 3,770 million years old.
Photo by Matthew Dodd
Evidence for early life in Earth’s oldest hydrothermal vent precipitates : Nature : Nature Research

Science is moving closer to an explanation of a process whereby the earliest proto-cells could have developed naturally on Earth. It's looking increasingly as though the best explanation of where suitable conditions could be found - in the rock precipitates around hydrothermal vents on ocean floors - is the right one.

It's also looking as though the process got going even earlier than we thought - when Earth was just few million years old, if the interpretation of the evidence presented in this paper is correct. It is strongly suggestive that the process may have got going at least 3.77 billion and maybe even 4.28 billion years ago.

The evidence was found in rocks from the Nuvvuagittuq belt in Quebec, Canada, which are believed to have been formed by precipitation around seafloor-hydrothermal vents.

Monday, 26 June 2017

Holy Smoke! Birds Use Cigarette Butts As Medication!

Urban house finch (Carpodacus mexicanus) nest.
Credit: JerryFriedman/CC BY-SA 4.0
An experimental demonstration that house finches add cigarette butts in response to ectoparasites - Suárez-Rodr-guez - 2017 - Journal of Avian Biology - Wiley Online Library

Here is yet another fascinating example of the ingenuity of biological adaptability - and an example that should make any self-respecting intelligent design advocate cringe with embarrassment.

Constantino Macías Garcia at the National Autonomous University of Mexico, and his colleagues have been studying a curious phenomenon observed in the Mexican urban house finch (Carpodacus mexicanus) in which they collect cigarette butts and place then in their nests. There was inconclusive evidence that the effect was to deter parasitic ticks and other nest parasites so they designed a simple experiment to settle the matter. It was strongly suspected that nicotine and other chemicals in the butts acts as a deterrent to parasites. House sparrows (Paser domesticus) have also been observed to use the same strategy.
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