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.

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.

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

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.

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.

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.

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.

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.

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?

100 Million Year-Old Flower

[left caption]

[Right caption/credit]

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 some 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 mammaliaform 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 a 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.

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.

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?

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.

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:

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.

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.

'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.

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.

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.

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.

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

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.

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.

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 16^th 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

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.

Source: AMS Education

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 article by A. J. T. Jull, a research scientist at the NSF Arizona AMS Facility and Department of Geosciences, University of Arizona, in Tucson, Arizona, USA.

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 in, desperately searching for as somewhere to fit their god.

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.

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.

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.

Anglican Church Colluded in Abuse Cover-up.

Peter Ball
Groomed and abused 18 vulnerable boys and young men.

Church 'colluded' with sex abuse bishop Peter Ball - BBC News

It's ironic really! Just when I go on holiday to Italy, the centre of the organised global Catholic paedophile ring that we discovered existed some ten to fifteen years ago, a similar, though smaller, scandal breaks in England and it's not even involving the Catholic Church!

This one involves a form Anglican bishop, Peter Ball, and a former Archbishop of Canterbury, Lord George Carey. Peter Ball had been Bishop of Lewes and then Bishop of Gloucester during which time he groomed, exploited and sexually abused eighteen young men and boys who went to him seeking spiritual guidance. He was jailed for thirty-two months in October 2015 for these offences but was released last February after just sixteen months.

Now a report into the church's handling of the affair, ordered by the current Archbishop of Canterbury, Justin Welby, and chaired by the former chief executive of Camden Council, Dame Moira Gibb, makes harrowing reading, according to Welby. Carey as Archbishop of Canterbury, a cabinet minister and a high court judge all conspired to protect Ball and wrote letters to the police and the Crown Prosecution Service in his defence.

Cretaceous Bird Mocks Creationists

Bird caught in amber 100 million years ago is best ever found | New Scientist.

It's not often we get to look at creatures from 100 million years ago, displayed in such detail. Normally we have to make do with distorted stone fossils which been subjected to all sorts of pressures and stresses, leaching by water and slow replacement by minerals over centuries. It's sometimes surprising that very much detail has been retained at all.

Preservation in amber is quite another matter, however. The specimen is trapped and coated in resin in a matter of minutes and sealed quickly away from any bacteria other than those trapped with it, and isolated from oxygen, other than the minuscule quantities that can slowly diffuse through the amber. It's almost as though the specimen has been sealed in a time capsule.

Yet Another Of Those 'Missing' Transitional Species

Map of the main Middle to early Upper Triassic outcrops in the state of Rio Grande do Sul, southern Brazil, highlighting the occurrence of Aleodon (A) and its skeletal reconstruction with available bones (in yellow) based on all known specimens (made by VDPN).

The African cynodont Aleodon (Cynodontia, Probainognathia) in the Triassic of southern Brazil and its biostratigraphic significance

At one time it became quite tedious writing yet another article about yet another of the transitional fossils that creationists dogma says aren't there. Who wants to read more or less the same thing several times a week with only the details changed? The problem of course is that every fossil is transitional because each represents a snapshot in time of a species that is evolving and changing over time.

But this latest one is interesting in that it is clearly transitional not between one genus and another or even between one family and another but between two or three major taxons. It is transitional between the reptiles and the mammals and comes close to the stem amniote that had earlier split from the amphibians to give rise to the land-based egg-laying tetrapods. This group went on to give rise to reptiles, mammals, dinosaurs and birds. The current consensus in palaeontology is that the amniotes probably radiated from a single ancestral species that had evolved an egg able to be laid out of water, so breaking the dependence of the amphibians on water.

More Nastiness From The 'Intelligent Designer'

Zombie soldier beetles: Epizootics in the goldenrod soldier beetle, Chauliognathus pensylvanicus (Coleoptera: Cantharidae) caused by Eryniopsis lampyridarum (Entomophthoromycotina: Entomophthoraceae):

The 'Intelligent (sic) Designer' is ever inventive in its sheer malevolent nastiness, continually coming up with ideas that would have been a credit to a Medieval torturer for the Spanish Inquisition or the organisers of 'entertainments' for a bloodthirsty Roman amphitheatre audience.

This one in particular is the epitome of casual malevolence and indifference to suffering. Its design turns a beetle into a zombie just before killing it, and then grotesquely reanimates its corpse so it can do it all over again to more victims.

Sadly, the copyright holders, Elsevier, want to charge me £22.43 to save you the trouble of clicking on this link, to read in the Journal of Invertebrate Pathology how the team from the University of Arkansas and Cornell University, led by Donald C. Steinkraus, discovered how it works.

The victim is the goldenrod soldier beetles, Chauliognathus pensylvanicus which survives by eating the flowers of frost aster, Symphyotrichum pilosum, common boneset, Eupatorium perfoliatum, and Canada goldenrod, Solidago canadensisnormally. They normally mate on top of a flower. It seems, if you subscribe to the notion of intelligent design, that the intelligent designer (who isn't God by the way, so it isn't religion it's biology and should be taught in schools, but he just happens to be identical in every way to the god of a literal interpretation of the Bible) spotted the opportunity for a bit of fun, so He it designed a fungus, Eryniopsis lampyridarum, to infect these beetles.

When the fungus, which has been living in and consuming the female beetle, is ready it first turns its host into a zombie and makes it clamp itself onto a flower stem with its jaws, immediately before killing it. Then it makes lots of spores inside the dead female's body before reanimating it! 15-22 hours after death the female spreads her wings out wide so the spores can escape through the spiracles she used to breathe through, then her body swells, making her more attractive to males who try to mate with her, so getting infected in the process.

They they find a living female to mate with and infect her with the fungus and the cycle repeats itself.

Neat, eh?

Now, although intelligent (sic) design is 'definitely-biology-not-religion', cDesign proponentsists (sic) will normally resort to 'The Fall' to explain parasites such as this. 'The Fall' is of course a purely religious construction found in the Bible and forming the basis of Christianity, but at least this enables them to dismiss these hideous examples of, if it were the intention of a real conscious being, malevolent intent, as not their god's the intelligent designer's fault. It doesn't explain how turning beetles into zombies and then reanimating them just to spread a fungus infection to the next generation of beetles relates to some mythical event in the Bible (which of course it doesn't because it's definitely-science-not-religion, except it does) but at least it nearly gets God the intelligent designer off the hook - if you don't think too much about it.

Using real science of course, this is exactly the sort of thing evolution predicts because there is no plan, no morality and no concept of punishing anything for 'sin', simply the allele frequency changing over time to maximise the number of reproducing offspring.

'via Blog this'

Dogs and Wolves Have a Sense of Justice Too

Vetmeduni Vienna : Sensitivity to inequity is in wolves’ and dogs’ blood

To listen to religious apologists you would think there is something special about humans that sets them apart from the rest of nature.

More often than not, in addition to babbling about a 'soul' (although they don't seem to agree whether that's unique to humans or not) they will quote morality, ethics, love, compassion, and a sense of fair-play or justice as setting us about the mere beasts.

This view has repeatedly been refuted by naturalists who can show that, for example, elephants grieve over lost friends and relatives, that several animals including the other apes show compassion and empathy. Now a paper by a team from the University of Veterinary Medicine, Vienna, Austria believe they have shown that not only domestic dogs but wolves have a sense of fairness and equity.

Highlights

• Pack-living dogs and wolves show both reward and quality inequity
• More dominant individuals were more inequity averse for both dogs and wolves
• Inequity conditions influenced social behaviors in subsequent interactions
• Inequity aversion is probably linked to the evolution of cooperation in dogs and wolves

Summary
Sensitivity to inequity is thought to be an important mechanism for recognizing undesirable cooperative partners and thus crucial for the evolution of human cooperation [ 1 ]. This link may not be unique to humans, as cooperative non-human primates also react to unequal outcomes [ 2 ], whereas non-cooperative species do not [ 3 ]. Although this hypothesis has not been tested in non-primate species, studies revealed that pet dogs show a limited form of inequity aversion, responding to reward, but not quality inequity [ 4–6 ]. It has been proposed that this primitive form of inequity aversion was selected for during domestication and thus absent in their ancestors, wolves. Alternatively, wolves, which hunt, raise pups, and defend their territory cooperatively, are similarly inequity averse as non-human primates, or at least to the same degree as pet dogs. Testing similarly raised and kept pack-living dogs and wolves, we found both to be inequity averse when their partner was being rewarded but they were not for performing the same action. Additionally, both wolves and dogs reacted to receiving a lower-quality reward than their partner. These results suggest that the inequity response found in pack-living dogs and wolves is comparable to that observed in non-human primates; results from studies on pet dogs may be confounded by the dogs’ relationship with humans. Consequently, our results suggest that inequity aversion was present already in the common—probably cooperative—ancestor of wolves and dogs and thus support the hypothesis of a close link of cooperation and inequity aversion.

Jennifer L. Essler, Sarah Marshall-Pescini, Friederike Range
Domestication Does Not Explain the Presence of Inequity Aversion in Dogs
Current Biology, Volume 0, Issue 0. DOI 10.1016/j.cub.2017.05.061

© 2017 Elsevier Ltd.

This basic instinct in humans is of course the basis of many legal systems including English Common Law - from which the laws of most American states are derived (the exception being that of Louisiana which is derived from French Law). The Law assumes an entitlement to equal and fair treatment in a trial, including the idea that what was good in an earlier case should be good in this one - hence the Law is the body of cases. As we say in English Law, the Law if the cases; the cases are the Law.

Religious apologists have long argued that this this is what makes us 'civilised' and that the moral basis of this is God-given morals (conveniently ignoring the amoral, even immoral nature of their own god according to their holy books).

What the researchers found was that, in experiments where of a pair of dogs completed a task but only one was given a reward, or one was given a lower value reward than the other, the dog treated less fairly refused to co-operate in future experiments. The same phenomenon was demonstrated in a captive wolf pack where the response was also affected by the individual wolf's ranking in the pack heirarchy, with high-ranking dogs reacting more quickly to inequity, presumably because they were less used to being treated unfavourably.

Because a sense of equity is common to wolves and domestic dogs, it is strongly indicative that it was present in their common ancestor.

So, where does this leave the notion that somehow human's are above the animals because they are conscious, have empathy and enjoy civilising morals handed down by an invisible law-giver? It leaves it in tatters, of course. There never was any basis for this anthropocentric arrogance. Morals and ethics are evolved characteristics in social animals where teamwork and cooperation are essential for success.

'via Blog this'

Morocco Mystery Man

[left caption]

[Right caption/credit]

A composite reconstruction of what its discovers believe is the earliest known Homo sapiens fossil (from Jebel Irhoud), based on scans of multiple specimens. The scientists say the virtual imprint of the braincase (blue) indicates that brain shape, and possibly brain function, evolved within the H. sapiens lineage.

Credit: Philipp Gunz, MPI EVA Leipzig

The age of the hominin fossils from Jebel Irhoud, Morocco, and the origins of the Middle Stone Age : Nature : Nature Research

The press are having one of those, "The textbooks are going to have to be rewritten" days.

Apparently, the textbooks are not just updated with the most recent findings and understanding when a new edition is published; they have to be rewritten because that one little bit of new information shows that everything we thought we knew was wrong. You sometimes wonder if the science news is written by creationists - except of course that the news media don't then make the absurdly childish leap of concluding that because one little bit of science has been revised this proves the entire body of science is wrong - about everything, so God did it!

But, in this case, the entire evolutionary story of humans now needs to be rewritten, so we are told. You might now be wondering what is this amazing discovery? Humans are not apes? Not African apes, maybe? We've evolved from guinea pigs or spontaneously generated? The truth is slightly more prosaic of course, in fact it barely rates as startling at all - interesting and thought-provoking, naturally, but startling? The 'startling' fact is some archaic human fossil remains including skulls, flint tools and animal remains found in Morocco have been dated to about 300,000 years old and may be the oldest fossil Homo sapiens so far discovered.

I Want To Tell You A Story!

How did almost nothing end up making you?

Don't tell the creationists and spoil their delusion but we've pretty much worked it out. It's not what they were hoping for!

From Chapter 10 of my latest book, "What Makes You So Special?":

From that small, unremarkable member of the Cambrian biota; those stiff little chordates that swam around amongst the trilobites and fearsome Anomalocaris with its huge, jaw–like appendages that were once thought to be a different species in their own right, big things were coming; in fact the biggest things to ever live – the blue whale. From that unpromising beginning were to evolve the fasted running animal, the fasted flying animal, birds that can soar on the wind and sing symphonies, two forms of powered flight, echolocation at least twice, a brain capable of doing calculus without realising it, and an ape that can go to the moon.

But first, it had to learn to walk on land and breathe air.