Sunday, 5 July 2015

Mistletoe Shoots Creationism in its Achilles Heel

Mistletoe species lacks genes found in all other complex organisms -- ScienceDaily

Creationism and the Intelligent Design hoax require a simple narrative to appeal to simple people who know little of science, have no intention of learning any and who believe their ignorant intuition is the best available measure of reality.

For the creation industry, this narrative includes the simplistic notion that the scientific theory of evolution states that all evolution involves increasing complexity brought about by mutation in functional genes.

This allows creationist frauds to sell the idea that evolution is impossible because a mutation will always be harmful and involve loss of function and that increased complexity is ruled out by some misrepresented version of the Second Law of Thermodynamic, which creationist dupes can be relied on to be impressed by because it makes it seem that creationism is scientific and that they understand fundamental things like the Laws of Thermodynamics.

This also explains why, when you know some basic biology, you can read a creationist article and wonder what on Earth its about, the biology and general science being almost unrecognisable sometimes barely even being parodies of the real thing.

This is also why creationists run a mile at the mere mention of parasitism and often start gibbering nonsense about Adam and Eve and 'sin' and quoting Bible verses to make it go away. Parasites of course, not only raise questions about why an omnibenevolent creator would create them. It's easy to present the supposed creation of an apex predator like humans as the act of a benevolent creator who made everything else for us; it's quite another to explain why it created parasites which have no utility value for anything other than themselves and which don't even impact on humans in any way.

The other frightening thing about parasites for creationists is that their evolution has almost invariably involved a loss of complexity, often, in extreme cases, a stripping down to the barest essentials for replicating their genome.

One such example is the mitochondrion, an integral part of all eukaryotic cells. Mitochondria are the degenerate remains of former bacteria which evolved the ability to release the energy in glucose and bind it up into a form which can be used to power other metabolic processes. At some point in the evolution of complex cells, these bacteria became first endoparasites, then endosymbionts of other prokaryotic cells and so gave rise to the first prokaryotic cells.

But this article isn't about mitochondria as such but about a specific mitochondrium found in another parasite - a species of mistletoe. Mistletoes are of course themselves parasites on other plants.

Mistletoe has long been regarded as a mystery plant and is still banned from Anglican churches because of its association with pre-Christian religions. Because it had supposed magical powers, it was used to kill the Greek demi-god Achilles who had been protected by being dipped in the magical river styx by his mother who held him by his heal, so leaving an unprotected area. He was also protected by a spell which meant he could not be killed by anything which came from the ground (i.e. everything apart from mistletoe which grows on other plants). So, he was killed by a spear made of mistletoe (or an arrow -accounts vary) striking him in the heel.

But it's not for this magical reputation that mistletoe is such an embarrassment for creationism which prefers a different set of myths, not one with lots of gods, some of whom have gods for mothers and can be killed.

Scientists investigating the mitochondrial genome (the mitogenome) of parasitic plants have made an astonishing discovery which should, if they could bring themselves to face up to it, be giving cold sweats to those creationist frauds who are currently earning their living peddling disinformation to their credulous dupes.

The mitochondria found in this species of mistletoe, Viscum scurruloideum, have degenerated to the point at which they don't even have the genes needed to carry out the normal functions of a mitochondrium. Presently, it's something of a mystery just how these essential functions are carried out, if indeed they are carried out in the mistletoe at all, rather than the host on which this mistletoe lives. What we could be seeing here is not only an extreme form of degenerate evolution in the mitochondria but also in the mistletoe, as 'superfluous' functions are lost because they are provided by the host plant.

The mitochondrial genomes of flowering plants are characterized by an extreme and often perplexing diversity in size, organization, and mutation rate, but their primary genetic function, in respiration, is extremely well conserved. Here we present the mitochondrial genome of an aerobic parasitic plant, the mistletoe Viscum scurruloideum. This genome is miniaturized, shows clear signs of rapid and degenerative evolution, and lacks all genes for complex I of the respiratory electron-transfer chain. To our knowledge, this is the first report of the loss of this key respiratory complex in any multicellular eukaryote. The Viscum mitochondrial genome has taken a unique overall tack in evolution that, to some extent, likely reflects the progression of a specialized parasitic lifestyle.

Despite the enormous diversity among parasitic angiosperms in form and structure, life-history strategies, and plastid genomes, little is known about the diversity of their mitogenomes. We report the sequence of the wonderfully bizarre mitogenome of the hemiparasitic aerial mistletoe Viscum scurruloideum. This genome is only 66 kb in size, making it the smallest known angiosperm mitogenome by a factor of more than three and the smallest land plant mitogenome. Accompanying this size reduction is exceptional reduction of gene content. Much of this reduction arises from the unexpected loss of respiratory complex I (NADH dehydrogenase), universally present in all 300+ other angiosperms examined, where it is encoded by nine mitochondrial and many nuclear nad genes. Loss of complex I in a multicellular organism is unprecedented. We explore the potential relationship between this loss in Viscum and its parasitic lifestyle. Despite its small size, the Viscum mitogenome is unusually rich in recombinationally active repeats, possessing unparalleled levels of predicted sublimons resulting from recombination across short repeats. Many mitochondrial gene products exhibit extraordinary levels of divergence in Viscum, indicative of highly relaxed if not positive selection. In addition, all Viscum mitochondrial protein genes have experienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of genomic streamlining in response to a high mutation rate but completely opposite to the pattern seen for the high-rate but enormous mitogenomes of Silene. In sum, the Viscum mitogenome possesses a unique constellation of extremely unusual features, a subset of which may be related to its parasitic lifestyle.

Elizabeth Skippingtona, Todd J. Barkmanb, Danny W. Ricea, and Jeffrey D. Palmera.
Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.
PNAS, 2015 DOI: 10.1073/pnas.1504491112

So, contrary to the essential creationist narrative of the ToE requiring ever-increasing complexity caused by mutation, the mitogenome in this mistletoe has degenerated beyond anything previously seen in the plant world even to the loss of essential functions. It could also be that the mistletoe has discarded this basic function itself and depends on its host for it.

And skulking in the background in all of this, for any ID proponents who haven't scuttled off for fear of what they're going to read next, there is the question of why on Earth an intelligent designer should have designed an entirely new way of performing a basic function which works perfectly well in other cells, and then made it look like this had evolved by degenerative evolution.

Any takers, or is it to be denialism yet again?

'via Blog this'

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Integrity - The Difference Between Science & Religion

Dong-Pyou Han, faked results.
Photo credit: Charlie Neibergall/AP
Scientist behind fake HIV breakthrough sentenced to prison after spiking results | Society | The Guardian

News that Dong-Pyou Han, a former scientist working at ISU, has been sentenced to four and a half years in prison for making a fraudulent misstatement so obtaining millions of dollars of government funding, should be a matter of pride for the scientific community because it shows how scientific fraud is exposed by the scientific method. In the long run, results which are not reproducible by other teams and which begin to stand out as outliers, come under closer and closer scrutiny and will eventually be discarded.

Friday, 3 July 2015

What a Shocker! Another Creationist is Lying Again!

When you don't have any evidence but you have a sacred dogma to not only defend at all costs but which you're desperate to get other people to believe too, in the belief that the more people who believe it the more true it will become, what else is there for creationists but to lie?

I came across this exchange on Twitter today. It's a claim that is currently doing the rounds on creationists sites and something I was challenged with on Facebook about a week ago. The claim is that scientists have isolated soft tissue from dinosaur 'bones' which has been carbon-dated to not more than four thousand years old, in a fossil which was believed to be 65 million years old.

When faced with this on Facebook, my reply was that if the recovered 'soft tissue' had been carbon-dated to four thousand years old then that would be evidence that sample had been contaminated. My proponent promptly disappeared and has not been seen since. It turns out he had been repeating a lie, knowingly or unknowingly anyway. Maybe he realised he'd been duped and ran in embarrassment.

We can see from the Twitter exchange that @crevinfo is quite confident. The sample contains C14 and so proves the sample is no more than 4 thousand years old. He/she even links to a creationist website which repeats the claim and where creationists are jubilantly congratulating themselves on have disproved evolution and proved dinosaurs were killed off in the biblical flood, et, etc.

Obviously none of them have bothered to check the original paper, even though @crevinfo smugly provides a link to it.

There is no mention whatsoever of carbon-dating, C14 or a 4000 year age anywhere in the paper. The claim is a lie.

No ifs or buts.

The claim that this sample contains C14 is a lie.

There is not even the excuse that the paper is behind a paywall, so the facts couldn't be checked. This paper, published in Nature Communications, is open access, freely reproducible under Creative Commons Licence.

It can be read in full here: Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens. Note, it doesn't even claim the dinosaur fossil was 65 million years old, as @crevinfo states, but 75 million years. Had @crevinfo even read the title of the paper he could have seen that for himself. Not only has he almost certainly not checked his source to ensure the accuracy of his claim, he almost certainly hasn't even read it.

So, what's behind this lie? Are all these creationists rushing online to deliberately lie to us, or have they been duped once again by creationist pseudo-scientists and people who run creationist disinformation sites? Creationists are noticeably reticent to read a proper scientific paper so they can usually be relied on never to check the facts. Being keen to have a scientific basis for their infantile magical beliefs (as though that were even remotely possible) they are the easy dupes of anyone unscrupulous enough to swallow these lies and constant drip of disinformation. No doubt we will still have creationists making this same claim in five years time and never one of them will have checked.

The ease with which these unfortunate people can be duped is why they are creationists in the first place of course; the entire belief is a hoax founded not on good scientific data but on carefully selected disinformation and misrepresentations in pursuit of a political agenda. There is absolutely no interest in truth; the entire purpose of creationism is to maintain a market in creationist literature for those who require confirmation for their bias and for whom maintaining a sacred conclusion is paramount, even at the expense of intellectual honesty and personal integrity.

Creationism is seen as a shortcut to credibility, avoiding any need to learn science or bother with fact checking, logical thinking and deductive reasoning. God did it! and any science which disagrees must be wrong. Any science which can be misrepresented as supporting creationism however, is absolutely conclusive proof! And no self-respecting creationist is going to risk spoiling a brilliant scientific proof like that by checking it; just in case it's not.

In fact, this paper is moderately interesting. I actually started to write a blog about it the day it was published then decided there wasn't enough new material. What the authors believe they have found is not 'soft tissue and dinosaur blood' (another creationist lie) but what looks very much like collagen and possibly remnants of red blood cells which have been retained inside fossilized dinosaur bone. The evidence for collagen is the appearance of banding, characteristic of fibrous structural proteins and due to the tertiary structure, and mass-spectroscopy analysis suggesting the presence of amino acids.

Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ~67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.*

(a) Amorphous carbon-rich material (red) surrounded by dense material (green). Scale bar, 5 μm. (b) Erythrocyte-like structures composed of carbon surrounded by cement. Scale bar, 1 μm. For comparison, fixed blood from an emu (Dromaius) is shown in Supplementary Fig. 2c, d. Fibrous structures. Scale bar, 5 μm in (c) and 1 μm in (d).*

There is absolutely nothing in the paper to suggest that these samples are evidence that the fossil is a mere four thousand years old. The interesting thing from a scientific point of view is that it suggests there may be special conditions in which these structural proteins may be retained, even in a mineralised form, for much longer than was generally assumed.

Collagen is a remarkably stable, tough, fibrous protein and a basic component of connective tissues such as bone, ligaments and tendons, as well as being found in skin and as other structures like blood vessels. It is very slow to break down in the absence of bacteria or fungi and especially when dry or in an anoxic environment so, if any structural components are going to be retained and become fixed during fossilisation, it's going to be collagen.

The controversy here is not that this paper shows dinosaurs were around just a few thousand years ago but that it might show that a structural protein which was assumed would be lost within a few thousand years may be retained for far longer. Controversy of this sort is normal in science and will be resolved by evidence. That evidence will not prove that life was created a few thousand years ago by magic.

Such an idiotic notion cannot be proven by science because it is intelligently designed by creationist frauds to be unfalsifiable, just in case. It's a touching tribute to their scientific illiteracy and skills at self-deception that creationists believe science is going to ever prove their childish, Bronze-Age superstition from the infancy of our species so they can believe they have a special relationship with a magic invisible friend who created everything for them.

*Published under Creative Commons CC-BY license.

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Wednesday, 1 July 2015

What Was Creationism's God Doing For Eight Billion Years?

Kepler-186f, first validated Earth-size planet to orbit a star in the habitable zone (artist's impression)
Credit: NASA Ames/SETI Institute/JPL-Caltech
Even stars older than 11 billion years have Earth-like planets: Precise ages of largest number of stars hosting planets ever measured -- ScienceDaily

A paper published a few days ago in Monthly Notices of the Royal Astronomical Society, a team of researchers from the Stellar Astrophysics Centre at Aarhus University, Denmark have shown what they believe is evidence of Earth-sized planets orbiting 33 stars in the Milky Way galaxy that are about 11 billion years old. In other words, these planets were formed at least 8 billion years before Earth in a Universe that appears to have had the right conditions for creating these planetary systems right here in our own galaxy.

What Idiot Designed a Worm That Injects Sperm Into Its Own Head?

Macrostomum hystrix
Hypodermic self-insemination as a reproductive assurance strategy | Proceedings of the Royal Society of London B: Biological Sciences

You really have to laugh at creationism's 'Intelligent (sic) Designer' when you see the idiot stuff it supposedly designs.

Take this hermaphroditic flatworm that uses its penis as a hypodermic syringe to inject sperm into it's own head, for example! What sort of idiot would come up with a solution like that to the occasional problem of not finding another flatworm of the same species to exchange sperm with?

But it gets worse! The sperm then have to swim all the way down the length of the flatworm's body to get to the eggs in the tail, so they can fertilise them and produce what are, in effect clones of their parent.

Monday, 29 June 2015

Unlike Fundamentalists, Chimps Can Tell Right From Wrong.

Chimpanzees’ Bystander Reactions to Infanticide | Human Nature

Unlike fundamentalist Christians, who proudly boast that they have to use their holy book to understand what's right and what's wrong, and so bizarrely claim to be more moral than people who don't need a handbook, it seems even chimpanzees understand the difference, either instinctively or through culturally-inherited memes. Ironically, this indicates that this ability may even have been present in the last common ancestor shared by chimpanzees and humans.

This was the conclusion of a team from the University of Zurich, Switzerland, who allowed chimpanzees to

Catholic Church Just Doesn't Get It!

Anthony Colin Fisher, Archbishop of Sydney. Inconceivable tht he would not have approved the letter.
Catholic church writes to companies that support same-sex marriage | World news | The Guardian

The Catholic Church really doesn't get it.

It's not just the paedophile priests and nuns, abuse of vulnerable adults, financial corruption, support for autocratic right-wing dictatorships, the sale of 'confiscated' children, the systematic, sometimes brutal, cover-ups, the habitual avoidance of responsibilities for their crimes and casual hypocrisy of the church and it's clerics, bad though they are, that are causing people to vote with their feet and stay away from church.

Thursday, 25 June 2015

Cardinal Brady Admits Official Abuse Coverup

Cardinal Seán Brady. Intimidated victims to keep abuses secret.
Historical Institutional Abuse Inquiry: Cardinal Seán Brady admits 'shroud of secrecy' over Church sex abuse inquiry - BBC News

Cardinal Seán Brady, former head of the Catholic Church in all Ireland, has admitted the official church enquiry into the sexual abuse of young boys by Catholic priest, Fr Brendan Smyth, was conducted under a cloak of secrecy designed not to reveal the truth and protect and compensate the victims, but to protect the abuser and the church against scandal.

For his part in this coverup, Cardinal Brady, who has never been officially sanctioned by even so much as being stripped of his title, was allowed to retire on a full pension at the normal retiring age for a priest, after spending a year on fully-paid gardening leave whilst an underling did his work for him.

Brady made this admission to the Northern Ireland Historical Institutional Abuse Inquiry and admitted that the questioning of a 14 year-old victim was intimidatory, intrusive and

Another Transitional Fossil Turtle!

Grandfather turtle, Pappochelys
Photo credit: Rainer Schoch. Source:
A Middle Triassic stem-turtle and the evolution of the turtle body plan : Nature : Nature Publishing Group

These examples of what creationists tell us don't exist - transitional fossils - are getting so frequent that I'm wondering whether it's worth writing yet another blog about yet another one being found, or whether it would be simpler to just publish a weekly list of the latest.

But, having almost certainly just shed any creationists who might have had the courage to read the blog at all with that shocking title, I'll carry on, as those interested in truth might find it interesting.

This example, published in Nature yesterday, is of a 240 million year-old fossil from Germany which is

Wednesday, 24 June 2015

Now Something Else For Creationists To Ignore!

One gene may drive leap from single cell to multicellular life - life - 22 June 2015 - New Scientist

Creationists need to isolate themselves as far as possible from the reality around them - which why they're oblivious to that fact that, to normal people, they resemble a comical King Canute, ordering the tide to retreat, except that they also have their eyes shut and are pretending to not even notice the tsunami of scientific evidence engulfing them.

Actually, to be fair to the much maligned Canute, whose tale was told by the eventual winners, he was almost certainly trying to demonstrate to his army that even a king's powers are limited, so he shouldn't really be compared to a creationist.

Monday, 22 June 2015

More Sex With Neanderthals But No Original Sin

Photo credit: AFP/Getty
An early modern human from Romania with a recent Neanderthal ancestor | Nature

This isn't so much new information as adding detail to what we already know.

We've known for several years now that all non-African populations have some Neanderthal DNA, showing without a doubt that humans came up against and interbred with, to a limited degree, the Neanderthal population that had evolved from members of an earlier migration out of Africa.

Does God Hate Vultures Too?

Lappet-Faced Vulture, Torgos tracheliotus
Another Continental Vulture Crisis: Africa's Vultures Collapsing toward Extinction | Conservation Letters - Wiley Online Library.

With so many species in serious decline and under threat of imminent extinction, creationists and Intelligent Design hoaxers have some explaining to do. They at least owe it to their followers to explain why their creator god either intended this to happen or is powerless to prevent it. Admittedly, they will need to face up to some unpleasant realities to do so, but at least they'll know they aren't living a lie.

What they need to grasp is that their notion, it it were any good, would be applicable across the entire range of biological science, not just the cherry-picked pieces that make their dupes feel important or to provide easy, default answers to the parts that are hard to understand without learning basic science, putting aside

Saturday, 20 June 2015

Watching Evolution As It Happens

Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli | bioRxiv

The world's longest running evolutionary experiment has just produced another embarrassing result; embarrassing for creationists that is. The result is, of course, exactly what the Theory of Evolution predicts.

This experiment, Richard Lenski's Long-term Experimental Evolution Project, has been running since 1988 when Lenski set up 12 cultures of a single strain of E. coli. Every day since then a sample of each culture has been taken and used to seed a new

Friday, 19 June 2015

Pope Is Part Of The Climate Change Problem

Generally, Popes talk what can only politely be called cobblers, and so far the current pope has been no exception. Normally it quite easy to read something a pope has said and to write an article pointing out the bigotry, superstition, scientific illiteracy or clerical self-interest which underpins it. A religious commentator might even regard popes as a godsend for the frequency with which they open their mouth just wide enough to get a red-booted foot in it.

But now we see a pope actually talking sense about climate change and man's responsibility for it and for once the Catholic Church isn't supporting the right-wing and the forces of reaction. From a quick skim through an English translation of his encyclical, Laudato Si', it appears to be well informed and even well-argued. No doubt Pope Francis is not personally the author of it and has depended a great deal on his science advisers to do the actual science but that doesn't detract from his responsibility for the contents, and he deserves praise for it.

Wednesday, 17 June 2015

Toothed Whales Laughing At Creationists

Laughing at creationists
Mx1 and Mx2 key antiviral proteins are surprisingly lost in toothed whales - PNAS

More evidence today that the supposed 'intelligent designer' is neither intelligent nor a designer. It's not clear yet whether the ID industry will become honest as a result of all this evidence against their daft notion and give up exploiting gullible people, or whether they will ignore it all as usual and rely on their victims' aversion to reading any science literature which might shake their 'unshakeable' faith.

Researchers have shown that the toothed whales all have broken versions of two genes (Mx1 and Mx2)

Rapid Human Evolution - Update

Fore victim of kuru
Eating human brains helped Papua New Guinea tribe resist disease, research shows | Science | The Guardian

Researchers have discovered that the gene which arose in the Fore people of Papua New Guinea in response to the prion disease, kuru, also gives protection against other prion diseases.

Some time ago I reported on an unarguable case of rapid Darwinian evolution in the Fore people of Papua New Guinea. Briefly, the local religious custom of ritually eating the brain of dead relatives had produced a high risk of contracting the transmissible prion disease, kuru, an invariably fatal dementia very similar to BSE (mad cow disease) in cattle, scrapie in sheep and CJD in humans. This placed the population under intense selection pressure where any resistance to this disease had high survival value.

Tuesday, 16 June 2015

Popes, Predators, Paedophiles And Priests

Józef Wesołowski
Photo credit: Manuel Diaz / AP
Vatican Sets Trial for Ex-Ambassador Accused of Sexual Abuse - The New York Times.

Archbishop of St. Paul and Minneapolis resigns after charges of sex abuse coverup - The Washington Post

For my 1000th blog, it's a pleasure to be presented with not one but two cases of senior Catholic clergy being involved in child abuse and coverup amounting to facilitation of child sexual abuse by Catholic clergy. These cases involve an ambassador for the Vatican, an archbishop and an auxiliary bishop.

On the day that the Vatican announced it is putting on trial it's former ambassador to the Dominican Republic, Archbishop Józef Wesołowski, for molesting young boys and posessing child pornograpy, came news that the Archbishop of St. Paul and Minneapolis, Archbishop John Nienstedt, along with his assistant, Auxiliary Bishop Lee Piché had resigned. The Vatican denies any link between the two cases.

The case of Archbishop Wesołowski is revealing and tells us much of the Vatican's basic instinct - to protect its own and keep them out of the reach of the law-enforcement agencies in the countries where they

Monday, 15 June 2015

Magna Carta - And Why The Pope Tried To Kill It

On this the 800th anniversary of Magna Carta, it's worth spending a few minutes remembering how fortunate we are that the Pope Innocent III didn't succeed in his determination to annul it and put an end to this dangerous idea of equality before the law.

Although it was probably never intended as such, Magna Carta has become one of the most important documents in history, being regarded as the origins of several basic principles now taken for granted:

  • The idea of equality before the law. This establishes the right to a fair trial and the rule of

Saturday, 13 June 2015

No Comfort For Ray As God Hits Bananas

Americas may be hit by catastrophic banana disease -- ScienceDaily

In a long-expected response to Ray Comfort's cruel attempt to make American Christian fundamentalists look even more stupid with his banana 'proof' of creationism and Intelligent Design, God is sending a disease, Fusarium wilt, to decimate the American Cavendish banana crop.

Comfort, readers may remember, hilariously exposed the credulity of his creationist followers and simultaneously showed his contempt for them by

Friday, 12 June 2015

Grand Canyon Catastrophe For Creationism

Geomorphic constraints on the age of the western Grand Canyon

It can't be easy being a creationist.

The problem is the need to be increasingly inventive to cope with the troublesome cognitive dissonance that comes from trying to stick to a belief while the evidence against it just keeps on piling up. This makes them prey to pseudoscience charlatans who will try to sell them spurious confirmation of their bias with lies, misinformation and misrepresentations of the data.

It also means they have to avoid reading proper science like a claustrophobe avoids lifts.


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