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Wednesday, 23 July 2014

Around the Bend with Ken Ham

2 January 2013: Astronomers have determined that the Milky Way may contain as many as 400 billion exoplanets, with almost every star hosting at least one planet.
"We'll find a new earth within 20 years" | Around the World with Ken Ham

Signs that Ken Ham may be beginning to panic at the thought that science could soon find evidence of life on another planet emerged recently with this desperate attempt to harness his fundamentalist audience in a bid to stop NASA looking for it, dismissing it as a waste of money which is bound to fail. His panic can be gaged from the horrible muddle he gets into with his argument where he inadvertently 'proves' that there isn't non-human life on Earth either.

He also showed his traditional propensity for making things up, even about the Bible, and relying on his ignorant audience not checking.

I'm shocked at the countless hundreds of millions of dollars that have been spent over the years in the desperate and fruitless search for extraterrestrial life. Even Bill Nye "the Science Guy," in our recent debate, happily gloated about tax dollars being spent toward this effort. And now, secular scientists are at it again.

Of course, secularists are desperate to find life in outer space, as they believe that would provide evidence that life can evolve in different locations and given the supposed right conditions! The search for extraterrestrial life is really driven by man's rebellion against God in a desperate attempt to supposedly prove evolution!

Judging by Hamster's snide swipe at him, it seems too that he may still be smarting at his recent public humiliation at the hands of Bill Nye "the Science Guy" in a widely publicised TV debate, which even many conservative Christians thought Nye had won.

How does Hamster know the search for evidence of life on the ever-expanding number of exoplanets (i.e planets orbiting other suns) will be fruitless? The Bible says so, of course.

The only problem is, he claims the Bible says things it simply doesn't say, even if what the Bronze-Age authors who believed Earth was flat, has a single landmass and a dome over it (Genesis 1:6-10) thought had any relevance. For example:

And I do believe there can't be other intelligent beings in outer space because of the meaning of the gospel. You see, the Bible makes it clear that Adam's sin affected the whole universe. This means that any aliens would also be affected by Adam's sin, but because they are not Adam’s descendants, they can't have salvation.

Er... actually Ken, the Bible says almost exactly the opposite.

Unto the woman he said, I will greatly multiply thy sorrow and thy conception; in sorrow thou shalt bring forth children; and thy desire shall be to thy husband, and he shall rule over thee.

And unto Adam he said, Because thou hast hearkened unto the voice of thy wife, and hast eaten of the tree, of which I commanded thee, saying, Thou shalt not eat of it: cursed is the ground for thy sake; in sorrow shalt thou eat of it all the days of thy life; Thorns also and thistles shall it bring forth to thee; and thou shalt eat the herb of the field; In the sweat of thy face shalt thou eat bread, till thou return unto the ground; for out of it wast thou taken: for dust thou art, and unto dust shalt thou return.

And Adam called his wife's name Eve; because she was the mother of all living.

Unto Adam also and to his wife did the Lord God make coats of skins, and clothed them. And the Lord God said, Behold, the man is become as one of us, to know good and evil: and now, lest he put forth his hand, and take also of the tree of life, and eat, and live for ever: Therefore the Lord God sent him forth from the garden of Eden, to till the ground from whence he was taken.

Genesis 3:16-23

No mention there that Adam's 'sin' affected the whole Universe or even the whole world. In fact, no awareness that there actually was a Universe. The only other species which seems to have been affected is the 'serpent' which gets a curse. There is only the merest hint even that this 'sin' is to be inherited by Adam's descendents even. It's certainly not spelled out with the certainty that Christian fundamentalists like to imagine.

But even if Ken's private version of his 'Holy Bible' were true, wouldn't this apply equally to non-human life on Earth as he says it does to hypothetical life on other planets? Mind you, even Hamsters carefully cultured ignorance of biology would need to go into overdrive to help him pretend there isn't non-human life on Earth, even if the logic of his own argument says there shouldn't be any.

And who was talking about intelligent life anyway? Is Ken preparing an escape hatch here just incase his prophecy is as phoney as that of Ezekiel when he prophesied the destruction of Egypt (Ezekiel 30:10-11) which history shows never happened? Will we be treated to a future creationist fraud confidently telling his audience that only intelligent life is actually living so the living things on other planets don't count?

Ham hasn't thought this through, has he. He's even forgotten now why he had to pretend the Bible said Adam's 'sin' affected the whole Universe. Now he's explaining why it only affected humans. Here he goes again:

Only descendants of Adam can be saved. God’s Son remains the "Godman" as our Savior. In fact, the Bible makes it clear that we see the Father through the Son (and we see the Son through His Word). To suggest that aliens could respond to the gospel is just totally wrong.

An understanding of the gospel makes it clear that salvation through Christ is only for the Adamic race—human beings who are all descendants of Adam.

So, Jesus isn't the saviour of anything non-human so Ken concludes that it can't exist. Er... Ken! Jesus isn't a "Godelephant" or a "Godbacterium" or even a "Godchimpanzee" either. Should we conclude then that elephants, bacteria and chimpanzees don't exist because Jesus can't save them?

In typical Hamster style, he can't help tell a lie about science and what science's aims are either. Remember, Ham's primary mission is to discredit the science he knows is undermining the very foundations of his wealth faith.

Of course, secularists are desperate to find life in outer space, as they believe that would provide evidence that life can evolve in different locations and given the supposed right conditions!

Many secularists want to discover alien life hoping that aliens can answer the deepest questions of life: "Where did we come from?" and "What is the purpose and meaning of life?"

Secularists = scientists, eh? And how would finding life on another planet answer those questions, anyway? Ken wants his audience to think those questions somehow obsess 'secularists' (scientists) because we don't have his glib platitude to save us the bother of asking.

The Creator has told us where we came from: "In the beginning God created the heavens and the earth" (Genesis 1:1; Nehemiah 9:6). And He told us what life's purpose is: "Fear God and keep His commandments" (Ecclesiastes 12:13).

In fact I know of no branch of biology which concerns itself with 'why' questions. There is no reason to suppose there is any purpose for the Universe, for planets or for life on them. These are the stuff of philosophy, charlatan clerics and creationist pseudo-scientists claiming to be able to answer a non question for an audience not too bothered about truth so long as they get a nice warm glow of smug self-importance.

And we know that life arose on Earth by virtue of the simple observation that there are living things on Earth, just as we know that raindrops form in clouds because we can see them. The only thing we are not yet sure of in both cases is the precise details of how it happened and, quite frankly, if we ever find out it will make not one iota of difference to anything very much, so there is no real reason to devote significant time and resource to it. The discovery of a plausible mechanism for abiogenesis will make even less difference to biology than the discovery of the precise details of how raindrops form in a cloud will make to the science of hydrology.

Ken knows the answers of course, because he has it on the authority of ignorant, pre-wheel Bronze-Age people who believed the highest mountains were about forty-five feet high (genesis 7:19-20), that the sun and moon were lamps hanging from a dome over the Earth (Genesis 1:16-17), that green plants were made before there was sunlight (Genesis 1:11-19) and Heaven was above the stars directly above the Middle-East and within reach of a manmade tower (Genesis 11:1-9). But then Ken Ham is in the business of selling easy answers to ignorant people who are less concerned with truth than with having simple certainties and an authority figure to give them a gloss of respectability.

At least we can see Ken Ham's real worry here - the thought that if life is found on another planet it will show that, in the right conditions, abiogenesis can occur, and if it can occur on another planet it could have occurred on Earth. And so much of creationism depends on their audience swallowing the lie that this is impossible, so creating an unfillable gap in which to sit their god. Ham's 'faith' looks a little shaky on this point.

But to show that life can arise in the right conditions we don't need to find intelligent life or even multicellular life, though that would be good. We don't even need to discover very complex life. All we need to discover is something capable of replicating and of using energy to maintain a degree of order so overcoming the tendency towards disorder, because at its most fundamental level, this is all that life is.

One thing we can be sure of though is that if a simple replicator has arisen on another planet, and has been replicating for a few billion years, as it has on Earth, it will have evolved and diversified and adapted as its home planet changed because this is the inevitable result of a selective environment inevitably selecting in favour of those minor variations in replicators best able to produce the most descendants.

Ken Ham knows this, hence his rather too transparently desperate attempt to stop us finding it out, even needing to invent 'evidence' from the Bible that simply isn't there.

And people still give him money.

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Monday, 21 July 2014

The Sacred Conclusion

Most theists will deny that they do it but it's usually easy to demonstrate that religious beliefs are not based an objective assessment of the evidence but on a received conclusion which is then protected and reinforced by highly selective cherry-picking of the evidence which is often heavily weighted whilst contradictory evidence is minimised, ignored or dismissed on spurious grounds.

'Evidence' can even include assumed evidence such as that 'list of eyewitnesses of the life of Jesus', 'all those fulfilled prophecies in the Bible which have been independently verified', or, in the case in point, 'all the historical names, places and events' mentioned in the Bible. Nothing wrong with these as examples of evidence, of course, apart from just one thing - they are all false. There are no authenticated eyewitness of the life of Jesus; there are no fulfilled prophecies in the Bible which can be independently verified and there are no historical names, places or events in the Bible which give it an authenticity as a holy book.

Quite the contrary, in fact. There are a couple of potential eyewitnesses to the life and acts of Jesus yet none of them mention him. None of the claimed list of authors actually do in ways which have any relevance as a historical source; there are very many demonstrably unfulfilled prophecies in the Bible, and many specific historical events and places mentioned are demonstrably wrong or are simple facts which would have been known to anyone such as the names of major cities and countries, the names of Kings or Roman governors and emperors that anyone writing a story claiming it to be true would have used. Does the name of London and Paris and the historical fact of the French Revolution render the novel A Tale of Two Cities by Charles Dickens a historical source document or the mention of Athens, Sparta, Troy and Macedonia turn Greek myths and gods into historical facts?
This is all, of course, an example of what Peter Boghossian calls 'doxastically closed'. The conclusion comes first and the 'evidence' is filled in later from wherever it can be gleaned without too much attention being paid to its authenticity. It fits the conclusion so it must be right because the conclusion is right. Above all, even the possibility of the conclusion being wrong must not be considered. The conclusion is immune to reason.

This can be easily tested and demonstrated by observing what happens when you show the claimed supporting evidence is false. Just as with a science when the previously accepted evidence for a theory is shown to be false, the intellectually honest - Peter Boghossian's 'doxastically open' - response should be to change the conclusion. In other words, when the evidence changes the honest thing to do is to change one's mind. Is this what we see in religious people?

Take a look at this exchange from Facebook. My original post to the 'Why Atheism?' group was:

Theists! If it's rational to believe the claims in your favourite holy book made by people you've never met, why is it not rational to believe the claims in other holy books made by people you've never met?

The following exchange ensued:

NM: At face value you could be addressing Hindus, asking why Hindus don't believe claims in the Bible... Actually they do. They claim Jesus as their own.

RR: I WAS addressing Hindus. Hindus are theists too. How about you give an honest answer the question instead of avoiding it?

NM: the claims in my "favorite holy book" made by people I've never met contain actual historical names, places and events. The claims in other holy books made by people I've never met do not contain actual historical names, places and events.

Okay, so the Quran does... But it's a plagiarization of my favorite holy book anyway.

RR: Where may we see the verified extra-biblical historical evidence which validates the Bible in ways no other holy book can be validated, please? Hint: the Bible is not evidence of it's own validity.

NM: Name me something historical that's also in the Bible and I'll do a search for you.

RR: Nope. YOU made the claim; YOU prove it. Did you not bother to check first? Do you remember who lied to you?

RR: So you believe the Bible because of all the verified historical facts in it - except you can't think of any and explain how they were verified, by whom and where we can see the evidence, eh?

Now you know the basis for your belief is false, will you be changing your belief or just thinking of some more arguments for it?
MN: I'll ask one last time before I give it up. Name me something historical that's also in the Bible and I'll do a search for you.

RR: Nope. If you can't prove your claim it fails by default. How about answering my question about what you do now your claimed basis for your belief in the Bible has been shown to be baseless? Do you do the intellectually honest thing and change your belief or do you try to think of another reason for it like someone too afraid to change their mind would?

RR: Aaaaand.... no answer.

A confident claim, made on the assumption that it must be true, presumably because he's been told it's true, as evidence that the Bible is unique amongst holy books and the only one to have such roof of authenticity, and yet he can't think of an example nor how it was authenticated. He doesn't actually know what he believes proves his faith; he only thought he knew it. His 'proof' had never even been tested!

And all he has is the desperate demand that I help him with his search or even go look for the evidence for him. The usual excuse to break off the debate quickly follows.

So, does our Christian fundamentalist change his mind, having been forced to confront the fact that his declared 'proof' is false? Of course not. He makes an excuse, assigns blame, guilt and responsibility to me and flounces off. He'll be on another Facebook group soon, offering the same proof and using the same tactic when called on it. It's no different to the insistent claims that there is no evidence for evolution; there is masses of evidence for the existence of God/Allah or that Atheists are rapists and murderers. There is no connection between the belief and reality and given the choice, between belief and reality, reality will be dismissed. It's all a test of faith!

The conclusion is sacred so facts must be ignored.

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Thursday, 17 July 2014

No Bread of Heaven for Creationism

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

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

As I explained in a recent blog about the genome of the Norwegian spruce (Christmas tree), one of their lines of attack on Darwinian Evolution is that it always moves from the simple to the more complex - something they imagine they can prove to be impossible with a misrepresentation of the Laws of Thermodynamics. They also habitually misrepresent evolution theory as a theory about the origin of humans. This parody puts humans at the top of some notional 'ladder of evolution' with lesser species arranged on the rungs below and making it look like the TOE says one species (represented by a single animal) spontaneously mutated into another in a single act of speciation (curiously, whilst leaving obligatory fossilised examples of 'transitional forms' as it did so).

So, taking these two together, creationist pseudo-scientists are in effect arguing the the TOE claims that humans are the most complex of all species being the most highly evolved. Evolution theory says nothing of the sort, of course. It's simply that creationists have constructed a ludicrous straw man to attack rather than deal with the real Theory of Evolution. More to the point, the idea that in increasingly complex genome means an increasingly complex organism is nonsensical.

Now, following on from the revelation that the Norwegian spruce has a genome seven times larger than that of humans and a functional (i.e. protein-coding) genome almost twice the size of our 17,000 functional genes, we have news that bread wheat (Triticum aestivum) has a genome more than five times as large as the human one.

Wheat got its large genome by a different route to that of the Christmas tree where the cause was a normally-corrected mistake in the DNA copying mechanism common to most species but in which the error-correction mechanism is broken too. So, over about 120 million years the Christmas tree has been accumulating an ever-expanding genome all to no discernible purpose. Not only would a hypothetical designer have made a fundamental error in the DNA copying mechanism but it would also have designed a broken mechanism for correcting its earlier error.

In the case of wheat, the genome came about by a doubling of the number of chromosomes to give a tetraploid form (i.e., one with four copies of each chromosome instead of the normal two) when two related normal diploid species hybridized to give a new species. This form then hybridized in another rare example of spontaneous speciation by hybridization when the tetraploid form again hybridized with another related diploid form to give a hexaploid genome containing six copies of each of seven chromosomes, giving 42 chromosomes in all divided into six sub-genomes. This is believed to have happened somewhere in the Tigris-Euphrates valley and was the environmental change which probably enabled wheat-based agriculture and urbanization to occur. Bread wheat now feeds 30% of the worlds people and provides 20% of our calories. I've already blogged about this rare example of evolution by hybridization so I'll resist the temptation to upset creationists with is again.

I'll simply point out how the example of bread wheat with its hugely complex genome not only represents all the problems for creationism that I outlined with the Christmas tree example but also gives the lie to another of their lines of attack - the idiotic claim that mutations are always harmful and so Natural Selection will never have an advantageous mutation to 'favour'. Given that bread wheat has six copies of every gene without even considering any gene duplication within each sub-genome, all these spare copies are free to mutate without having any detrimental effect whatsoever. If, however, one of these mutations gives a significant advantage, Natural Selection will ensure it spreads throughout the genepool.

Yes, it's been another bad week for creationism. They must pray for the day when scientists stop producing all this evidence against their daft notion.

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Clearing Up the Unintelligent Designer's Mistakes

Hamilton O. Smith. (Photo: Jane Gitschier ©PLoS Genetics)
I'm homing in on the genetic essence of life - opinion - 14 July 2014 - New Scientist

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

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

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

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

The aim is to strip the genome down to its bare essentials so it can be used experimentally by adding sequences that allow the organism to live in a different environment, make new substances or use something like photosynthesis. An incidental benefit is that we will discover more about what particular genes do. There are currently some 100 genes in M. mycoides whose function is not understood. Stripping the genome down and then adding or removing these could tell us what they do.

The only reason this is necessary, of course, is because evolution, unlike the design process, is such an unintelligent, utilitarian designer. Just so long as it works and gives the organism some sort of advantage it'll be retained and gradually spread throughout the organism's genepool. It matters not if a gene or group of genes for a specific function is scattered about throughout the genome and it matters not if occasionally chunks of DNA have been accidentally doubled to give two or more copies of the same gene, one of which can then mutate without being eliminated by making its carrier non-viable.

The only thing that matters is that it works. It's a bit like starting with a car to design a boat and retaining the wheels but reducing the drag by making them too small to function as wheels any more, but keeping them anyway because there is no particular benefit in getting rid of them. Another motoring analogy would be to design a sophisticated engine management system but continuing to fit a distributor and a choke cable. Not the act of an intelligent designer.

The J. Craig Venter Institute is a commercial organisation researching into, amongst other things, biofuels. It's objective is to make money. It's not difficult to see why they are using the knowledge they acquired from the study of Darwinian Evolution and have not opted for the idea currently fashionable amongst the religious right in America - so-called Intelligent Design, in other words, fundamentalist Christian biblical literalism. Quite simply, it isn't a scientific theory with any useful application because it's not based on scientific reality but fundamentalist religious dogma with a hidden political agenda.

It almost beggars belief that politically motivated organisations like the Discovery Institute and the Institute for Creation Research continue to get away with their nonsensical 'Intelligent Design' idea when one only needs to scratch the surface to see how much evidence there is against it. It takes profound ignorance, willfully maintained in the face of such an abundance of freely available information, to avoid seeing this evidence. It's almost as though creationists inhabit a different world to the rest of us - one in which the evidence of the world around them is of no importance.

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Wednesday, 16 July 2014

Altruism and Tits

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

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

The so-called long-tailed tit - it's actually closer to the warbler family than the tits - is one of the UK's smallest bird. Were it not for it's long tail it would actually equal the size of our smallest two, the goldcrest and the firecrest - also, as it happens, members of the warbler family. Both male and female cooperate in building one of the most remarkable of all bird nests made almost entirely out of cobwebs and lichen, lined with about 1,500 small feathers, and suspended in the small branches of, usually, thorny bushes. The nest is domed and has a small entrance hole in one side. It is elastic and remarkably strong. It needs to be because it will expand as the brood of 8-12, sometime more, grows.

Long-tailed tit's nest. Cobwebs and lichen.
I still remember finding my first long-tailed tits nest and taking one of the eggs for my collection when this was still legal in the UK in about 1957. I carried the miniscule egg home using an old egg-collector's trick when climbing back down a tree - placing it carefully under my tongue and keeping the tip of my tongue pressed against my lower teeth while riding home on my bike. I even succeeded in blowing it! I have even taken an incubating bird out of the nest and put it back in again and it continued to sit tight.

All this is thankfully illegal now but we really weren't aware of conservation issues then and, as a ten year-old inveterate collector of everything from birds eggs, to skulls, fossils, pressed leaves, and bird wings (taken from road and rail kills), adding another egg to my collection was probably uppermost in my mind. It's now illegal to disturb a nesting bird or to take wild bird eggs in the UK.

Anyway I digress.

Part of a winter flock (Japan)
What we have in the long-tailed tit is a lovely example of evolved altruism - something that creationists purport not to be able to understand, even claiming it's impossible for 'selfish' Darwinian evolution to create altruistic behaviour. This is either because they genuinely don't understand evolution or more probably because they are playing to an ignorant audience who like to imagine the only reason for altruism is because of the rewards their imaginary magic friend will give them later.

The obvious fact that altruistic and cooperative behaviour frequently evolved simply because that gives greater success than non-cooperation and selfishness, seem incomprehensible to them, but then the do earn their living selling lies, misinformation and spurious confirmation of their bias to ignorant and self-important people for money. Their failure, feigned or otherwise, to comprehend anything good being done if not for a reward, speaks volumes of creationist pseudo-scientists.


Due to high predation, there is a high nest failure rate. If nest failure occurs after the beginning of May, failed breeders will not try to re-nest, but may become helpers at a nest of another, usually related, pair. In one study, around 50% of nests had one or more helpers. By helping close relatives, helpers gain indirect fitness benefits by increasing the survivability of related offspring. Helpers may also gain greater access to mates and territories in the future. Helpers also gain experience raising young and therefore their future offspring have greater survivability rates.

Males and females are equally likely to become helpers. Parents may allow the care of helpers to be additive to their own efforts, or on the other extreme, they may reduce their efforts with the care of the helpers. Juvenile males have a higher survivability than juvenile females, although the survival rate for adults of the two sexes is the same. Offspring that were raised with helpers have a higher survivability than offspring raised without. Failed breeders that became helpers have a higher survivability than failed breeders who did not. This may be because of the reduced energy expenditure from sharing a nest. This is similar to Acorn Woodpeckers and Green Wood Hoopoes. However, failed breeders that did not help are more likely to breed successfully in subsequent years, so there may be a cost of helping. This may be due to helpers having relatively poorer body conditions at the end of the breeding season, similar to Pied Kingfisher and White-winged Chough. Successful breeders have a survivability rate around the survivability of failed breeders who became helpers1.

  1. Mcgowan, Andrew, Ben J. Hatchwell, and Richard J. W. Woodburn (2003). "The Effect of Helping Behaviour on the Survival of Juvenile and Adult Long-tailed Tits Aegithalos Caudatus". Journal of Animal Ecology 72 (3): 41-99

Next season's altruistic gene carriers
The only requirement for altruistic behaviour to evolve is that it results in more copies of the genes for it than alleles of those same genes which do not support it. In the case of the long-tailed tit, the 'helpers' are almost always the siblings of the parents which have either not bred or have lost their brood to a predator. Long-tailed tits are extremely gregarious and sociable animals with family groups normally banding together into small flocks in the winter. Walk through any UK woodland in winter and you will frequently become aware of a lot of small birds around you, keeping in touch with high-pitched tweets and foraging for small insects.

Because these flocks still stay in contact during the spring and summer, those helping to rear another pair's young will have a high probability of carrying the same genes as the young they are helping to rear. It has been shown that broods reared with helpers will be larger and more successful than those reared without help. There is no mystery to it because one thing follows inevitably from the other. Altruistic behaviour produces more copies of the genes for altruistic behaviour than non-altruistic behaviour produces copies of those genes for non-altruistic behaviour. There is no morality involved and no conscious decision to be kind. The genes for altruism are no less 'selfish' than they ever were.

Selfish genes produce altruistic behaviour if this results in more copies of themselves and in an otherwise weak and vulnerable, highly predated species like the long-tailed tit and humans evolving in leopard and lion country, this is usually the case. An example of evolved moral behaviour.

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Tuesday, 15 July 2014

A Message From 270 Million Years Ago

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

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

Exceptionally preserved Early Permian tetrapod trackways from the Orobic Basin (Central–Western Southern Alps) offer a unique opportunity to investigate in detail locomotion in fossil vertebrates that lived on continental European landmasses. Herein are reported the results of a study on several tetrapod trackways that display a large variety of behavioral, gait and substrate related extramorphologies. They clearly document the transition from terrestrial–underwater walking to swimming and are assigned to the compound ichnotaxon Batrachichnus C Lunichnium. The use of the “C” symbol is here introduced for the first time as nomenclatural indication of a Compound trace. Producers were probably small-sized temnospondyl or lepospondyl (microsaurs) amphibians. Comparisons with living urodelan anatomy and mechanics provide evidence for conservatism of locomotor mechanics in evolutionary history among amphibians. The derived model for locomotor kinematics in Early Permian amphibians provides a reference for interpreting transitional land-to-water trackways. The shift from walking to swimming behavior in early tetrapods, as in extant urodelan amphibians, is described as a complex balance between different dynamics.

Fabio M. Pettia, Massimo Bernardia, Miriam A. Ashley-Rossc, Fabrizio Berrad, Andrea Tessarollod, Marco Avanzinia;
Transition between terrestrial-submerged walking and swimming revealed by Early Permian amphibian trackways and a new proposal for the nomenclature of compound trace fossils;
Journal of Palaeogeography, Palaeoclimatology, Palaeoecology, P. 278-289 DOI: 10.1016/j.palaeo.2014.05.032

To begin with, the salamander was dragging its tail, showing the typical wiggling gait of salamanders and most tetrapodal reptiles which causes their tail to describe a series of curves. As it transitions to swimming all we have is the marks of the claws and the swirls left in the mud by the swimming motions.

This calls to mind something I was discussing only yesterday - how humans may well be the only species which can look at tracks like this and 'read' the information and build a narrative from it. We can see what I've described above, for example, how the salamander moved from shallow to deeper water and transitioned to swimming as it entered deeper water. So we know it could both walk and swim and was very probably semi-aquatic.

We can tell how big it was, that it had a long tail and that it walked with the typical wiggling gait typical of salamanders and lizards. This means we can begin to build an image of its basic body plan and especially how its limbs were attached to the rest of its skeleton.

Unlike mammals, dinosaurs and birds and the small mammal-like reptiles that survived the dinosaur mass extinction and evolved into mammals, the limbs of amphibians and lizards stick straight out from their body, then bend downwards at the elbow or knee joint. In birds, mammals and dinosaurs, the bend occurs at the joint with the pelvic or shoulder girdle. This means the spine can be kept in a straight line when walking, running or swimming and the weight of the body is supported on (normally) four limb with little muscular effort. Reptiles and amphibians need to use energy just to lift their body off the ground.


In typical early tetrapod posture, the upper arm and upper leg extended nearly straight horizontal from its body, and the forearm and the lower leg extended downward from the upper segment at a near right angle. The body weight was not centered over the limbs, but was rather transferred 90 degrees outward and down through the lower limbs, which touched the ground. Most of the animal's strength was used to just lift its body off the ground for walking, which was probably slow and difficult. With this sort of posture, it could only make short broad strides. This has been confirmed by fossilized footprints found in Carboniferous rocks.

So, we also know from that wiggly tail trace that the maker of those tracks belonged to a clade which may have been ancestral to our own but was not a member of our clade. A clade being a group that share a unique common feature. If we arrange species according to the features they have in common we end up with an evolutionary tree showing how we are related. It's fascinating to think that a little newt wrote all that information in the mud 270 million years ago and we can now read it. Our highly developed pattern-recognising ability and our deep-seated desire to tell the story allows us to read and understand that message and build a picture of its author.

These basic abilities have probably made us what we are today and created conditions in which evolving a brain capable of processing and interpreting this information and even relating it to others, especially our children who so can inherit our knowledge and stories, gave us a significant advantage over other evolving hominids in African and possibly Euro-Asia and allowed us to become the dominant and ultimately the only hominid.

Unfortunately, our ability to see patterns frequently where there are none and to invent stories to explain them, probably caused us to invent religions as simple narratives to explain what we did not understand. Some people are still unable to let go of the simplistic certainties that these simplistic explanations give them and accept that the real story was far more complicated and far more magnificent than pre-wheel Bronze-Age hunter-gatherers and nomadic goat-herders could ever have guessed.

So important is it to cling to these simple certainties that some people even go out and kill people who have a slightly different version of the same invented story.

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Christmas Tree Tease for Creationists

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

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

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.

Björn Nystedt, Nathaniel R. Street,, The Norway spruce genome sequence and conifer genome evolution;
Nature 497, 579–584 (30 May 2013) doi:10.1038/nature12211

This research was carried out by a team from Umeå Plant Science Centre (UPSC) in Umeå and the Science for Life Laboratory (SciLifeLab) in Stockholm, Sweden, led by Björn Nystedt. Apart from its economic importance in that it opens up avenues for plant breeding of this important commercial and ecological species, it is interesting from a evolutionary biology perspective too.

The genome is seven times larger than that of humans and has about 29,000 functional (protein-coding) genes compared to the 17,000 human functional genes, about which I blogged only recently. This of course begs the question, why does it need a genome seven times larger than ours for a functional genome of less than double the size of ours. And why does it take 29,000 functional genes to make a Christmas tree but only 17,000 to make a human being?

One way, common in plants, by which a genome can be increased in size is by gene doubling where a mistake in the production of the reproductive cells produces pollen or ovules with the full complement of chromosomes instead of the normal half set. If this is fertilised with a similar diploid gamete it can result in a tetraploid version. The Cox's Orange apple is a tetraploid apple, for example. Another way is a simple doubling of a length of DNA during its replication so the same length is replicated twice and becomes incorporated in the normal genome.

A third way is by using a crude, near enough is good enough approach to replication. Imagine you are a computer programmer who needs to write a routine for copying a table of data but you don't know how big the table is. So, you write a routine to copy a chunk at a time until you are well past the end of the table and just leave it at that. Much easier than including a routine to work out the exact end of the table and so the exact length of the last chunk to be copied.

You copy all the table and a lot of following junk as well. Next time the routine runs it copies everything you copied earlier and a whole lot of new junk as well. So far as the user is concerned, the table is there and all seems okay, until eventually the memory footprint of the application gets massive because your sloppy, near enough is good enough routine has filled up the hard drive. Not good programming, but evolution isn't bothered about the future because it can't plan. Near enough is good enough works for evolution because evolution is unplanned and utilitarian. As a piece if intelligent design however, it's stupid. The programmer should have been thrown off the programming course.

It is remarkable that the spruce is doing so well despite this unnecessary genetic load. Of course, some of this DNA has a function but it seems strange that it would be beneficial to have so very much. This appears to be something special for conifers.

Professor Pär Ingvarsson, UPSC
The pines are gymnosperms but the scientists who carried out this analysis point out that there is no such evidence of gene doubling in the gymnosperm lineage. The only feasible explanation is a gradual accumulation of mostly redundant DNA due to a faulty replication and a defective correction mechanism which, in other plants, helps correct this faulty mechanism. It's a normal feature of DNA replication in both animals and plants that the ends of DNA sequences are often replicated several times. These are replicated again in the next generation and, over time would lead to a huge amount of redundant coding. In most species this tendency is corrected and it is this which seems to have failed in the Norwegian spruce leading to this accumulation of DNA over about 200 million years.

Now, the obvious problem for creationist pseudo-scientists is how to handle this, apart from it needing 200 million years to accumulate.

Creationist Parodies
Creationism relies on perpetuating several myths about the science of evolution because these myths or parodies are what creationist pseudo-scientists earn their living attacking.

One of the myths is that biologists think that evolution is about how human beings came about and that the entire point of evolution has been to evolve human beings. This means that human beings have to be presented as the most highly evolved and most complex of species, at least in the pseudo-scientific view of evolution.

This is, of course, nonsense since evolution is all about how diversity arose and it has no aim or objective. No single species can be said to be more highly evolved than another since all living species have been diversifying for the same length of time. Never-the-less, if you go to a creationist website you'll see that parody of evolution attacked time and again.

Another myth is that evolution always involves increased complexity and new information. This makes it easier to attack evolution with a scientific-looking claim that it somehow contradicts basic laws of physics such as the Laws of Thermodynamics and some half-understood dogma that no new information can ever arise because that contradicts some fundamental law related somehow to thermodynamics too.

This too is nonsensical and based on a deliberate misrepresentation of the Laws of Thermodynamics, which neither preclude a local decrease in entropy nor prevent new meaning to existing information arising if the environmental context changes, or new information arising for that matter. If it did there could be no life because chemical processes could not occur, nor could automobiles work or any wealth ever be created by doing work.

Thirdly, creation pseudo-scientists present increased complexity in structure as reflecting increased complexity in the genome, so the more complex an organism is, the more complex its DNA must be. This plays to the myth that somehow DNA is like a computer program so more complex output must come from more complex input. This is also nonsense because DNA is more like a recipe than a construction manual. Complexity can come simply from switching controlling genes on or off at different times, hence the human genome has almost the same number of functional genes as chimpanzees and gorillas and only differs from that of a mouse by about ten functional genes. Same ingredients; slightly different recipe.

So, creation pseudo-scientist are faced with several dilemma here:

  1. How do they explain a manifestly less complex organism like a Norwegian spruce having such a vastly more complex genome and almost twice as many functional genes as humans? If their parody of evolution was correct, humans would have the most complex genomes.
  2. If additional DNA means additional information, what new information is there in all the redundant DNA in Picea abies and why does a spruce need seven times the information that humans need?
  3. How do they explain a species which diversified from the last common ancestor shared with humans about 500 million years ago having a more complex genome than humans? If their parody of evolution was correct the human genome should be the largest because humans are the most highly evolved of all creatures.
  4. How do they explain such a huge genome with so much redundant DNA? Why would any intelligent designer create so much redundant DNA?
  5. How do they explain a faulty DNA replication mechanism which needs an error-correction method to prevent it running out of control in the first place, and why would an intelligent designer then break the correcting mechanism it designed to compensate for its earlier mistake?

So what's it to be creationists?

Are you going to claim that the Christmas tree is more complex and more highly evolved than Humans; that genome complexity does not mean new information and increased phenotypic complexity or that the Intelligent Designer just messed up with the Christmas tree? Answers below, please.

I'll leave the problem of the salamanders with their huge genomes for another day.

*© 2013 Nature Publishing Group.
Reproduced for non-commercial/educational use under Creative Commons license (Attribution-Noncommercial 2.5)/

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Sunday, 13 July 2014

Catholic Church "Untrustworthy"

The Catholic Church in Germany is witnessing an astonishing collapse in public trust and is haemorrhaging members at an unprecedented rate. According to a Forsa poll recently 65% of Germans said they found the Catholic Church untrustworthy.

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

In Germany, a tax is levied on church members by the government unless they specifically deregister from the church with the local town hall. Officials in city after city across Germany have reported a huge increase in deregistrations not only from the Catholic Church but also from Protestant churches following this scandal. This has been dubbed the 'Tebartz effect' by officials.

Bishop Franz Peter Tebartz-van Elst, "The Bishop of Bling".
In Cologne the numbers deregistering from the Catholic Church doubled in October 2013 compared to the previous month and deregistrations from the Evangelical Protestant Church rose by 80 percent with long queues forming. In Paderborn, also in North Rhine-Westphalia, Catholics deregistrations tripled over the same period. Osnabrück and Bremen also reported increases.

The largely Catholic state of Bavaria also saw huge rises in deregistrations. In Munich the number double to 1250 and it tripled in Regensburg, Nuremberg and Passau between September and October 2013.

Detlef Pollack, a sociologist from Münster University, said that this sudden jump is part of a steady trend away from religion in Germany as living standards and standards of education rise.

This news is another blow for German Christianity following a poll by Forsa in former East Germany which found 52.1 percent self-identify as Atheists and only 25 percent self-identified as religious. Even more troubling for the Church, the same poll failed to find a single East German under the age of 28 who did not self-identify as Atheist! Many young people are still voluntarily undergoing a sort of Atheist confirmation ceremony known as Jugendweihe (literally, youth consecration) which was introduced under pre-unification Communism. The Protestant church in former East Germany is now losing twice as many members per year as it gains.

As Peter Thompson of the Guardian, writing before the 'Tebartz effect', pointed out, this process is not confined to Germany but is following the same trend across Europe:

Secularisation processes are under way throughout the continent and the role of religion and the church in modernity are being questioned everywhere, from gay marriage to women priests to abortion and on to whether the EU should identify itself as a Christian entity. The question should perhaps be whether it is actually folk atheism that represents the future of Europe.

The idea that the EU should formally identify itself as some sort of Christian entity is absurd given this steep decline in Christianity in member states and Christianity's increasing association with the conservative, authoritarian and reactionary wing of politics in an increasingly secular, Atheist Humanist Europe.

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Friday, 11 July 2014

Of Mice and Men and Evolution

Source: Iakes Ezkurdia, et. al., Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes*
Size of the human genome reduced to 19,000 genes - ScienceDaily

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

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

They also found no protein-coding genes unique to Homo sapiens and not common to all primates.

Their work has reduced the size of the functional human genome by a further 1,700 to just 19,000 functional genes, on the basis of a functional gene being one which codes for a protein. This is well below the original estimate of around 100,000 genes.

Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort. [My emphasis]

Iakes Ezkurdia, David Juan, Jose Manuel Rodriguez, Adam Frankish, Mark Diekhans, Jennifer Harrow, Jesus Vazquez, Alfonso Valencia, and Michael L. Tress
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
Hum. Mol. Genet. first published online June 16, 2014 doi:10.1093/hmg/ddu309

Our figures indicate that the differences between humans and primates at the level of genes and proteins are very small. The number of new genes that separate humans from mice may even be fewer than ten.

David Juan (one of the authors)
Apart from its significance for the Human Genome Project, the interesting result from this study is just how few new proteins it takes to make a new species and even whole new orders and families. It is becoming increasingly clear that it is not the number of proteins and so the number of genes coding for those proteins which matters so far as the difference between taxons is concerned but how they are uses, and especially how the genes are controlled.

The minor anatomical and physiological differences between Homo sapiens, Pan troglodytes, P. paniscus and Gorilla gorilla is probably almost all down to how and when genes producing controlling protein enzymes were switched on or off during embryological development, resulting in relative differences in the sizes of the same basic skeletal elements, muscles, brain and other organs. The same goes for the differences between a mouse and a primate or between a mouse and any other mammal. In other words, the same basic recipe, varying the ingredients and cooking times slightly, can produce a different cake. There is no real increase in complexity involved.

This piece of research, and the fact that it does not cause major ripples in the world of evolutionary biology or taxonomy because anyone who knows anything about the subject understands how it merely confirms what was already understood, highlights how far evolutionary biology differs from what creationists pseudo-scientists tell their audience evolution is. Creationist continue to attack an increasingly surreal parody of evolution which has become almost unrecognisable even in parody.

Despite the growing evidence that evolution does not necessarily involve any increase in complexity, we still get this blatant lie from creationists:

The popular syndicated columnist, Sydney Harris, recently commented on the evolution/entropy conflict as follows:

There is a factor called "entropy" in physics, indicating that the whole universe of matter is running down, and ultimately will reduce itself to uniform chaos. This follows from the Second Law of Thermodynamics, which seems about as basic and unquestionable to modern scientific minds as any truth can be. At the same time that this is happening on the physical level of existence, something quite different seems to be happening on the biological level: structure and species are becoming more complex, more sophisticated, more organized, with higher degrees of performance and consciousness.

As Harris points out, the law of increasing entropy is a universal law of decreasing complexity, whereas evolution is supposed to be a universal law of increasing complexity. Creationists have been pointing out this serious contradiction for years, and it is encouraging that at least some evolutionists (such as Harris) are beginning to be aware of it.

How can the forces of biological development and the forces of physical degeneration be operating at cross purposes? It would take, of course, a far greater mind than mine even to attempt to penetrate this riddle. I can only pose the question - because it seems to me the question most worth asking and working upon with all our intellectual and scientific resources.

This, indeed, is a good question, and one for which evolutionists so far have no answer. Some have tried to imagine exceptions to the Second Law at some time or times in the past, which allowed evolution to proceed in spite of entropy, but such ideas are nothing but wishful thinking.

The late Henry M. Morris, PhD, a hydrology engineer, not a biologist, was co-founder of the Institute for Creation Research. Sydney Harris was a journalist for the Chicago Daily News with no scientific training or qualifications. Despite the fact that this argument is easy to refute, and has not been revised since the 1980s, it is still trotted out regularly by creationist pseudo-scientists to misinform their audiences. A hydrolics engineer quoting a scientifically ignorant journalist and pronouncing authoritatively on biology and physics is considered perfectly good science in creationist circles, apparently.

Entropy, of course, only applies to a closed system which, for all practical purposes means the entire Universe. There is nothing in the Second Law of Thermodynamics which precludes a decrease in entropy in an open system if energy is supplied to the system, as it is with a biological organism in the form of nutrients and oxygen - energy which derives ultimately from the sun. It's as simple as that. If you want it said in a more detail see PZ Myer's blog, Entropy and Evolution.

With typical dishonesty, playing to the scientific ignorance of his audience, Morris waved aside this fundamental principle of science with:

It is amazing how many anti-creationist debaters and writers try to "sidestep" this serious problem with such a simplistic cliché as this. Creationists who cite the entropy principle against the evolutionary philosophy are, time and again, dismissed as either ignorant of thermodynamics or dishonest in their use of the second law. Such charges are inappropriate, to say the least.

In the first place, the entropy principle applies at least as much to open systems as to closed systems... [My emphasis]

Henry M. Morris, PhD; Op. cit.

He then follows this with an almost surreal piece of misinformation about thermodynamics followed by almost equally surreal display of misinformation about evolution:

Thus entropy in an open system always at least tends to increase, no matter how much external energy is available to it from the sun or any other source. To offset this tendency, the external energy must somehow be supplied to it, not as raw energy (like a bull in a china shop) but as organizing information. If the energy of the sun somehow is going to transform the non-living molecules of the primeval soup into intricately complex, highly organized, replicating living cells, and then to transmute populations of simple organisms like worms into complex, thinking human beings, then that energy has to be stored and converted into an intricate array of sophisticated machinery by an intricate array of complex codes and programs. If such codes and mechanisms are not available on the earth, then the incoming heat energy will simply disintegrate any organized systems that might accidentally have shown up there. [My emphasis]

Henry M. Morris, PhD; Op. cit.

And so the late Dr Henry M. Morris, spiritual founder of modern Young-Earth Creationism, displayed his dishonesty, prowess at building straw men, almost complete ignorance of basic physics and a cavalier attitude to the truth - to put it mildly. It's hard to imagine that even someone with an engineering degree would not have a grounding in basic science.

But all that is irelevent, and another creationist straw man anyway, because, as we are now understanding, there need be no increase in complexity whatsoever in evolution. All that is needed is a small change in the way genes are controlled by other genes. Studies such as that by the Spanish CNIO team are showing that the difference between related taxons are actually very small and more apparent than real. Most shockingly for creationists and religious people who like to flatter themselves with the thought that they are so important a god must have created a Universe just so it had somewhere to put its special creation, human beings, science is increasingly showing that we are simply another evolved species and very little different to any other evolved species.

*© The Author 2014. Published by Oxford University Press.
Reproduced for non-commercial re-use under the terms of the Creative Commons Attribution Non-Commercial License (

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Wednesday, 9 July 2014

Germ Warfare in Brazil

Credit: Gleison Miranda/FUNAI/Survival
Uncontacted tribe in Brazil ends its isolation | Science/AAAS | News

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

The reason for the 'no contact' policy is because of the very real threat to isolated people from the viruses we often take for granted such as influenza, measles and mumps. Between 1983 and 1985 some 60% of the newly-contacted Nahua population died of influenza, whooping cough and other diseases caught from loggers.

This illustrates well how successful memeplexes called cultures, like successful genetic organisms, are those which form alliances, in this case the European memeplex has formed an alliance with its viruses which act like an invisible advanced guard which wages biological warfare on a rival group, so weakening them and opening the way to a takeover of the people, their land and resources. There is, of course, rarely any consciousness involved although there was at least one instance of deliberate biological warfare when blankets were deliberately contaminated with smallpox and distributed to Native Americans.

For the most part, as Jared Diamond pointed out in Guns, Germs and Steel, cultural success was more a matter of luck and incidental biology than it was about racial or innate cultural superiority. The reason Christianity spread throughout so much of the world was not because it was culturally superior to other cultures or because Europeans were racially superior to other peoples, but because Christians took their viruses with them, as well as their guns.

In the pursuit of their conversions, the Jesuits sought to undermine the authority of the village shamans (the traditional religious leaders) and to gain the confidence of leaders who could influence others. The Black Robes used a variety of weapons to attain the desired end. Trained in rhetoric, they won admirers by their eloquence. Seemingly immune to smallpox, they explained epidemics among the Native Americans as God’s punishment for sin, their arguments aided by the ineffectiveness of the shaman’s traditional remedies for illness against that deadly disease.

But why did Europeans have so many novel viruses to take with them and introduce to previously isolated people? Because we had the great good fortune to live in or close to a part of the world such as the Middle East where so many animals are domesticable. We had acquired a whole range of domestic animals like pigs, goats, horses, cattle, sheep, hens, ducks, geese, dogs and cats, and we lived alongside several comensual species like rats, mice and pigeons, often in very close proximity.

We probably acquired their viruses as well, or viruses very closely related to theirs like smallpox, which almost certainly evolved from cowpox when it crossed the species barrier and infect man. Very few people outside Europe and Asia had so many domestic animals simply because there were few which could be domesticated.

Sub-Saharan Africa, for example, has a lot of big game but almost none of it is easy to domesticate and European domestic animals have no immunity to the parasite carried by the tsetse fly. As Jared Diamond asked, how different would history have been if a nascent Roman Empire had faced a cavalry of Bantu mounted on rhinoceruses? We would now be relating how slave ships from Africa had raided Western Europe and carried off white people who would now be forming an underclass in many economically advanced West African states, or maybe a United States of Africa superpower, while Europe remained economically dependent, under-developed and depleted of resources carried of to build the great civilisations of Africa?

So, these previously isolated Amazonian people now face possibly one of the most dangerous phases in their history because they have now come up against a culture which has formed alliances with fatal invisible agents. There are estimated to be about seventy other isolated groups of Amazonians living in the Amazon Forest.

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Sunday, 6 July 2014

More Trouble Down Under for Paedo-Protecting Pope

"We will not take one step backward with regards to how we will deal with this problem, and the sanctions that must be imposed. We have to be even stronger". Pope Francis, 11 April 2014
In stark contrast to Pope Francis' public professions of sorrow and wheedling apologies for the Catholic Church's role in facilitating institutionalised sexual abuse of vulnerable children by it clergy, and his assurances that the Vatican will do everything to bring them to justice, the Vatican has declined to cooperate with an Australian Royal Commission set up to investigate abuses by Catholic priests in Australia.

As reported by Lindy Kerin for ABC News:

The head of the Royal Commission into Institutional Responses to Child Sexual Abuse, Justice Peter McClellan, revealed last month that he had personally written to the Vatican, seeking copies of all documents relating to complaints about abuse involving priests in Australia.

The Vatican has provided documents to the royal commission relating to two cases, but Justice McClellan wanted more information to find out how church authorities in Australia, under the guidance or direction of the Vatican, responded to allegations of abuse.

In a written response, the Vatican says the Holy See maintains the confidentiality of internal deliberations, adding that it would be inappropriate to provide such documents.

Last June, Justice McClellan revealed that the Royal commission had received accounts of abuse from over 1,700 individuals involving more than 1,000 institutions of which a significant proportion were faith-based. He said that the Royal Commission had written to the Vatican requesting copies of all documents held in Rome relating to complaints of abuse by members of religious orders. He said:

We have asked for copies of documents which reveal the nature and extent of communications between Catholic congregations in Australia and the Holy See. From these documents we should be able to determine how church authorities in Australia, under the guidance or direction of the Vatican, have responded to individual allegations of abuse.

He also reported that he had referred 160 matters to the police for investigation.

This latest obstruction from the Vatican comes as no surprise:

I'm not surprised ... I feel like the Catholic Church believes it is above the laws of Australia and probably the world. It's just a replica of their behaviour for the last 200 years in this country. It's treating the Australian public with contempt, and the royal commission as well.

Leonie Sheedy, founder and chief executive of Care Leavers Australia Network, a support group for victims of child sexual abuse

It's not as if there's no material at all in Australia to assist - there is - and it's been of use, But I would simply say that it will certainly prevent the inquiry being as thorough as the royal commission wish it to be, and it's a lack of cooperation that's disappointing but unsurprising.

The Vatican claims the status of independent nation and in those circumstances there's nothing which can be done by government, let alone by the royal commission, to compel it to produce documents.

Andrew Morrison, Australians Lawyers Alliance spokesman who has represented many victims of church abuse.

Once again we see that the Vatican's perception of the problem of sexual abuse of vulnerable people by those under holy orders is not in terms of the harm it did and continues to do to the victims, but in terms of the damage it is doing to the Catholic Church. This follows just a few months after the Vatican committee established to deal with the problem, advised the Italian College of Cardinals to invoke a clause in the Lateran Treaty of 1929 by which Italian priests can refuse to cooperate with the Italian authorities if it involves information learned in the confessional - again in contrast to the Pope's assurance that nothing would be concealed.

The instinct of Vatican officials is still to cover up and prevent the truth getting out into the public domain, and the current Pope, as with his two immediate predecessors, appears unwilling or unable to change that modus operandum. The code of omerta still rules in the Vatican and secretive, unaccountable background figures still appear to hold the strings.

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