Unintelligent Design

It's amazing how, when you have a modicum of understanding of evolution - and I like to flatter myself that I know a little about it - you can find examples of it in other areas of life, not just in biology.



While waiting for the powers that be at Twitter to get their act together and decide what to do about my @RosaResurrected account being suspended for reasons which they just don't seem to be able to put their finger on right now, I'm busying myself with a pass-time I've had for some ten years or so now. I'm a volunteer transcriber for the FreeBMD website. This charity aims to put the official indices (sorry spell-checker but I refuse to call them indexes) of English & Welsh births, marriages and death registrations on line in an easily searchable format for people who want to research their family tree. To date I've transcribed over 1.25 million entries though rather fewer in recent years than I once did.



It suddenly occurred to me how an aspect of it is an almost perfect analogy for a feature which can sometimes be hard for non-biologists to understand about evolution - how redundancy can be built in and retained and why inefficiency is not always eliminated.



Briefly, and without being too technical, the indexes we transcribe are scans of alphabetical indices to the actual registrations of births, marriages and deaths, since the second half of 1837, giving enough information for people to obtain a copy of the birth, marriage or death certificate if they require one. The indices themselves can be use to confirm the dates and places of the events and, in later years, the mother's maiden surname, the age at death, or the spouse's surname without needing to buy the certificates from the UK Government's General Registration Office. This, together with census records, is often all a genealogist needs to build up a family tree.



The software most transcribers use is WinBMD, a brilliant piece, designed by software devoloper Ian Brooke and intended to make the transcription process as fast and as accurate as possible. To that end, when entering the forename, the numbers 1-9 on the keyboard are predefined with what were the nine most common forenames in England and Wales. This list is user-definable but comes with default settings along with several other background files.



The 'problem' is that this list was derived from transcriptions from around 1850-1880 which were some of the earliest indices we transcribed. Obviously the fashion for forenames changes over time and what were the most common in those days are not the most common ones in use when transcribing the 1967 indices for example.



But users like me are now used to the list and know that pressing '5' will enter the name 'James' or that '3' will enter 'Elizabeth', etc. We don't want the list to change because we would have to get used to a new one and would probably keep selecting the wrong one while we learned it. By repetitive usage of the software we have developed a set of reflexes so that when we see 'John' we hit '6' or when we see 'Mary' we press '7'. For other names we start typing then select from a drop-down list by number - a drop-down list we've built up over the years by adding 'new' names to it when we transcribe them for the first time.



To learn a new common names list, or even just to change it slightly by reordering it, would slow down the transcription process and introduce possible errors, so we are stuck with an increasingly illogical and inappropriate list which becomes more out of date as time goes on, yet the investment in effort and loss of productivity entailed in changing it is never a cost worth bearing.



Just so with evolving organisms where an intelligent designer would be able to scrap an increasingly inefficient design and start afresh with a new improved version, whereas Darwinian Evolution never has any mechanism for a radical redesign because any tendency to do so will always involve a loss of efficiency, so any carriers of these genes will be less successful, not more, and so will be eliminated. The process of Darwinian evolution is invariable upwards towards peaks in the evolutionary landscape but only in very rare and exceptional circumstances, such as genetic drift in a non-selective environment, is evolution ever to able to move a very small way down this fitness landscape.



This is exactly what we see with the mammalian eye where a redesign would result in a better eye yet any moves towards rearrangement would produce a loss of function and a complete reorganisation with a single mutation is simply not possible because of the way the eye develops in the embryo. Not a problem for an intelligent designer, who would not have made such a silly mistake in the first place anyway, but quite impossible for Darwinian Evolution.



We see a very similar problem with the mammalian recurrent laryngeal nerve where, even in the giraffe with it's long neck, the nerve takes a ludicrously long path to get from the brain to the larynx - via the thoracic cavity where it passed under one of the aortic arches before going back up the neck again. This path made sense in our remote fish ancestors with their short neck where the heart lies just a little below and behind the brain, but with evolution's small steps forward and the impossibility of going backwards, we've ended up with an unintelligent design because the overall change led to more descendants and the one small step at a time lengthening of the nerve never gave a disadvantage large enough to counter the overall improvements.

The extreme detour of this nerve (about 15 feet in the case of giraffes[16]) is cited as evidence of evolution. The nerve's route would have been direct in the fish-like ancestors of modern tetrapods, traveling from the brain, past the heart, to the gills (as it does in modern fish). Over the course of evolution, as the neck extended and the heart became lower in the body, the laryngeal nerve was caught on the wrong side of the heart. Natural selection gradually lengthened the nerve by tiny increments to accommodate, resulting in the circuitous route now observed.

Wikipedia - Recurrent laryngeal nerve.

This is how we can tell that life is not intelligently designed. It quite simply isn't what an intelligent designer would end up with.



I hasten to add that Ian Brooke's WinBMD design is far from unintelligent but even he can't avoid his designs being subject to the natural force of evolution and so accumulating some of the features of it such as the increasingly inefficient yet not easily redesigned 'commonest' names list.

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Religion And The History of Censorship

The recent phenomenon of the mass blocking campaign on Twitter and the various attempts to shut down blogs and websites is just another manifestation of the fear of dissent and debate that has always gripped religions. It tells us a great deal about the honesty and integrity of those who promote religion and who are desperate to suppress criticism. It tells us they know they will lose the argument in a free and open debate. It tells us they know they are pushing a lie and that their greatest fear is that they will be rumbled. It tells us their agenda is not what they claim and that they are too ashamed to tell us what it is.



One might expect a belief founded on good, established and unarguable evidence and principles of logical deduction would be confident enough in its methodology and basic philosophy to not only tolerate and allow dissent and argument but to positively welcome it, confident that it can win all arguments and dispel all doubts by good, honest argument and a dispassionate examination of evidence. One might also expect such a belief to be prepared to reassess, adapt and change whenever new evidence is found.



This, after all, is the proven methodology of scientific debate. No scientist worthy of the respect of his/her peers would present a paper to an audience of fellow scientists and then refuse to answer questions and demand that doubters be removed from the auditorium and even prohibited from practicing science. No scientist would publish a paper in a journal and demand the editor refuse to publish any papers which weren't in full agreement with it.



In fact, we would be fairly sure that seeking to suppress dissent and discourage discussion would betray a distinct lack of confidence. We might well suspect some low skulduggery or dishonest dealings; a deliberate attempt to mislead, probably in support of some secretive vested interest or in pursuit of a hidden agenda.



So, because all religions claim to know the truth with complete confidence, shouldn't we expect them all to welcome dissent and debate, confident that their beliefs are going to be strengthened by the ease with which doubt can be dispelled and misunderstandings or misinterpretations can be corrected?



Only if you are naive in the extreme.



Even the slightest contact with religion will show you that the last thing they will tolerate is doubt and disbelief. If you want to lose a religious friend, tell them you think their religion is wrong and another is right. Better still, tell them you think all religions are delusions and that only atheism makes any sense when the evidence, or lack of it, is examined objectively, honestly and dispassionately. Every atheist in the closet will tell you it's their religious friends' reactions they fear most.



No religion in the history of religion has ever tolerated dissent when it has had the power to prohibit it. They have all been keen on religious freedom when they were small minorities but that support is always inversely proportional to their strength in society. When they have gained absolute power, dissent is the first thing to be banned and no measure is considered too extreme to enforce it, as the long bloody history of religious persecutions, massacres and genocides shows. When the printing press was invented their first reaction was to control it and proscribe any printed matter which questioned religious dogma and especially religious authority and privilege.

Religious censorship is a form of censorship where freedom of expression is controlled or limited using religious authority or on the basis of the teachings of the religion. This form of censorship has a long history and is practiced in many societies and by many religions. Examples include the Edict of Compiègne, the Index Librorum Prohibitorum (list of prohibited books) and the condemnation of Salman Rushdie's novel The Satanic Verses by Iranian leader Ayatollah Ruhollah Khomeini.77

Wikipedia - Censorship by religion

The antics of religious fundamentalists and creationist frauds on Twitter is the equivalent of shouting, "Shut up! Shut up! La la la la la! Can't hear you!". Like frightened rabbits caught in the glare of headlights they've panicked and resorted to the only method they know - suppression and censorship, imagining that questions go away and arguments are won by ignoring them. And in so doing they've drawn attention to themselves, to the dishonesty of their faith and and to their own awareness of its fraud and vacuosity.



They have shown the world they know their faith is a lie and is used as an excuse for attitudes and behaviour which would otherwise be unacceptable in a decent society not conditioned to think of piety as something to be admired and of faith as a virtue.



But don't treat these frightened little rabbits as a joke, laughable and pitiable though their antics might be and how cowardly and socially inept they might be as individuals. The real lesson here is what these inadequate little people would do to other people in real life if only they had the power. The great challenge of the growing atheist movement is to make sure that we will never ever make the mistake of finding out. As it is the worst they can do is to sit in their rooms cowering in fear at what the next unanswerable question might be, what challenge they will need to run away from next, how much longer a pretence of piety is going to work as an excuse, and fantasising about what they would like to do to the person who had the temerity to stand up to them.



It's better they stay that way and hopefully never realise that their behaviour on the Internet is probably the biggest single cause of the recent phenomenal growth in atheism.

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Thanks For Your Support

Very many thanks to my many supporters on Twitter for your continuing support. It is very much appreciated and more than a little humbling. I see that some have offered to tweet links to my blog in my absence. This would be very much appreciated, as would posting links on other media such as Reddit and Facebook.



I'm hoping that Twitter will reinstate my @RosaResurrected account soon but given their refusal to with @RosaRubicondior one never knows. As with @RosaRubicondior, there is still no response from Twitter Safety to multiple requests for an explanation in terms of specific tweets and the rule(s) they breached, so I am left wondering what to avoid tweeting even if I am reinstated.



Is there anything specific or does their silence indicate that they don't have anything specific either, and have effectively handed over policing of Twitter to whicher cabal of extremists and control freaks can organise a mass censoring of opinions they don't want people reading? Spam-blocking may have originally been a means of reporting actual spamming but even a single original tweet can be reported as spam with no comeback on the person who is effectively filing a false report. Lies or genuine, it seems to make no different to the way Twitter handles it.



I suspect to avoid another suspension I would have to refrain from tweeting anything promoting atheism and anything critical of religion and creationism. I short, I would have to desist from exposing bigots, frauds and liars. I wonder it that's what Jack Dorsey had in mind when he set Twitter up.



One thing I am becoming convinced of is that the spam-block option on Twitter is their cowardly way out of bothering to police Twitter effectively - which would require staff, money and training. Spamming is quite simply not an abuse on the scale of threats of violence, lies, harassment, personal abuse, racism, sexism, child pornography, etc and can be handled just as effectively by blocking if a user does not want to see repeated tweets, advertising, etc.



On the other hand, spam-blocking, when used to trigger a suspension, puts another form of abuse in the hands of abusers to be used apparently with impunity - the unjustified suspension, and effective censoring of adverse opinion - which I would suggest is a far more serious form of abuse than spamming. Apparently when the 'secret' is known, by using spam-blocking at the right time, a user can be suspended almost instantaneously.



By contrast, I have now had outstanding for 8 days another explicit threats of actual violent to myself and my family from a Christian with nothing more that an automated acknowledgement. Recently it took Twitter 12 days to respond to a series of explicit death threat and then their action was a polite reminder to the abuser that threats are against the rules and please don't do it again. I say again: this was a response to a repeated death threat!



I also have outstanding complaints against a particularly obnoxious and probably clinically insane individual with a history of abusive tweets who currently has several accounts suspended, some for threats of sexually explicit violence against women. This has remained unanswered for 12 days following the standard acknowledgment.



All this make one call into question Twitter's handling of complaints when organised triggering of some algorithm can instantly auto-suspend an account without any checking, yet explicit death threats, threats of violence again a user's family and a continued campaign of harassment goes unchecked because it doesn't trigger an automated response and the few staff dealing with these complaints haven't gotten round to it yet, and can then only select a response from a pre-defined drop-down list.



Once again, thanks for your continued support, and thanks in advance for anything you can do to promote my blog and particularly the message it contains for truth, honesty, humanism and respect for all people.



I think it's time we organised a campaign to make Twitter more responsible in the way it handles abuse.

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How Early Cells May Have Got Complex DNA

DNA-grabbing bacteria hint at early phase of evolution - life - 26 September 2013 - New Scientist



How did the simplest cells early in the evolution of life build their DNA?



It has always been assumed that DNA evolved by three separate processes:

1. DNA transfer between living organisms.
2. Sexual reproduction where DNA is shuffled with that of a partner to produce descendants with different combinations.
3. Random mutation with natural selection sieving out the less fit mutations and favouring the more fit ones.

Now we can add a fourth: mopping up pieces of DNA from dead and decaying organisms and possibly viruses and incorporating them into the genome where they will be replicated in future generations.



DNA is notoriously stable as a molecule, which is why it can be recovered from long-dead bodies, dried up smears of body fluids and the partially fossilised remains of Neanderthals, mammoths and ancestral horses. Genetic material would have been more abundant in the environment in which early cells were evolving than in an adolescent boy's bedroom, especially since, prior to the evolution of photosynthesis, there would have been very low levels of free oxygen.



Søren Overballe-Petersen of the Natural History Museum of Denmark in Copenhagen found that when he fed fragments of DNA to a culture of Acinetobacter baylyi they were passively absorbed. They even absorbed fragments of 43,000 year-old mammoth DNA. The fact that this was a passive process suggests it may be a very primitive ability. By contrast, assimilating pieces of DNA passed across from another microorganism takes at least 40 genes.



So we have the possibility that very early cells acquired pieces of DNA from that sloshing about in their environment and that natural selection did the rest, sieving out those new combinations which were less successful at surviving to replicate and allowing through those which gave most descendants. With possibly billions of cells taking part in this process, it would have very quickly led to the accumulation of more and more complex and successful genomes. And of course the most successful organisms left more DNA fragments for others to mop up when they eventually died, so 'success' was not only inherited by descendants but could be picked up by the descendants of less successful organisms.



References:

Michael Marshall, DNA-grabbing bacteria hint at early phase of evolution, New Scientist Magazine issue 2936, 26 September 2013.

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How Can You Tell A Creationist Is Lying?

Entelognathus (Image: Brian Choo)

Fish fossil suggests our skeleton evolved face first - life - 25 September 2013 - New Scientist



Obviously you can tell when a professional creationist, like those who are paid to lie by the Discovery Institute, are lying because their lips are moving. What I'm talking about are the bog-standard creationist such as those who swarm onto the Internet every day to try to convince people they know more than biologists do about biology, more than geologists do about geology and more than physicists and cosmologists do about physics and cosmology and who can even spell the odd word of more than two syllables.



One sure fire way to tell they are lying is not so much the patently ludicrous claims they implicitly make about their own expertise and qualifications in science but the way the things they claim are not supported by the real-world facts.



One such patently false claim is that there are no transitional fossils as is predicted by Darwin's and Wallace's theory of descent with modification, and so no evidence to support the idea that living species evolved and diversified over time from earlier common ancestors.

Manta rays. More primitive?

As the above article in this week's New Scientist shows, these are in fact common in the fossil record. One such is the recently-found Entelognathus, a fish clearly displaying transitional features showing how bony fish evolved from the extinct primitive common ancestor of the bony and cartilaginous fish known as the placoderms.



To the consternation of creationists, Entelognathus from 419 million years ago, found very well preserved in a quarry near Qujing, Yunnan, China, has a typical placoderm skull and body and the jaw of a typical bony fish almost identical to that found in modern bony fish - features which were later to evolve into the typical amphibian, reptilian, mammalian and avian jaws in the descendants of those bony fish which evolved into the terrestrial vertebrates.



The find also suggests that, contrary to popular opinion which has sharks and rays as the more primitive fish because they lack the bones of bony fish, having cartilage instead, they may be the more highly evolved in they they could have replaced bone with cartilage. As so often with science, an answered question simple poses some more unanswered ones, and so we progress.



Just another transition fossil for creationists to lie to us about as they wait forlornly for a single drop of evidence supporting their infantile notion to be found, whilst trying not to see the tsunami of evidence for Darwinian Evolution engulfing them.



Reference:

Colin Barras, Fish fossil suggests our skeleton evolved face first, New Scientist, 25 September 2013 (subscription required).



Min Zhu, et al; A Silurian placoderm with osteichthyan-like marginal jaw bones, Nature, 2013

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Suspended Again

Sac O' Doughnuts

Yep! My Twitter account (@RosaResurrected)has been suspended again, and once again no specific reason has been given nor offending tweet identified.



And once again little Manuel de Dios Agosto is quite beside himself with delight and trying to claim the credit for it because he was once publicly humiliated by having to run away from a simple debate his infantile boasting had gotten him into, so exposing his claims of expertise in both science and theology to be fraudulent.



But before my followers understandably retaliate by filing complaints about him and his many accounts in an attempt to get him banned, think on what I said last time something like this happened.



Imagine what it would be like to have to live out your entire life fantasising and boasting about yourself on Twitter because your life is so meaningless and devoid of reason that you have no social life outside your room and the responses you can provoke on Twitter by being an unpleasant little abuser, liar and general nuisance. Your only claim to fame and your only sense of achievement came from conning a handful of credulous simpletons into believing that you were personally responsible for getting someones Twitter account suspended! And all this while desperately hoping no one makes public the reason you were expelled from seminary - the reason you have been ostracised and confined to your room by your community in the first place.



Do you really want to be responsible for depriving little Manny of the one thing he's achieved in life - being the reviled laughing stock of the Twitter #Atheist hashtag?



I'm not telling you what to do, merely asking you to consider the humanitarian aspect first.



A more effective remedy might be to get a campaign going to make Twitter adopt a fairer and consistent policy which is not open to the abuse of mass spam-blocking and in which offenders are given a specific reason for a suspension, including the offending tweet and the rule it contravenes, together with a right of appeal and review.

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Religious Sneaks

Why is God suddenly so big in the schools we all pay for? Zoe Williams, The Guardian



This article by Zoe Williams (@zoesqwilliams) reveals how religions - for that read religious people - are using the underhand tactics of the sneak who has no regard to democracy and whose morals are those of the market place where the bottom line is all that matters, to force their religion onto the most vulnerable section of UK society - our children.



The degree to which this is driven not so much by a misguided humanitarian motive (to be charitable to them) but by the perceived need to maintain control of the people through established religion can be gauged by the way it is being actively facilitated and encouraged by the right-wing coalition government with its cabinet full of aristocratic multimillionaires and public school grandees.



As Zoe Williams points out:

..what we're watching is the steady takeover of provision by groups whose influence is the result of something other than majority support. A freedom of information request by the Guardian revealed that 25% of free schools were faith schools. The true figure is higher, since a free school can have a "faith ethos" without being declared a faith school. There is massive variation in how many non-faith pupils a school will take, and the processes are opaque.



<snip>



We are a largely secular country. Only a third of adults even approve of state funding for faith schools, over half actively disapprove, and no more than a quarter of parents would be happy to send their children to a faith school. Well, parents are pragmatic, and there is plenty of expedient religiosity, which then raises accusations about the sharp elbows of the middle classes – an attempt to blame individual parents for a dishonesty that is built into the system. – we are handing over to religious institutions the education of the children of people who don't believe in God.



<snip>



[Accord Coalition] research shows that where fair admissions are being compromised, and the school intake does not reflect the social profile of the area, faith schools are the worst – their ranks include 18 of the 20 least representative schools, and 70 of the top 100.



There are schools in that bottom 20 where only 6.3% of the pupils are on free school meals [a measure of social deprivation], against 48.7% in the local area. That area, incidentally, is Hammersmith and Fulham, which has a preponderance of highly selective faith schools. The disadvantaged kids there are being systematically concentrated into the remaining, non-faith schools. This is social apartheid – a paradox, given that church schools only sprung up in the first place to educate the children of the poor.

Zoe Williams, Why is God suddenly so big in the schools we all pay for? The Guardian, Thursday 26 September, 2013

For those not familiar with the UK education system, the huge majority of children were educated until recently in schools run and regulated by the Education Departments of democratically-elected Local Authorities. Some of these were financed partly by Anglican and Catholic churches and Jewish communities as faith schools in which faith was a part of the daily life but the children were taught according to a national curriculum. A small number of children went to 'academies', which had started out as sixth-form colleges where children were prepared for A-level exams and then university. A small number, almost all the children of the rich, went to private schools confusingly and for historic reasons we needn't go into here, called Public Schools. A tiny number were educated at home under strict Local Authority supervision. It is a criminal offence in the UK to not send children to school or to provide them with an approved education between the ages of five and sixteen.

Michael Gove, Secretary of State for Education

Recently spent taxpayers' money to provide a new Bible

for every state school

The Coalition Government has now encouraged a vast expansion of the academies to cater for all ages and removed them entirely from Local Authority (i.e., democratic) control and placed them in the hands of boards of governors nominally accountable to parents but in practice, accountable only to themselves and their financiers. The plan appears to be to eventually take all schools away from Local Authorities and remove all democratic controls from them. The Tories seem to have noticed that it is invariably the wealthy middle classes who participate as school governors and who bother to turn up for meetings. In effect, the plan is to give control of education over to local Tories without them needing to bother with elections and all that democratic unpleasantness.



Some of the Christian groups are little more than chapters of American neo-con creationist Christian groups and cults. Needless to say, religious groups have seen this removal from democratic controls as a golden opportunity to get access to our children at their most susceptible and to indoctrinate them with the fear, superstitions and distrust of science and real-world evidence which will be used to control them later on as adults.



The British Humanist Association ran a partially successful campaign to force the Secretary for Education, Michael Gove, to ban the teaching of creationism, including it's pseudo-scientific under-cover version, intelligent (sic> design in faith schools, some of which had been actively advertising the fact that they intended to lie to children and tell them it was a valid scientific theory of the origin of life, so helping cast doubt in their minds about the validity of the scientific method and the integrity of the scientific community.



Eventually we managed to get assurances that teaching creationism in any form as as science would not be tolerated and that funding would be withdrawn from schools which did so. See I Have Mail. Seeing this as a bit wishy-washy with nothing to say how these schools would be monitored I asked my MP, Nichola Blackwood, MP (Oxford West & Abingdon) a right-wing Christian Tory who narrowly beat the Atheist Humanist, Dr Evan Harris in the 2010 General Election, to take up these concerns with the Department for Education. The email exchange can be read in I Have More Mail.



But it seems the systematic teaching of lies in pursuit of a religious agenda is not the only problem faith-based schools present and which even this right-wing government has been forced to control. They are now giving free reign to their class bias and creating poor, deprived ghetto schools as dumping-ground for the children of poor parents and those who are not dishonest enough to pretend to be religious and stump up donations to the local church, synagogue, mosque or temple. In short, they are creating social apartheid, and see nothing wrong with it.



One lesson from all this is that faith groups cannot be trusted when freed from democratic controls and jump at the chance to be undemocratic, unaccountable, prejudiced, selective and autocratic whenever the opportunity arises. In short, the temptation to be anything but decent humanitarians, even in the matter of educating our children, is too much for them to resist.



Faced with the haemorrhage of membership and drought in the income stream in recent years, religions have fallen back on their basic instinct for the dishonest tactics of the sneak and the parasite again.



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Apologists' Dilemma

Universe's baby pictures suggest a bubbly birth - life - 19 September 2013 - New Scientist



In this week's New Scientist we have another example of how detached modern religious apologetics has become from reality. The above article deals with the science behind the origins of our Universe and never once needs to invoke magic or deities. Instead it offers evidence for an explanation which has been mooted for many years - that our Universe arose by a perfectly natural (albeit difficult to comprehend) process, from a pre-existing metaverse. Nor is intuition invoked or an insistence that the explanation has to be easy to understand by people with little or no understanding of physics or advanced mathematics.



Contrast this with my recent public debate with Christian Apologist, Richard Bushey, who was trying to argue the line William Lane Craig takes that the so-called Kalam Cosmological Argument (KCA) leads to only one possible conclusion - that the Universe was created by magic by the locally popular god, who of course just happens to be the Christian one of whatever denomination you had the great good fortune to be born to parents who were believers of.



A great deal of that debate centred around the question of whether, even if we ignore the evidence of quantum mechanics that quantum events, of which the Big Bang is an example, do not require a cause, and that causality is a property of Relativity not of quantum mechanics, we have still not established that the only cause of the Big Bang must be supernatural because nature did not exists prior to it.



In fact this conclusion of the KCA is not only based on the circularity of assuming a priori that the god in the conclusion existed and was the only entity capable of creating a universe, but it also relies on the scientific ignorance of it's target audience. Any reading of the readily available literature will show that science offers several possible, perfectly natural, explanations for what the Big Bang could have occurred in and what could have caused it.



In this New Scientist article compelling evidence from a detailed analysis of the Cosmic Microwave Background (CMB) (the 'echo' of the Big Bang and one of the strongest pieces of evidence for it) suggests our Universe could have arisen by a process termed 'bubble nucleation'.

In this picture, our universe arose from quantum fluctuations in a much bigger cosmos called a metaverse. The quantum effects caused a phase transition in the fabric of the metaverse, and our universe popped into being, like an air bubble forming in boiling water.

Andrew Liddle of the University of Edinburgh, UK, quoted in Universe's baby pictures suggest a bubbly birth by Lisa Grossman, New Scientist, 19 September 2013, Magazine issue 2935

Incidentally, I could almost kick myself that in my debate with Richard Bushey I completely forgot Stephen Hawking's 1993 book, Black Holes and Baby Universes, in which the hypothesis that this Universe could have arisen in a non-zero energy field in a black hole in another universe was dealt with at length. It's not as though this hypothesis is new, since Hawking was writing about it twenty years ago. Surely this is enough time for people genuinely interested in scientific truth to have updated their knowledge.



And that's the dilemma for apologists. Do they update their arguments and incorporate the latest science into them, which would be honest but would mean continually abandoning old arguments, admitting they were wrong and having to think up some new ones and find smaller and smaller gaps in which to fit their shrinking god, or do they simply continue to try to fool a shrinking target audience and concentrate on those who know nothing about science and so won't have heard the science that refutes the lie they are being sold?



The contrast between science and religious apologetics is starkly revealed here. The KCA manifestly depends on the state of scientific knowledge and understanding of the Universe as it was when the KCA was first stated in its modern form a thousand years ago. This was a Universe centred on Earth where the debate still raged about whether Earth was flat or spherical and magic spirits and demons were assumed to be influencing things. It was a Universe where another physical realm was assumed to exist above the sky, inhabited by magical beings and operating the Universe as a mechanic operates his machines. It was a Universe where angels were assumed to be pushing the stars and planets on their daily circuit of the heavens.



To maintain this position, religious apologists need to avoid incorporating advances in scientific knowledge which undermine any of the basic assumptions which must have seemed intuitively true to people with that primitive level of knowledge and understanding in the eleventh century. As we saw with Richard Bushey's arguments and as we see with the identical ones put forward by people like William Lane Craig, advances in Quantum Mechanics, Relativity, Astrophysics, Particle Physics and Chaos Theory all have to be assiduously ignored because they never support their apologetic. And so religious apologetics becomes more and more detached from reality, increasingly only working in the scientifically illiterate parts of the world where religion's power-base resides and where an understanding of the world is closer to that of an early medieval camel trader or a Bronze-Age nomad than to someone from a twenty-first century, technological society.



They will happily wave science around when they imagine it supports them, or where they imagine their audience will think it does, yet where it destroys their basic premises and assumptions, and so destroys their apologetic altogether, science can be dismissed with the wave of a hand, can be wished away by pretending it isn't there or, with the arrogance of those who believe their faith is the best measure of reality available, can be rationalised as a conspiracy by evil scientists.



And those few apologists who are able to adjust their knowledge and update their thinking will undoubtedly show they will be unable to let go of the basic intellectual dishonesty which underpins their 'art'. They will still insist the metaverse must have begun to exist and that the god they are promoting was the only thing capable of creating it, so simply shifting their argument up one level. And they will still depend on the circularity of demanding we accept a priori that their cause of the metaverse exists and has the properties they have ascribed to it in order to make their conclusion come out the way they want it to.



None of them will do what science does and start from the premise that we don't know, yet, so let's go look at the evidence and see what we can make of it. For an apologist, their 'knowledge' of what the answer will be is the only evidence required. They call this 'faith' and claim the right to special respect and the power to make rules for us based on it.



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Fishy Fossil Monogamy

Coelacanths give birth to live young

Image: Peter Shunula

Zoologger: The fossil fish that's a serial monogamist - life - 20 September 2013 - New Scientist



Following close on my blog about so-called 'living fossils', our closest living fishy relative, the Coelacanth, is back in the news once again, with this New Scientist article by Andy Coghlan. As so often with science, the answer to one question leads to a couple more questions.



Female coelacanths give birth to a large number of large live young after a gestation lasting three years. This represents an enormous investment for the female, so we would expect her to use a spread bet strategy and mate with several males rather than risk all on a small number of mates. However, DNA analysis of two pregnant Latimeria chalumnae females caught in 1991 and 2007 respectively by Kathrin Lampert and colleagues of Ruhr University Bochum in Germany, showed that all the young had the same male parent.



Coelacanths are carnivorous and live mainly on squid and small fish. The reason for a long gestation and live birth of relatively large young could be because, living together in caves would put small young at risk of being quickly eaten by parents and other coelacanths. Being large and immediately independent would give them a fighting chance of escaping.



So, we now know that females are monogamous, admittedly based on just two examples, but that raises a couple of questions:

1. Why monogamy when polygamy would be expected?
2. How does internal mating occur when males don't appear to have the necessary apparatus for penetration?

These massive fish - up to 1.5 meters (nearly five feet) long - live in deep ocean volcanic caves in what are believed to be colonies of a few individuals. It is believed that there are only a few hundred coelacanths still alive, so it could be that males are in short supply. It could also be the mating is a prolonged process, maybe involving mating rituals intended to bring the male and female cloaca into the right alignment for sperm transfer to occur.



But the real answer is that we don't yet know and can only hazard educated guesses.



I wonder if one of my keen creationist readers could suggest an 'Intelligent' Design explanation for males not have the required equipment for internal fertilisation and why females put all their eggs in one basket as a mating strategy. Could it be that a slow lingering extinction is what the benevolent Intelligent Designer had in mind all along when he created coelacanths?



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Playing With Evolution

Probability = 1:100,000. Advantage factor = 51%

One of the things people sometimes find difficult to understand about evolution is the idea of a species evolving up an improbability gradient so that something which was highly improbable becomes the norm over time because of the multiplying effect of natural selection. Creationist frauds will point at an evolved characteristic and come up with some spurious notional estimate of the probability of it evolving 'by random chance alone' and dismiss the idea as too preposterous for words. It's the equivalent of standing at the bottom of a cliff and declaring that life can't possibly exist at the top of it because nothing could jump that high in a single bound.



Indeed, this is one of the stocks in trade of professional Discovery Institute liars who earn a living misrepresenting the mathematics of biology as part of the Wedge Strategy to discredit science because of the way an understanding of the Universe undermines religious superstition and makes it harder to retain the unelected political power that controlling the people's religion gives them.



Richard Dawkins devoted an entire book, Climbing Mount Improbable to explaining the idea of the improbability gradient.



Here's a very crude, simple spreadsheet for modelling in very simple terms how this works. You'll need Microsoft Excel^© and the ability to create a simple chart with it.



Here's what you do:



Open up a new Excel spreadsheet and type the following into the given cells. Have particular care with the formulae.

Cell	Content
A1	Population
A2	Advantage Factor
A3	Initial number of mutants
B1	100000
B2	51%
B3	1
D1	Generation
E1	Population A
F1	Population a
G1	Percentage of A
H1	Percentage of a
D2	=Row()-2
E2	=B1-F2
F2	=B3
G2	=100*E2/(E2+F2)
H2	=100*F2/(E2+F2)
D3	=Row()-3
E3	=($E$2+$F$2)*(E2*(100%-$B$2))/((E2*(100%-$B$2))+(F2*$B$2))
F3	=($E$2+$F$2)*(F2*$B$2)/((F2*$B$2)+(E2*(100%-$B$2)))
G3	=100*E3/(E3+F3)
H3	=100*F3/(E3+F3)

Now copy down all the formulae in columns D through F to at least row 500 or as many more rows as you wish. You can always add more later.



What this has done is set up a model for calculating the average number of alleles in each generation in a population of 100000 if the mutation (a) gives a differential probability of reproducing of 51:49 compared to the normal form (A). It also gives you the same figures expressed as a percentage of the population. It replicates what would happen if the probability of the initial mutation was one in one hundred thousand but ignores any future mutations. You can play with these settings to see what happens in a larger population or with a different probability. For example, to test out a 1 in a million chance, change the value in B1 to 1000000 and leave B3 with a value of 1. To change the modelled advantage change the parameter in B2. You may need to adjust the number of rows.



To appreciate fully how the numbers change over time, create a chart and plot either columns E and F, or Columns G and H, with column D as the X-axis. You can then make changes and see how the shape of the graph changes. I find a stacked bar-chart gives the best result but you can experiment with others.



If you want to use this as a starting model and build in things like random drift where there are no significant selection pressures, population growth from a small founder population or several co-evolving genes interacting, be my guest. Your skill and patience with Excel will be greater than mine, but I would be interested in seeing the results.



Enjoy.

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How The Common Cold Was Intelligently Designed

Intelligently designed coronaviruses

As I'm just getting over a nasty little cold I thought I would write a blog about the common cold for creationists, so they can appreciate the wonder of science too. (Hope the 's' word hasn't put them off already, because creationism is all about science really... isn't it?).



So what is a common cold?

The common cold (also known as nasopharyngitis, rhinopharyngitis, acute coryza, or a cold) is a viral infectious disease of the upper respiratory tract which primarily affects the nose. Symptoms include coughing, sore throat, runny nose, sneezing, and fever which usually resolve in seven to ten days, with some symptoms lasting up to three weeks. Well over 200 viruses are implicated in the cause of the common cold; the rhinoviruses are the most common.

Wikipedia - Common cold

All creationists understand that God er... sorry... The Intelligent Designer never makes any mistakes and knows exactly what His Its creations will do and designs them perfectly to do exactly what they do, nothing more and nothing less.



Why the Intelligent Designer wants us to feel miserable for a few days with a headache and high temperature, and to be susceptible to secondary infections causing things like pneumonia and sinus infections is not a matter for us to concern ourselves with. It knows best and is doing it for an ineffable reason. It also wants to cost industry billions in lost production every year for reasons us mere humans can't expect to understand. We just need to be grateful that it's all to the good in the long run.

We conclude that the economic cost of lost productivity due to the common cold approaches $25 billion, of which $16.6 billion is attributed to on-the-job productivity loss, $8 billion is attributed to absenteeism, and $230 million is attributed to caregiver absenteeism.

Bramley TJ, Lerner D, Sames M. J;

Productivity losses related to the common cold.

Occup Environ Med. 2002 Sep;44(9):822-9.

So how did the Intelligent Designer go about this?



He used a virus - basically some RNA wrapped up in proteins which gets into the cells in the lining of our noses and other parts of our respiratory system and converts our cells into machines for making more viruses. Our bodies react to this in ways which cause the typical symptoms of the common cold - high temperature, runny nose, coughs and sneezes (which help spread the virus to other people) headache, tiredness, etc.



But the Intelligent designer forgot that he had also designed humans to react to things like viruses by making antibodies which kill the viruses, so he had to think of a way to get round this intelligently designed problem.



So he came up with the brilliant idea of making over 200 different viruses which cause the common cold, all of which change a little bit over time so our bodies don't recognise them as the same one we got infected by some years ago. [Important note: this change over time should not be called 'evolution' because that's impossible. The Intelligent Designer does it!] With that many different viruses the Intelligent Designer made it so the average human in developed countries gets 2-4 colds a year on average and children can get 6-12 colds a year. At that rate it takes a whole lifetime to get through them all and by then they've all changed anyway. For some reason, the Intelligent designer decided it wouldn't make any difference whether people believe in him or not, everyone would have the same chance of catching a cold several times a year.



No! We don't need to know why He designed our bodies to fight the viruses he created. He must have had an intelligent reason because He's an intelligent designer! You see how easy Creation Science is? It always provides you with exactly the answer you wanted - which proves it's right.



So that's it, really. Everything a creationist needs to know about how the Intelligent Designer designed the common cold - which is obviously a much more sensible explanation than anything science can offer, and what we don't know we know really because God did it! No! Wait... The Intelligent Designer did it, because this has nothing to do with religion or the Bible and is all about science! Okay! It's not more sensible than science because it is science and should be taught in schools! Got that!

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Real Creationists Shouldn't Have Flu Jabs

If you're a genuine Bible-literalist creationist and don't believe in Darwinian Evolution you shouldn't get a flu jab. New flu jabs are brought out each year because scientists who believe the influenza virus evolves to produce new strains, produce new vaccines against these new strains. Obviously, if they are wrong and creationists are right, influenza viruses don't evolve to produce new strains so the new vaccines are a waste of time. Of course, that flies in the face of evidence but that should never be a problem for a genuine Bible literalist creationist who regards the Bible as the ultimate source of all knowledge, not mere things like facts.



Or maybe you're just a creationist in theory. In practice, you believe in Darwinian Evolution just like normal people do and especially where your health and well-being are at stake. Like a lot of other theory-only Bible literalists you don't make any connections between what you claim to believe and what you do. The Bible is just something you think everyone else should live by.

'Whatever the Bible says is so; whatever man says may or may not be so,' is the only [position] a Christian can take... If [scientific] conclusions contradict the Word of God, the conclusions are wrong, no matter how many scientific facts may appear to back them. Christians must disregard [scientific hypotheses or theories] that contradict the Bible.

William S. Pinkston; Biology For Christian Schools, Bob Jones University Press 1991

So let's take a look at the evidence which genuine, practicing Bible literalist creationists should ignore.



Influenza viruses are RNA viruses which infect mammals and birds and use the replicating mechanisms and resources of their cells to produce more influenza viruses. The cell is destroyed in the process. Dead cells and the resulting inflammation makes the infected organs ideal for opportunistic bacterial infection.



Influenza viruses have seven or eight strands of RNA which together contain eleven genes which code for specific enzymes and proteins. The other enzymes and proteins needed for RNA replication are 'borrowed' from the host's cells. Two of the proteins they code for form a protective coat around the RNA. These have antigens on their surface which our bodies recognise and which our antibodies can bind to to destroy the virus, once we have been infected, or vaccinated to produce antibodies in the first place.

New influenza viruses are constantly evolving by mutation or by reassortment. Mutations can cause small changes in the hemagglutinin and neuraminidase antigens on the surface of the virus. This is called antigenic drift, which slowly creates an increasing variety of strains until one evolves that can infect people who are immune to the pre-existing strains. This new variant then replaces the older strains as it rapidly sweeps through the human population, often causing an epidemic. However, since the strains produced by drift will still be reasonably similar to the older strains, some people will still be immune to them. In contrast, when influenza viruses reassort, they acquire completely new antigens—for example by reassortment between avian strains and human strains; this is called antigenic shift. If a human influenza virus is produced that has entirely new antigens, everybody will be susceptible, and the novel influenza will spread uncontrollably, causing a pandemic. In contrast to this model of pandemics based on antigenic drift and shift, an alternative approach has been proposed where the periodic pandemics are produced by interactions of a fixed set of viral strains with a human population with a constantly changing set of immunities to different viral strains.

Wikipedia - Influenza

They evolve in two main ways:

1. By genetic drift, ie the random imperfections in replication that lead to new genes.
2. By hybridizing with other related viruses and acquiring new genes

It helps to think in terms of a pig-duck-human complex, though other birds and mammals can be involved. Especially where these are in close proximity, like in many agrarian human societies, different strains of related virus can occasionally infect the same cell at the same time producing a new strain of virus. For example, a virulent strain of bird flu can hybridise with a human flu in one or other host to produce a new, virulent human flu.



This is where flu jabs come in. Scientists who accept that viruses evolve produce a new vaccination for the new strains so we can acquire immunity artificially and safely and without running the risks associated with acquiring it naturally.



Of course a Bible literalist creationist doesn't believe these new viruses exist, or if the do, they must have been created specially by their invisible, omnibenevolent magic friend, presumably to punish people because it loves them.



Or maybe they just compartmentalise their beliefs and behave like normal people and either get a flu jab or risk getting the flu. One thing we can be fairly sure of is that being a Christian or a Muslim, or whatever faith or sect is the one true one, doesn't convey any special immunity to influenza or we would have heard about it by now.



It's just as though there isn't a benevolent creator god punishing non-believers and sparing true believers, and viruses evolve by mindless, uncaring and non-directed neo-Darwinian genetic Evolution.

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Selfish Genes and Termite Indigestion

Creationist pseudo-scientists will assure their credulous customers that genetic evolution alone can only lead to selfish organisms. Maybe this mistake comes from assuming their own greed and selfishness is a result of their own genetic evolution. It isn't of course, it results from a sociopathic personality disorder.



But one only need to look at nature to see that cooperation is actually the norm - so common in fact that we either take it for granted or it's operating at a level which is too small for us to see easily. Just one example is the termite - if one can accurately even speak of them in the singular. Termites only exist as part of a cooperative colony.



But it's not the obvious cooperation in the termite colony that I'm talking about here.



Termites are a very old order of insects which branched off the group which gave rise to cockroaches about 150 million years ago so have been evolving into their specialised niche for a very long time. They are not at all closely related to the other social insects like the many hymenopterans like ants, wasps and bees. They live exclusively on decaying wood which presents them with very special digestive problems because decaying wood is almost completely cellulose and lignin (with fungal hyphae) and cellulose is notoriously stable and hard to break down. It is the main structural substance for plants and the last thing plants, especially long-lived ones like trees, need is for their structural material to break down.



In fact, very few animals can digest wood. Those which eat lots of plant matter have a specialised digestive system which normally contains a sizeable fermentation vat - which is one reason that herbivore mammals tend to be comparatively large. Termites are no different in this respect but have evolved a gut which achieves the same thing on a very small scale.



Termites depend entirely on cooperative symbiotic organisms living in their gut - and of course these organisms depend entirely on termites.

Interaction between the microbes in the termite gut is highly mutual, usually beneficial for both microbes.

Prokaryotes are closely associated with protists as symbionts, either attached to the cell surfaces or live within the cytoplasm or nucleus of the protists. For instance, Treponema spirochete bacteria are attached to the special bracket-like structures on the plasma membrane of mixotricha and contributes to the movement of the host protist known as “motility symbiosis”. Treponema also benefits by living on and within the protist, easily accessible to nutrients H₂ and CO₂ produced by mixotricha and utilize them to synthesize acetate and obtain energy for their own growth as well.



Another mutual relationship shown between Methanobrevibacter and parabasalids protist, H₂ plus CO₂ produced by protists also can be used by methanogens as energy source but they form methane,CH₄ in this case. Successful elimination of produced H₂ by endosymbiont’s H₂ evolution activity enables the protists to maintain optimal pH and stimulate its decomposition activity. These two groups of microorganism interact and work together to digest cellulose and enhance the cellulose fermentation.



Although most of the microbes act mutually, there is one exception between the relationship of methanogens and acetogens. Both take up H₂ and CO₂ as their substrates, thus they are likely to be in a compete relationship. Acetogenesis dominates methanogenesis from the same substrate, H₂ plus CO₂, because acetogenesis requires less energy loss of the termite by absorbing acetates but not methane as the energy source.

MicrobeWiki - Termite gut

The amazing thing is that not only do termites depend on microbes in their gut but that some of these microbes depend on symbiotic bacteria and archaea which live inside them. One protista, mixotricha, even has special brackets on its surface which the the flagellated spirochete, treponema fits into so they can move it about. It didn't need to evolve motility because it lived in close association with a spirochete which provided it for them, and it was in the spirochete's interest to cooperate.



This system evolved by natural selection, by genes appearing to mimic selfishness because the ones which produced the most descendents was the one which predominated in the genepool. There was no choice in the matter - whatever produced the most descendants won the race.



And by that process termites evolved together with their gut flora to become one of the most successful insect orders on the planet, and by utilising a food source which few other creatures could use.

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Rivers Out Of Africa

Lost river guided early humans out of Africa - environment - 16 September 2013 - New Scientist



I've noted before how science is often about finding missing pieces of the jigsaw and fitting them in place. This paper by Tom J. Coulthard, Jorge A. Ramirez, Nick Barton, Mike Rogerson, Tim Brücher, reported in New Scientist by Alyssa A. Botelho illustrates that as well as anything by adding a little bit more information to the account of human migration out of Africa.



The assumed routes Homo sapiens took out of Africa usually include migration north down the Nile which crosses the Sahara as a narrow fertile band in an otherwise arid desert, and by coastal spread from the Horn of Africa across the Red Sea and along the edge of the Arabian Peninsula. However, that didn't tie in with the archaeological evidence of stone tools in the western Sahara and Mediterranean coastal region which indicate human habitation much further west than the traditional routes suggest. For this reason, others had proposed a once-fertile Sahara with rivers running north to the Mediterranean. The problem was in working out how much water would have been in these rivers (and so whether they could have supported a human population) or where they were located.

Abstract

Human migration north through Africa is contentious. This paper uses a novel palaeohydrological and hydraulic modelling approach to test the hypothesis that under wetter climates c.100,000 years ago major river systems ran north across the Sahara to the Mediterranean, creating viable migration routes. We confirm that three of these now buried palaeo river systems could have been active at the key time of human migration across the Sahara. Unexpectedly, it is the most western of these three rivers, the Irharhar river, that represents the most likely route for human migration. The Irharhar river flows directly south to north, uniquely linking the mountain areas experiencing monsoon climates at these times to temperate Mediterranean environments where food and resources would have been abundant. The findings have major implications for our understanding of how humans migrated north through Africa, for the first time providing a quantitative perspective on the probabilities that these routes were viable for human habitation at these times.

Coulthard TJ, Ramirez JA, Barton N, Rogerson M, Brücher T (2013);

Were Rivers Flowing across the Sahara During the Last Interglacial? Implications for Human Migration through Africa.

PLoS ONE 8(9): e74834. doi:10.1371/journal.pone.0074834

So it looks likely that the most westerly river provided the route across the Sahara, bringing our ancestor up to the Atlas Mountains and eventually to the shores of the Mediterranean in the area of the present-day Tunisia-Algeria border - further west than we normally assume but consistent with the stone tool evidence. The suggestion is that we then spread eastward along the coast to the Nile Delta and then into the Middle East and eventually into Europe and Asia, where we found our cousins, the Neanderthals and Denisovans who had been living there for some 200,000 years - the descendants of an earlier migration out of Africa by our immediate ancestors, H. heidelbergensis.



And so another piece of the jigsaw has been fitted into the fascinating human story of the last 100,000 years or so.



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