F Rosa Rubicondior: September 2013

Sunday 29 September 2013

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 indices 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 invariably 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.

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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Saturday 28 September 2013

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

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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Thursday 26 September 2013

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.

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.

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, and the belief that their religion grants them the special privilege of being in charge, 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:

Saturday 21 September 2013

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.

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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Friday 20 September 2013

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.

A2Advantage Factor
A3Initial number of mutants
E1Population A
F1Population a
G1Percentage of A
H1Percentage of a
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.


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Thursday 19 September 2013

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.

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 anyway it's better science because it's written in a book, 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

Wednesday 18 September 2013

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.

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.

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.

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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Saturday 14 September 2013

How Thieves Exploit Religious Gullibility

[Although this site was taken off line soon after it was exposed here and in New Scientist, this doesn't affect the thrust of the article which is about how unscrupulous people exploit religious gullibility, apparently seeing religious people as especially good targets for this sort of scam, relying as it does on scientific ignorance and superstitious credulity. Fortunately, I copied all the relevant parts.]

Believe it or not, godparticle4u.com is a website set up to exploit the credulous gullibility of religious people, rather like all those emails from Nigeria looking for a kind Christian with a bank account where they would like to place a very large amount of money in return for a cut - just send your full account details including access codes, passwords, etc.

The site claims to be supplying parts of the Large Hadron Collider from CERN where the 'God Particle' was discovered and which they claim have magical properties curing almost everything from migraine to - you've probably guessed it already - sexual dysfunction. Apparently, the LHC has now been dismantled and sent to laboratories around the world for testing, presumably by Flying Pig Air Freight Services™.

Small parts of it - ball-bearing to be precise - can be yours for a mere $199.00 each inc. p&p.

Here's the bait they think will catch credulous, superstitious and scientifically illiterate (in other words, religious) suckers.

The God Particle, which was recently discovered by our colleagues in CERN, the world's largest particle physics laboratory, forever the Holy Grail of particle physics and nuclear research. The God particle is regarded as one of the fundamental forces of the cosmos. Many religious philosophers believe it constitutes the very ground of being, while others assert that it is the fabric of creation upon which the tapestry of the universe is woven. There are some who refer to the God particle as the clay of existence, whereas the Shaivites of India know it as Brahman and regard it quite reverently as sacred supreme Consciousness.

We still don't know if one of these theories is true, or maybe they all are. What we do know is that you are on the verge of a once in a lifetime opportunity of letting this infinite power into your life.

You deserve God's help, you deserve God's particle.

Making history - How they searched and found the boson in the particle accelerator
Using the particle accelerator, protons are accelerated to nearly the speed of light causing them to collide with each other. The collision creates many particles, among those particles the God Particle is found. The energy required is almost as enormous as the energy of the big bang which created the universe (sic). These particles are absorbed by huge detectors the size of an office building. The information obtained is then analyzed by 33,000 giant computers. The amount of electricity used is incredible - 120 Megawatts - about as much as all of the homes in the neighboring Swiss Canton of Geneva.

The conclusions, based on data collected in the past two years of research are now cleared for publication and there is now unequivocal evidence for the existence of the God Particle.

This discovery was crowned by the global scientific community as one of the defining moments of science and one of the most important steps towards understanding the universe.

The evidence found in the material remaining from the accelerated protons has been used to confirm the already well-established theoretical assumptions. Moreover, the new knowledge has opened a whole new world of practical possibilities.

Further surprising discovery
In addition, it turns out that the presence of the God Particle in the material has an unexpected effect. The days following the most talked about collision, were exciting for everyone involved. Meanwhile, an interesting phenomenon has emerged, which could be noticed only after the euphoria of the discovery slowly subsided. With the return to the normal work routine, most of the employees returned to their usual mental-emotional state, and except for an obvious sense of optimism, no unusual symptoms were registered.

However, an interesting occurrence had been noticed by some of the staff involved in the project. As the days passed their general mood was improving, accompanied by a significant sense of clarity, balance, relaxation and unusual vitality.
This phenomenon, realized and verified by those lucky workers led the researchers to an unequivocal conclusion: prolonged physical contact with the internal metal parts of the accelerator, is the cause of that phenomenon. Those employees, mostly technicians and engineers whose task required them to stay and work inside the accelerator were the ones diagnosed as being affected by the amazing phenomenon.

"God is in the small details"
Naturally to a place as teeming with scientists as CERN, researchers from a wide variety of scientific backgrounds decided to try and figure it out.

The employees who were most exposed to the particle energy were required to undertake an extensive series of tests.

Samples from the parts exposed to the surge of energy which showed substantial evidence of having the God Particle were sent to the leading universities and research centers in the world.

According to preliminary evidence found thus far by researches in the medical field, the energy of the God Particle has some amazing effects on migraine prevention, on treating different kinds of skin conditions, up to a surprising improvement among those who ailing from sexual dysfunction disorders. All those among a long list of other medical conditions.

The effects of the God Particle is also tested in the field of mental health and in this field the patients are also getting some surprising improvements in a wide range of medical cases, for example treating phobias and depressions of different kinds.
One of the theories being researched by the scientists is that the God Particle doesn't really cure the listed conditions but provides the human body with the energy needed to normalize and cure itself.

All those researches are performed in scientific methods demanding them to comply with a strict criteria before publication.
Therefore all the above should not be taken as a scientific fact, but should only be understood the way it is, a positive influence of material exposed to the God Particle on treating and preventing a wide range of medical problems.

The results of the researches are still censored. But there is an increasing assumption in the scientific community that in the future, when it becomes less expensive to produce the particle, it will completely change the face of modern medicine.

Providing a rare opportunity
We are a part of a maintenance team in CERN. Among our responsibilities is to replace some of the worn out parts inside the collider.

We notices (sic) that something amazing was happening to many people during those days, and when we were summoned for tests by the research groups we realized that we were not the only ones who felt that way.

When the moment came to replace some of the parts around the center of the collision, we felt that we cannot dispose this material as waste. Instead, we started collecting the remaining bearings from the section which is under our responsibility. This material was exposed to the most powerful energy. After the remaining bearings are collected, we remove them from the compound and later from the country, back to our countries of origin.

Initially we gave small spheres which came from the collected bearings to our relatives and friends. In a short period of time the spheres started to leave their mark, and along with great responses we were flooded with requests from other acquaintances who heard about the amazing experience.

When we realized what a significant finding we have in our possession, we decided to try and bring it also to other people who will want to seize this opportunity.

One of our team member’s wife, who works as a jewelry [sic] designer for a known fashion brand, was worried about losing the sphere while carrying it in her pocket. She decided to design a pendant to help her keep it close to her.
When the decision to start distributing the spheres was made, we recruited her to design a new pendant based on the one she made for herself. Our main goal was to enable the use of the sphere in a wider variety of ways, for both men and women, and to make it fashionable.

With that goal in mind, she created an original jewel, with a unisex modular design enabling a few different ways of 'wearing' the sphere. Using a leather band and designated magnets the sphere can be worn as a necklace or as a bracelet and the pendant design itself can be easily changed to satisfy everyone's personal preference.

The pendant comes in a designed gift box, and includes a throughout explanation about the sphere and the God Particle, so the receiver will truly appreciate its incredible value.

As the supply of the bearings is very limited and unstable (highly dependent on planned collision dates), we didn't feel right to throw away the outer parts of the bearings as well, even though their shape is not ideal for carrying, these parts were also exposed to the same energy as the inner spheres. We cut these parts to smaller pieces and they are also available for people who care less about carrying it around in their pockets.

May God be with you!

And may your money be with us!

A magic ball-bearing on a string! Now don't laugh! It's not nice.

Well, okay, laugh a little bit...<giggle>

Anyway, how is this claim any less credible that the claims of Islam and Christianity, and the claimed cures they provide for a non-existent problem with magical powers and spells in return for money and obedience? How much more credulous and gullible do you need to be to swallow this story than to swallow stories about talking snakes, flying horses, messengers from Heaven and the power of blood sacrifices to save us from imaginary sky bogeymen?

And are these frauds being any less moral than the clerics of religion who sell magic spells and phony cures to gullible and vulnerable people in return for an easy life and freedom from the bother of having to earn an honest living?

[Update 04 October 2013] The site is now 'down for maintenance'.

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Friday 13 September 2013

Evolving A Quickie

Related species, Gambusia puncticulata, showing the gonopodium
A lovely piece of research published in the Journal of Evolutionary Biology today illustrates perfectly how environmental differences can quickly lead to genetic divergence. It doesn't seem to be available online yet but is reported on in a New Scientist article by Victoria Druce

It was published by Justa Heinen-Kay of North Carolina State University who does most of her research in the Bahamas on the mosquitofish, Gambusia hubbsi, a small, promiscuous, live-bearing fish that inhabits blue holes. Mosquitofish eggs are fertilised internally and males have modified anal fins called gonopodia with which to deposit sperm into females in an act of copulation. The problem is, a big gonopodium makes fast swimming difficult and copulating pairs of fish are vulnerable to predators because they make a larger target and may well be distracted.

Typical blue hole
The blue holes in which these fish are found are vertical caves which filled with water when the sea-level rose at the end of the last ice-age, some 10,000 years ago. All blue holes have acquired their fauna since that time. They are also found in Mexico and Belize. Some of these holes have also acquired a large predator fish, the bigmouth sleeper (Gobiomorus dormitor), while others have remained predator free. Thus we have a ready-made laboratory test-bed to see what happens when a species is subject to predation while a control group is free to evolve without predators.

Heinen-Kay and her team caught and examined specimens of Ga. hubbsi and noticed that where predation was present, males had smaller gonopodia than those found in predator-free blue holes. She explains the idea in her profile:

In order to gain genetic benefits for their offspring, females should prefer males that are successful in their local environment. But, the most important type of whole-organism performance will depend on local selection pressures. Rapid-burst escape swimming speed is of utmost importance for Bahamas mosquitofish living with predatory fish, yet that performance is irrelevant in blue holes without predators. At the same time, although resource availability does not differ between high- and low-predation blue holes, low-predation populations have much greater population densities, so competition for resources and foraging efficiency will be more intense than in populations with predators.

Basically, when predators are present, it produces more descendants if mating is quick and fast swimming is possible. In predator-free environments, female selection for large gonopodia will ensure mating is more successful and so well-endowed males will produce more offspring.

To anyone with even a basic understanding of evolutionary biology and how the resulting phenotype is the product of several competing factors, this is probably astoundingly obvious, but to a creationist who believes an omni-benevolent magic man magicked everything into existence and everything is descended from a couple of ancestors who lived on a boat, is must seem incomprehensible.

Why would this magic man have given some varieties of Ga. hubbsi smaller gonopodia so they could get mating over with quickly to escape the predators he put there to eat them? Did this creator have a day when he was in favour of Go. dormitor, so he put them in blue holes with food in, then the next day, changed sides and gave Ga. hubbsi smaller gonopodia so they could avoid becoming Go. dormitor food?

And how on Earth can this be described as Intelligent Design by anyone with even a modicum of intelligence?

Victoria Druce, Mosquitofish are efficient lovers New Scientist 14 September 2013, Magazine issue 2934.

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Evolution's 'Big Bang' Explained

Marine life during the Cambrian explosion (~520 million years ago).

Image credit: Katrina Kenny & Nobumichi Tamura.
Copyright © 2010 The University of Adelaide
Biologists measure evolution's Big Bang

Unlike religion, where problems are disturbing and need special measures to explain them away or suppress them and keep knowledge of them away from the faithful, science thrives on them and actively looks for them.

One such problem has for a long time been the so-called 'Cambrian Explosion' in which a large number of very different major taxa suddenly seem to appear in the fossil record over a relatively short time scale, suggesting a rate of evolution which is hard to explain in conventional Darwinian terms.

However a paper published today in Current Biology PDF by Associate Professor Michael Lee of Adelaide University, Australia, and Dr Greg Edgecombe of the Natural History Museum of South Australia, to which the above link relates, shows that, although there was indeed rapid evolution immediately prior to and into the Cambrian Era, it was not inconsistent with Darwinian theory.

First a little background:

Wednesday 11 September 2013

Recent Evolution Underground

Culex pipens taking a meal
If you travel on the London Underground you might consider using a good insect repellent. We have a newly-evolved species of mosquito living there and it is a voracious blood-sucker. It has been classified by taxonomists as Culex pipiens f. molestus. It lives off the blood of rats, mice and especially humans, unlike the birds it's parent species lives off.

It has evolved very recently, certainly since the London Underground was built, starting in 1863, almost certainly from a population of C. pipens, and made life miserable for those who took shelter in London Underground stations during the blitz of WWII, as though Hitler wasn't making it miserable enough. The fact that hybrids between it and C. pipens are usually sterile suggests that speciation has occurred and the subterranean variety should more properly be classified as a new species rather than a variety or subspecies of C. pipens.

The evidence for this mosquito being a different species from C. pipiens comes from research by Kate Byrne and Richard Nichols. The species have very different behaviours, are extremely difficult to mate, and with different allele frequencies consistent with genetic drift during a founder event. More specifically, this mosquito, C. p. f. molestus, breeds all-year round, is cold intolerant, and bites rats, mice, and humans, in contrast to the above-ground species, which is cold tolerant, hibernates in the winter, and bites only birds. When the two varieties were cross-bred, the eggs were infertile, suggesting reproductive isolation.

I'd love a liar for Jesus/money/power from the Discovery Institute, Answers in Genesis, or any other pseudo-science creationist scam site to come here and explain to my readers how this fits with their infantile 'Intelligent (sic) Design' model. Why would a benevolent creator god suddenly come up with a subterranean mosquito in the last 150 years which seems to exist solely to make more mosquitos and for making the life of travellers, staff and maintenance workers on the London Underground a little less pleasant, unless he was on Hitler's side in WWII and was doing his bit to help by being an irritating little nuisance and has just left his secret weapon hanging around?

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