Friday, December 30, 2005

Christmas message

See Matthew 1:1-6.

We went to separate performances of three separate Christmas productions for each of our three children. In all of them there were tinsel halo-brights (as our youngest called them for a while). There were angels – mostly but not always girls in long flowing robes – not so much the sort of angels that would terrify you – as they terrified Mary, Zechariah and the shepherds – but the sort of angels that would make you say, “aaaaahhh!” There were reluctant innkeepers. There were multi-ethnic wise men or kings from the east; there were shepherds, there were a variety of animals, and there was a doll in a crib with straw in it.

Such is the pattern of the preparation for Christmas. The effect of all this is that people think that Christmas is just for the children – or at best for parents. It's lovely to see children dressed up in sparkly clothes, and stumblingly reciting versions of the words that we half-remember from when we went to school – but really, it has nothing to do with real life – nothing to do with me – and it's a bit of a nuisance and I could really do with getting back to sort out the Christmas cards, make sure the oven's come on and open some more presents.

But the reality is that the Christmas stories are very grown up. There's the obvious fact that Mary finds herself pregnant when she is not married – we tend not to explain to our children what “virgin” means, even when in the school play we get a seven-year old girl to say, “how can this be, since I am a virgin?” Mary and Joseph are probably very young – Joseph is a carpenter, but he evidently doesn't have much in the way of resources yet – they can't afford to sacrifice a lamb when Jesus is born, only the minimum offering of two small birds. How many people and families do we know today who face financial difficulty as they start out? We live in an affluent area – a lot of people only get married when they have a house already, and only start a family when they have paid loads of money into investments so the children can afford to go to private schools. If we heard about people in Mary and Joseph's situation, we would probably roll our eyes, and think to ourselves, “Vicky Pollard types! Why can't they be more responsible?” They are just the sort of family that would have Daily Mail readers asking “What is this country coming to?” And childbirth – well, again, we tend to go straight from the innkeeper offering some space in the stable to Mary and Joseph standing by the crib with straw in – but childbirth is anything but a nice experience – it's not the sort of thing that you really want children to know the details of until they have to.

There's the fact that Palestine finds itself under the rule of an indifferent occupying power, the Romans, and Mary and Joseph travelling to Bethlehem is just one small example of this power's complete indifference to the welfare of its subjects. In how many countries today are there people living under the authority of oppressive regimes? How often do we hear about how military or security forces have behaved in indifference to the welfare of civilian populations around them? In how many countries are there insurgencies that, in their desire to get back at occupying powers or the legal government, aren't bothered if there are civilians who suffer at the same time? Iraq – Afghanistan – Somalia – Eritrea – Columbia – Indonesia. Northern Ireland – the Basque country – Northern Nigeria – Saudi Arabia. Mary and Joseph's political situation finds echoes in that faced by people around the world today.

And then there's King Herod – who is happy to use his power to ethnically cleanse a town if he thinks that it will do anything to wipe out a pretender to the throne. Troops are sent into Bethlehem to kill any boys under two years old – an act of apparently random and callous violence. But Mary and Joseph slip away to Egypt – and become asylum seekers or refugees. I don't suppose they were able to escape with much, I don't suppose they were able to find out much about their family whilst they were there, I don't suppose that they felt that they could really return to Bethlehem when they came back, and I don't suppose the lot of foreigners in Egypt was particularly pleasant when they were there – but they were safe from the tyrant who was seeking to kill them. Again, aren't refugees and immigrants part of our experience today? There are people everywhere who know that it would be difficult for them to return to their home country because of the hostility of the regime. We have other people who have come to this country with the encouragement of this country in search of a better and more secure life. But the same is the case all over the world – this is a world in which people are moving around in search of a more secure future – or escaping from vicious regimes – or in some cases just exploring – many people cut off from parts of their family, from their heritage, unsure what the future will hold in the long term.

So the world in which Mary and Joseph lived wasn't a world full of tinsel halobrights, sweet angels and farm animals that looked like children. It was a violent, politically complicated world, in which people had to do what they could to make the best of their situation. Jesus – Immanuel – God with us – doesn't step into the world in a particularly nice, safe era with cuddly sheep and a round of applause from the audience. God comes into the world in a hint of scandal, to a family that will seek political asylum from a nation that is subject to an indifferent empire and under the rule of a vicious, paranoid tyrant.

And when we look at those first few verses in Matthew, we find something surprising. We find from Jesus' family tree that this isn't the exception, but the rule. Four times, women are included in the genealogy – and in each case, there is a story of scandal.

Tamar – I won't go into detail, but this is a scandalous story – Genesis 38 – the bit we skip over when we are telling children the story of Joseph – which is pretty scandalous in its own right, but won't lead to quite the level of embarrassing questions that the story of Tamar will. And yet, there she is – an ancestor of Jesus – God brings about his purposes through a family scandal.

Then there's Rahab – the mother of Boaz, who is the father of Obed, the father of Jesse, the father of King David. Who is Rahab? Well, she's a prostitute – she lives in Jericho – but she realises that God is coming in judgement against the city, and she trusts that God is able to save and protect her. And through her faith in God, she becomes a part of the people of God, and she is given an inheritance with them in the land – and in fact becomes part of God's plan to send Jesus into the world. If you want to read her story, see Joshua chapter 2 and the end of Joshua chapter 6.

Then there's Ruth – the wife of Boaz. She's a Midianite – the Midianites were God's enemies – they were people that the Israelites weren't supposed to deal with. But we know already how Naomi and her husband and sons leave Israel to escape the famine that is God's judgement on the Israelites – and how Naomi returns, bitter with God, with just her Midianite daughter-in-law some years later – and yet how God restores their inheritance through Boaz the redeemer. If you want to read more, read the book of Ruth.

And then we have mention of the wife of Uriah. Uriah was the general of King David's army that he arranged to get rid of to cover up the fact that he was having an affair with Bathsheba, his wife.

These awkwards details of the Christmas story, then – the bits that somehow don't get mentioned in the school nativity plays – we find that they are echoes of what has already happened in the line of Christ. We have refugees, illegitimate children, foreigners where they aren't supposed to be, kings misusing their power and so on. They are all there in the first few verses of Matthew's gospel – they aren't inconvenient details in the story to be quickly skipped over, they are an integral part of how God is at work amongst human beings.

So what? What difference does it make?

Firstly, does Christianity have anything to do with real life? Is it just sweet stories for the kids? Is it just myths that we can keep them happy with, like Father Christmas, whilst we get on with the hard work of sorting out everything that happens over Christmas?

No, it's not. Christmas is about God becoming involved in humanity. God getting his hands dirty. How much does God care about us? Does he care for us only enough to do things that frankly a child could do? No. The Christmas story tells us that God cares so much about humanity that Jesus was born to Mary – with Mary and Joseph putting up with the raised eyebrows and pursed lips of disapproving onlookers, because they both knew how God was at work. Jesus was born to a race oppressed by a foreign power. Jesus spent time as a stateless person. Jesus – God, in human form, knew from the start what it was to not fit in – to be unwelcome in the world.

And of course, as he was God in human form, this unwelcomeness grew, and led ultimately to the world putting to death their creator. Jesus faced all the hostility that the world could throw at him – and yet he lived and died in obedience to his Father's will. God brought about his purposes in the teeth of the rebellion of humanity – facing both the indifference of the world and its deliberate hostility, God came into the world to pay the price for its sin, to redeem it and bring it back to him. And that's what we celebrate at Christmas – not the “real meaning” of Christmas as some sentimental experience – but God loving us so much that all the opposition of the world, from the time of Adam to the time of Jesus, wouldn't deflect him from his purpose of redeeming people.

And the Christmas story brings us up to date, as well. Because I'm not an innocent child, that people will say, “Aaaaah!” over. I don't have a halobright over my head, and neither do you. My life is a mess. Things have gone wrong in it. The Christmas story tells us that God is involved in the lives of real people, with real problems in personal, economic, and political spheres. And that is what the angels sang about.

Habitability redux

Of course, we cannot prove that the equivalent of our planet's animal life is rare elsewhere in the Universe. Proof is a rarity in science. Our arguments are post hoc in the sense that we have examined Earth history and then tried to arrive at generalizations from what we have seen here. We are clearly bound by what has been called the Weak Anthropic Principle – that we, as observers in the solar system, have a strong bias in identifying habitats or factors leading to our own existence. To put it another way, it is very difficult to do statistics with an N of 1. But in our defense, we have staked out a position rarely articulated but increasingly accepted by many astrobiologists. We have formulated a null hypothesis, as it were ... that life ... is out there, or that even simple worm-like animals are commonly out there. Perhaps in spite of all the unnumbered stars, we are the only animals, or at least we number among a select few. What has been called the Principle of Mediocrity – the idea that Earth is but one of a myriad or like worlds harboring advanced life – deserves a counterpoint. Hence our book.
This could have been part of the introduction to “Privileged Planet.” In fact, it's not – it's from the preface to the first edition of “Rare Earth” by Peter Ward and Donald Brownlee. They put forward the idea that the environment in which earth appears is uniquely adapted to the presence of complex life. (Or at least, that's what I understand – I haven't got into the book yet.)

Gonzalez and Richards, in “Privileged Planet,” do the same, but note additionally that the factors that make the earth well-adapted to life (habitability) also make the earth well-adapted as an observation platform for the rest of the universe. Since there is no apparent obvious scientific reason for this to be the case, they conclude that this is a significant property of the universe.

Many of the observations that are made in PP echo those in RE, and conversely, Ward and Brownlee mention the influence of Gonzalez on their thoughts. And yet, whereas a great deal of fuss has been made by parts of the scientific community about PP (though admittedly not at the level of published papers or books), I am not aware of any such reaction against what Ward and Brownlee wrote, despite its fairly direct rebuttal of the Principle of Mediocrity.


Powers of ten

People get shaky when they use powers of ten. I wanted to post a quick reminder about some details about how to do maths with them – which will hopefully also have the benefit of helping me to clarify some of my thoughts on the argument about specification.

10 is ten to the power of 1. 100 is ten to the power of 2. This can be written more concisely as 102. 1000 is 103. And so on. 10150 is 1 followed by 150 zeroes.

This works the other way, as well. 0.1 – one tenth – is 10-1. 0.01 is 10-2. 10-150 is zero, followed by a decimal point, followed by 149 zeroes, followed by 1.

If you want to multiply two powers of 10 together, you can add the superscripted value. Thus, 100x100 – 102x102 is 104, or 10000. This works regardless of the sign of the superscript. 1080x10-25 is 1055.

William Dembski says that the universal probability bound is 10-150. What he means by this is that a specified event that is less probable than this value will not happen by chance. Unspecified improbable events happen by chance all the times – for example, if I toss a coin 500 times, I will obtain a sequence of 500 heads and tails which has an improbability of arising of about 10-150. This is an unspecified event. But supposing I write down a sequence of 500 heads and tails, starting as follows:
- and then toss a coin 500 times and get precisely this sequence of heads and tails – this is now a specified event.

This value of 10-150 is based on the number of measurable time steps (Planck Intervals – if I remember right, this is the time it takes a photon to travel the width of an atomic nucleus) that will occur in the universe, multiplied by the total number of fundamental particles in the universe. In effect, what Dembski is saying is that if the probability of a specified event is such that if everything in the whole universe was doing nothing for the entire history of the universe other than trying to match this specified event, and it was still less than likely that the event would happen at random, then it is a specified event that is less probable than the universal probability bound – and in this case, that this specified event should have happened by chance is less likely than that it should not have happened by chance.

Go back to those coins. Imagine a sequence of 500 heads. The UPB says that, if I toss a coin 500 times in a row, and it comes up heads every time, then it is reasonable to rule out “chance” as an explanation. In this case, it is unlikely that we would persist for 500 tosses anyway; most likely we would give up after less than 20 and assume the coin was loaded or something sneaky was happening.

However, suppose that we have very fast computers that are producing genuinely random numbers. These could generate sequences of simulated heads and tails much faster than humans. If such a computer could do a million simulated “coin tosses” per second, then it would expect to generate a sequence of 20 heads once per second, since the probability of such a sequence arising by chance is roughly one in a million (10-6).

But the UPB says that no matter how many people you have tossing coins, no matter how many simulated coin tosses you have on computers, no matter how fast they are, you will never see a sequence of 500 heads by chance. If you do, it is more likely that there is something happening in the computer which has caused it to generate this specific sequence.

The same applies to monkeys writing Shakespeare. The perception has always been: “Well, if enough monkeys type quickly enough, then surely it's only a matter of time before Hamlet's soliloquy appears.” Okay, then, let's consider a brief excerpt.

I make that 141 characters, from a range of 27 (A-Z plus space, to give the monkeys as much of a break as possible). How many possible sets of 141 characters are there? The answer is 27141. That's around 10200. So the probability of this sequence of letters being typed at random is the reciprocal of this – that is, 10-200. No matter how many monkeys you have, how fast they type, or even how many times you get incredibly fast computers to generate 141 character strings at random, you will not see this specified phrase generated at random, because it lies beyond the universal probability bound, of 10-150.

Now, the subtle thing here is the relationship between 10-150 and 10-200. People look at these two numbers and forget what those superscripts mean. It doesn't sound that far from one to the other – people have in mind the 50 difference between the superscripts, and subconsciously think that with all that improbability, something that is only something like 50 times less probable is really neither here nor there – they aren't all that far apart.

But suppose a specified event has a probability of 10-151. That means it is ten times less improbable than something with a probability of 10-150. That means that you need 10 universes all doing nothing but trying out random events to get to the improbability boundary of the event.

Take Macbeth's words above. The probability of this string being generated at random is such that you need 1050 universes, all doing nothing but generating random strings throughout their history, for this string to be likely to appear.

So what's the point of this? Well, I suppose what I'm getting at is that specified information is special. You don't need much of it to leave any random process that could be conceived of in the universe floundering. And yet, there's a lot of it about.

Saturday, December 24, 2005

Mind your language!

It is fun to watch how language develops in children, and the way that they make language work for them according to their own rules, prior to finding out what the actual rules are.

One of our favourite phrases from our eldest child was the whole phrase "look after" being used as a verb - as in: "Who's lookaftering us this evening? Jo lookaftered them after school."

Our youngest child today came up with a similar odd use of "left over" - "How much of the cream had you leftovered?" - i.e. "to leftover" is a verb, meaning to leave some over.

Thursday, December 22, 2005

Faith and materialism

The Constructive Curmudgeon posted a link to this article, which makes the point that philosophical materialism is - as much as anytheism - a faith position. I am linking it here because I know this topic has engaged people who have read my blog.

Intelligent Design - is it Creationism?

New Scientist says so. The American Association for the Advancement of Science says so. My former Cambridge colleagues say so. Most of the mainstream media say so. A federal judge in the U.S. has just said so. In fact, there are times when it feels as though there are only a few people who don't say so. But is it so? Am I really just being awkward? Or is it genuinely possible for so many people to be wrong and me - and what seems like a handful of others - to be right?

Firstly, what are the definitions? Are Creationism and ID formally the same? draws in information from various sources, and has the following definition of creationism:
Belief in the literal interpretation of the account of the creation of the universe and of all living things related in the Bible.
Intelligent Design doesn't have a separate definition, but the first line of the encyclopaedia entry for it is:
Theory that some complex biological structures and other aspects of nature show evidence of having been designed by an intelligence.
This would seem to encapsulate the essence of it.

So is there a formal connection between these definitions? No. Intelligent Design has empirical observation as their basis ("show evidence"); creationism has as its basis the "literal interpretation of the account of the creation".

Fair enough. But what about functional identity? One was once supposed only to eat oysters when there was an "R" in the month - in other words, not from May to August. The reason for this was that oysters spawn in the (Northern!) summer. So there is a functional connection between things formally defined in completely separate ways - there not being an "R" in the month, and it being spawning season for oysters. Are ID and creationism the same sort of thing - formally separately defined, but functionally the same?

That could be established by determining whether, despite the different definitions, it was the same people who aligned themselves with ID and creationism. But this turns out not to be the case. Creationists don't believe that ID proponents are adequately grounded in the Scriptures. ID proponents, for their turn, refuse to accept that it is possible to do science research starting with Scripture as a fixed reference point. So there is no functional equivalence, either.

In fact, a much better categorisation of the range of beliefs regarding origins can be found in this paper by Marcus Ross that I have linked to before.

But why is there such a determination to label Intelligent Design as creationism, when a few moments' consideration make it clear that this is not the case.

There are two groups of people who do this - again, this isn't new. There's the people who do understand the nature of Intelligent Design, and wilfully misrepresent it as creationism. Nobody who has fairly read "Darwin's Black Box" by Michael Behe could reasonably argue that it has much in common with the output of creationist organisations such as the Institute for Creation Research. Similarly "The Design Inference" by William Dembski. Similarly "Privileged Planet" by Gonzalez and Richards. But by labelling such books as "creationist", it is possible for their opponents to shut down debate - not on the basis of the content of the books (which as far as I know continue to be unchallenged in terms of the content of their science and maths), but because "everybody knows" that creationists are religiously motivated and "everybody knows" that there is no connection between religion and science - and therefore these books can't be scientific.

The majority of people who class ID as creationism simply do so because they have been told by somebody else that ID is creationism. They don't actually know anything about it first-hand - they haven't evaluated it for themselves. But (perhaps) they read New Scientist (whose "Intelligent Design Special" was a fine example of poor reporting), and if New Scientist says it is so, then it must be so.

So where do we go from here? The Kitzmiller vs Dover judgement is, in a sense, irrelevant (although humiliating). A person who, one assumes from the tone of writing in his judgement, was already pretty committed to a naturalistic worldview, takes the opportunity to slate the Intelligent Design movement and prevent ID from being proposed as an alternative to evolution in school. However, the questions that led to ID are still there - how come the universe is fine-tuned, and how come there seems to be a link between the presence of intelligent life and the ability to observe the univere? how come there is so much specified information in the universe? how come so much in biology looks designed with no apparent mechanism that could bring it about? Judge Jones didn't answer those questions. He just said that ID was wrong, and evolution was the truth. Perhaps he assumed that the answers were "out there" and just hadn't made it into court. Well, he was wrong. There are no answers to those questions. That's why I continue to have an Intelligent Design worldview.

Is ignoring the problems raised from a materialistic worldview going to enhance science? Or will it encourage people to think that science is more concerned about orthodoxy and toeing the line? We wait to see.

Tuesday, December 20, 2005

Christmas Present Idea

The British National Formulary is the reference book that provides up-to-date guidance on prescribing, dispensing and administering medicines in the UK. Here is a link to the 50th edition.

It was something of a surprise when I saw that Amazon suggested people buying it might also be interested in the British National Formulary for Children. I mean, are any children really likely to want to read such a specialist publication?

How not to get into a relationship (of the wrong sort)

(PARENTAL ADVISORY again - though, given that on their own testimony, up to 90% of 16 year olds are sexually active anyway, it's children from about year 8 upwards who need to know this!)

So, following the post below, what would I suggest? As an evangelical Christian, I have my opinions on how relationships are supposed to work, and I think that if people lived according to this pattern - sexual relationships are for marriage - they would be happier. But I also realise that most people don't share those beliefs. So if people aren't prepared to accept the Christian pattern, then what in practical terms can they do to avoid the worst of the messed-up relationship experiences that seem to be so common?

Unless you really are looking for casual sex (which in itself will probably help to mess up any future relationships that you have) don't start a sexual relationship with somebody unless you really know them. These days, it is a lot less painful to get into such a relationship than it is to get out of it. Sex isn't fundamentally a "casual" act - it changes you psychologically, emotionally and physically. This is even assuming that you know how to avoid unwanted pregnancy and sexually transmitted diseases.

It is a lie for somebody to say: "if you loved me, you would do this." If that person loved you, they wouldn't be pushing you to do something you didn't think was right.

Don't get into a relationship thinking that you will "change" the things you don't like about somebody. It is more common for relationships to break up with such things unchanged than it is for changes to happen.

Living together isn't a "trial marriage". The one thing that living together can't model is the one thing that is different about marriage - that it is supposed to be permanent. A marriage is more likely to break up if a couple lived together before they got married.

Finally, don't lie to yourself that your "heart" is more powerful than your "mind". You are in control of your actions.

Sunday, December 18, 2005

A substitute for carol singing

So far this year, we have had two lots of carol-singer substitutes call.

I don't know whether the idea of "carol-singers" is widely understood beyond England. Basically, as I understand it, people used to travel from house to house during evenings in the run up to Christmas. They would sing a carol (all of one - perhaps six or seven verses) then perhaps some verses from "We wish you a merry Christmas" - and for their time, they would be rewarded with something warming - perhaps (in the words of "We wish you a merry Christmas") some "Figgy Pudding".

The first lot of "carol singers" we have had are the Rotary Club. They have a kind of truck thing which has a mock up of Father Christmas's sleigh on the back. In addition to this, they have a PA system, through which they play recordings of a choir singing Christmas carols. The "outriders" (the Rotarians hunt in packs) go and knock on doors to collect the money, and point out to any children who may be resident that Father Christmas is afoot (in return for a donation to Rotary funds from the parents). The children are then supposed to look in wide-eyed wonder at the sight of the traditional Father Christmas accompanied by the sound of angelic trebles singing "I saw three ships come sailing in" or some other such carol that is now only sung on Christmas Carol CD's.

I have suggested to them in the past that I would be more willing to give them money if they actually sang themselves. To which their response was "Oh, no, you don't want to hear me singing." What I should have said was, "Yes, but that's not quite the point with carol singing." But I lost my nerve, and just coughed up my pound. There's a limit to what you can do to restore traditional Christmas values on your own.

The second lot of "carol singers" called last night. At about 9pm, we had a knock on the door - most people don't even bother opening the door at that time of night, I suspect. As soon as the door had started to open, I was regaled to five people (the oldest can't have been more than 17) singing "We wish you a merry Christmas" - just the chorus, somewhat out of tune - and then they lapsed into embarrassed, smiley silence, a small plastic tub with coins in held self-consciously in front of them. "Well done," I said, "are you collecting for charity, or just yourselves?" "For ourselves," said the oldest one, "and" - perhaps feeling that this sounded rather un-Christmassy, pointing at a young lad who must have been under 10 - "for the little one, so he can buy a present for his parents." "Yeah, right," I thought - and coughed up my pound. "Nice work if you can get it," I said to Liz after they had gone. "A pound for twelve seconds singing." "Would you have paid them two pounds if it had been six seconds?" she asked.

Tuesday, December 13, 2005

Street music

This post from the Witts reminded me of an experience we had. We were shopping when we only had one child (who was therefore less than 20 months old), but that one child was not happy - in fact, she had been making a loud fuss steadily for several minutes. In the street, a group of musicians were playing some fairly funky/folky/skiffly/Irish music - it wasn't easy to categorise. Anyway, our child was fascinated, and stopped making a fuss. So I stood there with her, listening to the music, whilst Liz finished the shopping. And then went and bought a cassette from them.

Some time after we got onto the Internet, it struck me that they were probably on it somewhere - and I found them after a short search. They had also progressed technologically, and I was able to buy copies of their CD's - which were just as much fun as the cassette had been.

The band was The Huckleberries. The cassette was "Live in the Garden". The CD's were "Reelgrass" and "Jigweed". And I see they have a new one now, called "Incahoots".

Monday, December 12, 2005

Seven things

From Tom

Seven things to do before I die (as the seconds tick away – tick, tock, tick tock [Bill Bailey])

1. Visit Patagonia
2. Write a novel
3. Play in an orchestra again
4. Plant a church
5. Become bilingual
6. See U2 in concert
7. Influence people

Seven things I cannot do

1. Sleep with somebody I’m not married to.
2. Play any sport at international level.
3. Play golf at any level.
4. Harm my children.
5. Say anything good about “The Family at One End Street” - the most tedious book I have ever read in my life.
6. Live my life again.
7. Put the toothpaste back in the tube.

Seven things that I like in my spouse/significant other/parents (apply in that order – unofficial expansion, for the sake of democracy and to get some revealing answers out of people who don’t have spouses)

1. She’s still here.
2.She will keep going when I run out of steam.
3.She likes me rubbing her back.
4.She understands me – and doesn’t give up in disgust.
5.Most of the time, she puts up with the fact that I don’t have the same awareness of when the house is untidy as she does.
6.She values what I value.
7.She looks lovely.

Seven things I say most often

1. Are you ready yet? (to the children)
2. Speed checked (– and similar – sorry, it’s a work thing)
3. My name’s Paul Fernandez and I’m your captain (work again)
4. Whereabouts do you live?
5. What did you do before you (do what you are doing now)?
6. What do you need me to do?
7. I just want to ....

Seven books (or series) I love (Bible not included)

1. Harry Potter by J.K.Rowling. Actually doesn’t really deserve first spot – good stories, but I think that most other entries on this list have changed my life, and I don’t think Harry has.
2. Lake Wobegon Days (plus spin-offs) by Garrison Keillor
3. Sophie’s World (... and if you can throw in the rest of the Jostein Gaarder collection, especially “Through a Glass Darkly” [even though I’m not sure I could bring myself to read it again – it is just too intense] that would be cool)
4. Swallows and Amazons series by Arthur Ransome
5. Francis Schaeffer Trilogy (The God who is There, He is There and He is not Silent, Escape from Reason)
6. The Dorling Kindersley series “Animal” “Earth” “Weather” “Universe” etc.
7. Darwin’s Black Box by Michael Behe

Seven movies I watch over and over again (or would watch over and over if I had the time)

1. Annie Hall
2. The Lord of the Rings
3. The Matrix
4. Minority Report
5. The Emperor’s New Groove
6. Lilo and Stitch
7. Dead Poets’ Society

Seven people I want to join in, too

This is tricky – most bloggers I know have already been hit by others – well, Tom, to be precise. So I’ll have to e-point various people who don’t have blogs to this post. If you want to set up a blogsite, then one way of doing it is to register at – they will host a blogsite for you free.


PS - I know it's cheating, but two/four more people - Rob/Vanessa and Jonathan/Amanda (except they've probably done it already)

Wednesday, December 07, 2005

"Come and see the violence inherent in the system"

The story so far.

Professor Paul Mirecki, at Kansas University, announced that he was going to run a course, entitled Special Topics in Religion: Intelligent Design, Creationism and other Religious Mythologies.

He backed this up with an email to a list server in which he wrote:
The fundies want it all taught in a science class, but this will be a nice slap in their big fat face by teaching it as a religious studies class under the category ‘mythology,’

Doing my part (to upset) the religious right, Evil Dr. P.
(He used stronger language).

It seems to have become apparent that this was inappropriate behaviour for a university professor, and he wrote an apology and withdrew the course - recorded here on Telic Thoughts.

And then he got beaten up.

Having been the victim of the sort of violence that Mirecki experienced - perhaps not quite as serious (I only had one assailant), though apparently Mirecki will live, I know what an unpleasant experience this is. It left me close to a nervous breakdown and had a major impact on my behaviour (I am of a sensitive disposition). There is never justification for this sort of behaviour. Period. It is loutish, unpleasant, and completely inappropriate in a civilised society. If the people doing it were doing it "in defence of Christianity", they did more to damage the cause of Christianity than could be imagined - look at this gathering of responses. He'd already apologised, for goodness' sake!

However, when I was beaten up, it wasn't because I had insulted anybody. It was just casual violence from a tanked-up local when I was a convenient student "target". If Mirecki had slagged off a local football team, it would hardly have been surprising had a couple of the fans caused him trouble. And yet, Christians are regarded as "fair game" today. They can be insulted, the things they hold holy can be derided, or mocked in art, they can be referred to as stupid, ignorant, evil child abusers simply because of their beliefs, and they are expected to put up with it. When they are seen to react (and I would point out again that this violent response was not a response from people who were acting in accordance with Christ's teaching), people say, "Aha! Now we see the fundamentalists' true colours coming out! Come and see the violence inherent in the system!" Anybody who made this sort of remark about Muslims would probably have a Fatwa issued against them; when a play that was regarded as "anti-Sikh" was put on in Birmingham, it caused riots. Just about anything that might be considered part of our Christian heritage is being "concealed" with more politically correct labels to make sure that nobody from any other faith could be offended. But one minor act of violence - unacceptable as it was - and all "Christian fundamentalists" are immediately classed as opponents of freedom of speech and tolerance. Hey, hang on! I didn't do this!

But this shouldn't come as a surprise. Jesus said, "Blessed are you when people insult you, persecute you, and say all manner of evil things about you." Opposition to Christian ideas isn't something new - because people are opposed to the Christian God. In "Rattle and Hum", Bono said in response to money-grabbing tele-evangelists, "The God I believe in isn't short of cash, mister." And neither does the God I believe in lack the ability to deal with people who wish to "break his chains".

Monday, December 05, 2005

"Where is the ID research?"

Intelligent Design (ID) is fundamentally a worldview, rather than something that is scientifically provable or disprovable in its own right. For that matter, so is philosophical naturalism (PN). So research can be interpreted in the light of ID - or PN - but because it is a metanarrative, in a sense it lies outside the realm of "provability". It is therefore no more valid to raise the question, "Where is the research that proves ID?" than to ask "Where is the research that proves PN?"

To somebody who has an ID worldview, evidence of the irreducibly complex nature of biochemical systems supports their opinions. For people who have a PN perspective, they KNOW that there must be a naturalistic explanation, so evidence that doesn't support their worldview must be flawed. What happens is that, as more evidence comes in, people have to decide whether the worldview that they have continues to provide an adequate explanation of the evidence. Eventually, if they don't believe their worldview is tenable any longer, they may change it. However, people have a great deal invested in their worldviews - it is not easy psychologically to change - and (for example in the case of phlogiston, the earth-centred cosmology, Newtonian vs Relativistic physics) may take something pretty convincing. One of the interesting phenomena about ID is that most of the people who subscribe to it don't seem to have arrived there from an originally creationist perspective, but because they have become convinced that evolutionary explanations aren't adequate.

I could work through a stack of papers, reinterpreting the research and writing new conclusions specifically on the basis of an ID worldview, or a naturalistic worldview, or a Young Earth Creationist worldview, or whatever. Not many papers have been written with conclusions that have a specifically ID perspective. The reasons for this are several. Firstly, ID faces opposition from the scientific mainstream, and so people who don't believe in PN may tend to shy away from research in areas where their beliefs will bring them into conflict with the rest of the department - particularly biology. A higher proportion of physicists aren't PN than biologists, and I think this is because biology as a discipline is so strongly committed to PN. The fact that many biologists don't have such a strong mathematical and statistical grounding as physicists may also have a bearing! Secondly, there is no reason why a scientist should court controversy and rejection by explicitly stating that he doesn't subscribe to PN in a paper if there's nothing in his research that is built on it - and except in evolutionary biology and cosmology, this is probably normally the case. I imagine that the hundreds of scientists who dissent from darwinism have papers to their names, but ID opponents would doubtless say that their research "doesn't support ID", because the conclusions of their papers don't make reference to ID.

Wednesday, November 30, 2005

Men are ... what's that word for illegitimate offspring?

Sorry, not terribly polite - and this is quite a blunt post. But I've just heard too many stories this week of men messing up women's lives.

There's the ex-husband who banned his wife from wearing slippers around the house because "they weren't sexy enough".

There's the ex-husband who rang his wife continually when she was away from home in an attempt to prevent her from doing anything socially.

There's the ex-partner who pushed his girlfriend down the stairs and then kicked her in the head.

There's the ex-lover who for a year refused to allow his woman to describe herself as "his girlfriend" - she came to the conclusion eventually that she was his "bit on the side".

There's the guy who got involved with a woman whose lover had relatively recently died when he already had a steady girlfriend.

There's the guy who rang his wife up whilst she was doing a presentation to say: "The baby won't eat her food. What should I do?"

That's just stories that I have heard in the last week. What is it with men?

Well, here are two suggestions. The first is the sexual "liberation" of women, and the casualisation of sexual relationships. Women are now considered free by society to sleep with whomever they want to. What this actually means is that, in most cases, if they want to get the attention of men, they have to sleep with them. So the big biological motivator for men is now being offered them in most relationships, to actually get them into the relationship in the first place.

Of course, this is miles removed from the "slavish" "Victorian" Christian morality that prevailed even until about 30 years ago. I would suggest that, within this paradigm, "living together" - in the sense of sexual relationships which were beyond the most casual encounters - was basically something that, if it existed outside marriage, was something which marked the most committed relationships. So if men were to get their biological "payoff" (as one might coarsely put it) they already had to be pretty committed to their women. Women weren't expected to become sexually involved with somebody before they were pretty sure that they were "the right sort of person". Nowadays, in most cases, the relationship is built the other way round - sex in many cases comes pretty early on, and you find out what the person is like later. So women can easily find themselves involved with men who, with more than five minutes thought and a few milligrams less hormones, they know are basically not the sort of person they want to be involved with. And whereas men - in biological terms - don't seem to care who they sleep with, women - in biological terms - are designed to want sexual relationships to be of the stable, child-rearing (i.e. years rather than minutes) kind.

The second phenomenon is the breakdown of families. This has impacts in all sorts of areas. In many cases, the dads of teenage girls are no longer around. This takes away a huge source of tension, of course - how many slammed doors are directed from the teenager to her dad? how many shouts are directed from the dad to his teenage daughter? But the reason for this tension in many homes is the fact that the dad is trying to protect his daughter - something that, in many cases in later teenage years (and particularly when a girl leaves home), she comes to see and appreciate. (At least, I hope!) And even if the girl is frustrated and tries to break away from the straitjacket that she perceives her parents protection to be, it still places some constraints on her, and no matter how much she rejects her parents' attitudes, she will still be affected by their opinions of different boys that wander in and out of her life. I suspect that fathers, in particular, will indicate the sort of boy/man that they think is appropriate for their daughters - and this will, regardless of her protestations, shape her thoughts.

It also has an impact on men when they are growing. Dads who stay around are role models for sons. How does a man know how to respond to the woman he is in love with? Well, the most likely role models will be the men he has seen relating to women that they love. If his dad showed love, care and affection for his mum, then as like as not, he will see that this is good, and will treat the women he loves in the same way.

These aren't cast iron conclusions - people can overcome all sorts of different backgrounds to become good at relationships - and people who have had everything good can still be lousy at them. But I wonder to what extent these factors do have an impact.

As Jon Mackenzie says at the bottom of his posts, "Go on, disagree. See if I care."

Tuesday, November 29, 2005

After some thought, (part of) a poem

Scott Adams has continued his explorations of issues related to intelligent design on his blog. It is hard to tell whether he is trolling or genuinely curious - after all, he is 'only' a cartoonist.

His latest post, which has (so far) garnered a mere 300 comments (sigh - have I had that many since I started?!) reminded me of a poem by Steve Turner - here's the last verse.

If Jesus was thirty-two today we'd have to
end it all. Heretic, fundamentalist, literalist,
puritan, pacifist, non-conformist, we'd take Him
away and quietly end the argument.
But the argument would rumble in the ground
at the end of three days and would break out
and walk around as though death was some bug,
saying 'I am the resurrection and the life . . .
No man cometh to the Father but by me'.
While the magicians researched new explanations
and the semanticists wondered exactly what
He meant by 'I' and 'No man' there would be those
who stand around amused, asking for something
called proof.

Steve Turner, "If Jesus was born today", Nice and Nasty

Anybody familiar with any of my poems will probably immediately recognise the influence that Turner has had on me, but that's not important right now.

Sunday, November 27, 2005

Technological evolution competition

Bill Dembski, at Uncommon Descent, has a few days to run on a competition to demonstrate gradual development/co-option in the technological realm.

When I had a connection with the RAF, they had standard issue sunglasses which were known as "Mark 14's". What interested me about this was how something as inherently simple conceptually as sunglasses should have gone through 13 previous design iterations prior to arriving at its current state of sophistication. It led me to construct stories akin to the evolutionary just-so stories that people suggest in nature as to what, exactly, the previous 13 "marks" might have looked like. For example, I wondered whether Mark 6's had been abandoned when they ripped off the ears of a fast jet pilot who ejected when wearing them, on account of the fact that the arms of the glasses were made out of cast iron and weighed five kilograms each. Or whether the primitive Mark 3's had been rejected when it was determined that plywood, although cheap, didn't make acceptable lenses for sunglasses.

Wednesday, November 23, 2005

Government's double standards?

The UK government failed in its attempt to push through legislation that would allow people to be detained for 90 days without being charged. Tony Blair emphasised over and over again that he was being asked for this by the police, that people shouldn't second-guess what the professionals thought - and there was a kerfuffle when police forces apparently made representation of these opinions to local MP's.

In the case of the legislation to extend licencing hours which comes into force in the next day or so, the opinions of the police seem (where expressed) to have been against the changes - extended opening hours and potential round-the-clock drinking are hardly going to make a policeman's lot a more happy one.

But whereas the opinions of the police seem to have led to Tony Blair placing his credibility on the line in the case of 90 day detention without charge, the government don't seem to have given a hoot for their opinions over licencing. And the funny thing is, whilst the potential threat from terrorists is doubtless greater, nobody has been able to make a coherent case for 90 day detention reducing the threat of terrorism (although plenty have pointed out the risks to civil liberties of such detention). But plenty of people know the impact that late night drinking has in turning city centres into no-go zones, and its relationship with anti-social behaviour.

So why is Tony Blair so concerned about the opinions of the police in one case - being prepared to alienate most of his party to fulfil their wishes - and so indifferent in the other case? Might it be that there are other issues at stake? ITWSBT

Tuesday, November 22, 2005

The Catholic position on Intelligent Design

Here, the Vatican's chief astronomer (! - the implication being that they have a whole department of astronomy!) says that ID isn't science:
According to the Italian news agency, ANSA, Father Coyne was speaking informally at a conference in Florence when he said that intelligent design "isn't science, even though it pretends to be."

This has been cited with glee in several places. What has not attracted so much attention in such places has been the opinion of the Pope, and a close associate of his, Cardinal Schonborn, who both argue that the universe requires intelligent agency (see here for Denyse O'Leary's analysis of this in English). Well, one would hope so!

Doubtless people will say something along the lines of, "Well, are they scientists?" But this isn't relevant, firstly because one's belief or otherwise in the supernatural is a matter of presuppositions, not evidence. Any and all observations are accommodated by people who believe in evolutionary explanations for all life - even when the evolutionary explanations are contradictory. This may partly be a symptom of a psychological phenomenon - called "confirmation bias" - evidence is fitted into one's existing mental framework rather than jettisoning the framework and adopting a new one. The same happened with the Aristotelian view of the universe with its epicycles; the same happened with phlogiston; the same happens with creationists for that matter - and the same happens to all of us when we are faced with odd circumstances that we need to find an explanation for.

Secondly, whilst Benedict and Schonborn may not be scientists, they aren't stupid - any more than Scott Adams is (despite his disingenuous blog to the contrary), or Denyse O'Leary was when she started researching "By Design or By Chance?", or Michael Behe was when he realised that there were weaknesses in evolutionary theory before he started writing "Darwin's Black Box". And unlike many scientists, Benedict and Schonborn also know the dangers of "unprofessional" intervention in science because they have a sense of history. Just because people aren't scientists doesn't mean that they are incapable of comprehending scientific arguments, and coming to their own conclusions about it.

Saturday, November 19, 2005

Hello, Phoebe

who are you,little i

(five or six years old)
peering from some high

window;at the gold

of november sunset

(and feeling:that if day
has to become night

this is a beautiful way)

e.e.cummings, "73 poems", 52
Actually, it wasn't evening - perhaps "if autumn has to become winter" would be more appropriate.

Wednesday, November 16, 2005

Our family - 3,500 years old.

One of the arguments against creationism and ID is that they tend to be funded by organisations that have a religious agenda.

Ateleological organisations have the advantage that in some settings, philosophical naturalism is considered to be inherent in the definition of science. As I have mentioned before, this is incorrect - most of the people who shaped modern science weren't philosophical naturalists, and in fact they believed that the pursuit of science was possible because the order in the universe had been put there by God. But because a naturalistic approach has been accepted as inherent to science, it is now possible for an organisation to adopt a "neutral" sounding name - Scientific American, American Association for the Advancement of Science, New Scientist - and pursue an agenda which excludes the possibility of ID by definition. Not because work in ID is not science - but because a narrow definition of science is being used specifically to exclude this as an option.

Any organisation that doesn't exclude a priori the possibility that there may be such a thing as an "external other" can be defined as "religious" - because it doesn't presuppose philosophical naturalism. In fact, it is impossible to have an organisation which accepts the possibility of teleology which won't be considered religious. Even an organisation which remained agnostic on the issue would be effectively being open to the possibility - which is not a naturalist position, and could therefore be classed as religious.

However, cast it the other way. Think about the (US) National Center for Science Education - which is actually about "Defending the Teaching of Evolution in the Public Schools", rather than about science education in general (nice neutral title). It's supported by people who have an anti-teleological agenda - they want to make sure that no form of teleology is promoted in public schools. Do we deconstruct their comments because they have a prior commitment to the teaching of evolution? Do we say that their opinions are invalid because they are seeking to oppose presentation of a teleological perspective in public schools? No. We accept that they are going to present material that is consistent with their foundation - but then we deal with that material on its merits.

In the same way, it isn't valid to dismiss the arguments of ID or creationist proponents on the basis of their worldview - or even the worldview of the people who are funding their research. People are bound to present research that they believe in. The way of refuting research isn't to say that the author doesn't share your worldview - no matter how invalid you think the other worldview is - that is postmodernism, not science. It's to show that their methods or conclusions are flawed. You can show that people haven't made a scientific case for their position - and that's what I was trying to do by interacting with the Avida and AFGP papers (see the side bar). Forget the fact that they wrote those papers because they didn't believe that ID or creationism was necessary - the papers simply don't show what it's claimed that they show. In the same way, criticisms of ID or creationist work has no need to look at how the work was funded. It should be able to show that the work is just scientifically wrong.

Aaaanyway, whilst trying to find out more about Charles Simonyi, who endowed Richard Dawkins' professorship (which is used more to "bash religion" than to promote the public understanding of science - I have talked about the upcoming TV shows that Dawkins is preparing below) I happened across this paper, which I thought was interesting.
Abstract: Questions concerning the common ancestors of all present-day humans have received considerable attention of late in both the scientific and lay communities. Principally, this attention has focused on `Mitochondrial Eve,' defined to be the woman who lies at the confluence of our maternal ancestry lines, and who is believed to have lived 100,000-200,000 years ago. More recent attention has been given to our common paternal ancestor, `Y Chromosome Adam,' who may have lived 35,000–-89,000 years ago. However, if we consider not just our all-female and all-male lines, but our ancestors along all parental lines, it turns out that everyone on earth may share a common ancestor who is remarkably recent. This study introduces a large-scale, detailed computer model of recent human history which suggests that the common ancestor of everyone alive today very likely lived between 2,000 and 5,000 years ago. Furthermore, the model indicates that nearly everyone living a few thousand years prior to that time is either the ancestor of no one or of all living humans.

I don't remember the media making much of this, but what is interesting is that the common ancestor would thus be comfortably in the era after the biblical flood.

P.S. Thinking about it, doesn't research that show we share a common ancestor 3500 years ago rather undermine research that shows we share common ancestors tens to hundreds of thousands of years ago? Doesn't it suggest that maybe the accuracy of their findings was the odd order of magnitude out? Or that their methodology was flawed? ITWSBT.

Monday, November 14, 2005

To which race of Middle Earth do you belong?

Apparently, I am ...


brought to you by Quizilla

(... though it ought to be observed that 40% of the people who took it got this result as well)

Saturday, November 12, 2005

Scott Adams and GROGGS

I plugged the Dilbert Blog (which perhaps, in the spirit of the strip, ought to be called the Dilblog) a little while ago. This was based on my experience of Scott Adams' insightful cartoon strips.

I have been startled at how thought-provoking his posts have been, and I was particularly startled by this recent post, which demonstrated a really keen analysis of many of the issues in the debate between evolution and ID.

Which is more than I can say for some ex-university acquaintances of mine, who are still convinced that:
a) ID is "God of the Gaps"
As a scientist, I see things every day that we can't yet explain. We tend not to put in papers `because we don't understand this, we conclude that someone designed it this way' not because `someone designed it this way' is a logically impossible conclusion, but because it raises far more questions than it answers.

b) ID has a political/religious agenda
discussion of the designer is deliberately discouraged by ID proponents, as part of the strategy to sidestep the US ban on teaching creationism in schools and to mask the religious motivation of most of those who support ID

c) ID should 'fess up to who the designer is
Doesn't ID rather beg the question of who the "intelligent designer" is? Given the lack of verifiable data, that strikes me as a rather religious question.

d) ID is the same as young earth creationism
Creationism is scientifically foolish because, in its strong form (God created everything just like it is now, just after having his breakfast on Sunday 23 October 4004 BC), it contradicts things that are observed, and in its weak form (created everything), it tells us nothing. Believe it, if you like, it may even be right, but it is not scientific.

... none of which errors Scott Adams falls into. Guess they must be too highly trained, or something ....

Friday, November 11, 2005


You gave me Christopher Robin, and then
You breathed new life in Pooh.
Whatever of each has left my pen
Goes homing back to you.
My book is ready, and comes to greet
The mother it longs to see -
It would be my present to you, my sweet,
If it weren't your gift to me.
A.A.Milne, Winnie-The-Pooh

Sometimes it's hard when, as a parent, you are lost in the chaos of messy rooms, a hectic round of children's activities, and children themselves who are permanently non-compliant, to remember the most amazing thing - that you are part of a unique family, and the interdependencies between the people within it are so tangled as to be inextricable.

The Winnie-The-Pooh stories are magical - I am just working through the series with my four year old. But what is even more magical is that they have their roots in a real (albeit now old-fashioned) family, where the son wanted his dad to tell him stories, and was spellbound when they turned out to be about him and his toys - and where the dad realised that there would be no magic were it not for his wife - who is, other than the dedication, completely invisible in the stories themselves.

Tuesday, November 08, 2005

Dawkins - religion is "the root of all evil"

In the new year, Richard Dawkins, Professor of Atheism - sorry, that should be Charles Simonyi Professor of the Public Understanding of Science - at Oxford University, will be airing a "provocative" two part documentary addressing this subject. In particular, he apparently wishes to point out the destructive force that the three monotheistic religions - Christianity, Muslim and Judaism - have been in Western civilisation.

Surprising? Hardly. His views on religion are well-known - he considers bringing children up within a religious tradition to be a form of child-abuse - see here for commentary - and he considers anybody who doubts darwinism (which "allows one to be an intellectually-fulfilled atheist") to be either mad, stupid, ignorant or evil. And the mainstream media in the UK are slanted against the expression of orthodox religious belief. So it was overwhelmingly likely that Dawkins would get the opportunity to continue what he started in the Royal Institution Christmas Lectures some years ago.

Neither is the theme likely to be surprising to most Christians who seek to present their beliefs in a public forum. "Look at all the suffering caused by religion" is probably in the top three intellectual objections to Christianity.

However, at risk of stealing his thunder, I have a couple of wonders. Firstly, is he going to address the fact that the twentieth century - the most bloody in human history (so far) - was so bloody because of anti-religious regimes? Stalin's Russia; Mao's China; Hitler's Germany; Pol Pot's Kampuchea. Of course, organised religion has wickedness to answer for - yes, there were the Crusades; yes, there has been sectarian violence in Northern Ireland for many decades; yes, there was the Inquisition, the Salem Witch Trials and the Counter Reformation. But do any of these compare with the systematic extermination of millions of Jews in Hitler's final solution? Or the Killing Fields?

Secondly, since I have no doubt that his focus will be on Christianity (being branded as anti-semitic is not what he would want, and it is always dangerous to publically condemn Islam), will he draw a distinction between the powerful organised religion represented by institutions such as the Catholic Church and the message of Jesus, which was the antithesis of power? Or will his research be as lazy as Robert Winston's was when he was preparing his "insightful, provocative" book on religion?

More scientific iconoclasm

I am writing with reference to: Chen et al. 1997. “Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish.” Proc. Natl. Acad. Sci. USA 94.
Here is a link to the full paper, and this is the abstract.
Freezing avoidance conferred by different types of antifreeze proteins in various polar and subpolar fishes represents a remarkable example of cold adaptation, but how these unique proteins arose is unknown. We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process by which this occurred through characterization and analyses of notothenioid AFGP and trypsinogen genes. The primordial AFGP gene apparently arose through recruitment of the 5 and 3 ends of an ancestral trypsinogen gene, which provided the secretory signal and the 3 untranslated region, respectively, plus de novo amplification of a 9-nt Thr-Ala-Ala coding element from the trypsinogen progenitor to create a new protein coding region for the repetitive tripeptide backbone of the antifreeze protein. The small sequence divergence (4-7%) between notothenioid AFGP and trypsinogen genes indicates that the transformation of the proteinase gene into the novel ice-binding protein gene occurred quite recently, about 5-14 million years ago (mya), which is highly consistent with the estimated times of the freezing of the Antarctic Ocean at 10-14 mya, and of the main phyletic divergence of the AFGP-bearing notothenioid families at 7-15 mya. The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly.

Firstly, I would like to say that this is a good paper. It is well-researched; the paper itself doesn’t make too strong claims for itself; and it is an example of exactly the sort of paper that darwinism needs to present if it is to move from the realm of story-telling to being on a solid scientific footing.
What I do not agree with, however, is the iconic status that this paper has in the darwinist community. Like the Avida paper that I discuss below, this paper crops up over and over again as a demonstration of how darwinism can – nay, has – solved all the problems that challenge it.

For example: it is cited here in a comment on a post by William Dembski; it is presented here on the NAS website as a “cool tale in molecular evolution”; and it is effectively the framework of one of the objections to the Meyer paper that Panda’s Thumb are reacting against to in Meyer’s Hopeless Monster.

If AFGPs arose in this way, this is a significant example of new – and highly useful – functionality arising. However, let’s think about the evolutionary process that has taken place, if this account of how AFGPs appeared is correct.

Firstly, presumably (since the trypsinogen gene continues to be used by the organism) the gene was duplicated. In organismal terms, this is a necessary first step; however, it is basically an evolutionarily neutral step. Then, a large section of the functional part of the trypsinogen gene was deleted – again, following duplication, this is a neutral step. Then comes the insertion or deletion of a couple of nucleotides to induce a frame shift within the gene that has lost its original functionality. This is analogous to where the computer model, Avida, mutates the genomes of its digital organisms. These are the evolutionarily significant steps. Then, having established the AFGP functionality, it was amplified. Once the functionality is there, it is possible to select for increased expression of the functionality. The significant step, then – to establish the functionality – requires only a couple of changes. Of course, the first neutral steps were significant in terms of evolution – but the likelihood is that these don’t provide anything that can be selected for.

It is significant that, even in this simple example of a beneficial process, all of the “difficult” evolution has happened elsewhere. The 5’ sequence of 67 nucleotides and the 3’ sequence of a couple of hundred nucleotides, is preserved in the AFGP gene from the trypsinogen gene. The 1.7 kbp insert in the AFGP gene is irrelevant to the gene. The spacer sequence is almost identical to an existing sequence that has undergone a frameshift. The backbone sequence has also been recruited from an already specified sequence. And the gene is highly repetitive, containing tens of copies of functionally identical sub-genes.

The fish breeding mechanism is also significant. The fish certainly aren’t sexually mature for many years. My reference books didn’t provide a definitive answer on this, but is it the case that these fish breed in the conventional fishy way – by mixing milt and roe? So many thousands of baby fish are released – presumably fully biochemically functional – but without the investment of huge amounts of energetic resources on the part of the parents. The significance of this is that this means of reproduction gives many opportunities for “beneficial mutations” to be present - and also tested - in every generation (compare mammals with litters or calves, birds or amphibians with a clutch of eggs). Furthermore, with sexual reproduction (compare bacteria) it is possible for beneficial mutations to spread through the population, rather than simply following one genetic line. This form of reproduction provides about the best possible framework within the animal kingdom for evolution.

So to summarize: this papers provides a coherent explanation of how the AFGP functionality might appear, and this is a significant evolutionary change. However, it is a long way removed from the appearance of complex polypeptides, and it is an evolutionary change that takes place in the reproductive environment which is most suited to evolution. Also, it is not a complicated evolutionary step – most of the complex evolution has already taken place elsewhere, and to use the analogy of “climbing Mount Improbable”, this evolutionary step represents climbing onto the trig point at the top of the mountain once the mountain itself has already been scaled. So it is presumptuous to argue – as many darwinists seem to think – that this paper suggests that darwinist explanations of all biological features are just around the corner.

Thursday, November 03, 2005

Visitors' book

I know that I have had hits on this blog from all around the world - every continent with the exception of Antarctica. I would love you to say "hi" when you stop by. I have just added a link to a frappr map in the sidebar. If you like, you can pin yourself onto the map, and leave a comment.

Wednesday, November 02, 2005

Some implications of probability bounds

It is argued that ID has little impact on anything in the world of “real science”. However, to consider at least one issue, there are some conclusions that can be drawn on the basis of work on probability bounds. The bounds place constraints on the starting point for evolution, and would perhaps assist in showing how evolution might happen – and also establishing whether evolutionary explanations are plausible.

For example, take as a starting point a random sequence of DNA bases. It is unclear from literature whether this is assumed to be a basis of evolutionary progress – whether having a random sequence of bases would be a starting point for natural selection. Actual proposed mechanisms by which novel proteins might appear is rarely addressed. But let's assume, for the sake of argument, that the engine of evolution is random DNA sequences which are then modified by natural selection.

However, three out of 64 of the DNA base codons code the STOP sequence – that is, if one of these codons is found, they will terminate a protein chain. Now, the probability of three bases NOT coding for STOP is thence 61/64 – or 0.953. The probability of two lots of three bases NOT coding for STOP is 0.953 squared – 0.908. The significance of the universal probability bound is that we can exclude chance as a reasonable explanation for an event if the probability of an event is less than this bound. And it turns out that the probability of 7000 lots of three bases NOT coding for stop is close to Dembski's conservative value for the universal probability bound of 10 to the power of -150.

In other words, we can exclude the possibility that a protein with a chain of over 7000 amino acids arose on its own. The likelihood of a DNA sequence of the required length arising at random can be excluded, using the universal probability bound – such a protein would have to arise by other mechanisms - perhaps as a consequence of adding together smaller components. Obviously, if as I suggested in an earlier post, higher probability bounds ought to apply to biological systems, then the maximum number of amino acids that could be present in a protein as a starting point for natural selection would be consequently smaller.

I would like to explore some further implications of the probability bounds in future posts.

Sunday, October 30, 2005

Full-time Christian workers - a danger

Tu Quoque has a thought-provoking article about the danger of “Senior pastor-itis” in large churches – a swollen sense of the significance of the senior pastor in the life of a church. What they have failed to do, though, is point out that this syndrome is simply a special case of a more general phenomenon. When a church has a full-time worker, there is a danger that the expectation will be that the people in the pews will “receive ministry” from the pastor, who is after all being paid to minister to them.

In churches where there is plenty of activity – children’s clubs, work in the community, and so on – there is still the expectation that the full-time person will be the main man, theologically. In churches where there is a plural eldership, in many cases, the elders defer to the full-time worker. This fails to get to grips with the fact that all elders are to teach (it is effectively what marks them out within the congregation, and is how they are to shepherd the flock) – and that more significantly if we are to fulfil the great commission, then we have to get beyond simply doing things in our own churches, and get people out of the church into the world.

It is understandable that the full-time minister would want a second worker if one is available, given the isolation he will experience in this elevated position. The church is likely to want a second worker as well - there is an element of pride for the members in a church having two full-time workers. But if a second worker is present, the danger is that the mentality will become even more marked. The number of main services probably won’t change – typically two main meetings on the Sunday. But with two full-time workers to “sing for their supper”, it becomes increasingly unlikely that the non-paid membership will ever be given the responsibility for teaching the church. And with two full-time workers, the self-perceived spiritual/theological gulf between the people in the pew and the people in the pulpit is even greater - “Oh, I’m only an amateur – far better to have the professionals preach.” Or, in the case of keen young men, they are regarded as too immature, and having more senior people ahead of them, so they are restrained from doing as much as they might be interested in. As likely as not, the "older generation" within the church will then bewail the "lack of commitment" in the "younger generation" that is preventing people coming forward for full-time work - when they haven't given them the opportunity!

Evangelical churches are committed to the idea of every-member ministry; they believe in the priesthood of all believers; they are committed to the fulfilment of the Great Commission. But the effect of this elevation of full-time workers above the rest of the congregation, in addition to the points made in the Tu Quoque article, is to undermine these principles in the key area of teaching.

It is salutory that Paul spends the first four chapters of 1 Corinthians addressing the problem of “leader-itis” in the church there – showing how it is undermining the message of the gospel, undermining the nature of the church, and undermining the spiritual lives of individual Christians. It is also worth noticing how Paul operated as a missionary. He went to a new place, taught there for a period of time (supporting himself as a tentmaker!), and then moved on, leaving the church to fend for itself. When he went back, he would appoint elders, and he would keep a spiritual eye on the church, writing to them to correct problems if necessary.

Elders might be appointed within a couple of years of Paul’s first arrival in a city. In how many of our churches would we consider somebody to be spiritually mature enough after a couple of decades to be considered for eldership? And this is after careful consistent ministry throughout that period. In fact, the danger is that most people in the congregation end up listening to much the same teaching being repeated – and they haven’t grown as Christians since they last heard it.

As Christians, we have lost the sense of urgency that the New Testament believers had. If the evangelical church is going to influence the nation for good in the future, it needs to recover a more biblical attitude to this, and many other things.

Thursday, October 27, 2005

Scott Adams

Scott Adams writes the Dilbert cartoon strip. I benefit from having this emailed to me free six days a week - so I am normally a day or two ahead of the syndicated version in the UK. In addition to my Christian faith, this has sustained me over the last eight years during which time I have had to contend with the absurdities of management.

Scott has also written some semi-philosophical books, and he has now started a Dilbert Blog. Actually, the Dilbert there is just the attention grabber - it provides the opportunity for more humour with enough social commentary to make it worth reading. Or if you rather, more social commentary with enough humour to make it worth reading.

Wednesday, October 26, 2005

Too little choice

In a post below, I argued that parents were being presented with too much choice in terms of secondary schools. Well, alea jacta est and all that - we've put our names down for our first and second choice for our oldest child.

However, in what was always intended to be a companion post to the earlier one, I wanted also to comment that parents have too little choice - yes, both too much and too little.

The trivial side of this is that there is no obvious school where children can go in which we will be confident that they will make the most of their potential. In a less trivial sense, for the Sept 2004 admission, of the 53 secondary schools in Surrey, 32 were oversubscribed on the basis of parental first choice (which in Surrey is frankly the only choice that has any significance). 2270 parents didn't receive their first choice of state secondary school in one county. This represents a huge level of stress and worry to a vast number of parents.

The government argues that the solution is increasing parental choice; making more options available; allowing successful schools to expand. But if schools get too large, they become unchangeable - and in many cases, the success or otherwise of a school is down to a couple of key people in the senior management team. Most parents aren't able to explore new school options for reasons of time and their own abilities - and in any case, the regulatory framework is such that this is simply never going to be a feasible option in more than a handful of cases.

The real solution has to be improving the quality of the schools. Parents need to be confident that regardless of where their children end up, they are going to get a good, consistent education, in which teachers were well-motivated, well-supervised, good practices propagate through the whole school, and in which failing or even coasting are simply not tolerated. Choice isn't the key thing - quality is - and regardless of political dogma, choice isn't guaranteed to bring quality.

Take Yahweh...

... on "How to Dismantle an Atomic Bomb", by U2.

When U2 were doing their postmodern bit (Zooropa, Achtung Baby), it seemed a great loss to mainstream Christianity. The quality of their songs was still great, but it was hard to argue that they were presenting an authentic Christian message. Bands like Delirious? tried to pick up their mantle, but although competent, just didn't quite seem to achieve the same quality.

With their latest album, U2 have returned to a position a lot closer to the mainstream of Christianity. Take Yahweh, for example.

Well, firstly it's a good enough song in its own right. Next, as has been observed elsewhere, it represents a modernisation of an older song, well loved by evangelical Christians: "Take my life and let it be", by Frances Havergal. The words are incredibly layered. For example, it includes the phrase:
Take this mouth,
so quick to criticise:
take this mouth,
give it a kiss.
In addition to asking God to kiss the mouth, the singer is asking God to make the mouth able to kiss. The same depth is present in the phrase:
Take these hands,
don't make a fist.
- not only "don't make these hands into a fist" but also (using a colloquial expression) "don't make a mess of these hands".

Then there's what they are doing with the song in the live shows. The last line of the song:
Take this heart and make it break
- a reference perhaps to Psalm 51:17 to
Take this city and keep it safe.
- a benediction (which comes almost at the end of the concert).

In one bound, then (or actually probably over the course of a decade - they have been heading back this way for some time), U2 have moved back to a much more orthodox, less ambiguous Christian position.

Monday, October 24, 2005

Thursday, October 20, 2005

More about Avida

As promised, here are some more comments on the Avida “artificial life” software. I am interacting with this paper – and unless I say otherwise, I am using the parameters used by the researchers in preparing this paper (see the Methods section at the end of their paper).

Firstly, as a piece of software, it is good. It does what it says on the tin – you can download it, adjust a vast array of parameters, run it, rerun it, rewrite the source and recompile it (apparently – I have been happy enough with the "basic package" not to try this myself yet) and so on. You can’t save it "mid-run", as far as I can tell – so I ended up with a computer running overnight – and (perhaps because I was using a beta version) it tended to fall over if you fiddled with the wrong things at the wrong time. You at least get the results saved as it goes along – but it was a little frustrating to have a run stop after several hours and 30,200 updates because I asked it to display the wrong thing. However, there aren’t many science experiments these days that you can try at home – but I have spent some time running Avida on a couple of PC’s, which has allowed me to evaluate the software, and also give consideration to the research that has already been done. Few areas of research can make themselves available to review by both professionals and amateurs – all credit to the Avida team for doing just that.

However, given my previous posts, it will hardly come as a surprise that my comments on what the software shows diverge from the researchers’ conclusions.

Interaction with the Avida software can be found on the ARN discussion forum (here is one of the threads), and the reason that I investigated it in more detail was because of reaction against this post in the ID: The Future blog, which various acquaintances thought weren’t taking the research seriously.

The software clearly demonstrates how a selective advantage will propagate through a population. In the paper, the digital organisms, through random mutation, may generate new functionality – in terms of giving as an output the result of a logical operation not built into the genetic language of the organism. In simple terms, the "harder" the logical operation – that is, the more instructions that would be needed in the genetic language to achieve the operation – the greater the "reward" - expressed in terms of a larger proportion of CPU time offered the organism that is expressing this functionality. In the paper, nine different logic operations are examined. The gain in functionality is cumulative, and also increases geometrically for the more complex functions. Thus, for expressing the simplest functions (NOT and NAND), the fitness of the organism is doubled. For expressing the most complex function (EQU), the fitness is multiplied by 32. The total impact of expressing all nine functions is that an organism would get 33 million times more CPU time than an organism of the same length expressing no functions.

The consequence of this is that, if a viable digital organism appears that expresses some of the more advanced functionality, the new functionality will rapidly dominate the population. For example, on a run of organisms of starting length 150, after a false start that didn’t get anywhere (perhaps the expression of the function was too sensitive to change, or perhaps it had appeared at the expense of a couple of other functions, resulting in a loss of overall fitness), the number of organisms expressing EQU rose from 2 (out of 3600) at update 15600 to 2000 at update 16600.

In a sense, this is kind of obvious – if an animal has a significant selective advantage, it is trivial that this advantage will spread across the population. Neither am I unhappy with the multiplicative nature of selective advantages. In the same way that protein functionality can easily and drastically be lost through even single changes to the amino acid sequence (as per the sickle cell anaemia mutation), it seems likely that comparatively small changes can result in abrupt improvements in functionality that can be expressed. There have been papers on how "anti-freeze" proteins arise in fish, and how small changes to genes can result in bacteria able to digest synthetic compounds that they would not have experienced in nature. However, the neat spread of a new colour across the map on Avida doesn’t generally correspond with nature, for various reasons.

Firstly, as I mentioned below, the domain space that relates to these digital organisms is much smaller than that of any organism in nature – the evolution that we are looking at is closer in scale to the evolution of a protein than an organism. The number of possible digital organisms of genome length 50 is getting on for 10^71 – which corresponds with a stretch of DNA with 120 bases, or a protein with a sequence of 55 amino acids. Within this, the simplest function that would give an increase in fitness would be coded for in only four or five codons. The most complex can be coded for in 19 codons. Of course, the likelihood of this arising by chance is small, but not vanishingly small. Dembski proposes a universal probability bound of 10^-150 – in other words, if a specified event is less likely than this to occur, then it is reasonable to assume that if it has occurred, it didn’t occur by chance. As Avida runs, it will end up randomly trying millions of candidate organisms for functional improvements – and it is obvious, given the size of the domain space, that this will yield organisms with increasing fitness.

But what is the likelihood of new functionality arising in a real organism that will give it a selective advantage? The antifreeze proteins and synthetic compound digesting enzymes mentioned above weren’t found through randomly trying everything – they were the result of minor changes of parts of the genome that had an existing role in the organism. What is the likelihood of (say) a proto-heme arising by chance, or being co-opted through minor modifications from another protein? What is the likelihood of the enzymes arising by chance that are at the heart of transcription and reproduction? As was observed in the ARN discussion, the developers of Avida didn’t wait for random changes to produce the genetic code of the digital organisms – and yet, this is a key step in a naturalistic biogenesis process. Similarly, the digital organisms don’t end up setting their own fitness criteria – they are constrained to what is programmed – they don’t break out of the code. Is this only a matter of time and chance? How many generations would that take?

Following on from this, whilst the genomic mutation rate – at 0.225 – may have been comparable to an organism (see Methods), the mutation rate per codon was consequently much higher, whilst the total number of codons was far lower. This means that evolution in the model will happen at a far higher rate than in real life.

All of these are acceptable simplifications for the purpose of modelling something – but it is important to be aware of how these simplifications impact the validity of the model when it is related to what it is supposed to be modelling.

To be continued ....

Tuesday, October 18, 2005

City of Blinding Lights

It's gratifying and occasionally disturbing how children adopt their parents' values. In all sorts of ways, we have to think about the way we present information - even about how we have discussions with one another. I am grateful to my parents for not seeking to indoctrinate me in any matters - particularly religious or political - though it really staggers me now how similar my opinions are to those of my own dad.

My son has almost completely taken on board my appreciation of U2 - as have the two girls, to a lesser extent. To begin with, I think it was just a family thing - "Who are your favourite band?" he would ask his friends, to which, if the reply was "Busted" or similar, he would say, "We like U2. They're much better than Busted, aren't they, dad?" However, it took more of a life of its own - he has his own particular favourites. And when he produced a picture on the computer - a very hard medium to work with for anybody to work with! - I realised that his own appreciation of U2 was no longer the same as mine.

I love it - more than just dad's love of his child's work - I really think it conveys something of the imagery of a "city of blinding lights". I've encouraged him to put it on his own blogsite, and to do some more - though as he then pointed out to me, it's a bit harder to do one based on "Sometimes you can't make it on your own" - his suggestions on the matter, if he is able to realise them, will also be interesting ....

P.S. 200 posts! 3000 visits! Only about 1000 by me! "Thanks for hanging around."

Sunday, October 16, 2005


On our first wedding anniversary ("Paper"), a close friend (no longer quite so close, but still dear) gave us one of those blank books that you can get at paper shops - but she had stuck in the first few pages copies of some of the poems that meant a lot to her. This is one of the few anniversary presents from anybody that I can still remember (okay, we don't often get anniversary presents, so the field is small, but it still means a lot) - and it was one of the reasons that my appreciation for poetry increased.

Anyway, I'll try and post some of the poems. They still mean as much to me as they did then (which being translated means: I end up reading them through a film of tears.)


Sometimes things don't go, after all,
from bad to worse. Some years, muscadel
faces down frost; green thrives; the crops don't fail,
sometimes a man aims high, and all goes well.

A people sometimes will step back from war;
elect an honest man; decide they care
enough, that they can't leave some stranger poor.
Some men become what they were born for.

Sometimes our best efforts do not go
amiss; sometimes we do as we meant to.
The sun will sometimes melt a field of sorrow
that seemed hard frozen: may it happen for you.

Sheenagh Pugh

And I pray that the violence
Of indifference will never

To care, to live, to create,
Or else.....


Monday, October 10, 2005

Avida Loca

ID: The Future published this article, which irritated some acquaintances of mine, who argued that IDTF had failed to seriously interact with this paper. So here are a couple of more formal informal comments on the paper.
... all populations explored only a tiny fraction of the total genotypic space. Given the ancestral genome of length 50 and 26 possible instructions at each site, there are c.5.6x10^70 genotypes; and even this number underestimates the genotypic space because length evolves.

This range of "genotypes" for the digital organisms is very small. For comparison, there are around this number of different DNA sequences for a length of 120 bases (coding 40 amino acids). Or, there are about 10^70 unique proteins with a length of 55 amino acids. This being the case, whilst this simulation might be appropriate to look at how the evolution of a single protein might occur (proteins, with secondary and tertiary structures, might themselves be considered to be "irreducibly complex" in their eventual form), it can hardly be said to model the evolution of organisms. The DNA of E.Coli is about 5 million bases long. The genotypic space of this "simple" bacterium is thus - well, ten to the power of several million. I didn't do logs at school, but I can see where that's going.

The significance of this is that the space over which Avida has to search for functionality is tiny compared to the space over which a "real live" organism would have to search for functionality. That means that it rapidly becomes harder to start from nothing and get "an answer" - especially if the answer, rather than being typically a sequence of the order of 40, was of the order of 400, or 4000.

The handwritten ancestral genome was 50 instructions long, of which 15 were required for efficient self replication; the other 35 were tandem copies of a single no-operation instruction that performed no function when executed

So Avida gives organisms a huge head start. In this simulation, the digital organisms are given a nice, 70% blank genotype (). This would be selected against in real life - it adds to the energetic burden on the organism, whilst providing no additional functionality. It seems unlikely that a real organism would actually arrive at a state where it had even 10% of its DNA "free" to be changed with no deleterious effect on the organism. And yet all of the digital organisms are conveniently started off in this state. This represents a huge "head start" in evolutionary terms - because changes to the majority of the "DNA" don't damage existing functionality.

Furthermore, in real life, the tools for transcribing DNA, reproduction etc etc also have to be encoded in the DNA. In Avida, the tools that interpret the instructions are coded in the computer, and are thus "safeguarded" - they won't be corrupted. (Though, by the same token I guess, they don't evolve, either). Again, this represents another significant evolutionary advantage.

Bottom line:
On the basis of what I've read so far, I have little reason to disagree with the ID:The Future comments that the claims made for the achievements of this study are substantially exaggerated. I suspect that if the authors were to go no further than to say that this was an analogue of how a protein might evolve, their claims might be considered more reasonable. The fact that they argue that this is not even a model of evolution, but describe this as "digital life", cries out for a close analysis of their claims, and in statistical terms, this simply highlights that the model substantially underestimates the problems of real life evolution.

Below the bottom line:
I have downloaded, installed, and run (several times) Avida. Despite the cheap joke in the title, it is an interesting piece of software. Further comments can be found here.