Tuesday, October 31, 2006

Humphrys in Search of God - to an extent

If you are going to ask somebody to try and convert you, it is unlikely to be the Archbishop of Canterbury. But then, neither are you likely to make a radio programme out of the conversation. These were two somewhat flawed premises of what was nonetheless an interesting programme on Radio 4. John Humphrys, a well-known and acerbic radio journalist, is inviting leaders of the three monotheistic religions to “convert” him in a half-hour radio programme. If you want to listen for yourself, you can listen to an extended version of the first interview through the link.

When Rowan Williams was appointed Archbishop of Canterbury – probably one of the most intellectual of the bishops in the Church of England, following George Carey who was considered to be an evangelical – many evangelicals had serious concerns that the church would be led abruptly in a liberal direction. We picked up various papers and talks he had given in the past in support of this view. But at least in this conversation, the archbishop presented Christianity in a form which, whilst perhaps not exactly as many evangelicals might have hoped for, was certainly as close as many of them would expect to get in a similar conversation at work, or down the pub.

What Rowan Williams did say.

He defended evil as the outcome of genuine free will. Along the lines of: “If God is going to give creatures free will, then there has to be a sense in which the outcome of this may be evil.” He nonetheless sought to defend the sovereignty and goodness of God. Whilst not quite saying that “death isn't actually the worst thing that can happen to somebody”, there was certainly that sense in what he did say. And whilst not quite saying that God has an overall plan which is good, there was again this sense in what he said.

He also didn't shy away from the exclusive claims of Christianity – in a setting in which it would have been easy and acceptable to do so. In talking about how he would engage with people of other faiths, he pointed to the fact that even in the New Testament (Paul's engagement with pagan cultures), engagement with different cultures was a process, not a simple assertion. Given his position, it would be difficult politically to go much further.

From an evangelistic point of view, he was also good at not offering formulaic answers, but getting John Humphries to explain what he thought – what it was exactly he “lost” when he lost his belief in God; what exactly he thought was the “faith” he was looking for (which to an extent, underlined the fact that this programme was somewhat artificial in its concept).

He also pointed out that, in considering the problem of suffering (why bad things happen to good people), there was a difference in thinking about it as an intellectual issue and as a pastoral issue.

What Rowan Williams didn't say.

He didn't mention Jesus in the whole programme, I think. He talked about the love that God has for people – without saying how that love is most visibly expressed.

He didn't mention eternal judgement (I don't think). Humphries tried to pin him down towards the end of the interview about this – but Williams leaned towards the idea that even after death, we still have the opportunity to respond to God. Similar ideas seem to be expressed in, for example, “The Great Divorce” by C.S.Lewis – but the weight even of this book is that the patterns that are established before somebody dies are pretty much final, and this is probably as far down the line of “non-final-judgement” that any evangelical would be prepared to go. In the archbishop's position, I would probably have wanted to point out that if somebody has rejected God throughout their life, then separation from the presence of God (which is part of the imagery of God's judgement) would seem as much an act of mercy as judgement. Also, God's love and the death of Jesus in place of the sinner are somewhat meaningless if you take away the idea of God's judgement.

This was an interesting programme, even though it had its flaws. I have no doubt that there will be other evangelicals who will be profoundly negative about what Rowan Williams said – but I thought it could have been an awful lot worse.

Monday, October 30, 2006

Global warming ...?

In the wake of the publication of the Stern report, and since I've probably already upset three or four of my five readers with what I said about Fair Trade coffee, what do I think about climate change - about which Tony Blair said:
This disaster is not set to happen in some science fiction future many years ahead, but in our lifetime
I think that there is plenty of evidence that temperatures are rising. Things like the fact that of the highest temperature summers on record in the UK, four or five have been in the last 10 years. Things like record sea temperatures in the tropics.

I think that this is likely to lead to more chaotic weather systems - El Niño recurring, exceptional hurricane years in the Caribbean like 2005 (though obviously this year hasn't seen anything like the same number), failure of monsoons, and droughts.

On the other hand, it is quite possible that this is fundamentally a cyclical change - that the human impact on the climate is marginal. It's possible that as the temperature rises, the cloud cover and vegetation levels will increase, providing a feedback system. It's conceivable, as suggested in a BBC Horizon programme, that the rising temperature will switch off the Atlantic Conveyor, causing a subsequent catastrophic fall in temperature. I'm neither of the apocalyptic camp, nor of the capitalist, laissez-faire camp, because I don't have enough information.

So what do I think we should do? Fundamentally, in my opinion, it comes back to theology. If humans are supposed to be stewards of creation, then we are to use the resources we have wisely. That means being careful about our use of limited resources, and doing what we can to protect the world about us - minimising our footprints, if you like. I don't think it means we have to be vegetarians - the Bible suggests that there is a divide between humans and animals which is reflected in their different nature (for example, with the exception of cats, few creatures attempt to organise humans ...), and that God specifically gave animals to humans for their "use" - but I do think we aren't free to abuse animals. I was also shocked to discover that, according to The Rough Guide to Ethical Shopping, it takes 100,000 litres of water to produce 1 kg of beef. I'm not opposed to nuclear power - but as with any form of power generation or industry, thought has to be given to the impact throughout its life - from construction to decommission and decontamination.

So that's it really. I believe that we should be careful about how we use resources not fundamentally for fear of climate change but because it is our job to take care of a limited resource.

Evolution and problem-solving

During my Computer Science studies, I was introduced to a problem where
the only known algorithms that produce optimal solutions are of the 'try-all-possibilities' variety and can have running times that are exponential in the size of the input” - the famous “traveling salesman problem (TSP).

(Aho, Hopcroft and Ullman, “Data Structures and Algorithms”)
You can find out about it on Wikipedia here.

The concept is simple. A road network connecting a number of cities is an undirected graph with weights (i.e. lengths) on the edges; a tour is a simple cycle that includes all the vertices, and the aim is to determine the shortest tour.

An exhaustive trawl through every single sequence connecting all vertices in all cases is computationally prohibitive – for example, in the Wikipedia article, an example is given:
In March 2005, the travelling salesman problem of visiting all 33,810 points in a circuit board was solved using CONCORDE: a tour of length 66,048,945 units was found and it was proven that no shorter tour exists, the computation took approximately 15.7 CPU years.
However, work has been done on algorithms that come up with results that are known to be close to (within a few percent of) the best answer.

People who are convinced about the ability of evolution to account for the appearance of all life work on the basis that, whilst evolutionary processes may not determine the single best answer, natural selection provides a means for determining one which is close to optimum. It is unfortunate that too much of the objection to evolution as a theory has been founded on the underlying thought that a single optimum solution has to be found for evolution to work. For example, many books talk about the probabilities of an exact 100 amino acid sequence appearing by chance – an argument that unsurprisingly receives short shrift from darwinists.

Proteins, with their enzymatic functions, can be considered “solutions” to the “problems” that an organism faces. For example, a cell has the “problem” of requiring energy. The large scale solution is to use ATP for this. However, this large scale solution has to be broken into many smaller steps – the organism must either find a source of ATP, or have a means of manufacturing it from other molecules. Then for ATP to be useful, other proteins must be able to harness the energy released in chemical processes involving it.

I wanted to give a couple of my own thoughts on whether random mutation and natural selection provide an adequate “problem-solving” mechanism for evolution to take place.

(Micro-evolution) Do mechanisms exist within organisms that permit a “solution” to be optimised in an organism, or for a solution to adapt to a gradually changing environment?

The short answer to this question is yes. A mutation within the gene coding for a protein will result in a change to that protein. The change may be neutral, beneficial or harmful. If beneficial, then the organism that bears the mutation will have a selective advantage, which will be reflected in its descendants.

However, I suspect that it isn't quite as simple as that. For natural selection to work, the number of mutations must be limited in each reproduction. If there are too many mutations, then the beneficial or harmful impact of any particular mutation will be lost. I don't think that Darwinism really has an explanation firstly as to how the DNA and protein mechanisms that allow the reliable duplication of the genetic material in an organism came about, and secondly how they could have a mutation rate that is neatly adapted to natural selection at all. Or rather, I suspect the answer is that “this was the evolutionary favoured rate” - which, without any real empirical foundation, would be a “evolution did it” sort of answer.

(Macro-evolution) Do mechanisms exist within organisms that allow for the appearance of functionality when it wasn't present before?

The short answer to this question, in my opinion, is no. There are exceptions – for example, the appearance of antifreeze glycoproteins in notothenioid fish, and the appearance of the ability to digest nylon in some bacteria. These are both significant evolutionary steps. But details of the changes have been analyzed in both cases, and the amount of new information added in either case was not significant. Also, in both cases, there is little investment on the part of the organism in any individual offspring – a situation not really typical of land-dwelling chordates in which we see today such a great variety of morphologies.

Macroevolution can't continually point to co-option of existing proteins into new roles. At some stage, new proteins have to be generated. This requires random – or randomised, or frameshifted – sequences, the generation of random polypeptides and their acceptance by the organism when the organism has no means of knowing whether they are going to be of any use, the presence or later addition of controlling mechanisms around the gene and so on. For the earliest organisms, the significant numbers of genes required (see the post below) have to be generated and organised – and many of these genes being shared as I understand by all life, they are likely to have been present in the earliest of our putative common ancestors. We don't even have a handle on the scale of the problems presented by macroevolution at this stage. The assertion that evolution did it has no empirical foundation – it is an assertion founded on the priority of the paradigm, rather than on scientific fact.

I will be challenged that I have no alternative mechanism, and that, in accordance with the scientific method, darwinists will at least continue to look for mechanisms whilst they can. I don't have a problem with that – and indeed, I have used and will in future probably use my time to see what can be done to model evolutionary processes. It is worth pointing out that few proponents of ID have a problem with that either. But based on my understanding of the problems involved, I am simply not convinced that darwinism will be able to offer a meaningful solution.

Fair Trade Coffee

We have bought Fair Trade coffee for ... well, as long as I can remember, and for some years, we have also avoided buying Nestlé products (and those of various other large corporations), on account of the questions that have been raised and not convincingly answered about their ethical standards. It's surprising how widely the tentacles of Nestlé reach. We eat supermarkets' own versions of KitKats, Shreddies and yoghurts. For that matter, we avoid artificial sweeteners and preservatives (which basically means buying High-Juice squash, and greatly restricts our options on fizzy soft drinks), limit our consumption of "junk" food, and try and keep an eye on the distance that food has travelled.

For people who are starting to get more concerned about ethics, I would recommend "The Rough Guide to Ethical Shopping" and the soon-to-be-published "The Rough Guide to Ethical Living". These are realistic books - they accept that we are part of a society in which it is hard to examine the consequences of all your actions, and that people draw the line at different points, and that in any case debates about ethics are rarely clearly one-sided.

For example, some people argue that Fair Trade coffee, by distorting the market and highlighting a particular weak area, are serving to prevent reforms. For us, from a Christian point of view, our choice is an extension of James' writing on behaviour:
Suppose a brother or sister is without clothes and daily food. If one of you says to him, "Go, I wish you well; keep warm and well fed," but does nothing about his physical needs, what good is it?"
This was written in relation to the way Christians treat other believers - but whilst they are a "special case", the general principle that Jesus sets out is that we have to think about how we treat "our neighbour" - which in days of globalization, can mean anybody in the whole world!

Others argue from "Sabbath" principles - and the fact that God's plan was that humans should rest for one day in seven - a pattern which I believe has shown itself to be good for humans throughout history. The idea behind the Sabbath was that not only the people of Israel were to enjoy rest, but also their animals, servants and the alien within their gate (Deuteronomy 5:12). This "compassion" for workers is now embedded in our society - an aspect of social concern from our Christian heritage that people probably don't think about - in the form of guaranteed holidays and days off - most people in the Europe and North America only have to work five days in seven, rather than six! But if I am paying so little for something that I buy or use that the person who supplies it isn't paid fairly for their time, and has to work 16 hour days and 7 day weeks to make ends meet, then I am failing to treat them with dignity or compassion.

One of the principle objections to Fair Trade coffee is "I don't like the taste". This is really not a compelling objection. In most cases, the first time that most people drank coffee, they "didn't like the taste" - but they got used to it, because they wanted the caffeine, or because they enjoyed the social side of coffee-drinking. There are several answers. The first is: get used to it! The people who are making the coffee don't have the luxury of consumer choice of brands - they hope for basic facilities, healthcare and education for their children. Choosing coffee which seeks to guarantee these things but doesn't taste quite as nice is a small price to pay for what it offers the people who make it.

Secondly: go and investigate the options. There is probably nearly as wide a variety of fairly traded filter coffee as there is of non-FT. I seriously doubt that most consumers who say "I don't like the taste" have seriously attempted to find a FT filter coffee they like. Few will even have investigated a range of instant coffees.

Finally: how was it made? The problem in a lot of cases is that FT instant coffee is used at worthy places - churches, social clubs - where they use half the amount of coffee that we would at home and skimmed or watered-down milk. Try making a FT cuppa with the amount of coffee you'd use at home, with the same sort of milk that you'd use at home. It wouldn't surprise me if it turned out just as palatable as your cup of instant coffee at home.

Both Nestlé and Kenco have made attempts to make themselves appear more ethical in coffee terms. For example, Nestlé have their "Partners" blend; Kenco (which is actually a Kraft brand) have a "Sustainable Development" coffee that they talk about here. (Incidentally the "independent, not-for-profit" Rainforest Alliance that the Kraft press release talks about acknowledges that they have a relationship with Kraft here). Personally, I would be gravely unhappy about buying these products. The concept of a multinational corporation having one coffee brand that is tagged as "ethical" but thirty that aren't to me simply underlines the fact that these corporations want to appear to be part of this, whilst continuing in fundamental indifference to their producers.

Sunday, October 29, 2006

Empathy ratings

We (Paul and Liz) were talking about the fact that we relate to different people – particularly men – in different ways. There are some people that we really like, but we don't feel that there is a connection there - no real meeting of minds. On the other hand, we feel that there are people with whom we have a genuine relationship – they understand our motivation, and we understand them.

In this context, we found the idea of “empathy” - as we have interpreted on our scale of 1-5 below – a fertile ground for discussion, and general agreement with each other, and we'd like to see what other people think. We were conscious of the fact that this was more than a little dangerous to judge from “our point of view”! However, here is the scale:

1 – least empathic. Is completely self-absorbed, and simply doesn't comprehend that anybody else has concerns or motivations that might be different from theirs.

2 – Is pretty self-absorbed. Is able to conceive of the possibility that somebody else might have a different motivation, but can't imagine why, or how these motivations can be as soundly founded as their own.

3 – Balance between self-absorbed and empathy. Generally has his or her own priorities, but will understand somebody else's perspective and will consider changing his or her actions in response to somebody else's concerns.

4 – Empathic. Is sensitive to the concerns and motivations of other people, and takes them into account in deciding a course of action or even a choice of words.

5 – Highly empathic. Understands other people's perspective and motivations, at times to a greater extent than they may do themselves. This can even lead to nervous problems if the person feels too much the clash of emotional demands from different people.

Women, in general, seem to score 1-2 higher than men on average. Another surprise was that men with higher education tended to come out more empathic than men without it – something that was most apparent in the “younger” generation – this trend was less marked in women - and there were certainly exceptions.

One of the most painful things in both of our experiences was seeing women in relationships with highly unempathic men – who fail to recognise that they have their own concerns and motivations. This might be reflected in their indifference towards the desire of the woman to have a family, for example, or a failure to realise that the woman has as much right to leisure activities as the man has to go out and play golf on all of his days off (to take an extreme example!).

Food for thought?

Friday, October 27, 2006

A Meaningful World

I've just finished Benjamin Wiker and Jonathan Witt's book, A Meaningful World. You can find another good review of it on Dave Heddle's blog.

The book's central thesis is that the whole universe is full of meaning, an idea which the authors say runs profoundly against the core materialist dogma that we are nothing more (ultimately) than atoms moving at random.

The most interesting science books I have read recently - well, ever, actually - have moved away from "reductionist" approaches (a focus on one small area) and towards crossing interdisciplinary boundaries, and "big pictures". The first was "Godel, Escher, Bach: An Eternal Golden Braid" by Douglas Hofstadter: more recently, I have enjoyed both "Rare Earth" (Ward and Brownlee) and "Privileged Planet" (Gonzalez and Richards), which have drawn upon astronomy, biology, geology, cosmology and many other -ologies as well.

A Meaningful World crosses boundaries as well - and, like the Hofstadter book, even crosses the traditional art/science divide - the authors start by looking at genius in the work of Shakespeare. They then move on to look at geometry as presented by Euclid, then the development of knowledge that discovered the Periodic Table, before moving into the more familiar ID territory of biology. They argue that the characteristics of genius are depth, clarity, harmony and elegance - all are present in all of these areas.

The book is being gently pushed in some quarters as a highly significant - perhaps even defining - philosophical/religious work - and it certainly presents a substantive case in support of the central thesis. That may be the case, and it is certainly enjoyable, thought-provoking, literate and informative. But the proof of the pudding is in the eating - I am simply not technically equipped to say whether it will prove to be as significant as that. What will be interesting is to see what response is drawn from materialists. A Meaningful World makes more clear the philosophy underlying the gradual development of ideas amongst proponents of Intelligent Design, and articulates a case for (for want of a better phrase) the genius of God. It will be interesting to see what will be done in attempts to refute the case.

Scott Adams hits the mark again.

Here's today's Dilbert cartoon.

It's the combination of Ratbert-like insecurity and self doubt, and amazement at the self confidence of people "out there". Knowledge isn't wisdom, after all.

Incidentally, if you want a feel-good story read Scott Adams' account of recovering his voice.

On the other hand, don't. There is no point in me (with my 30 hits per day) encouraging you to read his blog (with its number of hits on the other side of 1000 times that amount per day). *Sigh*

Wednesday, October 25, 2006

Minimally-specified organisms

(H/T Telic Thoughts)

At CreationEvolutionDesign, there is interaction from the author with current news about the genetically smallest organism yet found. It is a parasitic bacterium with 160,000 DNA bases and 182 protein-coding genes.

A couple of quick thoughts, in the context of the posts here about probability boundaries.

Firstly, this is a parasitic organism, so it is not capable of independent life. The author of the post points out that non-parasitic organisms generally need nearer 1500 genes. So "simple life" - life not requiring existing organisms to exist - is eight to ten times more complex than this organism.

Secondly, we are starting to home in on a figure for the amount of minimal information for life to exist. By comparing sequences of DNA for shared genes, like Cytochrome C, it ought to be possible to establish a maximum level of specification - that is, the shared sequences should give us an upper limit on how specified a DNA sequence has to be for it to function. It would be possible to determine a lower limit by systematically changing a gene and determining whether it continues to express its enzymatic function - if it expresses no function, then it is insufficiently specified to work. Once these upper and lower limits on specification have been established, we can then make a reasonable guess at how specified this organism is, for example. We can then use the mathematical work that Dembski has done (relating to the UPB and "No Free Lunch") to determine whether or not "life" can be considered to be chance or design.

Finally, there is no point in calculating the probability of correctly picking 160,000 DNA bases - it would be wildly above the UPB, and in any case, nobody is saying that all of the 160,000 bases need to be exactly right for the organism to "work". Let's suggest instead that there are 1800 candidate genes (sequences of DNA) (somehow) already floating around in a sympathetic medium, of which a proto-organism needs to (somehow) collect 180. Even this - which begs the questions of where the genes come from, how genes with suitable sequences might come about, how the control mechanisms might appear, why the medium in which this happens is so amenable to the process - still would be an event which was less probable than the UPB - one which couldn't be classed as a "random" event.

Monday, October 23, 2006

"But is it specified?"

Before I try to see whether the Universal Probability Bound has any relevance to biological systems, I would like to look at another issue. Given any sequence of cards in the example above – or any set of data derived through either design or a chance process, is it possible to establish that it definitely isn't specified? More generally, does the idea of specification that Dembski uses have any real meaning at all? The commenters on my earlier post suggest not.

Forget formal definitions for now, and notice first that intuitively, specification does have some meaning. If I look at a sequence of playing cards (as before), I will come to some conclusion as to whether it is a “specified” sequence. If the cards are set out and there is no obvious pattern, then I will just shrug at the magician who has set them out. If they are set out, and an order is evident, then I will assume that this is due to the cleverness of the magician. In both cases, I have some idea of what I am looking for in terms of specification, even without the magician speaking. For most magic tricks, the magician would specify exactly what card or cards we are expecting to see – perhaps a card we pulled out earlier, even if we don't know how the magician knows it. In this case, the specification is obvious. But even without this, if the cards are laid out in an obvious order having supposedly been shuffled beforehand, then we will be convinced that this order isn't a chance arrangement, but present due to the intention of the magician.

However, it is possible that a magician will have some subtle specification that he has to explain to me, as it isn't otherwise obvious. For example, the cards may be ordered so that if they are set out going round in a spiral, the pattern becomes visible. A part of the challenge to Dembski's proposals is that I can't exclude the possibility that data has some specification that I don't know about. Sequences of data can intuitively fall only into one of two classes:

1)Data with an obvious specification
2)Data without an obvious specification

Here's another example, to illustrate. Here is a sequence of letters:


They look random – they obviously don't say anything in English – but how do I establish that they are not specified? How do I know that they aren't saying something in English in a cipher? How do I know that they don't say anything in French in a cipher? In an obscure language spoken by only 500 people in the South Pacific? In a highly advanced code? It doesn't have an obvious specification, but I'm not able to conclude that it doesn't have a hidden specification.

What impact does this have on our consideration of the UPB?

Dembski argues that the significance of the UPB is that if a specified event is less probable than the UPB, then it is unreasonable to conclude that this is a chance occurrence. I think it is fair to say that, whilst people objecting to Dembski's proposals may not be happy that the concept of specification has been defined in watertight terms, it is quite clear that the cases with which he is concerned are nonetheless specified – and objections on the basis of what happens in unspecified events of low probability - like the hand obtained when dealing a shuffled pack of cards - are therefore not sound.

Consider a hypothetical new protein, novofunctionase (nfu), which enzymatically switches cis-reactol to trans-reactol. For the the function of nfu to be expressed, let's say that DNA must code for of a precise sequence of 50 amino acids. There is the specification, then. I haven't written a general definition of specification, but I have given a specification of what is required for this protein to appear. The specified event that would cause this new protein to appear when it was not present before is the random appearance of DNA that codes for this sequence of amino acids. The probability of such a sequence appearing in a random sequence of DNA would probably be of the order of 1 in (3/64)50 – that is, 3.5x10-67. Supposing instead we were talking about a precise sequence of 200 aa's – a much more demanding specification. The probability of such a sequence appearing in a random sequence of DNA would be well below the UPB – therefore the UPB says that the appearance of such a sequence (as a random event, with no precursor, and not from an intermediate) could not reasonably be classed as a “natural” event – it would require “design” or “intent”. That is the idea that Dembski is trying to get across. I think that Dembski's terminology is sufficiently precise for this to convey a meaningful proposition at least in particular cases, even if we can't define a general case.

In this case, I have defined the specification – I have said what is necessary for nfu to be expressed. My specification here is very tight - “a precise sequence of 50 amino acids”. However a more general specification would be possible, as the functionality of nfu might be expressed by a variety of proteins with completely different sequences. Such a specification might look as follows:

The protein would require a sensitive area of 6 amino acids from particular groups of amino acids, to be sensitive to the presence of cis-reactol in the cell, and cause it to bind with the active site on the enzyme. It would require another area including 10 specific amino acids that would utilise an ATP molecule to allow the enzyme to switch a binding cis-reactol to trans-reactol, and then unbind it. It would require another 6 specific amino acids as gene markers, and it would require 8 specific amino acids to allow this gene to be switched on at the appropriate time in the life cycle of the cell. This specification is more detailed, and yet less specific than “a precise sequence of 50 amino acids”. But it is still a specification.

For the appearance of new functionality, specification is required. The specification may be hardly anything at all – maybe a sequence of almost any three amino acids will have a catalytic effect on a range of biochemical reactions – but there is still a specification. The fact that it is not possible to tell that an event is an unspecified event of low probability, rather than a specified one, is not relevant, because all the biologically significant events that Dembski is interested in are specified events.

To come ... looking at the specification of some other events

That sounds strangely familiar ....

Darwinian explanations ... are often too supple: Natural selection makes humans self-centered and aggressive - except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed - except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behaviour, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery.

Philip S. Skell, "Why Do We Invoke Darwin," The Scientist 19, #4 (Aug 2005)
This is quoted in "A Meaningful World", by Benjamin Wiker and Jonathan Witt, which I am getting on well with, and I will comment on at some stage in the future.

Sunday, October 22, 2006

The Universal Probability Boundary and Specified low-probability events

A repeated challenge to the concept of the Universal Probability Boundary (UPB) as set out by William Dembski is that low probability events occur all the time. This challenge is flawed, and derives from a misunderstanding about the sort of events that Dembski is referring to. Let me illustrate.

Shuffle and deal a deck of 52 cards into a single line, for example. There are 52! - that is, factorial 52 - that is, about 8x1067 possible sequences of cards. So for a well-shuffled deck, it is fairly safe to say that nobody else will ever have seen that sequence before. In fact, the probability of that sequence arising is about 1.2x10-68. That is an incredibly small probability – and yet, there it is, in front of you! Which just goes to show that low probability events happen all the time. If you had a deck of 100 different playing cards, you would have over 10150 permutations, which means that the chance of any particular sequence of cards arising would be less than the UPB of 10-150. And yet, all you have to do for such an improbable event to occur is deal the cards.

This response to the UPB featured in the BBC Horizon programme about Intelligent Design, that I reviewed some time ago. However, it misses the point that Dembski makes in relation to the UPB. Dembski never suggests that improbable events don't occur. The UPB relates to whether or not a specified improbable event will occur by chance. The difference is important.

To explain this, take the sequence of cards that you got in the last part of the experiment, and write it down. Now, pick up the cards, shuffle them properly and deal them again. What is the likelihood that you get exactly the same sequence as you wrote down? Actually, it's exactly the same as the probability that you got it in the first case – 1.2x10-68. But whereas you know when you deal the deck of cards you are going to get some sequence of cards, you certainly don't know that you are going to get a specific sequence of cards. So for you to obtain the same sequence would be a specified event of low probability, as distinguished from an unspecified event of low probability, which was what we had with the first sequence of cards dealt.

Now imagine a magician, who with great ceremony shuffles a deck of cards, and for good measure encourages onlookers to cut and shuffle the deck as well. He then deals the cards in the way described above, and presents a random sequence of cards. That random sequence is no less improbable than dealing all the cards out in order of suit and value. But the audience would fail to be impressed, of course, because there was “nothing special” about that sequence – that is, more formally in Dembski's terms, it is not a specified sequence. But if the magician deals the cards by suit and value, then people would be impressed – because the sequence of cards dealt obviously is specified.

Our instinctive reaction when presented with such a feat with a deck of cards is to conclude that there is trickery – in other words, the pattern in the cards is there by design, not chance. The event is a low probability event that is specified – magicians attract audiences for this sort of trick precisely because we don't shrug our shoulders and say: “Well, the cards were bound to come out in a sequence, and each sequence is as improbable as any other.” However, there is a small possibility that a deck of cards dealt at random will come up with a sequence that is significant – perhaps suit by suit, or value by value – let's say that 90% of card sequences dealt are significant in some way. So the probability of getting a “significant” or “specified” sequence is 10 times greater (actually, this isn't quite right from a statistical point of view, but I think it will probably do). That would mean that the probability of dealing a sequence which was significant was about 10-67. This is still an incredibly low probability – however, Dembski sets the UPB – the point at which the occurrence of a specified event can be confidently assigned to intention rather than chance is a lot lower – namely, 10-150.

On the other hand, people would not be impressed by a magician presenting a sequence of cards that we were unable to clearly distinguish from a random sequence. The concept of specification is one that we are intuitively happy with, and arguing against Dembski's approach on these grounds either represents a failure to interact with what he has actually written, or a willful misrepresentation of his argument. Neither is commendable.

I hope to write more shortly about our intuitive sense of specification, and how this relates to the information content in organisms, in future posts. But I'm sure I've said that sort of thing before ....

Wednesday, October 18, 2006

Update of Haldane's Dilemma on ARN?

On the ARN bulletin board, there is discussion about this paper, "Estimate of the Mutation Rate per Nucleotide in Humans".

The first reply, by somebody with the handle "Life Engineer", says:
This has been discussed many times. The harmful and even neutral mutations predicted by Neo-Darwinian dogma don't actually occur. They are selectively eliminated by intelligent error correction mechanisms. As has been often discussed, the almost non-existent harmful mutations is an example of the evidence clearly contradicting the theory, but the soft science procedures intentionally ignoring the evidence in claiming the theory is still valid.
The argument then moves in a different direction, but I wanted to react specifically to this, without the 100 or so further responses that follow.

The assertion is that the harmful/neutral mutations are selectively eliminated. This sounds great, but I was left thinking - "at what stage?" My understanding was that gametes are formed by meiotic division, rather than mitotic - but in their nature, much of their functionality remains unexpressed whilst still in their haploid form. So, from the point of view of the parent, or for that matter the process of cell reproduction, there is no way to differentiate between harmful and beneficial mutations, let alone apply "intelligent error correction mechanisms" to get rid of harmful mutations. There is little evidence to show that the vast majority of human eggs contain harmful mutations - yes, up to 50% of fertilization events may not result in a live birth, but this doesn't approach the "female 40 offspring for 2 to survive" that the authors of the paper put forward. I also don't know whether there is evidence that this intelligent error correction occurs before the egg cells are included in the ovary - in other words, that the error correction takes place at an even earlier stage. And how would this relate to the production of male gametes?

On the other hand, it is interesting that this (5%) survival rate is consistent with what David Stove says Darwin's theory as he set it out implies.

More generally, as the original poster (Salvador, IDEA GMU) suggests, there does seem to be something circular happening in the argument here. Something along the lines of:

- We know that beneficial mutations (sorry - that implies teleology - what I mean by "beneficial" there is simply steps towards the new species that we see today) must be occuring at a specified rate, to allow for the evolution from (say) proto-hominid to homo sapiens.

- But this would entail a significant number of "harmful" mutations - that is, mutations that reduce the organism's fitness.

- Therefore, since evolution is true, either harmful mutations must be selectively eliminated (harmful mutations are "non-existent", according to Life Engineer - and the evidence in support of this is apparently the lack of harmful mutations, not a mechanism to eliminate them), or there must be another mechanism at work (the authors of the paper propose something called "synergistic epistasis").

Now this is a reasonable scientific approach. Here is a scientific "world-view" (macro-evolution). Here is an implication of it (required mutation rate). Here is an implication of that (the impact of harmful mutations). And here is a suggestion as to how this can be resolved (synergistic epistasis, or some mechanism for intelligent elimination of harmful mutations). However, it is important to think through the scientific implications. Macro-evolution was presented to start with as an assumption. You can't use an assertion of the truth of macro-evolution to support an argument when it is the truth of macro-evolution that you are seeking to demonstrate. Ultimately, if evidence doesn't support that assumption, then you have to throw away the assumption, and at least say: "We don't know".

In my job, we are warned about the danger of "confirmation bias". An event happens, which we have indications to interpret, and we come to some conclusion about what that event is. We then fit all subsequent evidence into that interpretive framework. We are told that, having dealt with what we perceive to be the problem, we need to be prepared to "review" evidence as carefully as time allows, in the hope that stepping back and looking again at everything might allow us to pick up something that will break the risk of confirmation bias.

My perception is that, in the case of evolution, confirmation bias has set in in a big way - exacerbated by what I would consider to be the erroneous assumption that good science requires philosophical naturalism. All evidence is fitted into the evolutionary paradigm, no matter how stretched it ends up, no matter how many contradictions it contains.

There are a limited number of ways in which this specific conundrum (the impact of harmful mutations) can be solved. I suspect that Life Engineer's solution is already moving too far in the direction of teleology for some people (he distinguishes himself from the "neo-darwinian dogma") in talking about "intelligent error correction mechanisms" - what does he mean by "intelligent"? can he reword this using concepts that don't imply purpose? What happens if and when these solutions are shown not to work, I wonder?

One more thought, relating to the bias against Intelligent Design as a worldview. Suppose this research had been done and written up by somebody from the Discovery Institute, and rather than proposing synergistic epistasis, they had simply highlighted this as a problem for macro-evolution. Would such a paper have been published in a mainstream journal? I would suggest not, despite the fact that synergistic epistasis currently has no more scientific basis than intelligent design - EXCEPT that it apparently avoids the risk of external agency, and so allows people to hold on to darwinian macro-evolution for a bit longer.

Tuesday, October 17, 2006

Unfortunate juxtaposition ...

... on the Phatfish lyrics page.
So lift your eyes
To the things as yet unseen,
That will remain now
For all eternity.
Though trouble's hard,
It's only momentary
And it's acheiving
Our future glory.

(Advert)Visit ba.com/amex to apply now. British Airways. Terms and Conditions apply.

Oh, the joys of contextual advertising.

Sunday, October 15, 2006

Where is everyone?

Not one blog on my Blogrolling list below is showing an update in the last 48 hours. Okay, so some don't have feeds, but even so .... Has everybody except me got a life, or something?

Here's a few useful abbreviations, while I'm at it, from the GROGGS era.

AFAIK - As far as I know
IAMFI - I ask merely for information
ITWSBT - I think we should be told
WTGROMT - Well, that's got rid of me, then

More can be found here. It's worth wondering the extent to which what happened there influenced the rest of the world. It's probably not worth wondering whether the list on that page pretty much constituted a full and sufficient definition of us as we were at the time. Or perhaps it was just me ....


Wednesday, October 11, 2006

Favourite U2 tracks

I'm far too keen on U2. I have just started using last.fm in an attempt to broaden my interests in music. For anybody who is as interested in U2's music as I am, here's a list of my favourite moments from their discography.

10. Acrobat (Achtung Baby)
And I'd join the movement
if there was one I could believe in.
Yeah, I'd break bread and wine
if there was a church I could receive in.

Disturbing first choice from a Christian band, I know - but this song is moving because of its incredible anguish. Achtung Baby dated, I think, from the time when Edge was going through a painful divorce, and many of the lyrics on the album have pain and betrayal as a side-tone.

9. 40 (Under a Blood Red Sky)
This is a staple of U2's live performances, and I suspect this song has had more influence on modern Christian music than almost anything else. Well, maybe not. But it's a bit more interesting than "this is one of the all-time best Christian rock songs."

8. Walk On (All That You Can't Leave Behind)
You're packing a suitcase for a place
None of us has been
Somewhere that has to be believed in
To be seen

Dedicated to Aung San Suu Kyi, but the first of many in this list that is more broadly full of eschatological longing.

7. Kite (All That You Can't Leave Behind)
In addition to the impact of breaking relationships, U2 have explored the loss of parents (Kite, Sometimes You Can't Make It On Your Own, Mofo), the permanence of relationships (A Man and a Woman), the growing-up of children (The Original of the Species). Somewhat more interesting than the typical "Boy-being meets girl-being under a moon which then explodes for no adequately explored reason". And also a longer lasting accompaniment to the average person's life.

The first time I heard Kite, I thought to myself: "Strange song. Who is Bono singing about?" It was finding out that kicked off the latest round of obsession with what U2 do.

6. Until the End of the World (Achtung Baby)
Judas Iscariot singing about Jesus, apparently. Another one of the eight or so fantastic and painful tracks on this album.

5. Vertigo (Live/Vertigo 2005)
The single and album versions were pretty good. But something happens when U2 get on stage - they just step up a gear. At least on the DVD's. Or maybe it was the direction. You'd have to ask somebody who was there. But this just rocks....

4. Yahweh (Acoustic live version/Vertigo 2005)
I've blogged about this song elsewhere. Again, the album version is okay - but in this stripped down version with Edge playing an acoustic guitar and a naive keyboard from Larry, this makes an amazing prayer/benediction at the end of the concert.

3. Where the Streets Have No Name (Rattle and Hum)
... where they switch to colour, and then turn on all the lights. This was the song that U2 turned down an offer of millions of pounds for the rights to it - I think from Apple - because it was so special to them and to the fans. I have to say that, whilst the African flags and the introduction to the One campaign in 2005 were good with this song, they weren't the same experience as the gigs where all the lights go on.

2. The Fly (Achtung Baby or Live)
Every artist is a cannibal,
Every poet is a thief,
All kill their inspiration
and sing about their grief.

... as evidenced by the choice of subject matter in the rest of the discography! Fantastic live.

1. Beautiful Day (All That You Can't Leave Behind)
See the bird with the leaf in her mouth
After the flood all the colours came out

This is a most sublime moment. I would be hard-pushed to choose between either the 2001 live, the 2005 live, the Charles de Gaulle, or the Dublin Rooftop video for this song. (Yes, I really must be a bit obsessive, I guess)

Just to point out that NOT on this list are Pride (In the Name of Love), One, Sunday Bloody Sunday or I Still Haven't Found What I'm Looking For. All of them worthy, but relatively dull (though I noticed for the first time that "Free at last!" in Pride references MLK directly this week). And definitely not "Mysterious Ways", which is probably one of my least favourite of their songs.

Tuesday, October 10, 2006

Looks interesting

BBC Newsnight Bookclub talks about a book called "The Goldilocks Enigma" - why the universe is "just right". Judging from the extracts, he (like Gonzalez and Richards) seems to suggest that this isn't simply an anthropic effect.

H/T John

Sunday, October 08, 2006

Frappr - hit me!

Currently, on my Frappr map, I have pins from:
- UK
- Canada
- United States (including Hawaii!)
- France
- Germany (though only through MySpace)

Hardly a large cross-section of the countries of the world. But I have had visits from many places. In the last 100 hits alone (courtesy of sitemeter), I have had visits from India, Australia, the Netherlands and Norway.

Just for the sheer fun of it, it would be great to see whether I can get a pin from every country in the world. If you know anybody in a country not yet pinned and think they would not consider it harrassment to be asked, please let them know, and let's see whether I can notch up any more.

Don't feel that, if your country has a pin already, you can't add one as well.

Saturday, October 07, 2006

Interpreting the Bible

Moore Theological College do a correspondence course in theology, which I followed for several years. One of the most useful sections of all my studies (which were all very helpful) was the second unit of "Introduction to the Bible", which they in turn based to an extent on The Lion Handbook to the Bible. Here are the contents of this module.
1. UNDERSTAND - What does the passage actually say?

1.1 Form - How, or in what form, was the passage written?
1.2 Words - What is the meaning of individual words?
1.3 Context - Where does the passage fit in the structure of the book?
1.4 Purpose- Why was the book or passage written?
1.5 Setting- In what situation or for what situation was the book or passage actually written?

2. EXPLAIN - What does the passage mean?
2.1 What is the main point or teaching of the passage?
2.2 Where does the passage fit into the Bible's overall message?
2.3 How does the passage compare with other Bible passages?
2.4 What general principles or theological truths does the passage set forth?

3. APPLY - What does the passage mean today?
3.1 Is there a warning to be heeded, an example to follow, a command to be obeyed or a promise to trust?
3.2 Is the main point of the passage some teaching about God or human beings or the church?
3.3 What is the equivalent situation today to that of the original readers?
3.4 Does it lead to prayer or praise?


5. The role of the Holy Spirit
Notice that the proportion of this that is "spooky" or "mystical" is very small. For example, in understanding the text, there is nothing that is done when reading the Bible that we don't do pretty much automatically when we read any book. In the explanation section, the only assumption that we are really making is that it is reasonable to work on the basis that the book has a unified message. If it doesn't have a unified message, then we would expect this process of explanation to break down.

The "apply" process is accepted by Christians because they believe that the Bible is not only a text addressed to its original readers, but also a message from the God who created the universe to anybody who reads it throughout history. That sounds like a pretty startling claim, but in justification of it, I would refer people to a short essay by Francis Schaeffer called "Is Propositional Revelation Nonsense?" A quick search has failed to find a copy of it on the internet, but here's a link to a post from somebody else who discusses the essay and introduces the main points. I also referenced it here.

Wednesday, October 04, 2006

More about "Darwinian Fairytales"

I have finished David Stove's book, which was a very interesting read. Stove was not a creationist, or even a Christian - he describes himself as "of no religion". However, he lays various charges at darwinism - both as it was presented by Darwin and his contemporaries and as it is presented today by neodarwinists.

The heart of the charge that he levels against darwinism is that, insofar as it is used to explain humans, it is "a ridiculous slander on human beings." He points out:

- human life is not a "continual free fight" in the sense that Darwin envisaged necessary as a driver of natural selection;

- the human population has never increased to the limit of the food available;

- specifically, more privileged (better educated, richer, more socially advanced) humans have generally shown themselves less successful at reproducing than those less privileged;

- infant mortality is nothing like the level that Darwin's theory expected it to be;

- the "problems" raised by sociobiology are actually not problems of organisms (they are observations) but problems within darwinism;

- the "discovery" of memes is not a scientific advance akin to the discovery of genes, but simply a truism - "Sometimes such things as beliefs, attitudes, etc., are transmitted non-genetically from one person to another";

- if altruism is linked to the number of shared genes (a widely held position), then people should be as altruistic towards their egg or sperm cells as they are to their offspring;

- in regarding genes as more intelligent and capable than humans, sociobiologists are effectively establishing a new religion;

- although neodarwinists claim that they don't believe in purposiveness, their language about genes contradicts this. "For every once that Dawkins says that genes are not purposive, he says a hundred things ... which imply that genes are purposive."

- it is stupid to describe homosexuality, altruism, celibacy etc. as "errors of heredity". They are simply observations. If there is an error, then it is with the theory that can't accommodate the observations.

This quick summary doesn't do the book justice. His writing is literate and funny. On every other page was a paragraph I would like to have quoted. There were issues where I felt that his arguments failed to reflect "the state of the art" in darwinism. But suffice it to say that his book at least does a great deal to undercut darwinism as it relates to humans at its popular level.

Sunday, October 01, 2006

Another quiz

(HT Bec)
You scored as Anselm. Anselm is the outstanding theologian of the medieval period.He sees man's primary problem as having failed to render unto God what we owe him, so God becomes man in Christ and gives God what he is due. You should read 'Cur Deus Homo?'



Karl Barth


Martin Luther


John Calvin


J�rgen Moltmann




Friedrich Schleiermacher


Paul Tillich


Jonathan Edwards


Charles Finney


Which theologian are you?
created with QuizFarm.com

Liz came out disturbingly close to the same result as me ....