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.
Sunday, October 30, 2005
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.
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.
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:
Then there's what they are doing with the song in the live shows. The last line of the song:
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.
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,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:
so quick to criticise:
take this mouth,
give it a kiss.
Take these hands,- not only "don't make these hands into a fist" but also (using a colloquial expression) "don't make a mess of these hands".
don't make a fist.
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
Breaking news
Look out for strange BMW's.
Also, Stephen Gould would not have signed up to Project Steve, says friend!
Also, Stephen Gould would not have signed up to Project Steve, says friend!
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 ....
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."
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
Poems
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.)
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
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
Suffocate
Us.
To care, to live, to create,
Or else.....
F.J.
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.
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.
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.
... 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.
Friday, October 07, 2005
Not Quite Me - Tess Wiley
"Another day gone.
Another sun I was frightened to see – a spotlight on me.
This stage is much too big for me."
Now that’s poetic imagery that only a teenager can write.
Such pathetic chemistry turning blessing into plight.
We all cry for something more,
but we stop just short of heaven’s door.
Somewhere right outside the lines that I’m drawn to be.
It’s not quite me.
The ground keeps turning.
One day the tears are a pity to cry.
You want to start learning how to keep them in your eyes.
The years I’ve wasted feigning self-sufficiency.
The weaker the better – there’s more room for God in me.
Another year gone.
Just singing the old songs time and again.
A little bit surer of the person I have been,
and who I will be when each song is through with me.
A little bit clearer – all the things that I’m supposed to see.
Another year gone.
Another lesson learned.
I love this song - in fact, I liked it so much, I bought the album (as one does - electronically, using iTunes, since it isn't available in non-virtual form in the UK). You can listen to the whole song on myspace, here. Tess's website is here.
At risk of doing the hateful thing of talking about people entirely in relationship to other people or things they have done, I found the song because Tess sang on "This Beautiful Mess" by Sixpence None The Richer - which is probably one of my top five albums of all time (pretty good, considering I'm not sure it has ever been available in the UK). Then I noticed her name when I found Leigh Nash's space on myspace. So I thought, "Well, where did Tess go next?" So I got to hear this in Tess's myspace. Thanks for writing and playing it, Tess - and for permission to post it here. It's lovely.
Better dead than ...?
Following the post linking with Denyse O'Leary yesterday, which highlighted the fact that ID proponents were facing direct challenges to their presence in university almost whenever they appeared, here is a link to a post on Telic Thoughts, which points out that the American Civil Liberties Union regard ID as a major threat to the American Way. Indeed, if you go to their website, you can see this for yourself.
Now this is interesting, and a little frightening. In the 1950's, communists were the enemy of choice. I only know about this by reputation, I hasten to add - but there was a national fear that there were communists hiding under every bed; Joseph Macarthy (sp?) launched his trials and witch-hunts under the Stars and Stripes to out every commie from wherever they were hiding. Some people with affiliations to communist groups were discovered; other innocent people lived in fear of malicious allegations. But an interesting question is: did it actually make any difference? Was there a communist conspiracy to overthrow the US? I suspect it had little effect beyond heightening the tension between the protagonists in the Cold War.
I am concerned by the fact that we see the same thing starting to happen now, in the opposition of liberals to the ID community. The truth of the matter is that the freedom of speech and thought of people is already being curtailed, supposedly in the name of separation of church and state ("Amendment 1! It's the most important rule in the book!"). In actual fact, that was nothing to do with what Amendment 1 was supposed to be for, and in closing down debate in this way, what is happening is that a liberal atheocracy is being enforced, in which it becomes intellectually intolerable for somebody to believe in a God who is actually capable of doing anything.
The paranoia might be cause for some people to giggle, but it disturbs me. In an era in which religious fundamentalism is regarded as the big enemy of civilisation, to be tagged as "threatening to introduce a theocracy" is to be branded as an enemy of the state. Separation of the state and religion was meant to guarantee religious freedom and tolerance; what is starting to happen is that the First Amendment is being distorted and used to restrict religious freedom. This distortion of the law is completely reversing its intent.
I am no real friend of GWB, but whilst the US continues to have a president who is part of the religious right, I think most people are relatively safe. However, if there were a significant movement towards the political left and liberalism, it is not hard to imagine that - rather than the political right pursuing enemies on the political left, as it did in the 50's - the liberal establishment would start to pursue and expel these "intolerant fundamentalists" in the name of "tolerant liberalism".
Now this is interesting, and a little frightening. In the 1950's, communists were the enemy of choice. I only know about this by reputation, I hasten to add - but there was a national fear that there were communists hiding under every bed; Joseph Macarthy (sp?) launched his trials and witch-hunts under the Stars and Stripes to out every commie from wherever they were hiding. Some people with affiliations to communist groups were discovered; other innocent people lived in fear of malicious allegations. But an interesting question is: did it actually make any difference? Was there a communist conspiracy to overthrow the US? I suspect it had little effect beyond heightening the tension between the protagonists in the Cold War.
I am concerned by the fact that we see the same thing starting to happen now, in the opposition of liberals to the ID community. The truth of the matter is that the freedom of speech and thought of people is already being curtailed, supposedly in the name of separation of church and state ("Amendment 1! It's the most important rule in the book!"). In actual fact, that was nothing to do with what Amendment 1 was supposed to be for, and in closing down debate in this way, what is happening is that a liberal atheocracy is being enforced, in which it becomes intellectually intolerable for somebody to believe in a God who is actually capable of doing anything.
The paranoia might be cause for some people to giggle, but it disturbs me. In an era in which religious fundamentalism is regarded as the big enemy of civilisation, to be tagged as "threatening to introduce a theocracy" is to be branded as an enemy of the state. Separation of the state and religion was meant to guarantee religious freedom and tolerance; what is starting to happen is that the First Amendment is being distorted and used to restrict religious freedom. This distortion of the law is completely reversing its intent.
I am no real friend of GWB, but whilst the US continues to have a president who is part of the religious right, I think most people are relatively safe. However, if there were a significant movement towards the political left and liberalism, it is not hard to imagine that - rather than the political right pursuing enemies on the political left, as it did in the 50's - the liberal establishment would start to pursue and expel these "intolerant fundamentalists" in the name of "tolerant liberalism".
Thursday, October 06, 2005
Academic freedom
Here is a link to a post on Denyse O'Leary's blogsite concerning academic freedom in various North American universities.
Wednesday, October 05, 2005
Hitting and feeding
For some time, I was frustrated that the number of times I looked at various blogs to see if they changed wasn't matched by the number of times I got hit by people who claimed to be avid readers. Then I was told about news feeds, and I understood, although I still spent far too much time on days off checking the same list of sites.
But I finally got round to doing something about it. On-line news aggregators didn't seem to work - I think I have subscriptions to a couple lying around, and I couldn't get into posting links on them, or going back to them to check them - I mean, if I'm online, why not just go and look at the blog? I have a blogroll - but there is a lag in the time it takes for updates to happen and for it to flag "NEW" material - and also it continues to flag it as such even when it is read. Also, it would have artificially boosted my own hit rate to keep checking what was new through my own blog, which seems a little dishonourable.
So a desktop version was what I needed, and after a bit of trawling around on the internet, I came up with RSS Reader. This stores links to all the blogs etc that I want to stay updated on, sits in the XP system tray, and changes colour when on one of its regular checks identifies new material. Pretty good. Sorry, all those people who were getting lots of hits from me (perhaps particularly this, this and this).
But I finally got round to doing something about it. On-line news aggregators didn't seem to work - I think I have subscriptions to a couple lying around, and I couldn't get into posting links on them, or going back to them to check them - I mean, if I'm online, why not just go and look at the blog? I have a blogroll - but there is a lag in the time it takes for updates to happen and for it to flag "NEW" material - and also it continues to flag it as such even when it is read. Also, it would have artificially boosted my own hit rate to keep checking what was new through my own blog, which seems a little dishonourable.
So a desktop version was what I needed, and after a bit of trawling around on the internet, I came up with RSS Reader. This stores links to all the blogs etc that I want to stay updated on, sits in the XP system tray, and changes colour when on one of its regular checks identifies new material. Pretty good. Sorry, all those people who were getting lots of hits from me (perhaps particularly this, this and this).
Tuesday, October 04, 2005
The eclipsed sun ...
... as viewed in the approved manner - through a small hole in a piece of paper, projecting it onto another white surface. The slimness of the crescent gives some idea of how significant the eclipse was (a thousand miles or so further south, it was annular, I understand).
Trees in evening light at 10 am
I had noted the fact that there was to be an eclipse on Monday, but put it to the back of my mind. Working on my computer, I noticed that the bright sunshine outside was not as bright as it ought to be - and then I remembered the eclipse. As with the total eclipse of 1999, the effect was a bit like "evening" arriving during the day - the intensity of the light dropped off a long way - I didn't notice a decrease in temperature, and some birds at least were still singing - but despite the blue sky and the sun being high, it just felt gloomy, or like sunset sort of time.
Other people I spoke to during the day had vaguely been aware of the eclipse, but had forgotten about it, and didn't notice anything at all.
In 1999, I was flying an aircraft back from Paris when the eclipse happened. We held mid-channel and gave the passengers a chance to have a look at it - it was about 98-99% total, but still definitely not dark. It was quite strange, however, for the sky to be so dim with the light source overhead (not on the horizon), but the horizon on either side East and West(hundreds of miles away) being brighter than where we were as the shadow was less deep there. I find the idea of the shadow of the moon racing across the earth at thousands of miles an hour fascinating.
Trees in early October
They are still largely green, but the yellows and reds are taking over now - even in the green, the notes of the other colours are starting to show.
Monday, October 03, 2005
An article that shames the journal it is in.
This article was published in the Journal of Religion and Society. It was cited approvingly by Ruth Gledhill - who ought to know better - in The Times.
It is a disgrace that the magazine should have picked up such a sloppy paper. It is a disgrace that, rather than challenging it, it should have been accepted by the liberal world because it fits with their beliefs. For interaction with it, see Telic Thoughts here, here, here, and here.
It is a disgrace that the magazine should have picked up such a sloppy paper. It is a disgrace that, rather than challenging it, it should have been accepted by the liberal world because it fits with their beliefs. For interaction with it, see Telic Thoughts here, here, here, and here.
Saturday, October 01, 2005
Too much choice
The problem with admissions to secondary schools where we are is that there is too much choice.
Of the local state secondary schools:
one has an integrated sixth form college, is a "Business and Enterprise Specialist School", and has an annual intake of 240.
one has had a bad reputation for many years, but is improving under the direction of a new head. It only has 160 children in each year.
one is a secondary school that is specifically ecumenical by foundation. Preference is given to people who can get the vicar of a nearby church to lie about how often they attend church. People who are actively involved in the wrong sort of evangelical churches will be discriminated against, the strength of their Christian commitment notwithstanding. It admits 270 children per year.
one is (basically) a state boarding school, again with an improving reputation, a small intake, long holidays and classes on Saturday mornings.
one is a very large comprehensive (300+ children per year), which has had a good reputation for a long time but now seems to be coasting.
This doesn't really take into consideration such issues as results, "value added", extra-curricular activities or ease of access. It also ignores out-of-area schools and private schools.
The government would have you think that this is what parents really want. But it isn't. All we want is a school in which our child will be treated as an individual and will fulfil his or her potential - both academically and in other areas.
In particular, I am concerned about the specialisation of schools. We were told that, being a "Business and Enterprise Specialist" school meant that the business studies and enterprise angle had an impact on all areas of the curriculum. Now, firstly, there is no need for any specialisation up to age 16 (unless children are sure they want to move in a particularly vocational direction) - there is no reason why education can't be completely "general" - in the sense of the old "General Certificate of Education" - it is learning about the world for the sake of learning. Secondly, I am troubled by a specific focus on business and enterprise. Of course, business and enterprise would love to have children educated to believe that business and enterprise is the goal of society - the summum bonum. But this is putting the cart before the horse. Business and enterprise ought to be informed by the ethical and social dimensions taught in a general education; they ought not to be controlling those dimensions. Forget schools that have a religious foundation, and the fact that this disturbs Richard Dawkins - what does he think the impact will be of children being brought up to believe that the world revolves around business and enterprise?
Other schools focus on "technology", "sports", "engineering", "modern languages" - or any number of other things. Perhaps these are potentially less harmful focuses (foci) - but I suspect that whilst they may attract the interest of sponsorship, they will lead children to believe that education has no value in itself, but only insofar as it is directed towards a specific goal.
But choice, we are told, is what we want, so choice is what we get - between a range of unsuitable and undesirable options.
Of the local state secondary schools:
This doesn't really take into consideration such issues as results, "value added", extra-curricular activities or ease of access. It also ignores out-of-area schools and private schools.
The government would have you think that this is what parents really want. But it isn't. All we want is a school in which our child will be treated as an individual and will fulfil his or her potential - both academically and in other areas.
In particular, I am concerned about the specialisation of schools. We were told that, being a "Business and Enterprise Specialist" school meant that the business studies and enterprise angle had an impact on all areas of the curriculum. Now, firstly, there is no need for any specialisation up to age 16 (unless children are sure they want to move in a particularly vocational direction) - there is no reason why education can't be completely "general" - in the sense of the old "General Certificate of Education" - it is learning about the world for the sake of learning. Secondly, I am troubled by a specific focus on business and enterprise. Of course, business and enterprise would love to have children educated to believe that business and enterprise is the goal of society - the summum bonum. But this is putting the cart before the horse. Business and enterprise ought to be informed by the ethical and social dimensions taught in a general education; they ought not to be controlling those dimensions. Forget schools that have a religious foundation, and the fact that this disturbs Richard Dawkins - what does he think the impact will be of children being brought up to believe that the world revolves around business and enterprise?
Other schools focus on "technology", "sports", "engineering", "modern languages" - or any number of other things. Perhaps these are potentially less harmful focuses (foci) - but I suspect that whilst they may attract the interest of sponsorship, they will lead children to believe that education has no value in itself, but only insofar as it is directed towards a specific goal.
But choice, we are told, is what we want, so choice is what we get - between a range of unsuitable and undesirable options.
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