Intelligent design - science, not religion

This post on ID: The future neatly summarizes my thoughts on why Intelligent Design is not a religious project, despite the obstinate insistence of its opponents otherwise. The reasons for this insistence are complex, but one of the key ones is that as long as it is considered to be a religious project, the US constitution can forbid evidence for design to be considered in public schools.

I wonder whether this means that evidence against naturalistic worldviews must also be banned from US public schools, as suggesting that they are wrong would imply that a religious worldview might be right, which might be unconstitutional.

Incidentally, a commenter said on the issue of bullying :that:

When the Discovery Institute actively promotes bullying of high school teachers who teach evolution, it's really poor form to complain about imagined bullying the other way.

When asked to back this up, he said:

Sure. Start here with Jonathan Wells' 'Ten Questions to Bully High School Teachers With'

Note that Wells is a "fellow" at DI, and note their defense of the bullying document:

The actual title of the paper is "Ten questions to ask your biology teacher about evolution." - which immediately softens the tone - by retitling the paper in this way, the commenter was already adding spin.

Why is it bullying to ask for evidence in support of a scientific theory? When we learnt about gravity, we learnt about Galileo's demonstrations. When we learnt about relativity, we learnt about how the 1919 eclipse and the precession of Mercury provided evidence in support of it. We can learn about the heliocentric model, and how the geocentric model with all its epicycles was really struggling beforehand.

But what evidence is presented in schools in support of evolution? The last thing scientists should be doing is being happy with inadequate evidence. I want to know that the things I have learnt really stand up. To be told to believe in something when no credible support for it is offered is not scientific.

So, commenter, I don't accept that as evidence of bullying "for a start" - unless you can show me in what sense it is bullying. Come up with something else.

Evening boat

Taken off Santa Catarina island, Southern Brazil, in October 2003.

Around Santa Catarina, there is still plenty of evidence of the traditional fishing/lacemaking lifestyle of the original Azorean settlers. Here is an introduction to this area of Brazil. 

Bono - Karma versus Grace

... at the centre of all religions is the idea of Karma. You know, what you put out comes back to you: an eye for an eye, a tooth for a tooth, or in physics - in physical laws - every action is met by an equal or [sic] an opposite one. It's clear to me that Karma is at the very heart of the universe. I'm absolutely sure of it. And yet, along comes this idea called Grace to upend all that "As you reap, so will you sow" stuff. Grace defies reason and logic. Love interrupts, if you like, the consequences of your actions, which in my case is very good news indeed, because I've done a lot of stupid stuff.... I'd be in big trouble if Karma was going to finally be my judge. It doesn't excuse my mistakes, but I'm holding out for Grace. I'm holding out that Jesus took my sins onto the Cross, because I know who I am, and I hope I don't have to depend on my own religiosity.

Bono on Bono, Conversations with Michka Assayas, Hodder and Stoughton 2005

On the basis of what I have read in the book, Assayas isn't a Christian. I'm impressed by the fact that Bono was able to communicate these deep Christian ideas to a non-Christian. If you are a Christian, how many non-Christians have you talked to about grace?

Slightly provocative passage from "The Spectator"

One of the great errors of political taxonomy is to classify Hitler as right-wing. He, and still more his closest colleague, Goebbels, were socialists, and the fact they were nationalists first did not orient them more to the right. There are six indispensable hallmarks of a conservative. First, firm belief in one, beneficent and omnipotent God. Second, absolute morality as the basis of public law. Third, strict limits on the size of the state. Fourth, respect for a multiplicity of traditional power centres. Fifth, restraint and self-restraint in all things. Sixth, search for the right balance between the individual and the traditional units of society. Hitler broke all these rules: he was an atheistic pagan, a moral relativist, a totalitarian, an ultra-centralist, an uninhibited exhibitionist and a collectivist. In many ways Stalin was to the right of him. There is a seventh point. A conservative is not afraid of force, or of using it thoroughly. But always as a last resort. With Hitler it was the first.

Who was the most right-wing man in history? - Paul Johnson, The Spectator, 25/2/2006

Hmm. And they styled themselves, after all, "national socialists". My dad always said that the difference between politics at its left and right extremes was less than you might think.

A (limited) retraction

In a comment before, I said that people were bullied into accepting evolution. I then wrote a post effectively to back up what I had said. However, on consideration, there are various aspects of this that I'm not happy with.

Firstly, I gave the example of a current email discussion between Ruse and Dennett as evidence in support of this position. I'm not happy with that; it does underline an interesting attitude from two different camps within darwinism, but without knowing much about things like motives and status, it isn't evidence of bullying. It just happened to be around at the time, and I was interested in linking to it. I should have left it at that.

Secondly, I think it is inappropriate to go back over my life and read "bullying" into my experiences, for the sake of fitting it into a comment I made. I would not say that I was bullied. I would say, however:
a) there was an assumption - both spoken and unspoken - that dissent from darwinism was intellectually untenable, and the email I recently received shows that this attitude is still present.
b) this assumption wasn't based on the presentation of evidence, either in school or university. In fact, it is only in the last couple of years that I have come across convincing evidence for common descent at any level (yes, Tim, that includes the non-functional Vitamin C gene in humans). Insofar as evidence was presented in support of evolution at earlier stages, it generally consisted of examples of very limited relevance to the concept of macroevolution - I knew a bit about industrial melanism, Darwin's finches, the Miller/Urey experiment and Haeckel's embryos before I read Denton's "Evolution: A Theory in Crisis". And the evidence in support of common descent is met by a lot of evidence that to me is fairly convincingly against it - lack of transitional fossils coupled with geologically sudden transitions; stick and leaf insects appearing before sticks and leaves; required changes in organisms being fundamentally "steppy" rather than gradual (eg. changes in numbers of chromosomes) as well as irreducible complexity and the amount of information contained in organisms.

So people aren't necessarily "bullied" into believing in evolution, as I said before - that is something else that I am retracting. Though there is a teacher in the school to which some of the teenagers I know go to who tells children that "God doesn't exist in this classroom". It is just that evolution is assumed with no reference to any supporting evidence. A suggestion, then. If people want to make a case for evolution, then they should be presenting the best evidence that they have, not evidence that has already been shown to be less than credible.

Remind me to talk about "Galileo was wrong" sometime.

Sermonti on Stick Insects

Giuseppe Sermonti's book "Why is a Fly not a Horse?" contains various challenges to the prevailing evolutionary orthodoxy. In Italian, the book is called "Dimenticare Darwin" ("To forget Darwin"). I wanted to quote a couple of sections which flagged up the issue of the accepted evolutionary chronology.

A strange order of insects, close to the coleopterans, has been given the name of phasmids (“phantoms”), indicating their ability to remain invisible to neighbours by imitating the forms and colors of the trees on which they alight. Stick insects and leaf insects belong to this order. These astute animals are taken as examples of mimetic adaptation, but they proved embarrassing when paleontologists started following their fossil traces and found them where they were not supposed to be. How these ghost insects – these incredible mimickers of leaves and sticks – ever came into the world remains a mystery, an unsolved scientific detective story. The reigning utilitarian interpretation would have it that these insects, before they were like leaf surfaces or dry sticks, got mixed up with leaves and twigs and, through mutation after mutation, came to resemble their background, until they arrived at the point of becoming the perfect models we see now (to the point that we don't see them!) on plants. Unfortunately for them and for the theory, these artful imitators derive no benefit from their mimetic capacity and are prey for their enemies, which have no difficulty in detecting them. But the most unforeseeable surprises have come from paleontology. The oldest phasmid fossils (they go back in Baltic amber to the Tertiary – i.e. about 50 million years ago) look identical to present-day species, showing that no gradations have occurred. It is thought that those phasmids originated from Chresmodids of the Upper Jurassic in Germany, fossils of which are encountered in deposits dating back some 150 million years. But the oldest fossils of stick or leaf insects (protophasmids) go back to even remoter periods, in the Permian (250 million years ago, in the Paleozoic). One might argue that these insects completed the process of imitating leaves at an extremely gradual rate beginning at a still earlier time. Yet things do not work out this way. Plants with flowers and leaves (phanerogams and latifoliae) appeared on earlier than the Cretaceous – in other words about 100 million years ago, long after the first protophasmids. This chronological anomaly places the imitators earlier in time than the objects of the imitation, leaving entomologists and paleontologists disconcerted.

That's a long paragraph! The two key points he is making are:
1. Having a leaf-like/stick-like appearance doesn't convey a survival advantage.
2. In any case, insects appeared that looked like leaves and sticks before leaves and sticks evolved.

I have little doubt about the initial guess at an evolutionary story that would be told concerning these insects. But given that it doesn't work, is there an alternative?

Short ID commentary from Germany

A friend happened across this the other day.

More about bullying

A commenter said, of my suggestion in a comment that people are being bullied into accepting the party line on evolution:

Bullshit. People who happen to be religious and practice science are not being bullied into parrotting the party line. Do you think people like Dr. Miller get up and give talks repeatedly - and testify in court - about the scientific vacuity of Intelligent Design because they are being bullied into it?

Perhaps he would care to comment on this exchange between Daniel Dennett and Michael Ruse, in which Ruse (a darwinist!) seems to be being warned about moving too far away from the fold.

In any case, bullying doesn't occur when people are in senior positions. It doesn't have to. Most dissent from a naturalistic science worldview is dealt with when people are much more vulnerable and impressionable - in high school, or when they are still undergraduates. I'm not talking about the serious bullying that leaves people crying in corners (though see the link below) - but just a continued intellectual assault on convictions that don't fit with the naturalistic worldview.

I went to university a creationist - I am not [in conventional terms!] one now, despite people's protestations otherwise. Within my first year I was made to feel that belief in anything other than straight-down-the-line darwinism was ridiculous and intellectually untenable. This didn't come through the lectures - in fact, I don't believe any evidence in support of evolution was presented in the course I was on (Natural Science, including Biology of Cells). It came instead in things like talks given to the CU, and the widespread respect in which people with naturalistic philosophies, such as Dawkins and Hawking, were regarded. Even this week, I had an email from an ex-university colleague "out of the blue" which suggested that only the mentally and religiously insecure had problems with evolution. (Incidentally, I pointed out that I don't have a problem with evolution anyway.)

Anyway, Ken Miller (or Coyne, the Vatican astronomer chappie) aren't "exceptions" that show there is no hard line. They are part of the system. Not because he sees it as his mission - but because he is pointed to by people like my commenter who then say: "Look, there's Ken Miller. He's religious and intelligent, and he's happy to be a darwinist. What's your problem?"

For more on more direct intimidation, see Denyse O'Leary's blog.

Another Venice street scene

... from last year

William Dembski believes in the Bible Code hoax!

Shock horror! William Dembski, with doctorates in mathematics and philosophy, and leading exponent in Intelligent Design, believes in the Bible Code books.

Well, not quite. That's the Panda's Thumb interpretation of a post over at Red State Rabble. Actually, it was the same post I looked at yesterday, oddly enough. To be fair to RSR, they were actually somewhat more guarded. What they said was:

Both Johnson and Dembski wrote favorable reviews of Cracking the Bible Code, a book touting the existence of a hidden code concealed in the Bible, by Jeffrey Satinover.

RSR then picked out the following section of Dembski's review:

At the same time that research in the Bible Code has taken off, research in a seemingly unrelated field has taken off as well, namely, biological design. These two fields are in fact closely related. Indeed, the same highly improbable, independently given patterns that appear as the equidistant letter sequences in the Bible Code appear in biology as functionally integrated ("irreducibly complex") biological systems, of the sort Michael Behe discussed in Darwin’s Black Box.

The relevant statistical methodology is identical for both fields. As a result, the two fields stand to profit from each other.

So Dembski doesn't believe in The Bible Code. Actually, he wrote a favourable review of a book about the Bible Code. Which really amounts to believing in The Bible Code books, doesn't it?

Well, not quite. Here's another extract from the start of Dembski's review:

Jeffrey Satinover’s Cracking the Bible Code is the place to begin for anyone interested in the subject. It is engagingly written, well-informed, and generally sober. In particular, it avoids the statistical fallacies too commonly associated with coverage of the Bible Code.

and

The Bible Code raises a number of sticking points. For instance, even if a nonhuman intelligence can convincingly be shown to have introduced information into the Bible, the identity of that intelligence remains controversial.

and

On the other hand, its speculative portions about the significance of the Bible Code are often diffuse and controversial.

That is actually quite guarded. He doesn't write off the theory, but he remains pretty agnostic about its validity, and about the claims it makes, although he points out that this approach to statistics can be used to detect design. To the best of my knowledge, a convincing case against this point has yet to be made.

Once again, if people are knowingly distorting the truth to support their arguments, to what extent should we be prepared to trust their other arguments?

Michael Behe believes in astrology!

Shock horror! Dr. Michael Behe, author of Darwin's Black Box and leading exponent of intelligent design, believes in astrology.

Well, not quite. It's probably only a matter of time before somebody says that, but to be fair, they haven't yet. What they have said is that Michael Behe has a "connection to the science of astrology". Look at this quote supposedly demonstrating this from Red State Rabble, a blog quoted approvingly by a much-beloved commenter.

Question: And using your definition, intelligent design is a scientific theory, correct?

Answer: Yes.

Q: Under that same definition astrology is a scientific theory under your definition, correct?

A: Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.

Q: The ether theory of light has been discarded, correct?

A: That is correct.

Q: But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?

A: Yes, that's correct…

So he believes that astrology is scientific.

Well, not quite. Look at the next section of the transcript - which Red State Rabble could have quoted, since it comes from the source they used, had they been concerned to present facts rather than spin. In fact, the ellipsis they inserted substitutes for the following continuation of Behe's reply!

... and let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.

Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?

A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.

Q And just to be clear, why don't we pull up the definition of astrology from Merriam-Webster.

MR. ROTHSCHILD: If you would highlight that.

BY MR. ROTHSCHILD:

Q And archaically it was astronomy; right, that's what it says there?

A Yes.

Q And now the term is used, "The divination of the supposed influences of the stars and planets on human affairs and terrestrial events by their positions and aspects."

That's the scientific theory of astrology?

A That's what it says right there, but let me direct your attention to the archaic definition, because the archaic definition is the one which was in effect when astrology was actually thought to perhaps describe real events, at least by the educated community.

Astrology -- I think astronomy began in, and things like astrology, and the history of science is replete with ideas that we now think to be wrong headed, nonetheless giving way to better ways or more accurate ways of describing the world.

And simply because an idea is old, and simply because in our time we see it to be foolish, does not mean when it was being discussed as a live possibility, that it was not actually a real scientific theory.

Q I didn't take your deposition in the 1500s, correct?

A I'm sorry?

Q I did not take your deposition in the 1500s, correct?

A It seems like that.

So, no, Michael Behe doesn't believe in astrology. He thinks it is "foolish" and points out that "the educated community has not accepted astrology as a science for a long long time". No, he doesn't think it has any scientific standing today. Which means that people who suggest otherwise when they have access to the facts - for example, New Scientist, Red State Rabble and Panda's Thumb - are all wilfully distorting the truth.

Question. If somebody is demonstrably distorting the truth in this way in support of an argument, to what extent should we be prepared to trust their other arguments?

ID on Radio 4 "Today"

"Today" is Radio 4's flagship morning news program - and sets a standard for authority in reporting that is matched in few places in the mainstream media in the UK ("Newsnight" on BBC2 TV is probably comparable). They had a short report on how things are developing for ID following Dover vs Kitzmiller this morning, followed by interviews with Eugenie Scott (NCSE, anti-ID) and John Henry (maths professor, pro-ID). Try this link for a feed - or alternatively, go here and scroll down to 0748. NB this second link probably won't work after today!!

Dr. Philip Skell in "Philadelphia Daily News"

Here's a link to an article by Dr Philip Skell, which argues that although "nothing in biology makes sense except in the light of evolution", in actual fact it is largely dispensible. This ties in with my comments about the NCSE survey, which sought to make much of the fact that ID wasn't necessary to most research - neither, it appears, is evolution (as I pointed out, and NCSE failed to).

Sudden Infant Death - Chance or Design?

Professor Sir Roy Meadows has won his appeal to overturn the decision that led to him being struck off the medical register.

Professor Meadows, one of the UK's leading paediatric doctors, acted as an expert witness in several cases. In the case that led to him being struck off, he said, according to the BBC report, that the chances of two natural unexplained cot deaths in a family was one in 73,000,000. My understanding is that on the basis of this testimony, a mother was found guilty of murdering two children. She was later freed on appeal.

The BBC adds:

The figure was later disputed by the Royal Statistical Society and other experts said that once genetic and environmental factors were taken into consideration, the odds were closer to 200 to one.

There are several issues here I wanted to comment on.

The first is the obvious "design inference" that was made by the jury when they found the accused guilty to start with. How probable is this specified event (that a family should have two natural unexplained cot deaths? If the answer is, as Prof. Meadows said, one in 73,000,000, then since there are probably only about 20,000,000 mothers in the country at any one time, this explanation doesn't seem likely. Of course, if the odds are one in 200 (by which I suspect they mean, "if a family has one cot death, the likelihood of their having a second one is about one in 200"), then the "chance" explanation is reasonable - even plausible.

The next is what he said at the original trial. Some justifications for reinstating him on the medical register were because expert witnesses need to be able to testify without fear of retribution, and (in effect) because he made an honest mistake with statistics. Now I agree that expert witnesses need to give their honest opinion, and I don't have a fundamental problem with him being reinstated - this case says little about his ability to practice as a doctor (and he has now retired in any case - his reinstatement was about restoring his credibility). What I disagree with is that he ought to be called an expert witness. On the basis that Prof. Meadows was a doctor, a paediatrician, a scientist and a knight, his testimony effectively represented the key plank of the prosecution case. As somebody with some scientific training, it took me about two minutes reading the account of the trial to raise questions - the key one being: "If there is one cot death in a family, can we exclude the possibility that further cot deaths won't have a causal link - genetic or environmental?" The answer to that is no. Which for all Meadows' years of teaching and training is effectively what discredits his "expert opinion". But if somebody is introduced as an "expert" to the jury, even if they have the training to understand the statistics and science involved, are they really likely to think that the expert could possibly be wrong?

And yet, the implication of the reinstatement judgement, as reported by the BBC, is that Meadows made an "honest mistake" over statistics. But that was the whole point of him being there. He was there to be an expert witness about the likelihood of this having a chance explanation - and it sounds as though this was the area in which he was not competent. Sure - no reason to be struck off the medical register - but how on earth did he end up as a credible expert witness in the first place?!

Finally, there's the issue of payment for expert witnesses. This typically ranges from £20 to £200 per hour. On the back of Meadows' testimony, someone was wrongfully imprisoned, and lost months or years of their life, in addition to having their reputation destroyed. In the circumstances, I'd have thought it would be a minimal matter of courtesy if Meadows paid the acquitted woman his fee.

Update - for more commentary and report from the Daily Telegraph, see here and here. These reports supply a lot more detail than I had been able to glean from the BBC reports I had heard. They do little to change my mind.

Today's Times

... contained two articles on evolution.

The first remarked on a report by David Deamer et al at University of California, Santa Cruz, which comes to a negative conclusion about the possibility of life evolving in ponds warmed by volcanic heat. The report concludes that this is unlikely, with reference to volcanic springs in Kamchatcka (Russia) and Mount Lassen, California.

However, my understanding was that life is thought to have evolved around volcanic vents in oceans. Evidence gleaned from experiments in warmed ponds around geysers isn't likely to have much bearing on whether or not life might have evolved in high-pressure thermal vents thousands of feet below sea level. Having said that, I really need to read the original paper ....

The second was an op-ed by Richard Morrison, on Intelligent Design. As with many commentators, he says, "Not for a moment have I ever doubted that I am descended from the apes." But he concludes, in commenting about the survey conducted in conjunction with the BBC Horizon programme on ID (the chances are if you are reading this post of mine, then you read my review of that...) "... I don't think that mankind is ready - not now, and maybe not ever - to accept that the soul is just a chemical trick of the brain."

He might be interested to know more about ID than he has apparently learnt from anti-ID media. For example, whilst there may be people who wish to exploit ID for the political end of getting a telic account of the origin of humanity into public schools, the scientists carrying out ID aren't fundamentally concerned with the politics at all. And whilst he might say that "... a monkey would never write [King Lear] except by freak accident", he apparently has little idea of the statistics involved. "One-in-a-zillion" doesn't come close.

A weakness in the Rare Earth hypothesis

Ward and Brownlee, in their book Rare Earth, advance the idea that intelligent life is very unusual in the universe. However, since simple life (single-celled organisms) are widespread on Earth, and can survive in hostile environments (high-temperature, low pH etc), they also suggest that simple life may be comparatively common.

The problem with this suggestion is that it assumes that the widespread presence of simple life, and the fact that it copes with a wide range of environmental conditions, means that its initial appearance is more likely. However, life may still only have appeared once, and be incredibly improbable - just that having appeared, it became very adept at adapting to new environments. If this is the case, then intelligent life (which, according to this theory, flows from simple life) may be even less common.

Even more so than Privileged Planet, the Rare Earth hypothesis is limited in its usefulness by virtue of the fact that it has a sample size of 1.

Priority of the paradigm

Another of the interesting things about Matzke's paper is that it draws attention to the fact that presuppositions have an impact upon the interpretation of data. Take the following paragraph:

A diversity of export systems of varying complexity exist, and there is a functional continuum of membrane complexes ranging from single proteins and passive pores through to active, gated export systems, indicating that there are no major evolutionary puzzles to solve. The cataloguing and categorizing of transport proteins is already yielding insights into their origin (Saier, 2003).

No assessment is made throughout the paper of exactly how likely the evolution of a membrane complex is. And yet the observation is made that the fact that there is a continuum of membrane complexes indicates that there are "no major evolutionary puzzles to solve".

But this statement is made having presumed that the membrane complexes can evolve. It is assumed that the answer to the key question - whether membrane complexes are likely evolve - is "yes" - and the evidence is then circularly interpreted in the light of this assumption.

Now let's suppose that we discover that, in fact, the likelihood of a membrane transport system arising is below the universal probability boundary. Does the evidence then suggest that there are no major evolutionary puzzles to solve? No. Instead, the evidence suggests now either that we have determined the likelihood incorrectly, or that intelligent design was responsible for the abundance of such systems.

Okay, now consider the actual state of knowledge - that is, we don't really know what the likelihood is of a membrane transport system arising. What does the fact that we have a continuum of such systems suggest? Well, if we assume that the likelihood is high, then Matzke is right - there are evidently no evolutionary problems here. If we assume that the likelihood is low, then the fact that there are a whole range of membrane transport options would appear to be evidence of design.

I am aware of the fact that membrane transport isn't considered an irreducibly complex system - not even, I would hazard, by the most ardent creationist, let alone by the ID camp. The point I am making is that the conclusion drawn by Matzke is dependent upon, but also conceals, his presuppositions.

Co-option - evidence of design?

Snatching a few minutes to post ...

Thanks to those people who have commented - positive and negative - it's great to have some thought-provoking debate stirred up following what I have written.

Tim posted a link to this paper, by Nick Matzke, relating to a proposed evolutionary pathway for the bacterial flagellum. I read this - it took some time, it runs to 58 pages (including lots of references), and my biochemistry isn't brilliantly up-to-speed - but I got there. My initial thoughts are that William Dembski has given an appropriate response to the paper. He highlights the fact that Matzke has in fact failed to achieve what he set out to achieve - a testable, verifiable model for flagellar evolution - but he has gone some way further than has been achieved by previous writers.

However, there was one particular aspect I wanted to comment on, and this was the issue of co-option. The idea of co-option is that a biochemical system (one or more proteins), used in one context, finds a use in another context following a minor modification. It is widely assumed to be a "Get out of jail free" for darwinist evolution - a means of avoiding the improbability barriers of coming up with new proteins from random sequences of DNA. For example, Matzke writes:

The hypothesis that the entirety of a primitive F1F0-ATP synthetase may have been coopted in toto into a primitive gated pore (proto-FliF and proto-FlhA/B) is certainly provocative; it would explain at a stroke the origin of most of the type III export apparatus and provide a phylogenetically basal precursor to the flagellum even though clearly basal type III secretion systems remain undiscovered.

My comment is: how improbable is this sort of event? Because it is certainly a specified event - in this case, it is necessary for an existing biochemical system (F1F0-ATP synthetase) to be co-opted to an entirely new role (proto-FliF and proto-FlhA/B). Of course, it isn't necessary that a specific protein is suitable for doing this, but it is necessary that a protein is available to do this. So there has to be a protein somewhere in the cell that will provide the primitive functionality that is required, that is the right shape to "fit" where it is needed, and that is expressed at the right time.

These probabilities could be estimated - what proportion of proteins are the right shape to fit on the gated pore? What proportion of proteins in the organism would provide the desired functionality? Is it possible to estimate the proportion of proteins that have ATP-synthetase activity that would also have the shape and size appropriate to provide this functionality. It would be possible to compare these probabilities with the number of opportunities available to bacteria, to determine whether this co-option event is feasible.

The probability is significant. Dawkins pointed out in (I think) "The Blind Watchmaker" that you couldn't have too much improbability, and Dembski's work on the Universal Probability Boundary effectively extended this. You can't rely over and over again on highly improbable events as an engine of evolution. What I am getting at, I guess, is that if co-option events turn out to be pretty improbable, then rather than being a handy tool that would allow evolution to progress, they would actually turn out to be evidence of prior design - design would be a more reasonable explanation of them than "lucky old evolution".

There are proponents of "front-loading" over at Telic Thoughts. They argue that one of the mechanisms by which evolution* proceeds is by information included in organisms at the start of the evolutionary process. If co-option is an improbable event (as it seems quite likely to be) then it would be the sort of event that would be likely to mark out front-loading, rather than a purely darwinian process. If it turns out that proto-F1F0-ATP synthetase is incredibly well specified for its role in the proto-bacterial flagellum, that wouldn't be evidence for darwinism at all.

Whilst I'm writing, and since my last post was on abiogenesis, I wanted to take the opportunity to draw readers' attention to the fact that (doubtless influenced by my post!!) David Berlinski has written an essay for Commentary on abiogenesis - which gives some idea of the problems associated with this field that is apparently completely unrelated to evolution.

* Please note the distinction here between evolution and darwinism. There are many proponents of ID who are happy with the idea of evolution but who don't accept darwinism.

In haste

Not much time for posting last week, and I can't see that changing this week, either - not even time to interact with the discussion on the previous post (43 comments! A record!). I will get back to it - there are a couple of very important threads to the discussion that will continue my journey into ID and evolution.

In the meantime, let me just post a link to Telic Thoughts, who have a post about labelling and propaganda, which covers familiar ground from a new angle.

I also wanted to re-emphasise the undisputed point made below - darwinism (the naturalistic explanation of how life develops) insists that it doesn't explain abiogenesis (the explanation of how life appeared). I'm not advocating a "God of the gaps" argument, but the fact that darwinism doesn't explain something that requires explanation (and which I would argue that "the man in the street" assumes it does explain) is significant.