Wednesday, August 29, 2007

Behe on Miller on Behe

Richard Dawkins, in "The God Delusion", encourages people to read what Ken Miller says about Michael Behe. The declared reason for this is because Ken Miller is both a Christian and a Darwinist. He is one of the "duty darwinists" employed by the media - both non-technical and technical - when they want to thump somebody with a teleological perspective. Arguably, since Dawkins shows little apparent understanding of what Behe has actually written, perhaps he feels out of his depth and is hoping that other scientists are able to offer a more convincing refutation.

Ken Miller wrote a review of "The Edge of Evolution" in Nature. Michael Behe's response to that review can be found in two posts on his Amazon blog, here and here. It is possible to infer from Behe's comments that Miller places his desire to see darwinism triumph ahead of the Christian principles of honesty and charity.

Thursday, August 23, 2007

Seven tips for atheists

From Richard Bewes, here.
5. Show us your virtues

It would be a help if you can show us around atheistic youth clubs and camps and summer houseparties and any work you may be doing among orphans; let’s see your family and play groups, and community centres.

Could you take us on a tour of your work among the down-and-outs and the homeless, and your equivalent of the Salvation Army’s soup kitchens? And your centres for Aids sufferers? And the hospice movement – had you thought of getting any homes established, and staffing them yourselves?

And – if we can be really adventurous – take us abroad for a peep at your leprosariums? I remember meeting Dr. Dennis Burkitt (of the Burkitt Lymphoma fame) out in Tanzania. He told me that he had been all over the tropics. Every single one of the leprosy hospitals he had ever visited were begun and run by Christians. Surely there must be one, run by an atheist organisation?

You see, I’m not absolutely sure that we have seen all that you have done, or could do, for suffering humanity. It’s only my tip….
Well, it cheered me up, anyway ....

Wednesday, August 22, 2007

Suppose for a moment ...

... that Dawkins is wrong when he says that teaching children about God is child abuse. Suppose that there actually is a god, and children were being brought up to be closed-minded to the possibility.

Wouldn't that be child abuse?

Del Ratzsch gets ID

From "Nature, Design and Science", on Behe:
Michael Behe in Darwin's Black Box has been widely misunderstood ... as holding a [God of the] gap account for what he calls "irreducible complexity." His conclusion from that is not that nature could not produce irreducible complexity, but that if (perhaps since) nature has produced it then Darwinianism (as gradualist and selectionist) is simply wrong. (Behe does not even necessarily reject common ancestry - that is not really his issue.) I do not believe that Behe wishes to rule out supernatural intervention, but it is not essential to his more basic contention, which is that certain types and degrees of complexity (irreducible complexity) in and of themselves constitute evidence for design regardless of how they were produced.
(Notes on Design in Nature, p.187)
And on Dembski:
... imagine that we have a complete causal explanation back to the Big Bang of the present moon crater jumble, an objective measure of inherent complexity of the jumble array, and that we know the probability of precisely that jumble being produced. Now, without changing any of that, imagine that we discover that the present jumble in actual fact spells out "John 3:16" in Martian script. With no changes in causal history, degree, or type of inherent complexity, the special mind correlativity now visible gives the case a vastly different complexion. On the other hand, suppose that human written language had developed in totally different directions, so that the inscription "John 3:16" carried no meaning whatever. In that case, nature's generating of that pattern in moon craters would have generated no surprise at all (or at least much less). Obviously, the unexpected match between our inscripted language and nature's production is a key element of the situation. This is related to the concept of specification in William Dembski's The Design Inference. It seems to me, however, that Dembski never gets beyond a purely formal indication of specification, which leaves the term without any of the content necessary to support actual design conclusions.
(Notes on Design in Nature, p.187)
Which seems to be the objection that many other people have to Dembski - or one of them, to be more precise. In defence of Dembski at this point, I think it may be worth saying that he has regarded his work hitherto as representing a mathematical foundation for more applied investigation into systems - biological or otherwise - and it is possible to see at least in principle how the idea can be applied. Indeed, I started doing just that for both biological systems and random texts, but my lack of time and my limited grasp of the maths somewhat hampered me. Nonetheless, I would suggest that, given Dembski's rules about probability boundaries, my proposition that a gene must initially code for a protein which is less than 7000 amino acids long is a non-trivial example of a prediction based on his theoretical work.

Tuesday, August 21, 2007

Del Ratzsch - an alternative to Dawkins

I've been reading "Nature, Design and Science", by Del Ratzsch. It's not an easy read. Ratzsch is a professor of philosophy, so this book is formal and careful, where "The God Delusion" is conversational but correspondingly casual. However, almost every paragraph has weight.
There is a widely held, vague supposition that the discovery that a phenomenon is purely natural removes any prospect of its being designed. That something is a product of unaided nature [Ratzsch terms this "pronautral"] does entail that its history does not involve any intervention into the historical course of the cosmos (i.e., that it is neither artifact nor natrifact [a term he uses for phenomena that are part of nature but which show signs of supernatural intervention]). But sinceboth the pronatural and the natrifactual can be intended results of agent activity deliberately aimed at producing the manifested patterns, the distinction between them is not one of presence or absence of designedness. Discovering a wholly natural process for producing some phenomenon in nature entails only that if it is designed, the relevant agent activity is primordial.

This distinction between design resulting from intervention and design produced by the unaided outworking of initiating structures has an extremely long history. Bacon, for instance:

God ... doth accomplish and fulfil his divine will [by ways] not immediate and direct, but by compass; not violating Nature, which is his own law upon the creation.

And in Whewell one finds explicit recognition of some of the implications - for example, that discovering purely natural processes for producing phenomena does not entail absence of design, but would involve a shift in the location of agent activity:

We have shown, we trust, that the notion of design and end is transferred by the researches of science, not from the domain of our knowledge to that of our ignorance, but merely from the region of facts to that of laws.

It is worth noting that both of the above quotes predate 1859. Contrary to common myth, this move was not simply and ad hoc attempt at salvaging some bit of design, while in forced retreat from Darwin.

In the absence of primary marks, there are relatively few means by which designedness could be identified. One of the possibilities is agent-initiated communication ....
Nature, Design and Science p.55
So much, in such a short extract. A couple of quick thoughts - I still have much reading to go, and I don't know where he is taking all this yet. This relates more to a deistic designer, rather than a theistic one. However, he is making the philosophical point already that whether or not there is empirical evidence for a designer does not necessarily have a bearing on whether such a designer exists, or is necessary. This is an answer from a philosopher to those people who say, "Show me the evidence".

This understanding of the nature of the universe doesn't logically rule out agent intervention in the universe - it just suggests that there may be no direct evidence of agent intervention in observable and measurable phenomena.

The last sentence is a bit of a teaser. Schaeffer covers similar ground in an essay called "Is propositional revelation nonsense?" - and the Bible makes a similar point, of course. Why would such a designer make himself invisible? Perhaps the nature of the universe is such that people will naturally look for a designer - it looks artifactual - something acknowledged by Dawkins (the word he uses is "designoid"). And if we are looking for a designer, but the evidence from the universe is ambiguous (why should there be so much evil and suffering, for example?) then perhaps we need a clearer self-revelation. Okay then, so let's look for one ....

Sunday, August 19, 2007

Shades of Carey

For me, one of the highlights at the Carey Family Conference concert this year was Mark Troughton, pastor of York Evangelical Church, singing a bossa nova in Portuguese, with simultaneous translation by Andrew King, in the style of Peter Cook. (Mark later confided that he didn't actually speak Portuguese - a fact that didn't inhibit his performance in any way.)

This works the other way around, as well - here's a video of "Breathe Your Name" by Sixpence None the Richer, with Portuguese subtitles ....


Explanatory note

From Wikipedia.
Oolon Colluphid är en person i Douglas Adams trilogi i fem delar om Liftarens guide till Galaxen, en debattör och författare som nämns som referens i en klassisk passage om hur framgångsrik Liftarens guide till galaxen är, i den text som i bokversionen av Adams verk är första bokens prolog.

(Liftarens guide till galaxen har...) "blivit mer populär än Den himmelska husmoderns alltiallo, mer såld än 53 tips för tyngdlösa och mer omdebatterad än Oolon Colluphids trilogi av filosofiska kvartersbomber: När Gud gjorde bort sig, Ytterligare några av Guds klavertramp och Vem i hela friden är Gud egentligen?

Saturday, August 18, 2007

Who is this Oolon Colluphid person anyway? - More on "The God Delusion"

See "Where Oolon Colluphid Went Wrong" and "Some More of Oolon Colluphid's Greatest Mistakes". The next section of the chapter “Why there almost certainly is no God” is entitled “The Worship of Gaps”, and it is in this section that Dawkins chooses to engage more directly with Behe, rather than in the section that was named after the concept that Dawkins acknowledges Behe named. This is itself something of a rhetorical ploy, of course. The idea of a “God of the Gaps” is of course theologically dubious, at best, and to implicitly mislead readers about what Irreducible Complexity is (as Dawkins does in the previous section by not engaging with what Behe wrote) and then imply that Behe is “worshipping gaps” (as he will do in this section) looks to me like a none-too-subtle attempt to discredit what Behe wrote without Dawkins having to actually do any of the dirty work of engaging with it himself.

Now if, like me, you post things on the internet, you expect that if you get something wrong – or even just don't make something clear – then somebody will come along and tell you so, especially if the issue is a controversial one. One would have thought that higher standards would be observed if somebody is going into print – obviously with publication of papers, but as much so with books. Unless, that is, you are telling lots of people what they want to hear. I really can't think of any other way of explaining the fact that Dawkins fails to fairly represent Behe's work.

I want to react to just three sentences from this section.
The speedy resort to a dramatic proclamation of 'irreducible complexity' represents a failure of the imagination. (TGD p.154)
This is, of course, correct to an extent. Indeed, Behe would agree with him – and there are no such speedy resorts to dramatic proclamations in Darwin's Black Box (DBB). Further, contrary to Dawkins' implication, no physiological structures, such as the eye or the weasel toad's elbow, are labelled as irreducibly complex by Behe. (No, Dawkins doesn't say that he does – he just spends a great deal of energy pointing out how such labelling would be wrong, giving the impression that this was what Behe had done.) Indeed, at the start of DBB, Behe specifically makes the point that he is not concerned with the gradual evolution of such structures. The concept of irreducible complexity is carefully defined (see below), related only to biochemical systems, and guardedly applied.

However, Dawkins' sentence is also misleading from a scientific point of view. An excess of imagination is not entirely a good thing for a scientist. Science is not simply story-telling – a story explaining how the multicellular organism got its immune system should not be a far-fetched “just-so” story. It has to be scientifically plausible. It is possible to write explanations of all sorts of complex observed phenomena, but more difficult to establish whether the descriptions provide a feasible or probable explanation. It seems to be considered an adequate scientific explanation if it is simply conceivable. In terms of the sort of biological structure that Dawkins is particularly interested in, it's worth reading this paper discussing different models for the evolution of the giraffe's neck. This post, however, is not the place to discuss such things. Suffice it to say that the speedy resort to a dramatic proclamation of 'scientifically explained' may represent in some cases a surfeit of imagination.
Without a word of justification, explanation or amplification, Behe simply proclaims the bacterial flagellar motor to be irreducibly complex. (TGD, p.158, emphasis in original)
This is incorrect. Behe defines quite carefully what he means by irreducible complexity. The concept itself is not hard to understand, and it was the fact that I quickly understood it that resulted in my being convinced that DBB made a compelling case. A biochemical system, Behe explains, is irreducibly complex if it contains multiple components, the absence of more than one of which would result in loss of functionality of the system. The bacterial flagellum was considered by Behe to be irreducibly complex because he claimed that removal of, or damage to, any of a number of the constituent proteins, would impair the flagellar function. Why is this significant? Because the system evolved from a state where those components were not originally present. If more than one component is essential to the operation of the system, then there is no selective advantage to the addition of one of the components without the simultaneous addition of the other essential ones. The simultaneous, random addition of two components is too low probability to be considered realistically possible.

This is substantially different from Dawkins' conception of “50% of an eye being more useful than 49%”, although there is little to suggest that Dawkins particularly understands this. Dawkins seems to view biological systems as evolving from monolithic sequences of DNA. To illustrate this, consider a random sequence of say 1000 letters, which has to mutate using Dawkins' METHINKS program into an English text. His argument is that if 510 letters are correct (51%), this is more accurate than 500 (50%), and so the more accurate version would have a “selective advantage”.

Behe's model is different. He argues that a biochemical system is more like a sequence of 1000 letters that actually breaks into 10 groups of 100. For the system to work, not only does each group of 100 letters have to make sense separately, but also until all of the groups make sense, the whole system has no function, and can't therefore provide anything that offers a selective advantage.

The discussion relating to the flagellum has moved on substantially from here since DBB was published. I won't go into that here, although to an extent, it follows below. The point I want to make is that this statement of Dawkins is simply not true. Behe does provide justification, explanation and amplification. Dawkins might not have bothered to read or been able to understand all of DBB: that doesn't mean that the rest of it doesn't exist.
The key to demonstrating irreducible complexity is to show that none of the parts could have been useful on its own. (p.158)
This relates to how the discussion about irreducible complexity has moved on since the publication of DBB, but this statement itself is also incorrect. The key to demonstrating irreducible complexity is to show that parts can't be removed without loss of functionality of the system – that is what irreducible complexity is. What Dawkins is talking about here is something different. A system may be irreducibly complex, but an evolutionary way around this can arguably be found if one or more of the required proteins is already present in a cell. If this is the case, it is possible to conceive of these proteins being co-opted to a new function. So whilst a biochemical pathway may irreducibly depend for its function on eight or twelve proteins, if proteins similar to those required are present in the organism already, then it is suggested that they could be relatively easily co-opted to their new role.

This does represent a hypothetical way forward, and to see what this might look like in the context of the bacterial flagellum, check out Nick Matzke's paper “Evolution in Brownian Space” – it goes some way further than Ken Miller's comments about the Type Three Secretory System that Dawkins refers to. However, just as Behe must be careful about labelling systems as irreducibly complex, I really think that the claims made for this means of getting around IC should be more guarded. To the best of my knowledge, there are few proteins that can definitively be said to have been co-opted to new roles. And an infinite regression can't be hypothesized – at some stage, new proteins have to be generated from scratch; new gene control mechanisms produced; new means of co-ordinating the function of groups of proteins to make biochemical systems need to be derived.

In short, Dawkins fails to go even as far as other researchers have in interacting with Behe in his book, and gives the impression either that he doesn't understand Behe's work, or that he is deliberately trying to misrepresent it to his readers.

Finally, all of this debate about irreducible complexity is, in a sense, yesterday's news. Behe's more recent book, “The Edge of Evolution”, suggests that undirected evolution is in any case able to achieve far less than the production of an irreducibly complex system. He has not backed away from irreducible complexity; he has strengthened his claim. As with DBB, most interaction with Behe's latest book – including Dawkins' own review of it in the New York Times – fails to get to grips with the issues it raises.

Tuesday, August 14, 2007

Well, that about wraps it up ...

... for Darwinism, then.
Natural selection based solely on mutation is probably not an adequate mechanism for evolving complexity.
(National Research Council, "The Limits of Organic Life in Planetary Systems"

Comments on Jennifer Government by Max Barry

What does your dystopia look like? The two most famous are probably those of Orwell (“Nineteen Eighty Four”) and Huxley (“Brave New World”). Max Barry offers another dystopic vision in “Jennifer Government”.

Here, it is the corporations who are all but sovereign – their relationship with government an uneasy balance of power, government being no more than another consumer choice. The police provide a service that can be paid for, as for that matter do the National Rifle Association. People bear their employer's name as a surname – John Nike joins the roll of great villains, a ruthless man who seeks to transcend even his own corporation. Jennifer Government is the “straight cop”, trying to prevent the corporations getting out of hand, but even her daughter has the surname “Mattel”, as she is in a school sponsored by the toy manufacturer. (Preferable, she feels, to the Macdonalds school....).

The heart of the story is a fictional promotion of urban footwear, in which some rogue Nike employees decide that nothing will make a particular range of trainers more desirable than assassinating a few of the people who own them. Hack, a much lower-level employee within Nike, finds himself the person tasked with carrying out this contract – but in a fit of conscience, he goes to the police, which leads to them offering to carry out the contract on his behalf. So far, so good – Nike, or more specifically, John Nike, goes from strength to strength, whilst Jennifer Government seeks to identify and make accountable the person who did this, as she tries to balance the needs of her patient, lonely daughter.

The book is an enjoyable read, though the number of characters is perhaps a little unwieldy. It reminded me of early Ben Elton (“Gridlock”, “Stark”) without the diatribes. I can't really disagree with those reviewers who suggest that it was written with a TV or film version in mind, though given the control of those media by corporations, one wonders how likely it is that this would ever be made! Also, sympathetic characters are somewhat light on the ground. This doesn't take away from a page-turning story, though, and if you are looking for a lightish read that fits ideologically with the reaction against consumerism, following a couple of months of reading Al Gore or Gore Vidal, this could be the book for you.

Max Barry's website is here, and here's a link to the Nationstates website, a semi-humorous country-management game which was where I first heard about Jennifer Government.

Monday, August 13, 2007

Plantinga on Dawkins

A more highly tuned philosophical mind than mine turns its attention to "The God Delusion" here.
Now despite the fact that this book is mainly philosophy, Dawkins is not a philosopher (he's a biologist). Even taking this into account, however, much of the philosophy he purveys is at best jejune. You might say that some of his forays into philosophy are at best sophomoric, but that would be unfair to sophomores; the fact is (grade inflation aside), many of his arguments would receive a failing grade in a sophomore philosophy class.

Tuesday, August 07, 2007

Theology of evolution/creationism/ID

(H/T Telic Thoughts, as usual)

A post here about some of the theological implications of evolution/ID/creationism. I guess I would agree with the theology of the original article. It is worth pointing out, however, that just because the media version of the creationist/ID God is limited by assumptions of deism doesn't mean that mine ever was. I have been pointing out for some time, for example, that the designer doesn't logically require a designer, so the "who designed the designer?" question need not be well-founded.

Good points, well made. However, since theology is "study without an object" and "the emperor has no clothes", I have little doubt that the article and review will stir no interest amongst the new atheists, those people who might have most to gain from reading it.