Saturday, 25 August 2007

Life, The Universe and Quote Mining

A blogosphere acquaintance of mine, Paul, has in my opinion recently outdone himself on the old quote-mining front. A record has been set for the depth plumbed but he has not stinted on the quality of the mine works and the mine walls are securely propped with misunderstanding and omission and, just like the mines of Moria, the walls glitter with half hidden bits of logical argument. I will show you what I mean.
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.
Dawkins actually tells his readers that God of the Gaps is considered unreliable by theologians. Didn't you read that bit Paul?

Behe's whole argument is one of trying to shoe horn a gap into biology where none exists. His argument attempts to prove that something could not have evolved. He has widely been shown to have done no such thing.

Where is this implication that Behe worships gaps? Paul neglects to give us this. In fact Dawkins hasn't even mentioned Behe's name yet. Didn't you read that Paul? How can Dawkins being implying something about Behe's argument when Behe hasn't even been named yet?

Bear in mind that Dawkins' book is about God not biology and also bear in mind that he has written several books directly addressing the litany of claims that this, that and the other could not possibly have evolved. I am left wondering on what basis Paul thinks that Behe's bogus molecular biology claims deserve special treatment.
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.
Cough, perhaps because it is bogus? Cough.
I want to react to just three sentences from this section.
Wow. He might as well as said, "Lets go into full quote mining mode here. . . "
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.
Once again Paul demonstrates a remarkable ignorance of the history of such claims of "irreducible complexity", "unevolvability", and straightforward "incontrovertible proof of creation" which stretches back over many many years. It is this which Dawkins is addressing, Behe has not even been mentioned by name yet.

So is Paul denying Dawkins account of the history of such claims? No he was simply saying they don't apply to Behe despite the fact that Dawkins wasn't applying them to Behe anyway.

Leaving aside the fact that Paul claims these arguments don't address Behe's points when Dawkins wasn't addressing Behe's point anyway, why does Paul think that Dawkins should be spending more time on Behe? I can understand that Paul would not want people to know that Behe is just the latest in a long line of such claimants, all of which have been shown to be false. But remember that Dawkins at this point hasn't even mentioned Behe's name. So Pauls claim that Dawkins is somehow inaccurately implying Behe's position is false.

Lets put Dawkins into some of its context - after all taking it out of context is the essence of Paul's "argument";

After some history of creationist claims he gives us a subtitle "The Worship of Gaps" and this introductory paragraph;
Searching for particular examples of irreducible complexity is a fundamentally unscientific way to proceed; a special case of arguing from present ignorance. It appeals to the same faulty logic as 'the God of the Gaps' strategy condemned by the theologian Dietrich Bonhoeffer. Creationists eagerly seek a new gap in present-day knowledge or understanding. If an apparent gap is found, it is assumed that God, be default, must fill it. What worries thoughtful theologians such as Bonhoeffer is that gaps shrink as science advances, and God is threatened with eventually having to nothing to do and nowhere to hide. What worries scientists is something else. It is an essential part of the scientific enterprise to admit ignorance, even to exult in ignorance as a challenge to future conquests. As my friend Matt Ridley has written, "Most scientists are bored by what they have already discovered. It is ignorance that drives them on." Mystics exult in mystery and want it to stay mysterious. Scientists exult in mystery for a different reason: it gives them something to do. More generally, as I shall repeat in Chapter 8, one of the truly bad effects of religion is that it teaches us that it is a virtue to be satisfied with not understanding.
Paul goes on to claim;
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.
Here Paul flirts with the truth, invites it out on a date but then stands it up at the last minute. Perhaps he even lurks about across the street and points and laughs at truth with his "finely tuned theological brained" friends as she waits patiently for him to show up.

It is the creationists argument that they have proved that something is impossible. Science relies on the many, many independent lines of evidence which support the Theory of Evolution Paul.

It is you who impose the false dichotomy, "either prove Behe wrong or it must be god".

Yes Behe's claims have been shown to be bogus.

It is you who ignores the multiple independent lines of supporting evidence for the Theory of Evolution.
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.
Lets just pop Paul's extract back into context to reveal the answer to Pauls comments shall we? (this is too easy);
Without a word of justification, explanation or amplification, Behe simply proclaims the bacterial falgellar motor to be irreducibly complex. Since he offers no argument in favour of his assertion, we may begin by suspecting a failure of his imagination. He further alleges that specialist biological literature has ignored the problem. The falsehood of this allegation was massively and (to Behe) embarrassingly documented in the court of Judge Jone E Jones in Pennsylvania in 2005, where Behe was testifying as an expert witness on behalf of a group of creationists who had tried to impose "intelligent design" creationism on the science curriculum of a local public school - a move of "breathtaking inanity" to quote Judge Jones (phrase and man surely destined for lasting fame). This wasn't the only embarrassment Behe suffered at the hearing as we shall see.

Dawkins goes on to detail the scientific reasons why even the theoretical basis for a claim of irreducible complexity is flawed as it ignores pre-adaption or aptation.

Paul seems to have casually ignored these points.

In fact Paul we now have your "quote mining technique" laid out before us.
  • Take a sentence out of context (let us say that it was originally part of argument for X).
  • Point out why it doesn't work as part of an argument for Y.
  • Ignore the real point it was making i.e. argument for X.
  • Continue to ignore the answers to the argument for Y in your discussion of the argument against Y anyway.
  • Keep your fingers crossed and hope that nobody reads the comment you have extracted in its full context.
Paul then makes some more breathtaking leaps;
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”.
Well yes Paul this is an analogy with the selective pressures artificially defined at the outset. And your point about the real world is . . .?
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.
As we already said this just casually ignores pre-adaption, which in essence shows us that these 100 letter groups have evolved themselves with their selective pressures in different circumstances. So the small step can now be these things inter-reacting.

In plain english ,and using the mousetrap analogy Behe is so fond of himself, which consists pf a piece of wood a spring a catch etc. The point is that Behe just assumes that there are no other uses for bits of wood springs and catches at all. See Behe on Colbert for a hilarious recantation of this argument.

Paul continues with this;
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.
Yes but evolution is about how things evolve Paul. Not about how you can or can't take them apart.
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.
Paul, hypothetical way forward, in this context means irreducible complexity is dead. Irreducible complexities sole claim is that there is no hypothetical way the evolution of this or that can be explained. This hypothetical way forward shows you how that can happen in theory. In other words you say it is impossible and science says well yes impossible apart from this possible way here.

Something can't be partly impossible Paul.
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.
Dawkins book is about god. He doesn't tackle the biology as much as other authors in biological contexts? Surprise surprise. Not a strong point Paul.
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.
Well yes Behe does seem to have abandoned the flagellar motor now doesn't he. Add it to the long, long list of gaps that creationists worship until science peeks in and shines the light of evidence.

2 comments:

  1. Er, I agree with Dawkins that "God of the Gaps" is theologically dubious. (It is, however, logically correct, as Del Ratzsch points out.) So I'm not sure what you're taking issue with there.

    The implication that "Behe worships gaps" comes because Behe's work is discussed in a section entitled "God of the gaps". I pointed that out. It isn't stated: it is an inference readers are invited to make.

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  2. Actually the god of the gaps argument is an often quoted example of the logical fallacy known as the argument from ignorance.

    Check it out.

    Your inference is very weak. I realise that Behe looms large in your own world view, but I think you would not argue that anything other than a small minority of Dawkins readers would have even heard of him.

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