Wednesday, August 23, 2006

What does the quote mean...in context?

I like to think that I am reasonably good at working out what someone meant when they wrote a particular piece of text. For those who think that I am defending the undefensible I include the preceding two paragraphs from the paragraph which Judge Jones and the Anti-ID-ers made so much of so that you can see for yourself the precise context in which it was made.

Another paper that gamely tries to account for a piece of the immune system is entitled "Evolution of the Complement System." Like the paper discussed above, it is very short and is a commentary article-in other words, not a research article. The authors make some imaginative guesses about what might come first and second, but inevitably they join Russell Doolittle in proposing unexplained proteins that are "unleashed" and "spring forth" ("At some point a critical gene fusion created a protease with a binding site for the primitive Cab"; "Evolution of the other alternative pathway components further improved the amplification and specificity"; and "C2, created by the duplication of the factor B gene, would then have allowed further divergence and specialization of the two pathways"). No quantitative calculations appear in the paper. Nor does an acknowledgment that gene duplications would not immediately make a new protein. Nor does any worry about a lack of controls to regulate the pathway. But then, it would be hard to fit those concerns in the four paragraphs of the paper that deal with molecular mechanisms.

There are other papers and books that discuss the evolution of the immune system. Most of them, however, are at the level of cell biology and thus unconcerned with detailed molecular mechanisms, or else they are concerned simply with comparison of DNA or protein sequences. Comparing sequences might be a good way to study relatedness, but the results can't tell us anything about the mechanism that first produced the systems.

We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.


Now you can decide for yourselves whether I have understood this particular piece of text when I say that the three things that Behe is looking for are:
1. Quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means.
2. Acknowledgement that gene duplication is different from new protein production.
3. Mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways.

9 Comments:

Anonymous Hrafn said...

Andrew: the fuller context does not support your interpretation.

1) Behe applied his "three prongs," in the first paragraph, to only a single article. This therefore provides no rational basis for interpreting the conclusion, which deals with all articles on the evolution of the immune system in the narrow context of these three prongs.

2) The first paragraph and the conclusion are seperated by a paragraph that makes no mention of the three prongs.

3) The first paragraph makes no mention of "answers" and the conclusion makes no mention of the three prongs - meaning that there is no tie between the two paragraphs other than the general flow of the argument (which as I have shown in (2) loses the three-prong thread entirely before reaching its conclusion).

4) When questioned about his conclusion in the Dover trial, Behe made no effort to tie them to his three prongs.

The inescapable conclusion is therefore that there is no evidence whatsover to support an interpretation of "no answers" to mean "no answers to the three prongs."

3:09 am  
Anonymous Matt Inlay said...

I agree with hrafn, the three prongs you keep mentioning were specific to the article Behe was describing in that paragraph.

I believe Behe brought up two articles in that section that he claimed were representative of the whole. However, both articles were commentaries, and not research articles. A significant portion of the 58 articles were published before DBB. Why didn't Behe read any of those? Since the two commentaries, "Molecular evolution of the vertebrate immune system" and "Evolution of the complement system", have titles that sound like definitive articles, Behe chose them based on a quick literature search.

I think it all boils down to what are considered "answers" to the question of the origin of the immune system. I would think that a model, developed over the course of the last 30 years, containing a number of details, that has been tested repeatedly and passed those tests, would constitute some answers.

4:01 am  
Blogger Andrew Rowell said...

hrafn,

Given that the second paragraph clearly states that Behe is looking for "detailed molecular mechanisms" and the first paragraph indicates in more detail what these are with a specific paper it seems entirely disingenuous to be that you make the kind of argument that you do.

I am entirely unpersuaded by your logic here. Behe has given us a detailed explanation of what he is looking for in para 1. In para 2 he explains he is looking for "detailed molecular mechanisms" and not simply DNA/Protein comparative studies. The para in question immediately follows. To disconnect it from the previous two in the way that you and others are doing would be shouted down (entirely legitimately) as quotemining if any
ID proponent used a piece of text from Gould or Dawkins in this way.

If you give me the reference to to the part in the trial where Behe gives his own evidence that I have understood him incorrectly then I would happily concede to his interpretation of his own words publically.

8:03 pm  
Anonymous Hrafn said...

"Given that the second paragraph clearly states that Behe is looking for "detailed molecular mechanisms" and the first paragraph indicates in more detail what these are with a specific paper it seems entirely disingenuous to be that you make the kind of argument that you do."

Andrew, I did not claim that the second paragraph was unrelated to the first, merely that it did not in any way continue the thread of the specific "three prongs" that could even conceivably lead them to be intended to be read into the meaning of "no answer."

It is your claims and your incompetent attempt at a rebutal that is "disingenuous"!

"To disconnect it from the previous two in the way that you and others are doing would be shouted down (entirely legitimately) as quotemining if any
ID proponent used a piece of text from Gould or Dawkins in this way."


No! It is not "quotemining" to expect a concluding paragraph to state its conclusion clearly and unambiguously, and to explicitly contain any qualifications or caveats. If they don't then they quite simply fail to perform the role of a "conclusion," in that they do not reach an endpoint but simply point back to the preceeding argument.

Behe concluded "no answers" without qualification or caveat, so "no answers" can, will and must mean "NO ANSWERS"!

4:08 am  
Anonymous Hrafn said...

"49 6 Q. We'll get back to that. Now, these
7 articles rebut your assertion that scientific
8 literature has no answers on the origin of the
9 vertebrate immune system?
10 A. No, they certainly do not. My answer,
11 or my argument is that the literature has no
12 detailed rigorous explanations for how complex
13 biochemical systems could arise by a random
14 mutation and natural selection and these
15 articles do not address that."


Note that in his testimony, Behe explicitly indicated that he meant "no answers" to mean "no detailed rigorous explanations" (which is, I suspect, a reasonable definition, but one which the available literature does provide "answers" for) and made no mention of his "three prongs."

If you wish to claim that Behe meant "no detailed rigorous explanations" to equate to "no answers to his three prongs" you would have to prove that Behe purports them to be a general criteria to evaluating all articles, not an ad hoc framework for criticising a single article.

Has Behe mentioned these "three prongs" anywhere other than in the context of this single article? Are they even sufficiently generalised a set of question that they even can be applied to any article on the evolution of the immune system (let alone were intended to be)?

4:24 am  
Blogger Andrew Rowell said...

Hrafn,

Thanks for that section of the transcript.
Here he tals about:
"no detailed rigorous explanations"

In DBB he gives an example for a particular review paper of what he is looking for.

You are right that there may well be other prongs in his "detailed and rigorous" He is clearly qualifying what he meant by "no answers"

I think that you are expecting too much from a concluding paragraph in an argument. Obviously Behe is the best interpreter of what he means by his writing but given the context I still think that you are divorcing that section too radically from the previous two.

7:06 pm  
Anonymous Hrafn said...

"Here he tals about:
"no detailed rigorous explanations"

In DBB he gives an example for a particular review paper of what he is looking for. "


And here you have the crux of the problem Andrew! Behe is looking for detailed explanations in a review paper! THIS IS BLATANTLY DISINGENUOUS!

"Obviously Behe is the best interpreter of what he means by his writing but given the context I still think that you are divorcing that section too radically from the previous two."

No, Andrew. I have not "divorced" the conclusion from the immediately prior paragraph, which makes no mention of your "three prongs." It is you who is attempting to hard-wire a link to the wording of the first paragraph, ignoring the second (which makes no mention of it).

And you have ignored my questions:
Has Behe mentioned these "three prongs" anywhere other than in the context of this single article? Are they even sufficiently generalised a set of questions that they even can be applied to any article on the evolution of the immune system (let alone were intended to be)?

1:44 pm  
Blogger Andrew Rowell said...

Hrafn,

There is no contradiction between detailed explanation and a review. Reviews should distill the relevant details from many papers to build up a larger story.

Sorry to ignore your question.
"Has Behe mentioned these "three prongs" anywhere other than in the context of this single article?"

Not that I am aware of. Probably I overdid the emphasis on them and probably you are right that they are not sufficiently generalised. However they do give us a flavour of the sort of thing that Behe is looking for and which he maintains is absent from the literature.

He may be right or wrong. That is what I am trying to make up my mind about in questions to Matt and Ian. Is that OK?

7:01 pm  
Anonymous Hrafn said...

"There is no contradiction between detailed explanation and a review. Reviews should distill the relevant details from many papers to build up a larger story."

Baloney! Review articles necessarily sacrifice depth for breadth. They cannot, while still keeping to a readible length, cover all the details of the research articles they review. They provide an overview of the state of research and, quite reasonably, expect anybody wanting more detail to read the reviewed articles for themselves. I honestly cannot see any reason why Behe has not done this.

"That is what I am trying to make up my mind about in questions to Matt and Ian. Is that OK?"

It is. I was only objecting to equating "no answers" to "no answers to the three prongs." Equating it to "no detailed rigorous explanations" seems reasonable, and I will leave Matt and Ian to provide evidence that such explanations exist (noting however my disbelief, stated above, that Behe himself has made reasonable efforts to discover whether such detailed explanations exist).

3:48 am  

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