Friday, August 25, 2006

System 2

Just a few thoughts after having read Matt Inlay’s response to Behe’s immunology chapter section 2.

The mechanism explaining the origin of a rearranging gene segment system to generate antibody diversity.

(CAUTION – I am a self confessed delusional crank with no immunology or evolutionary biology qualifications.)

As I understand it this is a summary of the best guess currently available for the origin of the gene rearranging system to generate variable antibodies.

1. A transposon became inserted either into a sperm cell, and egg cell or a very early embryo cell. Presumably at this stage it is a transposon that only becomes active in transcribed genes rather than having eukaryotic transcription control sequences. It must have initially integrated into an active gene in such a way that it could transpose when that gene was expressed. This is something that is presumably a selective disadvantage.

2. After jumping around the genome for x generations it happened to insert into an innate immune system receptor at the point where its eventual excision would cause variation in the antigen binding site and thus be an advantage to the cell. This is also presumably an exceedingly rare event.

At this point in the description the proposed pathway becomes very sketchy. By means of 4(or 5) genetic duplication events plus an incorrect recombination event we produce a set of variable antibody producing genes with heavy and light chains which fit together beautifully and a set of T-cell receptors using a similar process for a totally different function.

If this is the best that is currently available then I would agree with Behe that it is time someone got their act together or was ready to admit publically that at the moment we really have got lots of major problems explaining the origin of variable antibodies.

(Please note I am not intending to belittle Matt Inlay’s essay. I think he has done an excellent job explaining this to a non-specialist for the web. Thank you Matt!)

(Please note I am not intending to belittle the work of evolutionary immunologists comparing immune systems in different organisms and trying to put together a scheme for its evolution. I am very appreciative indeed of research immunologists. I am merely saying that this account is very sletchy indeed and for it to be convincing you need to already believe that it really did evolve without any intelligent input.)

(BTW are there different RSS sequences at the two join sites and different RAG proteins…what stops them getting muddled?)

Wednesday, August 23, 2006

System 1.

I have read and thought about the first part of Matt Inlay’s response to Behe’s Immunology IC (irreducibly complex) argument. This section is written to rebut Behe’s claim that a simple Antibody receptor system is IC.

Behe claims that there are 3 components each of which is needed for the system to function.
1. A membrane bound form of the antibody
2. Messenger system
3. Secreted form of the antibody.

As far as I understand Matt Inlay’s response he is saying that the whole system came as a working variant of some other 3 component system.

He suggests macrophage scavenger receptor, CD14, and Beta2 or hemolin (which is described in more detail.)

Thus Matt Inlay’s answer to the origin of this simplified antibody system is to pick another such system from those available, duplicate the genetic information and modify the relevant parts.

The problem with this answer is that it simply takes the IC issue somewhere else. You have to develop an example of one of these systems in the first place.

It is a bit like the Panspermia idea of Anaxigorus, Arrhenius, Hoyle and Wickramasinghe the origin of life issue is just taken somewhere else in the universe only in this case somewhere else in the genome.

Having looked (very briefly) at some of the control pathways for some of the suggested origins explaining their origin is indeed a matter of some difficulty. It is especially in the messenger and control pathways that the IC argument is I believe strongest.

What does the quote 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.

Behe and the Literature – Who is bluffing?

These series of Posts (here, here and here) started as a result of reading Behe’s response to the Dover legal opinion of Judge Jones.

As a result of the discussion one commenter pointed me in the direction of Matt Inlay’s essay responding to Behe’s immunology chapter in DBB.

In the paper he looks at three systems which Behe suggests exhibit IC (irreducible complexity) and provides suggestions as to how they could come about as a result of gradual step by step change (RMNS)

I had argued from the context of the much quoted claim “The scientific literature has no answers to the question of the origin of the immune system”

That Behe intended to be understood to be asking the following three questions:
1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

With regard to Matt Inlays essay we must conclude that there is no attempt to address question 1. (Anti-IDers I think respond by stating that this is asking for unreasonable detail…or even impossible detail.)
Question 2 is satisfied I am sure.
With regard to question 3 there is an attempt at least partially to address this issue.

Matt Inlay divides his essay into three sections with each section dealing with one of the claims for IC in the immune system.

1. The production of a clonal selection system
2. A rearranging antigen receptor.
3. The origin of the complement system.
I would like to go through these three sections seperately in following posts.

Matt Inlay I assume did not write his essay for research immunologists. It was focused at people with a reasonable background in biology who were interested in the response of immunologists to Behe’s arguments…. In other words for people like me who are ceratinly not immunologists!

Forgive me therefore if I demonstrate publically that I am not an immunologist!

Thursday, August 17, 2006

Unreasonable Detail?

The argument over whether Behe is asking for unreasonable detail regarding the origin of the immune system will be determined either way by how one defines “unreasonable.” We should I think acknowledge that this will be affected by whether we have a basically materialist/naturalistic view of the universe or not.

A naturalist will tend to look at homologies between systems in different organisms and be happy to take this as proof that evolution has occurred.

A ID sympathiser will tend to say that we need a clear possible pathway to explain these interconnected complex systems.

The Immunology Chapter in DBB has three sections arguing that the system contains irreducibly complex mechanisms.

1. The production of Plasma Antibody.

The process by which the randomly produced antibodies become bound on the membrane of the B-cell. The process by which the binding of the antigen to the surface antibody triggers the ingestion of the antigen/antibody complex. The process by which a fragment of a foreign protein become attached to the MHC protein. The interaction of the B cell with the helper T cell producing interlekin. The interaction of the interleukin with the B cell to produce plasma cells and free antibody.
Behe concentrates upon the production of a clonal selection system. The need for there to be a genetic connection between the membrane bound antibody and the genetic information coding for that antibody. There needs to be a message system to transmit ON signal from the surface to the antibody gene in side the cell.
Behe imagines a system of data transfer involving only one other protein (thus missing out the T cell/MHC interaction problem) He argues that such a system therefore has three ingredients
(a) The membrane bound antibody
(b) The exported form of the antibody
(c) The messenger protein.
This would constitute an ICS
Behe argues that even this simplified system needs all of these items to produce a properly working system even without the issue of involving the T cell system.

2. The Complement System.
The problem that the complement system needs the antibody system and the anitobody system needs the complement system. This cascade system Behe argues suffers from the same problems as the gradual production of a blood clotting system.

3. The Antibody diversity generation system.
Behe argues that there is need for accurate developmental triggers to rearrange the DNA to form particular B cells.
There is need for carefully controlled somatic hypermutation. He argues that an ICS will be composed of:

The antibody coding fragments.
Signal identifying start and end of the coding fragments
Mechanism for cutting out the intervening sequences.

Behe argues that such a system must exhibit a selective advantage at each stage of its development.

Behe mentions the RAG protein as a function that could have come from a bacterium and been luckily transferred to an animal. It has the ability to rearrange DNA fragments.

But this is a very far cry from explaining the step by step process to a properly functioning immune system.

The question that needs to be asked is whether (in the face of the evidence currently available) it has been demonstrated beyond all reasonable doubt that the immune system was produced without any intelligent input.

Has it even been demonstrated beyond reasonable doubt that these kind of systems can be assembled without intelligent input.

Are Behe’s doubts reasonable?

Calling someone’s bluff…..

I have attempted to discover precisely what Behe was saying when he made his statement about the literature concerning the origin of the immune system (here).

3 aspects.
1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

My point here is that Behe cannot be both wrong and at the same time be making unreasonable demands.

If he is just plain wrong then the papers from the literature which refute the two remaining prongs need to be listed. A paper which provides evidence that the control system was coopted from somewhere else is not a satisfactory prong 3 refutation as it does not explain anything about the origin of the control system.

If he is making unreasonable demands for evidence then this is a different matter entirely and much more difficult to resolve. However if this is the Anti-ID response then I would say that presenting a large pile of papers etc and claiming that they have demonstrated that Behe is wrong is not a very helpful way of making their argument that he is making unreasonable demands. It does not deal with the precise point that Behe is making.

If Behe is making unreasonable demands for evidence then this is a tacit admission that at least technically he made a correct statement about the current origin of the immune system literature.

He cannot be both wrong – (the papers and evidence are there staring him in the face but he refuses to look at them poor fool!)
Be making unreasonable demands for proof – (he is asking for a complete unedited DVD of the history of life on earth … doesn’t he realise that DVD recorders were not around in the Cambrian!)

So let me be clear are you arguing–
Behe is technically correct but asking for a DVD that Amazon do not sell or have the technology to make at present.
Behe is wrong and here are the references.

I personally find a mixture of the two confusing.

Wednesday, August 16, 2006

Putting the Polls together…

There have been three fairly recent polls regarding UK beliefs in origins.

1. Ipsos MORI for the BBC's Horizon series (see here).
22% chose creationism
A further 17% favoured intelligent design.
(39% combined)
48% chose evolution.
Uncommitted 13%

2. The UK section of the Science magazine article by J.Miller (See here and here and here)
67-68% Accept Evolution as true using it seems a combination measure of several questions about evolution.
15% unsure
17% rejecting.

3. The recent Opinion panel Research poll reported in the guardian. (See here)
(This is focused on students.)
In this poll 12% of students chose creationsism.
A further 19% favoured intelligent design.
(31% combined)
56% chose evolution.
Uncommitted 13%

What these results show it seems to me (as always) is that a great deal depends on the precise questions that are asked and perhaps the context of the questions. The Ipsos and the Opinion Panel results are comparable. If they are broadly correct then it appears that the Science survey seems to include some intelligent design supporters as those who believe evolution is true.

Saturday, August 12, 2006

Behe and the Dover “Literature Bluff”

So Who is Bluffing?

Useful links:

Barry A's original thoughts on the Literature Bluff here.
Barry A's further musings on the Literature Bluff here.
Wesley Elsberry's take on the Literature Bluff here.

"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."

It was this proposition of Behe (Darwin’s Black Box p138, 2003 paperback ed) that the pile of books, articles and journals was intended to refute at the Dover trial and which Judge Jones mentioned in his opinion.

"However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system."

What exactly did Behe mean?

The quote comes in the section of his book which examines the mechanism of the immune system looking at the complement pathway and the function and contruction of antibodies. (Chapter 6 – A Dangerous World)

In the concluding sections of this chapter Behe appears to be seeking to present the current understanding of the mechanism by which this system cam to exist. He maintains that the best efforts to do this are in two short papers:

1. David Baltimore’s 1994 article “Molecular Evolution of the Vertebrate Immune System.” PNAS 91, 10769-10770
Behe says that Baltimore suggests that the 3 sets of proteins are required for a functioning immune system (antigen receptors, antigen presentation molecules and the gene rearranging proteins.) They then argue that sharks have all three and note that immunoglobulin and TCR genes both require RAG proteins for rearrangement. On the other hand, RAG proteins (RAG is the component that rearranges the genes) require specific recombination signals to rearrange immunoglobulin and TCR genes. In this paper Behe notes that the authors speculate that a gene from a bacterium might have luckily been transferred to an animal. Luckily the protein coded by the gene could itself rearrange genes; and luckily in the animals DNA there were signals that were near antibody genes; and so on.

2. Farries, T.C., and Atkinson, J.P. (1991) Evolution of the Complement System. Immunology Today, 12, 295-300. In this paper the authors, says Behe, join Russel Doolittle in proposing unexplained proteins that are “unleashed” and “spring forth”

Behe acknowledges that there are other papers, articles and books on the subject but maintains that most of them are at the level of cell biology and are thus unconcerned about molecular mechanisms, or else they are concerned simply with comparison of DNA or protein sequences. He maintains that comparing sequences may be a good method to study relatedness, but the results can’t tell us anything about the mechanism that first produced the systems.

Behe complains that the papers fail to present quantitative calculations. He complains that they fail to acknowledge that gene duplications do not immediately make a new protein. He complains that none of them worry about the control mechanisms to regulate the pathway.

The “literature bluff” which was set up in the Dover trial presumably by Ken Miller presented a series of 8 articles in the pre trial documentation and a further "fifty- eight peer-reviewed publications, nine books, and several immunology textbook chapters" in the pile in the courtroom.

The question that I wish to ask is this… Who was right about the stack of papers. Behe mantains that these papers do not affect his proposition that the scientific literature has no answers to the origin of the immune system. Was Behe right when he made that proposition? Is he still correct?

So let us put this formally into what I will call the 3 pronged Behe test.

1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

Monday, August 07, 2006

Dover- Behe's response to the Immunology document stack.

Added insert(....10-8-06)
I just read BarryA's description here of Rule 803(18) which he says applies directly to this situation and demonstrates Judge Jones incompetence in his reliance upon this stunt.

Appenix A of the booklet is Behe’s response to the judgement which contains this little rather funny snippet:
(11) In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” (23:19 (Behe)).
Several points:
1) Although the opinion’s phrasing makes it seem to come from my mouth, the remark about the studies being “not good enough” was the cross-examining attorney’s, not mine.
2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously.
3) The Court here speaks of “evidence for evolution”. Throughout the trial I carefully distinguished between the various meanings of the word “evolution”, and I made it abundantly clear that I was challenging Darwin’s proposed mechanism of random mutation coupled to natural selection. Unfortunately, the Court here, as in many other places in its opinion, ignores the distinction between evolution and Darwinism. I said in my testimony that the studies may have been fine as far as they went, but that they certainly did not present detailed, rigorous explanations for the evolution of the immune system by random mutation and natural selection — if they had, that knowledge would be reflected in more recent studies that I had had a chance to read (see below).
4) This is the most blatant example of the Court’s simply accepting the Plaintiffs’ say-so on the state of the science and disregarding the opinions of the defendants’ experts. I strongly suspect the Court did not itself read the “fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system” and determine from its own expertise that they demonstrated Darwinian claims. How can the Court declare that a stack of publications shows anything at all if the defense expert disputes it and the Court has not itself read and understood them?
In my own direct testimony I went through the papers referenced by Professor Miller in his testimony and showed they didn’t even contain the phrase “random mutation”; that is, they assumed Darwinian evolution by random mutation and natural selection was true — they did not even try to demonstrate it. I further showed in particular that several very recent immunology papers cited by Miller were highly speculative, in other words, that there is no current rigorous Darwinian explanation for the immune system. The Court does not mention this testimony.

Dover - The History of ID

The discussion of the history of the intelligent design movement in Judge Jones opinion comes in the section in which the Judge seeks to determine whether the Dover school Board were guilty of endorsing or disapproving a particular religious viewpoint.

Judge Jones seeks to establish the proposition that ID is a religious strategy that evolved from earlier forms of creationism. He concludes:

“the evidence at trial demonstrates that ID is nothing less than the progeny of creationism.”

(I understand that to mean- ID is nothing but the progeny of creationism.
I understand creationism to mean - the Fundamentalist effort to get God and the bible into state funded science lessons.)

This argument swallows the false idea that ID is nothing but creationism in a new box. It is exactly the same product with a new label.

There are at least 4 problems with this argument.

1. He argues that the strongest evidence supporting this finding is the history and pedigree of the book Pandas and People which is mentioned in the text that teachers were to read to pupils.

In coming to his conclusion Judge Jones places great weight upon the implied intentions of changes of language in the text of “Pandas and People” (the text that was mentioned in the paragraphs to be read to students) to establish the point that ID is a religious matter. Barbara Forest’s analysis and interpretation of the textual changes is swallowed hook line and sinker despite the fact that it conflicts with the explicit testimony of one of the authors Charles Thaxton included as part of his deposition:

“I wasn’t comfortable with the typical vocabulary that for most part creationists were using because it didn’t express what I was trying to do. They were wanting to bring God into the discussion, and I was wanting to stay within the empirical domain and do what you can do legitimately there.”

Why should Barbara Forest have a better insight into the intentions of the authors than one of the authors themselves? Why does the Judge describes Forest’s book “Creationism’s Trojan Horse” as a “thorough and exhaustive chronicle of the history of ID”? Why should we accept Forest’s description of ID as entirely objective and non-partisan?

2. It fails to recognise the ancient nature of the argument.
These arguments did not spring into Aquinas’s brain from nowhere. There are two more ancient streams of thought one of which is not of Judeo-Christian. Socrates, Plato and Aristotle argued that mind is a prerequisite for life, Heraclitus, Empedocles, Democritus and Anaximander argued the reverse. Cicero argued for design well before the Christain Era.

3. It fails to do just to the nature of the recent revival of the design argument stimulated by the discoveries of nano-technology and information systems in molecular biology. It was the significance of these discoveries that cause chemist and philosopher Michael Polanyi to argue in 1967 that “machines are not reducible to physics and chemistry” and that “likewise the mechanistic structures of living beings appear to be likewise irreducible.”

It was Michael Denton’s book “Evolution - a Theory in Crisis” that caused the radical change in direction for Micahel Behe. Denton’s book has no connection to Christianity or creationism and Denton himself was not a Christian.

Several other leading ID thinkers testify that it is the molecular biology that led them to ID not the bible.

4. It fails to recognise the importance of the design debate in physics and Cosmology going back to Fred Hoyles conviction that the carbon 12 resonance evidence pointed to “some superintellect has monkeyed with physics as well as chemistry and biology.”

Dover - Introduction

Judge Jones’ opinion stretches to 139 pages. There are two main sections to his arguments after his legal background and introductory sections.

The first (Section E p14-90) deals with his application of the “Endorsement Test” to the case. The second (Section F p90-132)deals with his application of the Lemon test to the case.

It is the first of these two main sections with which I am concerned. It is in this section that he seeks to present the history of ID and to determine whether it is Science or not.

If the Judge had limited his judgement to section F then I probably would not be very interested in it… but when a Judge is presenting a verdict concerning the history of ID and coming to a final verdict on whether ID is science or not then I cannot help but be interested.

Dover - preliminary thoughts.

1. I think the Dover policy was a clumsy misguided policy.
2. I do not think that ID should be a specified part of a national curriculum in science at present but I am in favour of a teachers freedom to discuss ideas about origins including intelligent design and to state their own views. Schools with a religious ethos may wish to explore the way in which science and religion interact in society with a more detailed look at the history of the conflict regarding evolution and the way in which developments in physics and cosmology and molecular biology have resulted in a revival of the design argument in the minds of some scientists.
3. I think that students need to be taught the theory of evolution and the evidence for it and should also be made aware of the areas in which the evidence is weak and where scientists do not have full and detailed explanations of how certain features arose. When we don’t know we should say we don’t know and not give the impression that evolution has a full and detailed explanation for everything in biology when it does not.

Saturday, August 05, 2006

The Kitzmiller vs Dover Decision.

I have decided to look at this decison by means of a review of the Discovery Insitute booklet entitled "Traipsing into Evolution" by DeWolf, West, Luskinand Witt. I had been reluctant to do this without the booklet and I was reluctant to pay the £9.78 necessary to get the booklet. I was hoping that the bulk of the arguments would come out clearly on the web and I could spend my gold on other books. I have finally succumbed to the pressure and purchased the booklet.

There has been a recent brief review of the book at the NRO here. Which resulted in an interesting back and forth between Casy Luskin (here, here and here) and Wesley Elsberry (here)

The criticism in the book is divided into 4 sections:
1. The partisam history of Intelligent Design.
2. The unpersuasive case against the scientific status of ID.
3. The failure to treat religion in a neutral manner
4. The limited value as precedent.

I intend to look at these 4 sections in separate posts. I trust that visitors who remember my promise to look at this decision at some point in the future will be satisfied with this as a fulfillment of my promise.

One sentence that stood out in my reading of the introduction was this...

"... he asserted (that is Judge Jones asserted) that scientists who support ID have published no peer-reviewed articles or research..."

(I wrote in the margin....Did he in fact assert this?)