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?

15 Comments:

Anonymous Anonymous said...

In the immune system chapter, Behe asserts at various points that evolution could not have produced the systems, because intermediates would be nonfunctional. These claims are falsified by demonstration that modern functional systems exist with just these intermediate characteristics. This was all shown here in 2002:

Evolving Immunity: A Response to Chapter 6 of Darwin's Black Box
http://www.talkdesign.org/faqs/Evolving_Immunity.html

It doesn't take very many of these failures to realize that Behe's assertions about why evolution couldn't produce these various subsystems are unreliable.

12:43 am  
Anonymous Anonymous said...

Regarding how to determine what is a reasonable level of detail: do we have to have an actual up-close photo of an extrasolar planet to determine than an extrasolar planet is orbiting a star?

Whatever standard of detail you decide is appropriate has to be applied consistently to all of science. Currently the IDers just make a special exception for evolution and require infinite detail from it -- but when it comes to astronomy, or molecular biology, or New Testament history for that matter, it suddenly becomes perfectly OK to say "Well, we don't know everything, but the evidence points strongly to these specific conclusions."

The IDers employ this special standard only in order to rationalize away the massive data that does exist that contradicts their position that complex structures can and have evolved.

12:48 am  
Anonymous Hrafn said...

Andrew, this question has already been answered a couple of threads ago.

1) Behe has no standing whatsoever (due to his lack of qualifications and detailed knowledge in the area) in the study of Evolution of the Immune System to determine what is "reasonable."

2) As Ian Musgrave and a post I linked to from Dispatches from the Culture Wars have shown, Behe's standard is impossible for any historical science to meet and therefore clearly unreasonable.

This is now your fourth thread on Behe's Dover testimony. You have left questions in prior threads unanswered, and raised in new threads questions and/or statements already throughly answered and/or rebutted in prior threads.

None of this attempted evasion has in any way succeeded in hiding the vacuity of Behe's position, nor his dishonesty, incompetence, and lack of connection to scientific reality.

What then are you hoping to achieve?

3:58 am  
Anonymous Hrafn said...

"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."

Andrew, this is a fairly obvious strawman caricature of the wealth of scientific evidence for the evolution of these systems.

7:40 am  
Blogger Andrew Rowell said...

Anonymous,

I am sure that you are aware of the tenacity and power or religious belief. The extraordinary grip that a person's religious upbringing has upon a person's whole life. Changing a whole world view of a person is a traumatic experience. Becoming a materialist for a theist could be a traumatic experience.

Do you accept that there might be likewise a difficulty going the other way?

The origins issue has always been a foundational world view issue. There is a lot more at stake here than how many exoplanets there are.

It is like the standard of evidence required to put a new drug into a human being as opposed to putting a new drug into a mouse.

Expecting one level of evidence accross all areas is not realistic... I do not know if you can really measure evidence like that anyway.

6:50 pm  
Anonymous Matt Inlay said...

Andrew,

In biology, there is essentially nothing for which there is absolute proof. The degree of our certainty that a given conclusion is "true" is proportional to the strength of the evidence that supports it. I would contend that science is not so much about the "truth" as it is about the search for the "truth". For that, we must rely on the scientific method as the best method of determining what is or is not "true".

With regards to immune system evolution, we have a general model for how the adaptive immune system evolved, a model which makes predictions and can therefore be tested, a model that researchers are actively testing, and a model for which data is steadily accumulating in favor of. This is the epitome of the scientific method.

The 58 papers presented to Behe at the Dover trial are an outline of some of the more significant discoveries made in that field. Every few years, a major piece of the puzzle is added, as can be seen in that list. The major point of the presentation of those articles was to demonstrate to the judge how disconnected Behe is from the reality of science.

The papers do not provide absolute proof. They do not provide detailed calculations of selection constraints or a step-by-step, mutation-by-mutation account of the evolution of this system. What they do show is progress in a field that Behe claims is a dead end. What they do show are detailed, testable models that Behe claims doesn't exist. What they do show are hard results where Behe claims there are none.

Compare this to ID. In the 10 years since the publication of Darwin's Black Box, what progress has ID made in studying the origins of any IC biological system? Have they even done a single experiment to support their model? Do they even have a "detailed, testable" model?

So yes, given the total failure of ID to produce any type of experimental plan that even resembles the scientific method, and given the continuing advances in the field of evolutionary immunology, I'd say it's unreasonable to demand the level of evidence that Behe does. Of course, Behe chose that level of evidence specifically because he knew it could never be achieved. All you have to do is contrast it with existing levels of evidence for other fields (especially ID), and you'll see just how unreasonable it is.

12:37 am  
Blogger Ian Musgrave said...

G'Day All

I'm in the middle of a heavy workload at the moment, students starting projects, grants to be sent in and a couple of papers to be finalised and sent off to journals. Hence I can only pop in briefly and occasionally. However, I will make a couple of points.

Andrew wrote:
"The argument over whether Behe is asking for unreasonable detail"
As I have previously demonstrated, it is not just unreasonable. Behe asks for a level of detail which is impossible in principle to provide.

Andrew wrote:
"The problem that the complement system needs the antibody system and the antibody system needs the complement system."
Tell that to Sea Squirts, that have a simple, two step complement system and no antibodies, or amphioxus, which has a slightly more complicated complement system and no antibodies or Hagfish that have a more advanced (but still simpler than mammals) complement system and no rearranging antibodies.

This is just one example of sheer ignorance, there are many more, but I don't have time to go into it. But how many times does it have to be demonstrated that Behe is completely ignorant of the biology of, extensive research into, the immune system before you understand this point Andrew? (As always, the annotated bibliography of the immune system is a good place to start for all your immune system needs)

3:15 am  
Blogger Andrew Rowell said...

Ian,
You said:

"As I have previously demonstrated, it is not just unreasonable. Behe asks for a level of detail which is impossible in principle to provide."

Can you point me to where you demonstrated this again?? Thanks.

7:40 am  
Blogger Andrew Rowell said...

Ian,
Re
"The problem that the complement system needs the antibody system and the antibody system needs the complement system."

That is my ignorance rather than Behe's. He does not say what I thought he said regarding complement. It is the control system in the complement cascade upon which he pins the IC argument not on the need for both Antibody and complement.

7:46 am  
Blogger Ian Musgrave said...

G'Day All

Andrew wrote: "It is like the standard of evidence required to put a new drug into a human being as opposed to putting a new drug into a mouse.

Expecting one level of evidence across all areas is not realistic... I do not know if you can really measure evidence like that anyway."

As one of my areas of expertise is drug development, I can tell you this argument is (mostly) nonsense. Exactly the same levels of evidence are needed.
1) Evidence that the drug binds to relevant receptors in the target tissue.
2) Evidence that the drug modifies the relevant tissue response
3) Evidence that the drug modifies the relevant organ response
4) Evidence that the drug is not toxic at the dose to be used.

The one area where there is difference is 4, where drugs are (usually) monitored for chronic toxicity before first doses studies in humans, but otherwise it's exactly the same level and detail involved. I use the example of the development of Bosetan for pulmonary hypertension in my classes, where these steps were carefully observed before first use in rats (rather than mice).

Note that there are two different issues that are being conflated here 1) whether a drug works and 2) whether it is safe. When giving a drug for first use in humans, we usually demand more evidence of safety than we do for rats and mice, but it's the same kind of evidence. For example, we usually want safety evidence from rats and rabbits and dogs before going to first use in humans, but it’s the same kind of evidence, not an infinitely detailed amount of evidence. Behe's argument would require we test for safety in all mammals, examining all tissues before we go to first use in man, whereas we generally go to first use with very limited safety data. Note fist use and clinical approval are different things; we give experimental drugs to humans way before the kinds of long term tests that are required for approving the drug for use in the clinic Also in cases where the disease is severe and there is no existing treatment we often go to clinical use before we have done extensive safety trials (which are minimal by Behe's standard; eg AZT).

And again, Behe's argument is not just "we need lots of evidence". His claim is that we need impossible levels of evidence (such as resurrecting Cambrian jawless fish) before he will even consider there is any evidence of an evolutionary explanation. Remember he said " 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 evidence…" not weak evidence, not evidence that doesn't convince him, but no evidence.

This is like claiming that there is no evidence that Bosetan is an endothelin antagonist, because despite it displacing endothelin in radioligand binding assays, blocking endothelins action in isolated blood vessels and reducing bllod pressure in rat models of pulmonary hypertension, long term safety studies have not been done on all mammal species known to humans. (And then, after long term safety stuidies in rats, rabbits and dogs is published, saying "these papers do not affect my proposition that the scientific literature has no evidence that Bosetan is an endothelin blocker"

3:25 am  
Blogger Ian Musgrave said...

Andrew wrote
Ian, You said:

"As I have previously demonstrated, it is not just unreasonable. Behe asks for a level of detail which is impossible in principle to provide."

Can you point me to where you demonstrated this again?? Thanks."


Comment 33 in the "Behe and the Dover “Literature Bluff”" tread, you even commented on my comment.

4:20 am  
Blogger Ian Musgrave said...

Andrew wrote: It is the control system in the complement cascade upon which [Behe] pins the IC argument not on the need for both Antibody and complement.

Again, this shows his ignorance, as the control mechanism is rather simple, and can be traced from very simple systems like those in the sea squirt, through to the more complex systems of vertebrates (there are papers out there on this).

For 10 points, describe the control system of the complement system to me, and explain why it is impossible to evolve.

4:22 am  
Blogger Andrew Rowell said...

Ian,

1. I think that you are misinterpreting the standard of evidence Behe is looking for. Where do you get the idea from that he wants living Cambrian fish?

2. I am going through Matt Inlays response to Behe's Immunology chapter and one of the sections is on the complement system so when I get there I will attempt your challenge. What is the prize for 10 points?

7:46 pm  
Blogger Ian Musgrave said...

Andrew wrote
"1. I think that you are misinterpreting the standard of evidence Behe is looking for. Where do you get the idea from that he wants living Cambrian fish?"

Read my post, the kinds of eviodence he wants cannot be obtained unless we ressurect Cambrian Jawless fish.

"2. I am going through Matt Inlays response to Behe's Immunology chapter and one of the sections is on the complement system so when I get there I will attempt your challenge. What is the prize for 10 points?"

A squashy Brain with my Uni's logo (I was going to send a jar of my wifes Lillypilly jam, but the customs problems are horrendous)

1:58 am  
Blogger Ian Musgrave said...

I wrote:
"A squashy Brain with my Uni's logo (I was going to send a jar of my wifes Lillypilly jam, but the customs problems are horrendous)"

Duh!! And a copy of the latest Sky&Space magazine (with fantastic articles on Pluto). That should be woth a bit of brain exercise. I keep forgetting that I am a contributing editor to this magazine.

2:47 am  

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