Casey Luskin email debate

Over a year ago I decided to contact the Discovery Institute to ask them a very simple question. I wanted to know what scientific data there was to support intelligent design. I had never heard of Casey Luskin before but within a few weeks I received a very polite reply from him ensuring me that there was indeed scientific data to support ID. Naturally, I disagreed with him. Over the next month or two we engaged in an email debate, until Casey withdrew. I thought I would post the whole debate unedited below the fold. I'm sure Casey won't mind... (Edit: he did)

From: rhiggs
Sent: Tuesday, January 22, 2008 9:31 AM
To: Mollie Tschida
Subject: ID research

Hello,

I am aware of the multitude of publications on ID and related topics. However, on reading these I haven't found any direct research which has provided positive evidence of ID. It seems to be more philosophy-based. Surely someone has done some actual experiments to verify the claims of the ID community as opposed to simply casting doubt on other theories. I would be interested in reading about them. Could you please direct me to the appropriate sources?

Many thanks,

Rhiggs

Subject: RE: ID research

Date: Sat, 9 Feb 2008 11:42:35 -0800
From: cluskin@discovery.org
To: rhiggs

Dear Rhiggs,

Geretings and thanks for your e-mail. I'm sorry that it took a couple weeks to get back to you. In fact, there is much positive, research-based evidence for ID, and ID is not merely "philosophy-based." I would refer you to the following sources:

(1) An explanation of the "positive case for design":

http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=546

(2) An explanation of how ID uses the scientific method, a positive method of making scientific claims:

http://www.ideacenter.org/contentmgr/showdetails.php/id/1154

(3) A listing of much peer-reviewed research supporting ID, presenting much data that represents research done by ID proponents supporting ID's claims:

http://www.discovery.org/a/2640

(4) Some of the pro-ID experimental research is specifically discussed at places such as:

http://www.evolutionnews.org/2007/01/journal_of_molecular_biology_a.html

http://www.evolutionaryinformatics.org/

http://www.evolutionnews.org/2006/10/response_to_barbara_forrests_k_7.html

It's worth noting that ID proponents cite innumerable research studies, even when done by pro-Darwin scientists, as presenting research that predicts intelligent design. As one example, Michael Behe discusses MUCH research by other scientists in Darwin's Black Box that show that various systems are irreducibly complex and support intelligent design.

In this regard, while ID proponents themselves are doing much research, there is nothing wrong with expounding a theory that can explain and predict the results of other scientists. In fact, if you read Darwin's Origin of Species, you'll find that this is EXACTLY what Darwin commonly did: he presented a new theory and found that it explained the results of other scientists. Thus, in science, it is considered good practice to propose positive new theories that explain and predict the data that has been uncovered by other scientists. This is how "positive" scientific theories are commonly argued for in the scientific community. Darwinists do it all the time, and there's nothing wrong when ID proponents do it as well. Thanks again for your e-mail and take care.

Sincerely,

Casey Luskin

From: rhiggs

Sent: Mon 2/11/2008 6:56 AM
To: Casey Luskin
Subject: RE: ID research

Dear Mr. Luskin,

Thank you for the reply. I have gone to the links you sent me and despite your claim that "there is much positive, research-based evidence for ID", I have failed to find any. The link you sent me to "peer-reviewed research supporting ID, presenting much data that represents research done by ID proponents supporting ID's claims" DOES NOT present much data. It predominantly presents essays from ID proponents in which they 'argue' for a central ID idea, although they never seem to 'show' that this idea is correct, thus they cannot and should not 'conclude' that ID is the best explanation.

It is the experimental evidence for ID that I am interested in. From what I read in the links there seems to be only two real attempts to use scientific experimentation to test ID. These are a) Douglas Axe's papers and b) Scott Minnich's flagellum experiments. However, both of these examples fail to provide evidence for ID for the same reason: They only test for a specific function, penicillin resistance in Axe's case and bacterial motility in Minnich's case.

Both sets of experiments essentially take a protein or protein complex with known function, remove or mutate specific residues and test for the same function. When the functionality is lost, Minnich claims that this proves irreducible complexity (Axe does not go this far). But it is fundamentally wrong to conclude this without testing the mutated protein for other functions. Obviously, this would entail much more laboratory time and would be a very difficult task, but nevertheless, it cannot be termed irreducibly complex unless the mutated forms are proven to have absolutely no function. To do so is BAD science and why Minnich's testimony did not convince credible scientists or Judge Jones.

I am a molecular biologist and have done some work on protein structure-function relationships in avian antimicrobial peptides. We showed a loss of function by mutating single amino acids from a functional peptide, similarly to Minnich, however the mutated peptides still had plenty of other biological activity, including chemotactic and immunostimulatory functions. These secondary functions are proof against irreducible complexity, and the 'mutated flagellums' in Minnich's experiments were not tested for secondary functions, hence cannot be called irreducibly complex.

I have read that you are a lawyer with some qualifications in geology. Perhaps you do not realise that there are many many proteins that we know to exist in cells but we do not know what their functions are (this is why people like me have jobs!). Also, there are many many proteins which have several distinct functions, including my example of antimicrobial peptides above. Because of this, irreducible complexity is BAD science. We still have a lot to learn and shouldn't jump to unscientific conclusions.

As an aside, I read your personal website in which you quote Michael Behe:

"I myself do believe in a benevolent God … But a scientific argument for design in biology does not reach that far. This while I argue for design, the question of the identity of the designer is left open. Possible candidates for the role of designer include: the God of Christianity; an angel--fallen or not; Plato's demi-urge; some mystical new age force; space aliens from Alpha Centauri; time travelers; or some utterly unknown intelligent being. … [A]s regards the identity of the designer, modern ID theory happily echoes Isaac Newton's phrase hypothesis non fingo.” (Behe, 2001)

If you believe that ID does not appeal to the supernatural, I assume that you agree with the above quote by Behe. If it is possible that a number of intelligent sources could be responsible, then I don't understand why 'the question of the identity of the designer is left open'. If indeed it is space aliens or time travellers then it is not supernatural at all and there may be physical evidence that could be open to scientific investigation. In this case, it is strange that ID proponents do not want to look into it, and instead leave the question open, as it would certainly help to prove their case.

It seems more likely that all ID proponents believe that 'the God of Christianity' is the designer, but as this cannot be tested scientifically, the ID stance is that they are not concerned with the identity of the designer. You may disagree, but this an unscientific stance, and appears to the majority of the scientific community as a 'cover-up' to get religion into the science class.

I look forward to hearing your comments. Also, I would be interested in hearing what you have to say about PZ Myers' blog in which he points out the basic flaws in your rebuttal of Ken Miller's testimony. I admit that I have not read your rebuttal (please link it to me if possible), but if the quotes attributed to you are correct, then you really don't understand genetics and you are in no position to argue Miller's testimony...

http://pharyngula.org/index/weblog/comments/luskins_ludicrous_genetics/

Kind regards,

Rhiggs

From: Casey Luskin (cluskin@discovery.org)
Sent: 13 February 2008 22:06:31
To: Rhiggs
Subject: ID research

Dear Rhiggs,

Greetings and thank you for your kind reply. At first approximation, I am puzzled by your reply. You stated "I have failed to find any" research supporting ID. But then you stated that the pages "DOES NOT present much data," and it seemed like you were saying that there is some, but not "much." I just wanted to clarify and allow you to explain what you are trying to say: are you saying there is "not any" research, or potentially "some" research supporting ID?

That is just a point of clarification, however, and I'm happy to discuss with you some of your other comments. I pointed you to much research supporting ID and it seems clear to me that it exists, thus satisfying your original request for information. Now, will the goal-posts shift?

In my previous e-mail to you, I prefaced the discussion by explaining how we detect design, giving you a link explaining the positive case for design. I presume that you read this article, and if you did then you would have seen that the very first table gives various quotes from ID proponents explaining the positive case for design:

“Agents can arrange matter with distant goals in mind. In their use of language, they routinely ‘find’ highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities.” (Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design, pg. 388 (William A. Dembski and Michael W. Ruse eds., Cambridge University Press, 2004).)

“[W]e have repeated experience of rational and conscious agents-in particular ourselves-generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. … Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent.” (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

Both of these articles are peer-reviewed articles listed on the page I sent you. While Meyer's work here are admittedly review papers, he does discuss experimental evidence, and he explains why it supports ID using the positive arguments given above. Thus, I believe that your statement "they never seem to 'show' that this idea is correct, thus they cannot and should not 'conclude' that ID is the best explanation," is simply wrong.

Meyer gives extensive discussion regarding why ID is the best explanation for the origin of large amounts of specified complexity. I think you would find it helpful to re-read Dr. Meyer's article in Proceedings of the Biological Society of Washington at http://www.discovery.org/a/2177 to understand the positive argument for design.

Also, you raised some good points about irreducible complexity, however I think they are ultimately flawed. First, however, I want to address you wrote: "Perhaps you do not realise that there are many many proteins that we know to exist in cells but we do not know what their functions are (this is why people like me have jobs!). Also, there are many many proteins which have several distinct functions, including my example of antimicrobial peptides above. Because of this, irreducible complexity is BAD science. We still have a lot to learn and shouldn't jump to unscientific conclusions."

I reply: I agree that we "shouldn't jump to unscientific conclusions." In that spirit, I’d like to propose that we take some historical perspective here: It is the neo-Darwinian-side that has long been making the grand claim that all of the complexity of life can be explained by a process of blind natural selection acting upon random mutations. Great claims require sufficient evidence. We "shouldn't jump to unscientific conclusions" and we should NOT engage if "evolution-of-the-gaps" reasoning.

But that’s precisely what seems to typically be done by neo-Darwinists.

And I would respectfully say to you that your e-mail engages in "evolution-of-the-gaps" reasoning.

For example, you wrote, that there are many proteins in a cell "but we do not know what their functions are". If that’s the case, how do we know that such complexity can evolve in a step-by-step neo-Darwinian fashion? Take ID out of the equation here, and you have an entire field that operates under the grand assumption that all proteins and pathways and systems in a cell both can and did evolve via a step-by-step neo-Darwinian process.

I don’t make this argument to claim that we should reject neo-Darwinian evolution out of our ignorance. Hardly. My criticisms of evolution are based upon what we do know, not what we don’t know. Rather, my argument is that we should also be careful not to accept evolution out of our ignorance as well. It’s OK for a scientist to say, “We don’t know, but we’re working on it.”

Furthermore, you made the bold claim:

"Obviously, this would entail much more laboratory time and would be a very difficult task, but nevertheless, it cannot be termed irreducibly complex unless the mutated forms are proven to have absolutely no function.”

I reply: This expects people to do an impossible experiment because you can’t prove an absolute negative, so you’ve set up an impossibly high standard. And this is why it’s clear that this kind of neo-Darwinism is based upon “evolution-of-the-gaps” reasoning—it’s based upon the fundamental presumption that intermediate states DO EXIST, even if they are not found.

Additionally, you wrote, “it cannot be termed irreducibly complex unless the mutated forms are proven to have absolutely no function.” That statement misunderstands the definition of irreducible complexity. This is how Behe defines irreducible complexity:

“In The Origin of Species Darwin stated: 'If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.' A system which meets Darwin's criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.” (Michael Behe, Darwin's Black Box, pg. 39 (Free Press, 1996).)

Thus, I wrote at http://www.iscid.org/papers/Luskin_EngineLugnuts_042706.pdf ...

“evolution requires that a system, or its sub-parts, be functional along each small step of their evolution to the final system. Yet one could find a sub-part that could be useful outside of the final system, and yet the total system would still face many points along an "evolutionary pathway" where it could not remain functional along "numerous, successive, slight modifications" that would be necessary for its gradual evolution. Thus, [Ken] Miller mischaracterizes Behe's argument as one which focuses on the non-functionality of subparts, when in fact, Behe’s argument actually focuses on the ability of the entire system to assemble, even if sub-parts can have functions outside of the final system.”

Therein lies the rub: ID proponents find it implausible that a sub-system (or multiple sub-systems) of flagella could be transformed and simultaneously brought together so as to spontaneously form a functional flagellum. Such models of co-option seem highly implausible, and most certainly do not represent “slight modifications” required by neo-Darwinian evolution. Such transformation would require great modifications to effect the required change to produce the systems we observe.

Similarly, Michael Behe wrote in a response titled, “Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions”:

“[O]pponents of design want to assert that if the individual parts of a putatively IC structure can be used for anything at all other than their role in the system under consideration, then the system itself is not IC. So, for example, Kenneth Miller has seriously argued that a part of a mousetrap could be used as a paperweight, so not even a mousetrap is IC. Now, anything that has mass could be used as a paperweight. Thus by Miller’s tendentious reasoning any part of any system at all has a separate “function”. Presto! There is no such thing as irreducible complexity …

I never wrote that individual parts of an IC system couldn’t be used for any other purpose. (That would be silly--who would ever claim that a part of a mousetrap couldn’t be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin’s Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention.

In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn’t form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system. (Darwin’s Black Box, page 66)

… Miller’s argument is that since a subset of the proteins of the flagellum can have a function of their own, then the flagellum is not IC and Darwinian evolution could produce it. That’s it! He doesn’t show how natural selection could do so; he doesn’t cite experiments showing that such a thing is possible; he doesn’t give a theoretical model. He just points to the greater-than-expected complexity of the flagellum (which Darwinists did not predict or expect) and declares that Darwinian processes could produce it. This is clearly not a fellow who wants to look into the topic too closely.” (http://www.discovery.org/a/1831)

Does the same logic hold true for individual protein evolution? You wrote: “We showed a loss of function by mutating single amino acids from a functional peptide, similarly to Minnich, however the mutated peptides still had plenty of other biological activity, including chemotactic and immunostimulatory functions”

This does not rise to the level of complexity studied in Axe’s research. Axe’s work tried to determine the likelihood of finding functional protein folds. Peptides are extremely short chains and they don’t fold into folded structures like longer proteins, and thus they don’t fold tertiary folded structures like real proteins and they can’t perform the complicated structures that enzymes can do. Short peptides can have all kinds of biological activities but they can’t function the way a folded protein can—they can’t do what enzymes normally do. Ultimately, you have to answer the question, how did life get the larger folded protein structures? Axe’s work dealt with protein folds and enzyme function, so I’m skeptical that your work explains away his data. Some of his other work has even showed that short peptides (20 amino acids or less) can have multiple functions.

I’ve seen other papers that slightly tweak fully-functional proteins to perform a highly similar function and then over-extrapolate from the results. Such studies never address how any function is acquired in the first place, and they represent trivial changes in function. To give an analogy, these kinds of studies don’t show how evolution scales mountains, it simply shows that neo-Darwinism can get you the last 10 yards after you’ve already spent 10 hours hiking.

In the end, I’d love to see your papers—if you have published this material—would you mind sharing the work? I ask because I’m interested to learn if the other activity it retained was upon targets that were highly similar to the original activity. I’m also interested in the overall length and complexity of the peptides. Regardless, I’ll gladly admit that if you can mutate one amino acid that causes loss-of-original function, and still find other functions, that this could represent the kind of “slight-modification” required for protein evolution. But this is a far cry from what is required for neo-Darwinism to meet its required burden of proof, and it doesn’t show that folded enzymes can arise in a step-by-step fashion.

You wrote: “To do so is BAD science and why Minnich's testimony did not convince credible scientists or Judge Jones."

I reply: Are you suggesting that neither Scott Minnich nor any other pro-ID scientists who hold these views are credible scientists? Also, I must note that while Judge Jones was surely convinced of his views, he simply copied the vast majority of his section on whether ID is science from an ACLU brief (please see http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1186 for details). I don’t consider judge’s opinions to be authoritative on scientific issues, and I’m sure you feel the same as I do.

Finally, regarding the identity of the designer, you asked some questions:

“If it is possible that a number of intelligent sources could be responsible, then I don't understand why 'the question of the identity of the designer is left open'. If indeed it is space aliens or time travellers then it is not supernatural at all and there may be physical evidence that could be open to scientific investigation. In this case, it is strange that ID proponents do not want to look into it, and instead leave the question open, as it would certainly help to prove their case.”

Intelligent design is not so much focused on studying the designer as it is on studying natural objects to determine if they have the type of informational signature that in our experience comes only from intelligence. The ground-rule that you must keep in mind here always is that ID is takes a strictly scientific approach, and does not make claims that go beyond the data. ID is not inherently opposed to studying the designer. But right now, absent a time-machine, we don’t know how. I’ll briefly explain why:

“Thomas Woodward clearly explains the principled reasons why the biological evidence for ID may not allow us to identify the designer:

‘There is no ‘Made by Yahweh’ engraved on the side of the bacterial rotary motor—the flagellum. In order to find out what or who its designer is, one must go outside the narrow discipline of biology. Cross-disciplinary dialogue must begin with the fields of philosophy, sociology, history, anthropology, and theology. Design itself, however, is a direct scientific inference; it does not depend on a single religious premise for its conclusions. ‘ (Thomas Woodward, Darwin Strikes Back: Defending the Science of Intelligent Design, pg. 15 (Baker Books, 2006).)

In other words, the flagellar machine itself indicates that it did not arise by a random and unguided process like Darwinian evolution, but rather arose by a non-random and intelligently directed process such as intelligent design. However, while biological structures may be scientifically explained via intelligent design, the structures themselves have no way of directly telling us whether the designer is Yahweh, Buddha, Yoda, or some other type of intelligent agency.” (http://www.discovery.org/a/4306)

Thus, while the DNA encoding the irreducibly complex flagellum might indicate an intelligent cause origin, I don’t know how to use that DNA evidence to determine whether the designer is natural or supernatural. If you have any ideas how to do that, I’m all ears. Until you explain to me how I could look at the DNA in the flagellum to determine the identity of the designer, then you have no basis for telling me that I should be trying to make such a study, because I can’t think of a way. Thus, the interface between ID and the identity of the designer presently stands as follows:

ID does·“ not address religious questions about the identity of the designer, and in fact ID proponents have diverse views about the identity of the designer; ID proponents give principled reasons why ID does not identify the designer, stemming from ID’s intent to respect the limits of science and not attempt to address religious questions that go beyond what can be scientifically inferred from the empirical data;

Whether traditional theists or not, ID proponents are entirely open about their views on the identity of the designer; ID proponents make it clear that their views about the identity of the designer are their personal religious views, and not conclusions of ID.” (http://www.discovery.org/a/4306)

…perhaps someday we will be able to scientifically study the identity of the designer, but I can’t think of how to do that right now using scientific methods. Unless you can tell me how I can look at the information in DNA and determine the identity of the designer, I’m not sure what else to say here on this topic. It’s not central to ID.

In any case, I think that’s enough material for now. If you want to talk about other subjects, I’m happy to do that. But let’s finish our conversation about the relevant topics at-hand before we jump to other topics.

Thanks again for your e-mail and your civil reply—and happy Darwin day!

Sincerely,

Casey

From: rhiggs

Sent: Friday, February 15, 2008 15:57
To: Casey Luskin (cluskin@discovery.org)
Subject: ID research

Dear Mr. Luskin,

Thank you again for your reply. Let me first clear up the confusion over whether I think there is NO or SOME evidence for ID. Having read the link you sent me in your original email that you described as containing…

“…peer-reviewed research supporting ID, presenting much data that represents research done by ID proponents supporting ID's claims”

…I did not find any data that provides positive evidence for ID, thus I worded my response that this link ‘DOES NOT present much data’ because this is what YOU claimed (see the bold letters in your original sentence). My position is that there is definitely NO evidence. You may disagree, but in my opinion, review-type articles which discuss others work and make new arguments are NOT evidence of the arguments in their own right. These arguments need to be validated by experimentation. Otherwise they are simply interesting ideas and hypotheses.

You wrote…

“I pointed you to much research supporting ID and it seems clear to me that it exists, thus satisfying your original request for information. Now, will the goal-posts shift?”

Please explain to me in your own words (without linking or quoting) all of the direct experiments that have been performed by pro-ID scientists which provide the much evidence that you continually claim exists…..I ask this because I’m not sure if you realise how little supposed direct experimental evidence there actually is (although I don’t consider any of it to be evidence of ID)

You use this quote from Meyer – “Agents can arrange matter with distant goals in mind. In their use of language, they routinely ‘find’ highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities.”……..

The appearance of design or improbable functional sequences are not empirical evidence of ID, they are what you might call philosophical evidence. Furthermore, they are improbable sequences when you predict the probability of the entire sequence assembling spontaneously, but this is actually what ID proposes, not neo-Darwinism. ID is simply an easy answer which does not attempt to explain these things scientifically. There may be sub-sections of ID theory that can claim to be scientific, but the whole idea is based on an unscientific premise, an intelligent designer who is beyond scientific testing.

As Douglas Theobald writes on http://www.talkorigins.org/faqs/comdesc/

“Scientific theories are validated by empirical testing against physical observations. Theories are not judged simply by their logical compatibility with the available data. Independent empirical testability is the hallmark of science—in science, an explanation must not only be compatible with the observed data, it must also be testable. By "testable" we mean that the hypothesis makes predictions about what observable evidence would be consistent and what would be incompatible with the hypothesis. Simple compatibility, in itself, is insufficient as scientific evidence, because all physical observations are consistent with an infinite number of unscientific conjectures. Furthermore, a scientific explanation must make risky predictions— the predictions should be necessary if the theory is correct, and few other theories should make the same necessary predictions.”

In this same article, Theobald explains 30 different predictions based on evolution and common descent that have been upheld by experimentation. He states that…

“No alternate explanations compete scientifically with common descent, primarily for four main reasons: (1) so many of the predictions of common descent have been confirmed from independent areas of science, (2) no significant contradictory evidence has yet been found, (3) competing possibilities have been contradicted by enormous amounts of scientific data, and (4) many other explanations are untestable, though they may be trivially consistent with biological data.”

I believe point 4 in the above quote applies to ID.

You wrote…

“While Meyer's work here are admittedly review papers, he does discuss experimental evidence, and he explains why it supports ID using the positive arguments given above.”

Just because Meyer discusses experimental evidence performed by others that he claims supports ID, this does not provide evidence for ID. This can only be provided by direct experimentation using a testable hypothesis, not retrospectively reinterpreting another’s results.

When I suggested you need to test the mutated flagella for other functions, you wrote…

“This expects people to do an impossible experiment because you can’t prove an absolute negative, so you’ve set up an impossibly high standard. And this is why it’s clear that this kind of neo-Darwinism is based upon “evolution-of-the-gaps” reasoning—it’s based upon the fundamental presumption that intermediate states DO EXIST, even if they are not found.”

I agree that it is impossible to test for every possible function, but for the same reason it is equally as impossible to thus term something irreducibly complex, because you are claiming to know that it has no other function through which it could have evolved. You seem to agree that subparts of an apparently irreducibley complex structure can have other functions, but you still strangely claim that the initial structure is irreducibly complex. Incidentally, you refer to my “evolution-of -the-gaps” reasoning, which is fair enough, but at least scientists are trying to fill in those gaps using proper experimental methods. ID proponents, on the other hand, use “God-of-the-gaps” reasoning, cleverly disguised as “designer-of-the-gaps” reasoning, which is also based on a fundamental presumption which cannot be tested and so will NEVER be found, hence NEVER proved wrong. How convenient!

Perhaps, as you say, I don’t understand the concept of irreducible complexity, so I will take Behe’s definition. If irreducible complexity is to be defined as Behe states…

“By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning”

…then of course irreducible complexity DOES exist. It fact, it exists everywhere. It has been shown in labs many times that removing “parts” of “systems” results in loss of function. But, crucially, this does not strengthen the ID argument, because these ‘irreducibly complex’ systems CAN evolve through step-by-step neo-Darwinian evolution. Herman Muller described the process back in 1918. For example, take a relatively complex system that performs a function. Next, gradually make that system more efficient and sophisticated by step-by-step addition of new “parts”. Then, remove some of the earlier redundant “parts” (as happens in evolution) thus increasing efficiency. You now have a more complex system than the previous one, however, if you were to artificially remove a “part” of this new system, it would cease to function. As you should be able to see, this does not mean that it couldn’t have evolved.

I may not have explained that very well. Here is a well known analogy that you may be familiar with. Imagine a river with three stepping stones forming a rudimentary bridge. The stones constitute a system with a function. If you add a long piece of wood across all three stones it is now a slightly more complex system, still with the same function. The middle stone can now be removed without loss of function, and this newer (slightly) more complex system is more efficient in that you can walk across it rather than hopping from stone to stone. If you now remove any of the other parts of this system, ie the wood or the two outer stones, it will lose its function, and thus the bridge can be termed irreducibly complex. However, it came about in a step-by-step fashion (which includes removal of redundant parts) without loss of function.

You wrote…

“…the flagellar machine itself indicates that it did not arise by a random and unguided process like Darwinian evolution, but rather arose by a non-random and intelligently directed process such as intelligent design.”

This is wrong as I have explained. You assume that the “flagellar machine” is an example of ID because it is irreducibly complex, but irreducible complexity is everywhere in nature and does not have any bearing on neo-Darwinism. Behe is fundamentally wrong because he assumes that evolution is only an additive process.

Behe and the ID community ignore the fact that there is more than one way for a complex structure to evolve. The actual precursor may have had more parts, not fewer. Or, if the individual parts evolve, the precursor may have had the same number of parts, not yet codependent. Take the common mouse-trap analogy. I am sure that prior to the common-day mousetrap, there were other less efficient systems, which used many more parts in order to catch a mouse. These systems may have been refined over time, with unnecessary parts removed until we arrived at the mouse-trap as we know it today. This does not mean it didn’t undergo slight modifications during its ‘evolution’.

Now, based on this, it seems obvious to me that irreducible complexity is a real thing, but it does not debunk neo-Darwinian evolution, in fact it is an effect of neo-Darwinian evolution. More to the point, it says ABSOLUTELY NOTHING about ID. If you understand science at all, the presence of irreducibly complex structures DOES NOT indicate design no matter how much you want it to, so should not be used as positive evidence of ID.

When I described my research on antimicrobial peptides, in which a mutated protein still has secondary functions, you wrote…

“I’ve seen other papers that slightly tweak fully-functional proteins to perform a highly similar function and then over-extrapolate from the results. Such studies never address how any function is acquired in the first place, and they represent trivial changes in function. To give an analogy, these kinds of studies don’t show how evolution scales mountains, it simply shows that neo-Darwinism can get you the last 10 yards after you’ve already spent 10 hours hiking.”

On the contrary, using irreducible complexity as evidence for ID is most certainly “over-extrapolating from the results”. ID does not address how any function is acquired, it just assumes that a designer did it all, but conveniently shies away from explaining it in any more detail. To give the same analogy, ID simply states that we arrived on the top of the mountain but does not explain how we got there scientifically. If, as you implied, neo-Darwinism has shown how we arrived from 10 yards away, then this is 10 yards better than ID is doing. By simple inductive thought, if we know how we arrived from 10 yards away, then it is logical to think that in the past we arrived in that spot from 20 yards away, and so on…

If you accept the 10 yards of Neo-Darwinism, why are you unable to suppose that it might go further than that? Excuse the crude analogy, but 1,000,000 – 10 = 999,990, therefore 1,000,000 – 10 -10 -10 -10 -10 -10, etc……= an ancestral species. Given many millions of years to act, I think this is a reasonable hypothesis. Much more likely than just appearing out of thin air due to the handiwork of a designer, of whom we know nothing about and there is no evidence of at all.

Also, neo-Darwinism does not suggest that any individuals climbed a mountain. Just that a population of individuals made a “10-yard” journey, and that those better equipped to successfully make the journey are the ones who successfully completed it. The population then reproduced and a new population with slightly better “mountain-climbing” properties engaged on the next “10-yard” journey, before reproducing again. And so on, until we arrive at the modern day and we look to the base of the mountain and see that our distant relatives look nothing at all like us. Then we wonder how we made the journey?? You presume that a designer had to intervene at some stage or at many stages, with no evidence, and expect biologists to explain the full journey step-by-step…

No one expects to do one set of experiments to show exactly step-by-step how we got from a single-celled organism to a human being. This is akin to me asking you to describe in a step-by-step way how a designer made every living thing and what exact mechanisms were used to do so. We have to start by describing one step at a time. Neo-Darwinism is doing this, as you admitted yourself, but ID jumps straight to the whole answer at once without considering the steps at all.

In terms of my research I described, the work is still ongoing and not yet published, however I can direct you to several other papers which discuss how antimicrobial peptides (called peptides but are really short proteins, generally over 40-50 amino acids), which directly kill pathogens, also have other functions, including acting as chemokines, wound healing and immunomodulatory. These ‘secondary’ functions were discovered long after the ‘primary’ antimicrobial function was established.

Immunomodulatory properties of defensins and cathelicidins. Curr Top Microbiol Immunol. 2006;306:27-66

A re-evaluation of the role of host defence peptides in mammalian immunity Curr Protein Pept Sci. 2005 Feb;6(1):35-51.

Mammalian defensins in immunity: more than just microbicidal. Trends Immunol. 2002 Jun;23(6):291-6

It may be the case that many proteins have other functions we don’t know about yet, thus filling up the intermediate evolutionary stages that ID proponents claim are non-functional. The answer to this question should be lets do the research and find out, NOT lets assume a designer made it because we haven’t yet shown how it happened. That is unscientific.

Concerning the identity of the designer, you wrote…

“ ID does not address religious questions about the identity of the designer”

and

“But right now, absent a time-machine, we don’t know how.”

By saying that ID is not concerned with finding out who the designer is simply renders the whole hypothesis as unscientific. It would be like the pro-Darwin community claiming that it is not concerned with the origin of life because it is “absent a time-machine”. It is an easy way out and constitutes BAD scientific morals as it just stunts progress. Thankfully, for the majority this is not the case and many groups are doing actual experiments to try and determine how life arose on this planet, unlike the ID community, who strangely claim that they are not concerned with the answer, as if this is a scientifically valid position. In fact, I believe that the only reason ID distances itself from the identity of the designer is because, as God is the obvious candidate, this would diminish their much sought-after scientific credentials.

You wrote…

“ Whether traditional theists or not, ID proponents are entirely open about their views on the identity of the designer”

If so, then what are your personal views on this question? I assume you believe the designer is God. Are there other possibilities apart from God? If so, what are they and who believes in them? This must mean that there are some possible designers that are not part of the supernatural realm. Therefore, there might be physical evidence out there. Why not look for it?

“…I don’t know how to use that DNA evidence to determine whether the designer is natural or supernatural. If you have any ideas how to do that, I’m all ears.”

I’m not talking about only biochemical evidence. Why doesn’t ID branch out into archaeology and look for any signs of greater than normal intelligence in the past. Surely someone intelligent enough to create flagella and eyes and immune systems would have left some non-biological signs of their presence.

I think this is a reasonable request of the ID community, go and look for non-biological evidence of the designer, there simply must be some out there. An archaeologist doesn’t just find an ancient relic and then declare ‘I have no interest in researching who made this’. If IDists are unwilling to do this, then they are essentially admitting that the designer is in the supernatural realm, which has the knock-on effect on the whole hypothesis as being unscientific. If ID wants to be respected by the scientific community, it cannot make a claim, and then stick its head in the sand when asked about a direct prerequisite for that claim.

To summarise there are two positions you can take:

1. The designer is God or some other supernatural being

2. The designer is not supernatural and is a physical being

If you believe #1 then your whole hypothesis is not scientific and will never be accepted as such. In fact, it is becoming a form of creationism, irrespective of the fact that you claim ID is about the design and not the designer.

If you believe #2 then branch into archaeology and look for some non-biological evidence to back up your claim. At least make an effort to do so. Your apparent lack of interest makes it look as though you already know there is no evidence out there.

What happens though is that IDists adopt an ambiguous stance where either #1 or #2 is possible. Thus, this means that option #1 is possible and by default this means that ID is based on an unscientific premise.

To conclude, if a person who was scientifically minded but knew nothing much about evolution or ID and was impartial to religion was to hear the arguments for both and see
the evidence for both, I strongly believe that person would deduce that evolution was the only plausible explanation for complex life. In fact, that is what happened at Dover. Both sides had their expert witnesses and both sides had a fair chance to argue their case. I have read the court transcripts and Behe was on the stand for a few days backing up his claims but still didn’t make a convincing argument and even had to admit that technically ID was akin to astrology. The fact that Judge Jones may have plagiarised sections of his decision is not acceptable, I agree with you there, but I am quite sure this was a simple case of laziness. Do you think he had a differing opinion on the case and at the last minute decided against it and instead opted to just copy someone else’s opinion? No, of course not. He was quite sure of his ruling but stupidly plagiarised some of it.

I think Mr Rothschild summed it up nicely in his closing comments…

“The board's behaviour mimics the intelligent design movement at large. The Dover board discussed teaching creationism, switched to the term "intelligent design" to carry out the same objective, and then pretended they had never talked about creationism. As we learned from Dr. Forrest's testimony, the intelligent design movement used the same sleight of hand in creating the Pandas textbook. They wrote it as a creationist book and then, after the Edwards decision outlawed teaching creationism, simply inserted the term "intelligent design" where "creationism" had been before.”

You may say that ID has nothing to do with creationism, but creationists don’t agree with you and love to use ID as a central piece of their ‘evidence’. ID supposes the presence of an intelligent designer, the most obvious candidate being God, a fact that I’m sure you yourself believe, thus ID and creationism are not mutually exclusive.

Anyway, that’s enough for now. I look forward to your comments,

Kind Regards

Rhiggs

From: Rhiggs
Sent: 12 March 2008 11:48:17
To: Casey Luskin (cluskin@discovery.org)
Subject: ID research

Dear Mr. Luskin,

As I did not get a reply to my last email, I thought I would send it to you again (see below). I appreciate that you may have been busy however I hope that you aren't simply ignoring my arguments. You clearly stated in your last email that...

"If you want to talk about other subjects, I’m happy to do that. But let’s finish our conversation about the relevant topics at-hand before we jump to other topics."

...so it seemed to me that you were keen to continue our discussion, as am I.

I hope to hear from you at your earliest convenience,

Regards,

Rhiggs

From: Casey Luskin (cluskin@discovery.org)
Sent: 12 March 2008 13:39:14
To: Rhiggs
Subject: ID research

Dear Rhiggs,

Hi again—thanks for your kind reply. I assure you that I don’t ignore arguments. You don’t know me and I am not that kind of person. In fact, I’ve been traveling a lot for work lately, but in the last week over the course of 2 long plane flights I’ve managed to find time to work on replying to you. I’m nearly done with the reply and I hope to finish it on another flight I have later this week. FYI, my reply is already over 5000 words, and it begins by saying, “Greetings after an undesired delay on my part. I appreciate the time you took in your extensive reply. Because you put in so much time, you deserve a reply. I apologize that it took a while to reply--I've been busy a lot over the past couple weeks, including much traveling, and in fact I'm finally getting some free time now that I'm on a flight.” Thanks again—I hope you will hear from me soon.

Sincerely,

Casey

Its been 13 months since then so Casey must be writing one hell of a long reply...