Critique of Behe and Snoke (2004) to be Published

| 122 Comments

Last year Ian, Steve, and I wrote a critique of a flawed anti-“Darwinian processes” paper by Michael Behe and David Snoke. At the time we had been discussing turning it into a publication, but we set aside the idea after we learned that the editors of Protein Science had asked an expert on gene evolution, Michael Lynch from Indiana University, to write a response to Behe and Snoke (2004).

Now it comes to pass that Michael Lynch’s response and a reply by Behe and Snoke is going to be published in next month’s Protein Science.

We’ll keep our readers informed about Lynch’s analysis of Behe and Snoke’s science.

122 Comments

The best thing about that,

They call it the BS model.

Its going to be sweet I tells ya.

I still think you guys should have just submitted.

I’d be interested to see Behe’s response, bearing in mind his rather novel way of responding to criticism and evidence countering his views.

Just a thought:

Won’t it be utterly amazing if it one day turns out that Ian, Steve and Reed, upon learning that the editors of Protein Science had asked Michael Lynch to respond to Behe and Snoke (2004), immediately put themselves in contact with Michael and tried to be ever so useful, offering in so many words to help his fingers find their way around his keyboard? Why, I know I’d be simply shocked to find that out!

Maybe we won’t find that out, but something about this post says otherwise.

Was this the same Michael Lynch who said:

Michael Lynch on ID

Two factors have facilitated the promotion of ID. First, IDers like to portray evolution as being built entirely on an edifice of darwinian natural selection. This caricature of evolutionary biology is not too surprising. Most molecular, cell and developmental biologists subscribe to the same creed, as do many popular science writers. However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity. Building a straw man based on natural selection alone makes it easy for opponents to poke holes in evolution.

So, according to Lynch, most molecular, cell, and developmental biologists subscribe to the caricauture of evolution called “evolution by natural selection” alone. What! Most biologists believe in a caricature of evolution, rather than true evolution? How regrettable.

What is a caricature of evolution by IDists is an accepted creed by many biologists. Reminds me of the old saying, “what’s one man’s garbage is another man’s treasure.”

neurode Wrote:

Michael Lynch to respond to Behe … immediately put themselves in contact with Michael and tried to be ever so useful, offering in so many words to help his fingers find their way around his keyboard?

You can’t even troll well. Ambiguous antecedent.

Serious question: It seems to me that although the “issues” that IDers raise are ideologically rather than scientifically motivated, they do sometimes suggest intersting avenues of investigation. My question is, are these areas that are being/have been/would have been investigated anyway? Are these areas of investigation that are not scientifically fruitful, but a mere distraction? Or is it the case that, however unscientifically motivated, ID sometimes motivates some inquiries that provide interesting new data? I don’t mean to imply that ID will have all been worth it if only we can build a mousetrap without a spring or something; I just wonder–do they ever push research in an interesting direction with the questions they pose?

the irrepressible Cordova Wrote:

So, according to Lynch, most molecular, cell, and developmental biologists subscribe to the caricauture of evolution called “evolution by natural selection” alone. What! Most biologists believe in a caricature of evolution, rather than true evolution? How regrettable.

Hey Sal: what do you suppose Lynch might be alluding to as underappreciated foundations of the edifice of evolution, other than natural selection? I think you and Lynch should co-author a post here on PT to enlighten us.

neurode Wrote:

Maybe we won’t find that out, but something about this post says otherwise.

We also learned that he had read our critique.

But let me be honest here, I doubt there is little we could do to help Lynch, who has published several papers on the topic discussed by BS04.

Sal, in his usual quote mining has come across a quote by Lynch but fails to see the larger picture

What is a caricature of evolution by IDists is an accepted creed by many biologists.

In other words, ID proponents are attacking a strawman namely that natural selection is the only component of evolution. Of course, ID itself proposes no explanations or mechanisms itself and remains not only a caricature but also scientifically vacuous.

I am looking forward to Lynch’s article addressing the strawmen of the Snoke and Behe paper. PT set a high bar here…

More from Lynch

Lynch Wrote:

But features of the genome, such as genomic parasites or non-coding introns, which aren’t so evolutionarily favourable (nor obviously ‘intelligent’ innovations), can be more readily explained by models that include random genetic drift and mutation as substantial evolutionary forces.

What does ID have to propose again Sal?…

Poof?…

Greg: The central “issues” raised by ID proponents ultimately have to do with the overall nature of reality, and the primary source of order in the various patterns it displays.

The problem: some definitions of “science”, the nominal purpose of which is to study reality (aka “nature”), exclude certain possible features of reality from scientific consideration on an a priori basis, and are thus oxymoronic. However, I regret to inform you that you are highly unlikely to get any garden-variety ID critic to admit that the overall nature of reality, and the primary source(s) of natural order, are accessible to science as they conceive it.

On another note, Bayesian Bouffant apparently considers himself to have been semantically victimized by an “ambiguous antecedent” in my last post, namely, “Michael”. In other words, Bayesian thinks that I might have meant that Ian, Steve and Reed may have wanted to help Michael Behe rather than, or in addition to, Michael Lynch.

First, this confirms for all to see that the verbal milieu, i.e. language, favored by Bayesian is strictly context-free, each of its expressions properly standing alone and requiring no interpretation in light of context. And given that this would make language accessible even to readers with memory capacities of no more than one sentence, it suggests that Bayesian possesses every bit of the acuity which he was already credited.

The problem: some definitions of “science”, the nominal purpose of which is to study reality (aka “nature”), exclude certain possible features of reality from scientific consideration on an a priori basis, and are thus oxymoronic. However, I regret to inform you that you are highly unlikely to get any garden-variety ID critic to admit that the overall nature of reality, and the primary source(s) of natural order, are accessible to science as they conceive it.

Unfortunately, the only problem here is that this statement is factually incorrect. Science does NOT exclude anything but those things it cannot investigate - are you stating that ID is inherently untestable? That would accord with the usual nonsense that Dembski, Behe, et. al. promulgate, and is completely in line with the essentially vacuous statements of “Sallie” Cordova.

Clearly ‘intelligent design’ exists - we have genetically modified organisms; bred-species; beaver dams; etc. Science investigates all those things - so the claim that it doesn’t permit ID a priori remains a farcical distortion of science based on lack of knowledge.

Rilke’s Granddaughter: “Science does NOT exclude anything but those things it cannot investigate - are you stating that ID is inherently untestable?”

No, I’m stating that to meaningfully use the term “science”, we need a comprehensive account of what science is, including its proper domain of inquiry and range of application.

Regarding the former, you say that science excludes only “those things it cannot investigate”. However, in order to decide what science “cannot” investigate, we need to logically establish the boundaries of science independently of any particular scientific theory or preferred model of science.

Since this has not yet been accomplished, we are regrettably unable to exhaustively characterize what science does or does not exclude. This means that the issues ultimately addressed by ID theory cannot be summarily excluded from science.

In other words, any reasonable definition of science makes science contingent on its domain of inquiry, reality. To instead make reality contingent on a preferred mode of scientific inquiry is to engage in a logically unacceptable kind of circular reasoning.

But haven’t there been a preponderance of critiques of ID literature that shoot holes through Dembski’s CSI and Behe’s Irreducible Complexity, etc, etc..

The issues addressed by ID theory (what is that theory again? I think you have “theory” confused with “proponents”) have been countered many times. these “issues” have been measured and found wanting.

“No, I’m stating that to meaningfully use the term “science”, we need a comprehensive account of what science is, including its proper domain of inquiry and range of application.”

I’ll make it simple for you then.

1) Make a prediction about some observation from the natural world

2) Test the prediction using some form of experimental procedure

3) Publish the result and importantly, have your experimental predictions repeated by other researchers

4) Repeat from step 1 now with the new information in mind.

This is very simple and is the basis for ALL science. ID fails at step 2, because not only do they lack a theory, they don’t even have the beginnings of a proper hypothesis (which is really quite sad after all this time). They think science works like this:

1) Say “Goddidit” and then hide behind the same creationist arguments that were broken down years earlier, with new technical jargon so they sound like new ‘science’.

2) Don’t bother experimentally verifying it in any way, instead whine about ‘Darwinist’ conspiracies and try to stack school boards to get various idiocy taught (ID proper, failed creationist criticisms of evolution or whatever nonsense is required)

3) Keep whinging through political channels

Without experiments and actual science, as in making testable predictions about the designer, which would require naming said designer incidently. It’s little wonder why IDists are so afraid to do such basic science seeing as they are terrified of naming their designer.

Honestly, science isn’t hard to grasp or understand. You make predictions based on what you observe and then experimentally test this in a laboratory. What seperates science from witchcraft, quackery, ID and everything else from this point is that those predictions and experiments must stand up to replication by independant parties. If someone else can’t replicate your results then it’s time to be asking serious questions about the legitimacy of the original paper and its methodology.

However, in order to decide what science “cannot” investigate, we need to logically establish the boundaries of science independently of any particular scientific theory or preferred model of science.

No, I don’t think we do. My observation is that scientists attempt to bring the scientific method to bear on matters that method is inherently incapable of addressing, on a regular basis. Generally, this is the case because what is being investigated is not well understood, or clearly articulated, or well-bounded. So the idea is, something *might* be testable, or might not, and the practical way to make this determine is not by potificating about logic, but about actually going out and making the effort to do the investigation.

This isn’t either a bad or a dumb thing, because some notions are as broad as they are hazy, and the attempt to operationalize them into “what we are looking at using method X” clarifies which portions if any are testable, and which are more definitional or more matters of social convention.

As an example, consider those experiments looking into the efficacy of prayer to ameliorate medical problems. Now, DOES prayer actually “do” anything beyond the placebo effects? Is there a real intercession effect that can be isolated from anything else involved? It’s entirely possible that prayer helps only the state of mind of those doing the praying, there being nobody “out there” to hear the appeals. But maybe there ARE some gods listening out there who have medical skills and are flattered to apply them. Until the scientific effort is made, how can we know (other than just SAYING we know)?

The results of these studies suggest that the target of the investigation (some otherwise indetectible agency) was indeed beyond the “proper domain of inquiry and range of application” of science. But science can only learn this by practical trial and error, where there is any fuzziness in the description of what’s going on.

This means that the issues ultimately addressed by ID theory cannot be summarily excluded from science.

I don’t think this is an issue here. My reading is that nearly everyone here has been just begging the ID people to produce anything even remotely resembling “ID theory” and not one single testable idea has been forthcoming. If you can tell us what “ID theory” predicts, even if (like Behe) you don’t bother to suggest a single test, much less attempt to test your own ideas, leaving it up to everyone else, people here would be most grateful.

But claiming that there IS an “ID theory” without ever producing one is nugatory.

Salvador Cordova said: “So, according to Lynch, most molecular, cell, and developmental biologists subscribe to the caricauture of evolution called “evolution by natural selection” alone. What! Most biologists believe in a caricature of evolution, rather than true evolution? How regrettable.”

Yes, it is. Of course, I am sure few of these biologists claim to be experts on the mechanisms of evolution, vs. topics in their subfields. Didn’t the fields mention give you a clue? Those who claim to have a great insight on evolution, however, should at least know that natural selection is not all of evolution. For heaven’s sake, haven’t they ever read Stephen Jay Gould?

Salvador: “What is a caricature of evolution by IDists is an accepted creed by many biologists.”

Believing something because that was the way it was taught “way back when” is somewhat excusable, except for a lack of curiosity about some of the major issues in biology outside their field. Attacking a caricature when it is known to be a caricature AND you should know better is totally inexcusable.

Comment #44617

Posted by neurode on August 24, 2005 11:35 AM (e) (s)

The problem: some definitions of “science”, the nominal purpose of which is to study reality (aka “nature”), exclude certain possible features of reality from scientific consideration on an a priori basis, and are thus oxymoronic. However, I regret to inform you that you are highly unlikely to get any garden-variety ID critic to admit that the overall nature of reality, and the primary source(s) of natural order, are accessible to science as they conceive it.

Saying that science precludes supernatural considerations is utterly irrelevant to ID. If you will recall, IDers have stated, numerous times, that there is nothing religious here. This is just science. No supernatural beings are required by ID. From Wikipedia:

Most ID advocates state that their focus is on detecting evidence of design in nature, without regard to who or what the designer might be. However, ID advocate William Dembski in his book “The Design Inference”[1] lists a god or an “alien life force” as two possible options.

Science obviously doesn’t preclude, a priori, the study of alien life forces.

Comment #44649

Posted by Tracy P. Hamilton on August 24, 2005 01:07 PM (e) (s)

Salvador Cordova said: “So, according to Lynch, most molecular, cell, and developmental biologists subscribe to the caricauture of evolution called “evolution by natural selection” alone. What! Most biologists believe in a caricature of evolution, rather than true evolution? How regrettable.”

A caricature version of a given theory is likely still more useful than Puff Of Smoke, or POS, Theory.

Joseph O’Donnell may be a bit off the track when he writes that “science isn’t hard to grasp or understand.”

The nature and methodology of science is in fact a very involved and difficult topic. Contrary to what Joseph seems to believe, most scientists are not trained to function adequately on this level of discourse.

For example, what sort of hypothesis is one permitted to formulate, and what kind of prediction is one permitted to make? What sort of experiment is one permitted to run, and how is one permitted to run it (for example, can one use mathematical simulations that correspond to reality only at certain junctures, but not at others)? How are experimental outcomes to be interpreted? What are the limits of scientific confirmation? And what are the proper editorial criteria for scientific publication?

These issues really are important, and I’m afraid that until Joseph realizes this, he has little business laying down the law for ID.

Flint says that “scientists attempt to bring the scientific method to bear on matters that method is inherently incapable of addressing, on a regular basis.”

I’m pleased to say that I’m in full agreement on this point. However, simply “going out and making the effort to do the investigation” does not provide sufficient grounds for restricting the domain of scientific inquiry.

ID predicts order in nature, specifically in the biological realm. Neo-Darwinism also predicts biological order, but only as predicated on a restricted form of nature itself; hence, it relies on the order already implicit in “nature” (as they define it) prior to its biological manifestations. The difference: in its most fundamental form, the ID hypothesis is about the primary source of this order and the process by which it arose, while neo-Darwinism simply addresses (e.g.) statistical transformations of this order once it is given.

For reasons already given above, it would be premature to say that the primary source of biological order, and the means of its generation, cannot be scientifically investigated.

neurode:

However, simply “going out and making the effort to do the investigation” does not provide sufficient grounds for restricting the domain of scientific inquiry.

Not so. The domain of scientific inquiry is established by this very process. Where misguided attempts are made, in all honest ignorance, to investigate the imaginary, the investigations fail. And this is HOW WE KNOW what is imaginary. It’s perfectly “permissible” (whatever you mean by that term) to attempt to apply the scientific method to the untestable, although by implication the effort must miss the point, and be “testing” something other than what was (poorly) described. The scientific enterprise does not know its limits a priori, it learns those limits day by day.

it would be premature to say that the primary source of biological order, and the means of its generation, cannot be scientifically investigated.

I doubt anyone would disagree with this, and in fact abiogenesis is an active field of investigation. Most speculation I’ve seen (we’re still in the speculative phase) is that the die could have been cast in any of a wide variety of initial directions: right-handed chirality, different possible RNA models, who knows? The notion here is that evolutionary processes build on what precedes in a cumulative fashion. Right at the beginning, the very first successful forms (whatever they were) became pretty much willy nilly the “primary source of biological order” and sheer chance (within the scope of workability) set up permanent biases we see forever after.

Neurode Wrote:

For reasons already given above, it would be premature to say that the primary source of biological order, and the means of its generation, cannot be scientifically investigated.

Then perhaps Neurode can predict for us when the ID “scientists” are going to get off their fat asses and do some actual work, or explain why they remain in a catatonically recumbent posture when there’s so much important work to be done.

The nature and methodology of science is in fact a very involved and difficult topic. Contrary to what Joseph seems to believe, most scientists are not trained to function adequately on this level of discourse.

Considering that I happen to actually do science (of the laboratory kind even) I happen to know quite a lot about this area, as anyone who actually does science learns (often the hard way). Once again, despite what people try to claim science ‘is’ it really boils down to being able to make predictions that can be tested and then replicated. The hard part of the methodology of science is knowing exactly what methodology to employ to answer your question, but even so that is why the point about replication is so important. Other researchers have to agree that your method is suitable and accounts for the observation you claim it does, hence the whole importance of being able to repeat other scientists methodology. Evidently, the importance of this and why it distinguishes science from just making wild guesses (like ID does) is not clear to you. Everything else you’ve gibbered about is relatively meaningless however, because once again, science works by replicating the results of other researchers and building upon previously made hypotheses. If someone had a computer simulation that was flawed, it would likely be discovered because someone attempted to replicate their results and found it deficient in that area.

They could then propose a new hypothesis that purports to explain that better than the previous group. Slowly but surely, after repeated rounds of challenge and revisal the original hypothesis will either be supported or it will get replaced by one that fits the evidence better. Evidently, Neurode seems to think that science ‘suddenly’ comes out with the best methodology immediately and doesn’t appreciate the sheer amount of effort, work and time that goes into perfecting new methods (IE: producing monoclonal antibodies, using specialised adenovirus vectors carrying modified thymidine kinase genes to destroy cells with latent papilloma virus etc). Ultimately, all of these are developed in exactly the way I described, despite what neurode ‘thinks’ science works.

Once again:

1) Make a prediction about some observation from the natural world

2) Test the prediction using some form of experimental procedure

3) Publish the result and importantly, have your experimental predictions repeated by other researchers

4) Repeat from step 1 now with the new information in mind.

I think it’s simple, if you cannot design a suitable test for the prediction you are proposing then it’s simply put not science. This is why I straight up said ID fails at step 2. Simple isn’t it.

ID predicts order in nature, specifically in the biological realm.

And funny that Neurode, it fails to answer that question exactly as I described above. They don’t bother doing actual experiments that can be repeated and independantly verified. It’s also interesting that they’ve never done anything more than present strawman creationist caricatures of evolution rather than actual data for said intelligent design. That in itself speaks volumes about ID as ‘science’.

good carl zimmer article about new research into why people behave as essentialists. http://www.corante.com/loom/archive[…]za_virus.php

Essentialism, of course, being the mistake behind the ‘A fly doesn’t give birth to a horse’ line of creationist thinking talking.

Flint: “Not so. The domain of scientific inquiry is established by this very process.”

Translation: “The domain of scientific inquiry, that is, objective reality, is established by the (frequently over-restricted or wrong-headed) process of scientific inquiry.”

Reality exists prior to any particular formal definition or informal conception of science or its methodology. Therefore, although science often attempts to define its own domain in practice, it can at best describe that domain to some imperfect level of accuracy. Reality is not actually subject to the inaccuracy of any particular description of it, and cannot thereby be limited without danger of fatal circularity.

Joseph, I’m afraid you’re just not getting it. The issue is “what can be interpreted as evidence of the ID hypothesis?” ID proponents cite biological order as evidence of their hypothesis, and I assure you that observations of biological order are highly replicable.

“But wait!” you ejaculate. “Neo-Darwinism already owns that evidence!”

I regret to inform you that neo-Darwinism owns nothing of the kind. As I’ve already attempted to explain, it owns the evidence only within the range of its hypothesis, i.e., with respect to the order implicit in already-existing organisms and its causally restricted model of nature. Unfortunately, you have not yet established that this amount of order suffices to explain evolution, unless you simply regard evolution as a mere set of statistical effects revealing nothing about intergenerational transformations of biological form and function.

On the other hand, the ID hypothesis owns the evidence within the range of its hypothesis, which has to do with the primary source of order in biology and nature at large.

I strongly suggest that you turn down the arrogance on your end, lest I turn it up on this end and make you look even worse than you already do.

Can we please stay on topic?

Joseph, I’m afraid you’re just not getting it. The issue is “what can be interpreted as evidence of the ID hypothesis?” ID proponents cite biological order as evidence of their hypothesis, and I assure you that observations of biological order are highly replicable.

Wrong. Once again, their results have failed to be replicated. Once again, every system they have claimed is ‘evidence’ of design (the Flagellum, blood clotting cascade) has failed. Further, they have yet to put forward testable claims of any sort that have survived experimental verification. It’s really that simple Neurode.

On the other hand, the ID hypothesis owns the evidence within the range of its hypothesis, which has to do with the primary source of order in biology and nature at large.

Once again, you imply they have a hypothesis. Yet, as all ID advocates fail to do, you fail to establish what experimental procedures and methods were employed to actually test these hypotheses. As I said, if you don’t have experiments that people can repeat you’re not doing science. It’s pretty simple here Neurode.

I strongly suggest that you turn down the arrogance on your end, lest I turn it up on this end and make you look even worse than you already do.

I’m not scared :) You’re all bark and no teeth Neurode, because as I’ve already pointed out, ID has no experimental evidence supporting it. That’s why it’s nothing more than a political movement using technical language to pretend it’s a science. Can you point me to papers published on ID that actually put forward testable predictions about the designer, what methodology the designer used to create life and how this accounts for the observations better than evolution?

steve:

“A caricature version of a given theory is likely still more useful than Puff Of Smoke, or POS, Theory.”

Actually, The Puff of Smoke hypothesis can generate testable predictions:

Prediction 1. At least some mutations will be accompanied by a puff of smoke.

Test 1. Look for tiny puffs of smoke inside cells and see if there are now new genetic sequences.

If this is, in fact, observed, we should also be able to identify the residue of the smoke and the look for that residue inside other cells. If this residue is then identified in other cells that also have new genetic sequences, the hypothesis will be confirmed.

Prediction 2. At least some speciation events will be accompanied by a puff of smoke.

Test 2. All smoke that is not readily identified as coming from a known source should be investigated to see if there are any new species at that location.

If this is observed, we should also be able to identify the residue of the smoke and then look for that residue elsewhere to see if it is accompanied by speciation events. If the traces of the puff of smoke are non degradable, or degradable in a predictive fashion, we may also be able to do atmospheric studies to estimate the rate and time frame of speciation events. (Considering that this could conceivably give a lower level limit to species creation, YEC’s would also be very interested in this type study).

So, here we are, the POS hypothesis makes testable predictions. I breathlessly await the announcement of funding for these projects by the ID scientists. Considering that the ID movement has fairly deep pockets, this announcement should come anytime now.

Shenda

Lenny, I checked out the site to look for predictions made based upon evolution, which could be tested by experimentation.

http://www.don-lindsay-archive.org/creation/evo

The predictions listed aren’t predictions in the usual sense, where you make predictions based upon a hypothesis and don’t yet know the the outcome of the experiment.

They are more like explanations of how past events gave rise to present observations.

Are there any experimental predictions that evolution makes for events that have not yet occurred (fortelling a future outcome as opposed to a past outcome)?

John,

I’m spending the entire semester explaining the basics of these five forces to undergrads. I don’t have the time to provide the same information to you on this blog.

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This page contains a single entry by Reed A. Cartwright published on August 23, 2005 8:02 PM.

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