The Pro-ID Paper That Wasn’t.

| 274 Comments

Bill Dembski and company are having a self-congratulatory session about a new “pro-ID” paper published by Finnish researchers Matti Leisola and Ossi Turunen in Applied Microbiology and Biotechnology. Looking at the paper, you wouldn’t know that it’s a “pro-ID” paper at all because it contains not one shred of evidence in favor of ID, nor does it even try directly arguing for ID (compare this to the Meyer paper, which while riddled with errors, at least put forth pro-ID arguments). On what basis could it possibly be a pro-ID paper? If it weren’t for the fact that Matti Leisola is a creationist, there would be no reason to believe it was intended as such at all.

Nevertheless, Dembski apparently thinks that it’s a pro-ID paper on the basis of its content, presumably because he conflates rational design methodology as used in protein engineering with ID. Of course this is nonsense, and in reality the paper is merely a redundant review of the current state of protein engineering techniques, with most of the space dedicated to the very long list of successes enjoyed by evolutionary methods. There are much better reviews out there, but nevertheless Leisola and Turunen give a decent (if too limited) overview of directed evolution experiments. Then they proceed to argue that rational design methods will start working better once we have more detailed knowledge of the mechanism by which the primary sequence of a protein determines its structure and function. This is an obvious and noncontroversial conclusion, so one is still left wondering how this could possibly be spun as “pro-ID”. I’ll say more about that in a minute, but first let me give a quick overview of the state of protein engineering as it exists today.

There are generally two ways one can go about trying to engineer a protein. The first is to use what is commonly called “rational design”. As the name implies, this simply means taking what you know about the structure and function of a protein and trying to predict which changes you need to make in order to get a desired result. The problem with this approach is, first of all, that you need detailed knowledge of the protein’s structure and function. Not all proteins have had their structures solved, and many of their functions are either poorly characterized or not characterized at all. Obtaining this knowledge is an expensive and time consuming process. And secondly, no one really knows what the exact relationship is between sequence, structure, and function. Even if you know everything there is to know about a protein’s current structure and function, it is very difficult to predict what’s going to happen when you start changing things around.

So protein engineers employ a second technique known as “directed evolution”. Again, the name tells you essentially what the technique involves: you apply random mutagenesis to whole or part of your protein, you screen for the properties you’re looking for, and you repeat the process as necessary. In other words, you use the Darwinian mechanism, the very mechanism that ID advocates have spent the last decade fruitlessly arguing is incapable of doing the very things we see it doing in the lab. And as it turns out, directed evolution methods are generally superior to rational design methods, so much so that a number of successful biotech companies such as Diversa and Applied Molecular Evolution use directed evolution as their primary engineering tool. (Incidentally, creationists who argue that evolution has no practical applications – paging Michael Egnor! – should sit down and have a talk with the officers of these companies.) But in spite of the success of directed evolution techniques, they’re not without drawbacks. You need a means of screening large numbers of mutants quickly (known as high-throughput) in order to find the rose among thorns. This means using expensive automated equipment and/or a lot of researchers. Plus such screens often have to be developed independently for each individual protein, and lots of proteins just aren’t going to be easy to screen. So both rational design and directed evolution each have their advantages and disadvantages. Luckily, researchers are not limited in which approach they use, and when applicable, they will use both directed evolution and rational design approaches together.

Okay, now back to the paper. One of the central deceits of the ID movement is to claim that anytime a human being designs something, she is using the theory of “intelligent design”. Sorry, but no. Researchers who employ rational design techniques do not operate under the premise that natural proteins were “designed” by some unknown intelligence using unknown methods. And if for some reason they did, it would be entirely unhelpful. The paper does not argue directly that rational design methodology somehow supports “intelligent design”, but given Leisola’s creationist sympathies, this might be what he intended. And this is certainly what Bill Dembski is implying, going so far as to claim that it is “pro-ID article without the usual disclaimers…” But absent the glaringly illogical attempt to connect protein engineering with ID, there is no support for ID to be found anywhere in the paper. (In fact, the phrase “intelligent design” does not even appear in the article – how could it be a “pro-ID article without disclaimers” if ID never even gets mentioned?)

The only claim that might be relevant to the ID/evolution debate is in one small section titled “Obstacles in protein engineering” in which the authors argue that there is an “Overreliance on the Darwinian methodology”. But this argument is made very tepidly, and little if any support is provided for it. Leisola and Turunen are forced to conceded throughout the paper that Darwinian methods are not only highly successful, but are more successful than rational design approaches. They merely contend that as our knowledge of protein structure and function improves, rational design approaches will also improve. Well, yeah, that’s kind of obvious. If someday we obtain perfect knowledge of the relationship between protein sequence, structure, and function, then rational design methods will definitely be superior. How could they not? If you can make a precise prediction about which mutations will generate which functions, you can skip the messy high-throughput methods and just go straight to the desired result. It’s no secret that evolution is a slow and wasteful process requiring a lot of trial and error. That’s why life on Earth took billions of years to reach its present state; if the ID people were correct, one would imagine that the goals of the “designer” would have been reached instantaneously.

In the meantime however, directed evolutionary approaches are very powerful, and even rational design approaches are increasingly incorporating evolutionary methods. (This is one major weakness of the paper – rational design and evolutionary methods are presented as an either/or dichotomy, when in fact rational design approaches, particularly those derived from computational models, make extensive use of evolutionary theory.) Most importantly, directed evolution refutes one of the central tenets of ID argumentation, which is that the Darwinian mechanism — random mutation plus selection – cannot generate new “information”, protein functions, or whatever. We knew this was false long before the ID movement ever began. Now they’re reduced to arguing that just because directed evolution methods are less than perfect, or that researchers can design stuff directly, that this somehow supports ID. And of course there’s the annoying spectacle of pretending as if an ID advocate getting a paper of any kind published is some sort of coup. Dembski claims that “perhaps this is a sign of things to come.” Actually we’ve been seeing it for quite awhile now.

274 Comments

When I saw it I just thought it was another case of claiming that every biology paper is in fact an ID paper.

But oh yeah, rational design methods will be better if we have exhaustive knowledge of protein structure and function, as well as a huge computing ability.

What these people forget is that such rational design methods won’t be finding the same solutions, certainly not in many cases, because rational design won’t be hamstrung by past evolutionary histories. Extremely good rational design methods will simply further confirm what we already know, that evolution has worked with limitations that a god-like designer would not, and that the proteins and morphologies that we have reveal exactly those sorts of limitations (and not the kinds of poor design found in Pintos).

I suppose they have to claim triumphs wherever, even when they are pointing out the pro-evolutionary fact that everything from the time it took to evolve to the results of evolution are consistent with undirected evolution, not with rational design.

Glen D http://tinyurl.com/35s39o

Steve,

On what basis could it possibly be a pro-ID paper?

I’m surprised you needed to ask this question. Probably, you’re looking at the paper from the point of view of someone who actually knows what “rational design”, “random techniques”, and “Darwinian blind search” all mean in the context of protein engineering.

But you aren’t the DI’s target audience.

Try and think of this from the perspective of a lay-person who’s inherently both sympathetic to ID creationism and unfamiliar with the jargon and concepts of protein engineering. Such a person is going to go to the Uncommon Descent website and see the following abstract…

Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

Now, if you want ID creationism to be true and you don’t know anything about protein engineering, you’re going to think that says: 1) there is “rapid progress” being made in “rational design”, 2) “Darwinian” methods are over-relied upon and don’t give practical results, and 3) “random methods” are being replaced by “design”.

If you’re an ID creationist, that all sounds wonderful! And when Dembski tells you it’s a pro-ID paper, well that just seals the deal!

All that context you explained about what the terminology means and how it’s applied in this specific field is great for people like me who are genuinely interested in understanding things like this, but it’s all just white noise to ID creationists who feed on being told what they want to hear.

To them, this paper looks very much like it’s bashing random Darwinian methods and trumpeting the virtues of design.

Know your enemy and know thier audience.

Now I’ve really heard it all. For the first time I come to understand there are “evolutionary methods” as if to say evolution is methodical and not purely random-based. So if evolution is methodical, who devised the method? The experimenter? Would such a method select the “fittest” for “survival”? With logic such as this is it any wonder you guys are having to spend huge amounts of energy the past few years arguing and insulting us ignoramuses, on the controversy that supposedly doesn’t exist, you know, the one that dominates discussion on PT?

Now I’ve really heard it all. For the first time I come to understand there are “evolutionary methods” as if to say evolution is methodical and not purely random-based.

There are evolutionary methods—when humans are utilizing an evolutionary process. Steve is not writing about evolutionary methods existing out in “nature”.

So if evolution is methodical, who devised the method? The experimenter?

Methodical evolution is designed by the researcher.

Would such a method select the “fittest” for “survival”?

Actually, you have to work your method to deal with the fact that the “fittest” will “survive”. That is, you have to set the parameters so that the design, molecule, etc., will evolve to become fit for certain purposes.

With logic such as this is it any wonder you guys are having to spend huge amounts of energy the past few years arguing and insulting us ignoramuses, on the controversy that supposedly doesn’t exist, you know, the one that dominates discussion on PT?

Unfortunately, the faulty “logic” is your own, since you confused methods which are designed to mimic “natural” evolution in the lab or on the computer, with the evolution which occurs in nature.

Glen D http://tinyurl.com/35s39o

Jason F Wrote:

I’m surprised you needed to ask this question. Probably, you’re looking at the paper from the point of view of someone who actually knows what “rational design”, “random techniques”, and “Darwinian blind search” all mean in the context of protein engineering.

But you aren’t the DI’s target audience.

Well yeah, that kind of goes without saying. I took the time to write this in case there are people who 1) aren’t already committed to Dembski’s point of view, and 2) may not know enough about protein engineering to realize that the authors weren’t talking about what Dembski implies they were talking about. I imagine there are quite a lot of such people. It’s important for them to know that there is no basis on which to call this a “pro-ID” paper, other than perhaps the intent of the authors.

Now I’ve really heard it all. For the first time I come to understand there are “evolutionary methods” as if to say evolution is methodical and not purely random-based. So if evolution is methodical, who devised the method? The experimenter? Would such a method select the “fittest” for “survival”? With logic such as this is it any wonder you guys are having to spend huge amounts of energy the past few years arguing and insulting us ignoramuses, on the controversy that supposedly doesn’t exist, you know, the one that dominates discussion on PT?

It boils down to the fact evolutionists think they can deceive God by deceiving themselves. One day evolutionist will claim their ersatz process of natural selection is random one day and methodical the next. It’s like the bisexuality most of them practice, they do know what it’s going to be from day day.

Steve,

It’s important for them to know that there is no basis on which to call this a “pro-ID” paper, other than perhaps the intent of the authors.

Oh, absolutely! Your time and effort are greatly appreciated.

Two things that should stand out to any objective observer: 1) it’s the “evolutionist” side who provides all the details, definitions, and background necessary to put the cited paper in proper context (OTOH, Dembski just throws out an abstract and declares “It’s pro-ID!” without anything further), and 2) all ID-creationists are still able to do is falsely claim non-ID creationist papers as their own, rather than generating their own research.

And remember, “The Wedge Strategy” made it very clear…

Without solid scholarship, research and argument, the project would be just another attempt to indoctrinate instead of persuade.

…and there you have it.

The “creationist” link points to the “8th European Creationist Conference” and features talks by Leisola and even the DI’s own token YEC (pseudo-YEC?) Paul Nelson. The titles of the talks suggest that it not only promotes creationism, but from the papers about the Flood and the Fall, specifically YEC, or at least a non-progressive OEC (e.g. day-age). But wait. It also promotes ID, which makes it one more thing that undermines the DI’s futile attempts to distance itself from classic creationism. Not that their target audience cares of course; the whole “ID is not creationism” thing is just to get critics to take the bait.

When IDers whine that they are shut out from publishing by those oppressive “Darwinists,” I remind them that all they have to do is drop the design language, just as they do for public school lesson plans. The problem, of which chief IDers are completely aware, is that with or without design language, there’s nothing in their work that challenges evolution; if anything it even adds further support. They can fool high school students, but not scientists, and they know it.

When the few papers by IDers (or classic creationists) get published, they gush about how ID is legitimized by peer review. But when one notes how pathetically few papers have been published by IDers (or classic creationists), and that none provide a shred of support for ID (or the mutually contradictory creationist accounts), they again whine about being shut out. They know that it’s one more thing that ID tries to have both ways. But as long as their cheerleaders don’t care, why should they?

I guess the fact that someone designed a process that mimics nature proves that nature was designed.… NOT!!

Pumpkinhead: the effort you are having to make to keep your creationist beliefs intact is beginning to show.

I was pretty sure that after Dover, the ID crowd would get the message that they had to publish evidence for ID in reputable, peer-reviewed journals. I also figured that, since there isn’t any such evidence, they would find a way to fake it to their audience.

What they will do is publish papers that are pretty mundane and uninteresting while avoiding ID terminology to get by reviewers, but their papers will have enough code words in them that they can brag to their followers that they are now publishing articles that prove ID. Their followers will swallow it hook, line, and sinker, and armed with this belief, will step up their political attacks on legislatures and school boards.

If we point out that none of their papers argue for ID or that they have started no research programs nor improved the scientific understanding of our universe, they will argue that we have moved the goalposts.

None of their followers know what a significant paper does in the world of research. It has to be confirmed, cited in many other research papers, and it has to get a trend going that leads to significant advances in our understanding. I can see other ID/Creationist leaders jumping on the bandwagon to cite and “confirm” the papers of their co-conspirators, but the only “change” in science they can hope to generate will be caused by a massive political campaign that declares that ID is now a “proven” science.

I think we are seeing the beginning of this process. It’s another case of fundamentalists gaming the system to gain the appearance of legitimacy.

Isn’t it common for creationists to parasitize the work of real scientists? They also like to twist the meaning of scientific work so that it seems to say the opposite of what the original author intended. (Carl Zimmer needs to add a new chapter to Parasite Rex.)

Pumpkinhead wrote:

“One day evolutionist will claim their ersatz process of natural selection is random one day and methodical the next.”

You only have to look at the equations to see that natural selection is a completely deterministic process. Anyone who claims any different is not telling the truth. Of course there are still elements of chance and drift that are important for the entire process of evolution, but that is not the point. Can you give any examples of anyone who told you natural selection was “random”? If so, why did you believe them?

People, I’m pretty sure Pumpkinhead is pulling our chain. After all, he called us all bisexuals. Only another evolutionist would know that we’re all bisexuals.

“nor can we specify a sequence that folds to a target structure”

Odd statement. Pulling out a book on Protein Design (called Protein Design), page 5/section 1.1.3, talks about specified sequences that fold into a desired alpha helix (in an aqueous environ). Beta sheets starting on page 27…design of entire protein complexes on page 113. (Methods in Molecular Biology - 340 - Protein Design: Methods and Applications)

In a paper, Biotechnology Advances (vol 23 page 271-281), mesophiles such as us are used as the example of what not to do. In example we have undesirable beta branched residues (I, T, V) incorporated in helices causing conformational strain, increasing the ease of destabilization.

Protein design shows that we are poorly designed, heck we have to take most of our “what we desire to have” from thermophilic bacteria. Amoral processes best explain our poorly placed residues.

Weird authors.

Matti Leisola is a well-known YEC-creationist in Finland. He has translated various anti-evolution books in Finnish including Dembski’s “The design inference” and co-authored with German creationist Siegfried Scherer book “Evolution:The critical analysis”. He even maintains a website that promotes intelligent design: http://www.intelligentdesign.fi/ In 2004 he arranged a lecture series at the Helsinki University of Technology called “Tackling Ultimate Complexity” in which lecturers included Paul Nelson and Richard Sternberg. That year the Finnish skeptic association gave him and to his laboratory the annual “bullshit award” for promoting pseudoscience.

Pumpkinhead Wrote:

It boils down to the fact evolutionists think they can deceive God by deceiving themselves. One day evolutionist will claim their ersatz process of natural selection is random one day and methodical the next. It’s like the bisexuality most of them practice, they do know what it’s going to be from day day.

Wait, that’s a parody right? Brilliant! Nice work Pumpkinhead, I love it!

Matti Leisola is a creationist

Referencing a creationist conference in Sweden 2003. Ouch! And if you can’t read the swedish, they had three presentations on lecturing ‘our origin’.

Public school is supposedly protected from pseudoscience hurting the development and minds of children. But private school is freer. They still has to pass the inspections and requirements of the school authority, which now has stopped the recent attempt of presenting creationism in one school. Now I know what originated that trial balloon.

I also understand why Paul Nelson visited Sweden. IIRC it was that year he snuck [What? Such a simple word not in Firefox spell checker! Why do I have to teach it non-conservative english; am I supposed to know that? Yet another wrong order of things. :-| ] into the swedish national Museum of Natural History, talked with reporters in one of the galleries, and later claimed he had made a presentation at the premises.

Tom Groover Wrote:

Now I’ve really heard it all. For the first time I come to understand there are “evolutionary methods” as if to say evolution is methodical and not purely random-based. So if evolution is methodical, who devised the method? The experimenter? Would such a method select the “fittest” for “survival”? With logic such as this is it any wonder you guys are having to spend huge amounts of energy the past few years arguing and insulting us ignoramuses, on the controversy that supposedly doesn’t exist, you know, the one that dominates discussion on PT?

I know others have already responded pretty well to this but it always bears repeating. We have evolutionary processes in nature, and we have cases where we take what we know about those processes and put them to use in the lab. Directed Evolution for the purposes of Protein Engineering, Genetic Algorithms, etc. Here we determine what we want the evolutionary pressures and selective constraints to be in order to produce a desired outcome (such as with Directed Evolution) or we set the constraints to allow a for a search towards reasonable solutions (such as Genetic Algorithms). It is much like the basis of Animal Husbandry, where our ancestors observed variation and selection in nature and realized they could breed for specific desired traits.

Here in this type of experiment and methodology we are emulating what we know about nature but unlike nature we may have a specific goal in mind (Protein Engineering) and se we set the constraints and environment appropriately. Nature of course does not have a pre-set goal.

Re “talked with reporters in one of the galleries, and later claimed he had made a presentation at the premises.”

Well heck, if he was present there, and talked to some people, isn’t that making a “presentation” there? LOL

Public school is supposedly protected from pseudoscience hurting the development and minds of children. But private school is freer. They still has to pass the inspections and requirements of the school authority, which now has stopped the recent attempt of presenting creationism in one school. Now I know what originated that trial balloon.

Like his Viking ancestors who made their living raping, killing, pillaging, and burning peaceful Christian communities, this Scandinavian evolutionist can not tolerate any dissent from the evolutionary theology of the modern secular state.

The zeal to which Darwiniacs will persecute dissidents never ceases to amaze me. Even in an area where popular opinion veers toward the evolutionists side; they still hysterically try to stamp out all traces of Christianity.

Wait, that’s a parody right? Brilliant! Nice work Pumpkinhead, I love it!

Not everything that appears to be a parody actually is. This movie starring Don Johnson based on Robert Rimmer’s book was actually based on the author’s observations of college life in the increasingly Darwinian ethical framework that began to dominate American campuses in the 1950’s.

Like his Viking ancestors who made their living raping, killing, pillaging,…

Reminds me of a joke.

A Viking and his three grown sons are getting off of their long-boat, about to sack a town. The Viking lays out his strategy: V: “Ok, we’re gonna have a really good sacking today.

V: [To his eldest son] “Ok, Lars, you’re in charge of killing.”

Eldest son: “Woohoo!”

V: [To his second oldest son] “Gunther, you’ll be in charge of the pillaging.”

2n eldest son: “Alright! Pillaging rocks!”

Youngest son: “Awww, not raping, again…”

Hi pumpkinhead, back again? How about answering some of my questions? Or did you just make all that stuff up?

Finns are not Scandinavians and did not, AFAIK, go a-viking…

Finns were not vikings (although, perhaps some of us were: it may be possible that some people from Finland have joined the Swedish Vikings, when they travelled to Russia). It is also possible that some of Swedish vikings married Finns… and that’s why some of us could have viking ancestors…

Pumpkinhead Wrote:

Like his Viking ancestors who made their living raping, killing, pillaging, and burning peaceful Christian communities, this Scandinavian evolutionist can not tolerate any dissent from the evolutionary theology of the modern secular state.

Normally I don’t answer trolls, but you made it personal.

First, it is highly unlikely I have Viking ancestors even being a Swede by many generations.

My lineage is a mix mainly from central west Europe and northern Sweden. The later can mean such ancestors as Same (genetically traced to northern Africa) or Fins (again central Europe, but east).

Worse, Vikings were a social, and not ethnic, group. Since records doesn’t go that far back it is impossible to tell which were and were not. Vikings were more specifically some of the men of mainly coastal settlements that chose to live by travel, and they were only out as viking (“dra i viking”) when they pillaged. Most scandinavians were never Vikings at any time, but all were “nordmän”.

Second, the traveling people mostly made their living by trade, especially slaves (which they of course could also got from pillaging and not only by population growth among the thralls).

Third, not all of Europe was christian at the time. For example, the Kievan Rus’ principality was probably founded just by scandinavian traders, and it wasn’t christianized until about 200 years after the travels had started to pass the region.

Fourth, I’m not a biologist. That I support science instead of anti-science doesn’t make me an expert in evolutionary biology. So please refrain from mislabeling me and my expertise.

Fifth, and you know this because you are only trying to parody and put up easy targets, a secular state is separated from theology of all kinds.

So let’s see, what remains that you did get right?

Oh, yes, “modern secular state”. That sounds about right.

Torbjeorn Larrson — Well done!

And a third of the way around the globe, it is highly likely that I have Viking ancestors on my father’s side…

So, let’t summarize shall we? So far pumpkinhead has, (anonomously): made claims without evidence; failed to answer questions posed to him; and failed to acknowledge when answers were given to his questions. Then, when all else fails, he has stooped to racism and descriptions of sexual preference as arguments.

OK, let’s play shall we? Everyone knows that pumpkinheads are bulbous, orange skined and totally hollow inside. Oh yea, and they scare small children on holloween and undoubtedly have deviant sexual preferences.

Until this guy answere questions put to him I suggest we all ignore him

Dembski: “Just because the word “evolution” is used doesn’t mean that homage is being paid to Darwin. “Directed evolution” properly falls under ID.”

It’s nice to know that eugenics is an ID thing now. ;)

He floundered? Should he ask for help from the piranha of science?

(did I say that?)

I’m still here, waiting patiently, keeping any and all fish jokes to myself.

I don’t know about the problem with links. Why don’t you try it with dead urls that we can cut ‘n’ paste if we need to and see if that works.

I too await your response with great eagerness. I make a point of not playing silly games with people’s names. I grew up with a name begging to be mauled and made fun of, and my schoolmates didn’t disappoint, so I know how annoying that can be.

I’m much more interested in seeing if you are going to try the “front-loaded” gambit with the EAs, or its demented cousin, the TE = ID canard. I’ll be somewhat disappointed if you do, given the sheer idiocy of those arguments, and you seem capable of better. But nonetheless, demolishing poor arguments will always be far more amusing to me than making fun of someone’s poor choice of parents.

It’s like the bisexuality most of them practice, they do know what it’s going to be from day day.

I think this pretty much rules Pumpkinhead out as a serious commentator on any subject; and possibly nothing more than a junior-high redneck with bad teeth and a stupid-looking automotive-product T-shirt. What will he do next – call us “faggits?”

Umm, no, I’m just debating whether arguing with you recalcitrants is worth my time…

Right – the fish-boy posts a lot of nonsense, then, when it’s all been refuted and he’s left with a lot of questions he can’t answer, he suddenly pretends to wonder whether we’re worth the time. In other words, he’s not worth our time either.

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This page contains a single entry by Steve Reuland published on April 9, 2007 10:01 AM.

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