Bipod, I'm closing comments for now.

Have I designed my car if I change the headlight bulbs from stock to blue?

As that all this result is analogous to, changing the color of a bulb?

Citations are not links, just as intelligent modification is not intelligent design.

This is rich. Intelligent modification is not intelligent design. So "the designer" can only *poof* things into existence. No modifications allowed.

The bottom line remains the same - the entire universe of terpene chemistry in nature is eminently accessible to RM+NS.

While over at ARN they assert that RM+NS is a straw-man.

Crikey. Bipod claimed that there was a LINK to the Nature paper. His/her claim was patently false. Citations are not links, just as intelligent modification is not intelligent design. Therefore, it is reasonable to hypothesize that bipod didn't bother to read the Nature paper.

Smokey, you have a serious reading comprehension problem. Here is what Bipod said:

The intelligent design of evolution (link takes you to Nature article)

The link does indeed take you to the Nature article with the title "The intelligent design of evolution". (note the journal is a "joint endeavor" by EMBO and Nature Publishing Group).

Which followed this: "The combinations of mutations were SELECTED so as to decrease the m value and to maintain Pm."

I already mentioned this.

This means that they were chosen by artificial selection, not designed. The design went into the selection of residues and the construction of a screen.

Once again, you have a serious reading comprehension problem. The entire point of the paper was this:"The systematic recombination approach described herein enabled us to design enzyme specificity rapidly and efficiently without a screen for the desired activity." They did use a screen on the previous step. But, they used site-directed saturation mutagenesis and site-directed mutagenesis to actually construct the enzyme specificity.

The quote you mined just makes the authors look illiterate, as one doesn't add mutations to an enzyme, one makes mutations in a gene encoding an enzyme. The resulting enzyme is a mutant enzyme, not a mutation.

That isn't even coherent. I never claimed that this was not an example of intelligent design of evolution, thats the whole point this particular blog.

The authors' speculations aren't the relevant piece, the data are the relevant pieces.

The data provide the basis for their conclusion that rational design of evolution is possible and can be done on a greater scale.

Moreover, the authors are pointing out that the only thing being rationally designed here is the evolution. Do you know what "saturation mutagenesis" means, Guts?

Do you know what site directed saturation mutagenesis and site directed mutagenesis is Smokey?

I didn't refer to *a* paper. I referred to our work, which is published in multiple papers in Cell, JBC, Neuron, and PNAS.

You mentioned a single experiment, just cite the one you did. I find it strange that this is the umpteenth post that you've mentioned this in and you still havn't cited it.

Where is this claim? The full citation is found within that commentary.
Crikey. Bipod claimed that there was a LINK to the Nature paper. His/her claim was patently false. Citations are not links, just as intelligent modification is not intelligent design. Therefore, it is reasonable to hypothesize that bipod didn't bother to read the Nature paper.

…[the experimental design] includes this: "the selected mutations were added to -humulene synthase"
Which followed this: "The combinations of mutations were SELECTED so as to decrease the m value and to maintain Pm." This means that they were chosen by artificial selection, not designed. The design went into the selection of residues and the construction of a screen. The quote you mined just makes the authors look illiterate, as one doesn't add mutations to an enzyme, one makes mutations in a gene encoding an enzyme. The resulting enzyme is a mutant enzyme, not a mutation.

You keep leaving out the relevant piece, they also concluded:"divergent evolution by rational design may be feasible on a significantly larger scale than currently possible"
The authors' speculations aren't the relevant piece, the data are the relevant pieces. Moreover, the authors are pointing out that the only thing being rationally designed here is the evolution. Do you know what "saturation mutagenesis" means, Guts?

Are you claiming to have done something here?
Obviously, yes. What tipped you off?
Who are you?
I'm someone who works in this field of intelligent mutating of proteins to change their substrates and/or products; therefore, according to the analogy favored by the IDists here, I am analogous to God. Who are you?
What paper are you referring to?
I didn't refer to *a* paper. I referred to our work, which is published in multiple papers in Cell, JBC, Neuron, and PNAS.

Duh - one thing the cited study shows is how very modest variations, subtle differences in how the substrate is bound, can lead to dramatically different chemistries.

Duh, any protein with a function probably has plasticity residues. Enzymes especially, they need to form specific chemicals, catalyze the right chemical reaction, recognize substrates. This requires obtaining residues that exclude cross reactivity,accelerate any of those things, etc. If you have a group of proteins that do not have these residues, they might be just random peptides without any functions.

Art:

I think yer making things up here, Guts.

Naa, I'm not an anti-IDist.

Art:

Do you know how these enzymes work? Specifically, do you know what active roles the enzyme plays in determining the steps subsequent to cation formation? How many of these come into play after initial substrate binding? Feel free to expound and provide pointers.

The reason I gave contradicts your assertion of sloppy simplicity, I'm happy to play the reference game, you first.

It's probably far more complicated since similar protein folds can lead to different products in different enzymes,

Duh - one thing the cited study shows is how very modest variations, subtle differences in how the substrate is bound, can lead to dramatically different chemistries.

and the enzyme must trigger the generation of the cation and then control when and where it is quenched.

I think yer making things up here, Guts. Do you know how these enzymes work? Specifically, do you know what active roles the enzyme plays in determining the steps subsequent to cation formation? How many of these come into play after initial substrate binding? Feel free to expound and provide pointers.

The bottom line remains the same - the entire universe of terpene chemistry in nature is eminently accessible to RM+NS.

This phenomenon is consistent with MET, but not with intelligent design.

I left it out because I was correcting bipod's & Joy's initial misunderstanding of the method.

I don't see any misunderstanding in either of their posts.

"Intelligently combining them" still doesn't get you to "intelligent design," Guts.

I have no idea what a better example of intelligent design might be.

Again, bipod clearly only read the commentary and didn't bother reading the paper, falsely claiming that he had provided a link to it. The commentary was inaccurate.

Now you're making things up? Where is this claim? The full citation is found within that commentary. The commentary was not inaccurate.

The only "design methodology" here is experimental design.

Which includes this: "the selected mutations were added to -humulene synthase"

They were simply testing the hypothesis that the changes were additive. They were, which was surprising, which is why the paper that bipod didn't bother to read made it into Nature.

You keep leaving out the relevant piece, they also concluded:"divergent evolution by rational design may be feasible on a significantly larger scale than currently possible"

As Art says, there's no good news here for ID. Our data make it even worse: we changed an almost completely conserved residue in the active site that contacts the substrate to something not found in nature, without losing the original function. This demolishes a major assumption underlying all the probabilistic attacks on MET by Dembski, Behe, et al.

Are you claiming to have done something here? Who are you? What paper are you referring to?

I left it out because I was correcting bipod's & Joy's initial misunderstanding of the method.

…they then used the data collected from the single mutations to recombine them and constructed enzymes with high product selectivity.

"Intelligently combining them" still doesn't get you to "intelligent design," Guts.

The design methodology described in the commentary…

Again, bipod clearly only read the commentary and didn't bother reading the paper, falsely claiming that he had provided a link to it. The commentary was inaccurate.

The only "design methodology" here is experimental design. They were simply testing the hypothesis that the changes were additive. They were, which was surprising, which is why the paper that bipod didn't bother to read made it into Nature. As Art says, there's no good news here for ID. Our data make it even worse: we changed an almost completely conserved residue in the active site that contacts the substrate to something not found in nature, without losing the original function. This demolishes a major assumption underlying all the probabilistic attacks on MET by Dembski, Behe, et al.

…and used by the researchers is called "adaptive walking", and bipod's point is that this methodology can likely be gleaned from the experiment.

As bipod and Joy didn't bother to read the paper, they didn't really have a point. It was just wishful thinking.

I'm interested in how Eric can claim "the *complete lack* of evidence" when it is clear that he hasn't bothered to examine the evidence in good faith. Doesn't a negative claim like that require reams of research?